Evaluating and Mitigating the Immunogenicity of Therapeutic Proteins.

Therapeutic proteins provide interventions for some of the most complex and intractable diseases and are an essential part of modern medicine. Immunogenicity is the development of immune responses, usually measured by antibodies, to therapeutic proteins. These responses can adversely affect the safety and efficacy of the therapeutic agent and may have the following consequences: neutralization of a life-saving biotherapeutic, crossreactivity to non-redundant endogenous proteins, and hypersensitivity responses. These concerns have been underscored by the discontinuation of development of several drugs in recent years owing to immunogenicity issues. We review here recent progress in technological approaches that are useful for the clinical and non-clinical risk assessment of immunogenicity as well as mitigation strategies including deimmunizing protein molecules and inducing immune tolerance to the therapeutic protein.

[1]  S. Reddy.  Immunology: The patterns of T-cell target recognition , 2017, Nature.

[2]  W. Jiskoot,et al.  Mouse Models for Assessing Protein Immunogenicity: Lessons and Challenges. , 2016, Journal of pharmaceutical sciences.

[3]  Bernhard Hemmer,et al.  Recommendations for clinical use of data on neutralising antibodies to interferon-beta therapy in multiple sclerosis , 2010, The Lancet Neurology.

[4]  John Sidney,et al.  A Systematic Assessment of MHC Class II Peptide Binding Predictions and Evaluation of a Consensus Approach , 2008, PLoS Comput. Biol..

[5]  P. Ridker,et al.  Lipid‐Reduction Variability and Antidrug‐Antibody Formation with Bococizumab , 2017, The New England journal of medicine.

[6]  James E Crowe,et al.  Epitope-Specific Human Influenza Antibody Repertoires Diversify by B Cell Intraclonal Sequence Divergence and Interclonal Convergence , 2011, The Journal of Immunology.

[7]  S. Quake,et al.  The promise and challenge of high-throughput sequencing of the antibody repertoire , 2014, Nature Biotechnology.

[8]  Chris Bailey-Kellogg,et al.  Optimization of Therapeutic proteins to Delete T-Cell epitopes while Maintaining Beneficial Residue Interactions , 2011, J. Bioinform. Comput. Biol..

[9]  N. Raben,et al.  Pompe disease: from pathophysiology to therapy and back again , 2014, Front. Aging Neurosci..

[10]  D. Okita,et al.  Human CD4+ T‐cell epitope repertoire on the C2 domain of coagulation factor VIII , 2003, Journal of thrombosis and haemostasis : JTH.

[11]  J. Voorberg,et al.  von Willebrand factor binds to the surface of dendritic cells and modulates peptide presentation of factor VIII , 2016, Haematologica.

[12]  H. Schwarz,et al.  Blockade of CD40/CD40 Ligand Interactions Prevents Induction of Factor VIII Inhibitors in Hemophilic Mice but Does not Induce Lasting Immune Tolerance , 2001, Thrombosis and Haemostasis.

[13]  A. Sewell,et al.  T-cell libraries allow simple parallel generation of multiple peptide-specific human T-cell clones , 2016, Journal of immunological methods.

[14]  George Georgiou,et al.  High-throughput sequencing of the paired human immunoglobulin heavy and light chain repertoire , 2013, Nature Biotechnology.

[15]  D. Stockton,et al.  Durable and sustained immune tolerance to ERT in Pompe disease with entrenched immune responses. , 2016, JCI insight.

[16]  J. Zehnder,et al.  Development of antibodies to thrombin and factor V with recurrent bleeding in a patient exposed to topical bovine thrombin. , 1990, Blood.

[17]  D. Miller,et al.  The incidence and significance of anti-natalizumab antibodies , 2007, Neurology.

[18]  Chris Bailey-Kellogg,et al.  Design and analysis of immune-evading enzymes for ADEPT therapy. , 2012, Protein engineering, design & selection : PEDS.

[19]  A. ten Brinke,et al.  Limited Promiscuity of HLA-DRB1 Presented Peptides Derived of Blood Coagulation Factor VIII , 2013, PloS one.

[20]  David Baker,et al.  Removing T-cell epitopes with computational protein design , 2014, Proceedings of the National Academy of Sciences.

[21]  N. Chirmule,et al.  Considerations for optimization and validation of an in vitro PBMC derived T cell assay for immunogenicity prediction of biotherapeutics. , 2010, Clinical immunology.

[22]  Andrew W. Liu,et al.  Tetramer-Guided Epitope Mapping: Rapid Identification and Characterization of Immunodominant CD4+ T Cell Epitopes from Complex Antigens1 , 2001, The Journal of Immunology.

[23]  D. Scott,et al.  Engineered antigen-specific human regulatory T cells: immunosuppression of FVIII-specific T- and B-cell responses. , 2015, Blood.

[24]  R. Preissner,et al.  Development of Immune-Specific Interaction Potentials and Their Application in the Multi-Agent-System VaccImm , 2011, PloS one.

[25]  K. Lamberth,et al.  Quantitative analysis of the CD4+ T cell response to therapeutic antibodies in healthy donors using a novel T cell:PBMC assay , 2017, PloS one.

[26]  K. Sheng,et al.  Methods to measure T-cell responses , 2010, Expert review of vaccines.

[27]  J. Demengeot,et al.  The immunogenicity of anti-TNF therapy in immune-mediated inflammatory diseases: a systematic review of the literature with a meta-analysis , 2012, Annals of the rheumatic diseases.

[28]  C. Yanover,et al.  Pharmacogenetics and the immunogenicity of protein therapeutics , 2011, Nature Biotechnology.

[29]  F. Sallusto,et al.  Human naive and memory CD4+ T cell repertoires specific for naturally processed antigens analyzed using libraries of amplified T cells , 2009, The Journal of experimental medicine.

[30]  Jing Zhang,et al.  The real cost of sequencing: scaling computation to keep pace with data generation , 2016, Genome biology.

[31]  H. Schwarz,et al.  Opportunities and limitations of mouse models humanized for HLA class II antigens , 2009, Journal of thrombosis and haemostasis : JTH.

[32]  Alessandro Sette,et al.  Identifying specificity groups in the T cell receptor repertoire , 2017, Nature.

[33]  D. Baker,et al.  Recombinant immunotoxin for cancer treatment with low immunogenicity by identification and silencing of human T-cell epitopes , 2014, Proceedings of the National Academy of Sciences.

[34]  P. Roche,et al.  The ins and outs of MHC class II-mediated antigen processing and presentation , 2015, Nature Reviews Immunology.

[35]  H. Hartung,et al.  Development and Validation of an Enzyme-Linked Immunosorbent Assay for the Detection of Binding Anti-Drug Antibodies against Interferon Beta , 2017, Front. Neurol..

[36]  William W. Kwok,et al.  Antibiotic-refractory Lyme arthritis is associated with HLA-DR molecules that bind a Borrelia burgdorferi peptide , 2006, The Journal of experimental medicine.

[37]  Yingyu Chen,et al.  Lentivirus‐mediated platelet gene therapy of murine hemophilia A with pre‐existing anti‐factor VIII immunity , 2012, Journal of thrombosis and haemostasis : JTH.

[38]  Søren Buus,et al.  Functional recombinant MHC class II molecules and high-throughput peptide-binding assays , 2009, Immunome research.

[39]  Ira Pastan,et al.  Immunotoxin therapy of cancer , 2006, Nature Reviews Cancer.

[40]  Gopi Shankar,et al.  A risk-based bioanalytical strategy for the assessment of antibody immune responses against biological drugs , 2007, Nature Biotechnology.

[41]  J. Voorberg,et al.  Comparative profiling of HLA-DR and HLA-DQ associated factor VIII peptides presented by monocyte-derived dendritic cells , 2017, Haematologica.

[42]  A. ten Brinke,et al.  HLA-DR-presented Peptide Repertoires Derived From Human Monocyte-derived Dendritic Cells Pulsed With Blood Coagulation Factor VIII , 2011, Molecular & Cellular Proteomics.

[43]  J. Goedert,et al.  Loss of high‐responder inhibitors in patients with severe hemophilia A and human immunodeficiency virus type 1 infection: A report from the multi‐center hemophilia cohort study , 1993, American journal of hematology.

[44]  Z. Sauna,et al.  Immunogenicity assessment during the development of protein therapeutics , 2018, The Journal of pharmacy and pharmacology.

[45]  J. Kalden,et al.  Immunogenicity and loss of response to TNF inhibitors: implications for rheumatoid arthritis treatment , 2017, Nature Reviews Rheumatology.

[46]  Leonard Moise,et al.  Effect of HLA DR epitope de-immunization of Factor VIII in vitro and in vivo. , 2012, Clinical immunology.

[47]  T. Ortel,et al.  Recent developments in topical thrombins , 2009, Thrombosis and Haemostasis.

[48]  P. Bradley,et al.  Quantifiable predictive features define epitope-specific T cell receptor repertoires , 2017, Nature.

[49]  K. Chester,et al.  Overcoming the immunologic response to foreign enzymes in cancer therapy , 2005, Expert review of clinical immunology.

[50]  R. Herzog,et al.  Ex vivo expanded autologous polyclonal regulatory T cells suppress inhibitor formation in hemophilia , 2014, Molecular therapy. Methods & clinical development.

[51]  Etienne Caron,et al.  Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry* , 2015, Molecular & Cellular Proteomics.

[52]  C. Pozzilli,et al.  Guidelines on use of anti‐IFN‐β antibody measurements in multiple sclerosis: report of an EFNS Task Force on IFN‐β antibodies in multiple sclerosis , 2005, European journal of neurology.

[53]  D. Okita,et al.  Epitope repertoire of human CD4+ T cells on the A3 domain of coagulation factor VIII , 2004, Journal of thrombosis and haemostasis : JTH.

[54]  R. Liesner,et al.  Incidence of factor VIII inhibitors throughout life in severe hemophilia A in the United Kingdom. , 2011, Blood.

[55]  Eugen Koren,et al.  An acid dissociation bridging ELISA for detection of antibodies directed against therapeutic proteins in the presence of antigen. , 2005, Journal of immunological methods.

[56]  C. David,et al.  HLA-DR4 (DRB1*0401) transgenic mice expressing an altered CD4-binding site: specificity and magnitude of DR4-restricted T cell response. , 1998, Journal of immunology.

[57]  S. Ziegler,et al.  CD4+FOXP3+ regulatory T cells confer long-term regulation of factor VIII-specific immune responses in plasmid-mediated gene therapy-treated hemophilia mice. , 2009, Blood.

[58]  I. Pastan,et al.  Recombinant immunotoxin engineered for low immunogenicity and antigenicity by identifying and silencing human B-cell epitopes , 2012, Proceedings of the National Academy of Sciences.

[59]  K. Bagshawe.  Antibody-directed enzyme prodrug therapy (ADEPT) for cancer , 2006, Expert review of anticancer therapy.

[60]  I. Pastan,et al.  Dual B- and T-cell de-immunization of recombinant immunotoxin targeting mesothelin with high cytotoxic activity , 2016, Oncotarget.

[61]  L. Aarden,et al.  The antibody response against human and chimeric anti-TNF therapeutic antibodies primarily targets the TNF binding region , 2014, Annals of the rheumatic diseases.

[62]  M. Recht,et al.  Changes in the amino acid sequence of the recombinant human factor VIIa analog, vatreptacog alfa, are associated with clinical immunogenicity , 2015, Journal of thrombosis and haemostasis : JTH.

[63]  Hidde L. Ploegh,et al.  The known unknowns of antigen processing and presentation , 2008, Nature Reviews Immunology.

[64]  C. Yang,et al.  Thrombocytopenia caused by the development of antibodies to thrombopoietin. , 2001, Blood.

[65]  D. DiMichele,et al.  Immune tolerance in haemophilia: the long journey to the fork in the road , 2012, British journal of haematology.

[66]  Scott D Boyd,et al.  Deep sequencing and human antibody repertoire analysis. , 2016, Current opinion in immunology.

[67]  Massimo Bernaschi,et al.  ImmunoGrid: towards agent-based simulations of the human immune system at a natural scale† , 2010, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

[68]  Jörn Dengjel,et al.  Mass spectrometry analysis and quantitation of peptides presented on the MHC II molecules of mouse spleen dendritic cells. , 2011, Journal of proteome research.

[69]  X. Mariette,et al.  Characterization of CD4 T Cell Epitopes of Infliximab and Rituximab Identified from Healthy Donors , 2017, Front. Immunol..

[70]  T. Hickling,et al.  Contribution of enhanced engagement of antigen presentation machinery to the clinical immunogenicity of a human interleukin (IL)‐21 receptor‐blocking therapeutic antibody , 2016, Clinical and experimental immunology.

[71]  Ryan M. Pearson,et al.  An antigen-encapsulating nanoparticle platform for TH1/17 immune tolerance therapy. , 2017, Nanomedicine : nanotechnology, biology, and medicine.

[72]  E. Lázár-Molnár,et al.  Immunogenicity Assessment of Tumor Necrosis Factor Antagonists in the Clinical Laboratory. , 2016, Clinical chemistry.

[73]  J. Gokemeijer,et al.  How Close Are We to Profiling Immunogenicity Risk Using In Silico Algorithms and In Vitro Methods?: an Industry Perspective , 2017, The AAPS Journal.

[74]  R. Dubridge,et al.  The immunogenicity of humanized and fully human antibodies , 2010, mAbs.

[75]  Viswanath Devanarayan,et al.  Recommendations on risk-based strategies for detection and characterization of antibodies against biotechnology products. , 2008, Journal of immunological methods.

[76]  P. Paz,et al.  T cells from hemophilia A subjects recognize the same HLA-restricted FVIII epitope with a narrow TCR repertoire. , 2016, Blood.

[77]  I. Pastan,et al.  Low-Dose Methotrexate Prevents Primary and Secondary Humoral Immune Responses and Induces Immune Tolerance to a Recombinant Immunotoxin , 2018, The Journal of Immunology.

[78]  Chris Bailey-Kellogg,et al.  Open Access Methodology Article Optimization Algorithms for Functional Deimmunization of Therapeutic Proteins , 2022 .

[79]  L. Aarden,et al.  Differential effect of drug interference in immunogenicity assays. , 2011, Journal of immunological methods.

[80]  P. Lenting,et al.  Life in the shadow of a dominant partner: the FVIII-VWF association and its clinical implications for hemophilia A. , 2016, Blood.

[81]  George Georgiou,et al.  In-depth determination and analysis of the human paired heavy- and light-chain antibody repertoire , 2014, Nature Medicine.

[82]  George Scott,et al.  Recommendations for the design and optimization of immunoassays used in the detection of host antibodies against biotechnology products. , 2004, Journal of immunological methods.

[83]  Roberto A. Maldonado,et al.  Polymeric synthetic nanoparticles for the induction of antigen-specific immunological tolerance , 2014, Proceedings of the National Academy of Sciences.

[84]  Patrick Mayeux,et al.  Pure red-cell aplasia and antierythropoietin antibodies in patients treated with recombinant erythropoietin. , 2002, The New England journal of medicine.

[85]  X. Montalban,et al.  Clinical practice of analysis of anti-drug antibodies against interferon beta and natalizumab in multiple sclerosis patients in Europe: A descriptive study of test results , 2017, PloS one.

[86]  W. Jiskoot,et al.  Small Amounts of Sub-Visible Aggregates Enhance the Immunogenic Potential of Monoclonal Antibody Therapeutics , 2014, Pharmaceutical Research.

[87]  D. Okita,et al.  T cell recognition of the A2 domain of coagulation factor VIII in hemophilia patients and healthy subjects , 2004, Journal of thrombosis and haemostasis : JTH.

[88]  Sur Sharma,et al.  Translating antibody directed enzyme prodrug therapy (ADEPT) and prospects for combination , 2017, Expert opinion on biological therapy.

[89]  J. Cizeau,et al.  Engineering and Biological Characterization of VB6-845, an Anti-EpCAM Immunotoxin Containing a T-cell Epitope-depleted Variant of the Plant Toxin Bouganin , 2009, Journal of immunotherapy.

[90]  Jian Li,et al.  Detection of low-affinity anti-drug antibodies and improved drug tolerance in immunogenicity testing by Octet(®) biolayer interferometry. , 2011, Journal of pharmaceutical and biomedical analysis.

[91]  B. Maillère,et al.  Quantitative analysis of the CD4 T‐cell repertoire specific to therapeutic antibodies in healthy donors , 2011, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[92]  S. Rosen,et al.  Membranous glomerulonephritis and nephrosis post factor IX infusions in hemophilia B , 1998, Pediatric Nephrology.

[93]  H. Weiner,et al.  Induction of partial immune tolerance to factor VIII through prior mucosal exposure to the factor VIII C2 domain , 2006, Journal of thrombosis and haemostasis : JTH.

[94]  Catherine E Costello,et al.  Immunogenic HLA-DR-Presented Self-Peptides Identified Directly from Clinical Samples of Synovial Tissue, Synovial Fluid, or Peripheral Blood in Patients with Rheumatoid Arthritis or Lyme Arthritis. , 2017, Journal of proteome research.

[95]  H. Daniell,et al.  Suppression of inhibitor formation against FVIII in a murine model of hemophilia A by oral delivery of antigens bioencapsulated in plant cells. , 2014, Blood.

[96]  B. Dijkmans,et al.  Development of antidrug antibodies against adalimumab and association with disease activity and treatment failure during long-term follow-up. , 2011, JAMA.

[97]  Renuka Pillutla,et al.  Recommendations for the characterization of immunogenicity response to multiple domain biotherapeutics. , 2014, Journal of immunological methods.

[98]  C. Rehder,et al.  CRIM-negative infantile Pompe disease: Characterization of immune responses in patients treated with ERT monotherapy , 2015, Genetics in Medicine.

[99]  G. S. Pandey,et al.  Post hoc assessment of the immunogenicity of bioengineered factor VIIa demonstrates the use of preclinical tools , 2017, Science Translational Medicine.

[100]  James R. Apgar,et al.  Augmented Binary Substitution: Single-pass CDR germ-lining and stabilization of therapeutic antibodies , 2015, Proceedings of the National Academy of Sciences.

[101]  Zuben E. Sauna,et al.  Recent advances in (therapeutic protein) drug development , 2017, F1000Research.

[102]  Julie McMurry,et al.  Prediction of immunogenicity: in silico paradigms, ex vivo and in vivo correlates. , 2008, Current opinion in pharmacology.

[103]  E. James,et al.  Efficient ex vivo analysis of CD4+ T-cell responses using combinatorial HLA class II tetramer staining , 2016, Nature Communications.

[104]  R. Giugliani,et al.  Newborn Screening for Pompe Disease , 2017, Pediatrics.

[105]  D. Eslin,et al.  Factor VIII ectopically expressed in platelets: efficacy in hemophilia A treatment. , 2003, Blood.

[106]  I. Pastan,et al.  Tolerogenic nanoparticles restore the antitumor activity of recombinant immunotoxins by mitigating immunogenicity , 2018, Proceedings of the National Academy of Sciences.

[107]  Y. Latchman,et al.  Suppression of the immune response to FVIII in hemophilia A mice by transgene modified tolerogenic dendritic cells. , 2011, Molecular therapy : the journal of the American Society of Gene Therapy.

[108]  Vibha Jawa,et al.  T-cell dependent immunogenicity of protein therapeutics: Preclinical assessment and mitigation. , 2013, Clinical immunology.

[109]  Mario Roederer,et al.  Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep Sequencing , 2011, Science.

[110]  L. Santambrogio,et al.  The melting pot of the MHC II peptidome. , 2016, Current opinion in immunology.

[111]  D. Lillicrap,et al.  The molecular mechanisms of immunomodulation and tolerance induction to factor VIII , 2009, Journal of thrombosis and haemostasis : JTH.

[112]  P Vicini,et al.  A Mechanistic, Multiscale Mathematical Model of Immunogenicity for Therapeutic Proteins: Part 1—Theoretical Model , 2014, CPT: pharmacometrics & systems pharmacology.

[113]  Sri H. Ramarathinam,et al.  A Systems Approach to Understand Antigen Presentation and the Immune Response. , 2016, Methods in molecular biology.

[114]  O. Abdul-Rahman,et al.  Sustained immune tolerance induction in enzyme replacement therapy-treated CRIM-negative patients with infantile Pompe disease. , 2017, JCI insight.

[115]  Gopi Shankar,et al.  Scientific and regulatory considerations on the immunogenicity of biologics. , 2006, Trends in biotechnology.

[116]  Chen Yanover,et al.  Polymorphisms in the F8 Gene and MHC-II Variants as Risk Factors for the Development of Inhibitory Anti-Factor VIII Antibodies during the Treatment of Hemophilia A: A Computational Assessment , 2013, PLoS Comput. Biol..

[117]  Roberto A. Maldonado,et al.  Improving the efficacy and safety of biologic drugs with tolerogenic nanoparticles. , 2016, Nature nanotechnology.