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Moeckel C, Mareboina M, Konnaris MA, Chan CS, Mouratidis I, Montgomery A, Chantzi N, Pavlopoulos GA, Georgakopoulos-Soares I. A survey of k-mer methods and applications in bioinformatics. Comput Struct Biotechnol J 2024; 23:2289-2303. [PMID: 38840832 PMCID: PMC11152613 DOI: 10.1016/j.csbj.2024.05.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 06/07/2024] Open
Abstract
The rapid progression of genomics and proteomics has been driven by the advent of advanced sequencing technologies, large, diverse, and readily available omics datasets, and the evolution of computational data processing capabilities. The vast amount of data generated by these advancements necessitates efficient algorithms to extract meaningful information. K-mers serve as a valuable tool when working with large sequencing datasets, offering several advantages in computational speed and memory efficiency and carrying the potential for intrinsic biological functionality. This review provides an overview of the methods, applications, and significance of k-mers in genomic and proteomic data analyses, as well as the utility of absent sequences, including nullomers and nullpeptides, in disease detection, vaccine development, therapeutics, and forensic science. Therefore, the review highlights the pivotal role of k-mers in addressing current genomic and proteomic problems and underscores their potential for future breakthroughs in research.
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Affiliation(s)
- Camille Moeckel
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Manvita Mareboina
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Maxwell A. Konnaris
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Candace S.Y. Chan
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Ioannis Mouratidis
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
- Huck Institute of the Life Sciences, Penn State University, University Park, Pennsylvania, USA
| | - Austin Montgomery
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Nikol Chantzi
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | | | - Ilias Georgakopoulos-Soares
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
- Huck Institute of the Life Sciences, Penn State University, University Park, Pennsylvania, USA
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Koncz B, Balogh GM, Manczinger M. A journey to your self: The vague definition of immune self and its practical implications. Proc Natl Acad Sci U S A 2024; 121:e2309674121. [PMID: 38722806 PMCID: PMC11161755 DOI: 10.1073/pnas.2309674121] [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] [Indexed: 06/10/2024] Open
Abstract
The identification of immunogenic peptides has become essential in an increasing number of fields in immunology, ranging from tumor immunotherapy to vaccine development. The nature of the adaptive immune response is shaped by the similarity between foreign and self-protein sequences, a concept extensively applied in numerous studies. Can we precisely define the degree of similarity to self? Furthermore, do we accurately define immune self? In the current work, we aim to unravel the conceptual and mechanistic vagueness hindering the assessment of self-similarity. Accordingly, we demonstrate the remarkably low consistency among commonly employed measures and highlight potential avenues for future research.
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Affiliation(s)
- Balázs Koncz
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Hungarian Research Network (HUN-REN) Biological Research Centre, Szeged6726, Hungary
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre (HCEMM-BRC) Systems Immunology Research Group, Szeged6726, Hungary
- Department of Dermatology and Allergology, University of Szeged, Szeged6720, Hungary
| | - Gergő Mihály Balogh
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Hungarian Research Network (HUN-REN) Biological Research Centre, Szeged6726, Hungary
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre (HCEMM-BRC) Systems Immunology Research Group, Szeged6726, Hungary
- Department of Dermatology and Allergology, University of Szeged, Szeged6720, Hungary
| | - Máté Manczinger
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Hungarian Research Network (HUN-REN) Biological Research Centre, Szeged6726, Hungary
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre (HCEMM-BRC) Systems Immunology Research Group, Szeged6726, Hungary
- Department of Dermatology and Allergology, University of Szeged, Szeged6720, Hungary
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3
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Kanduc D. On the Pentapeptide as the Measurement Unit in Immunology. Glob Med Genet 2024; 11:34-35. [PMID: 38239806 PMCID: PMC10796194 DOI: 10.1055/s-0044-1779041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2024] Open
Abstract
This communication concerns a crucial query in immunology, that is, the dimension of an epitope. The issue has essential implications in vaccine formulations.
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Affiliation(s)
- Darja Kanduc
- Department of Biosciences, Biotechnologies, and Biopharmaceutics, University of Bari, Bari, Italy
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4
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Kanduc D. Oligopeptides for Immunotherapy Approaches in Ovarian Cancer Treatment. Curr Drug Discov Technol 2020; 16:285-289. [PMID: 29793409 DOI: 10.2174/1570163815666180525071740] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 05/11/2018] [Accepted: 05/21/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Anti-ovarian cancer vaccines based on minimal immune determinants uniquely expressed in ovarian cancer biomarkers appear to promise a high level of sensitivity and specificity for ovarian cancer immunodiagnostics, immunoprevention, and immunotherapy. METHODS Using the Pir Peptide Match program, three ovarian cancer biomarkers - namely, sperm surface protein Sp17, WAP four-disulfide core domain protein 2, and müllerian-inhibiting substance - were searched for unique peptide segments not shared with other human proteins. Then, the unique peptide segments were assembled to define oligopeptides potentially usable as synthetic ovarian cancer antigens. RESULTS AND CONCLUSION This study describes a methodology for constructing ovarian cancer biomarkerderived oligopeptide constructs that might induce powerful, specific, and non-crossreactive immune responses against ovarian cancer.
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Affiliation(s)
- Darja Kanduc
- Department of Biosciences, Biotechnologies & Biopharmaceutics, University of Bari, Bari, Italy
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Bersanelli M, Giannarelli D, Castrignanò P, Fornarini G, Panni S, Mazzoni F, Tiseo M, Rossetti S, Gambale E, Rossi E, Papa A, Cortellini A, Lolli C, Ratta R, Michiara M, Milella M, De Luca E, Sorarù M, Mucciarini C, Atzori F, Banna GL, La Torre L, Vitale MG, Massari F, Rebuzzi SE, Facchini G, Schinzari G, Tomao S, Bui S, Vaccaro V, Procopio G, De Giorgi U, Santoni M, Ficorella C, Sabbatini R, Maestri A, Natoli C, De Tursi M, Di Maio M, Rapacchi E, Pireddu A, Sava T, Lipari H, Comito F, Verzoni E, Leonardi F, Buti S. INfluenza Vaccine Indication During therapy with Immune checkpoint inhibitors: a transversal challenge. The INVIDIa study. Immunotherapy 2019; 10:1229-1239. [PMID: 30326787 DOI: 10.2217/imt-2018-0080] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
AIM Considering the unmet need for the counseling of cancer patients treated with immune checkpoint inhibitors (CKI) about influenza vaccination, an explorative study was planned to assess flu vaccine efficacy in this population. METHODS INVIDIa was a retrospective, multicenter study, enrolling consecutive advanced cancer outpatients receiving CKI during the influenza season 2016-2017. RESULTS Of 300 patients, 79 received flu vaccine. The incidence of influenza syndrome was 24.1% among vaccinated, versus 11.8% of controls; odds ratio: 2.4; 95% CI: 1.23-4.59; p = 0.009. The clinical ineffectiveness of vaccine was more pronounced among elderly: 37.8% among vaccinated patients, versus 6.1% of unvaccinated, odds ratio: 9.28; 95% CI: 2.77-31.14; p < 0.0001. CONCLUSION Although influenza vaccine may be clinically ineffective in advanced cancer patients receiving CKI, it seems not to negatively impact the efficacy of anticancer therapy.
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Affiliation(s)
| | - Diana Giannarelli
- Biostatistical Unit, Regina Elena National Cancer Institute, Rome, Italy
| | | | - Giuseppe Fornarini
- Medical Oncology Unit 1, IRCCS Policlinico San Martino Hospital, Genova, Italy
| | - Stefano Panni
- Medical Oncology Unit, ASST - Istituti Ospitalieri Cremona Hospital, Cremona, Italy
| | | | - Marcello Tiseo
- Medical Oncology Unit, University Hospital of Parma, Parma, Italy
| | - Sabrina Rossetti
- SSD Oncologia Clinica Sperimentale Uro-Andrologica, Dipartimento Corp-S Assistenziale dei Percorsi Oncologici Uro-Genitale, Istituto Nazionale Tumori "Fondazione G. Pascale", IRCCS, Napoli, Italy
| | - Elisabetta Gambale
- Department of Medical, Oral & Biotechnological Sciences & CeSI-MeT, University G. D'Annunzio, Chieti-Pescara, Italy
| | - Ernesto Rossi
- Medical Oncology, Catholic University of Sacred Heart, Rome, Italy
| | - Anselmo Papa
- Department of Medical & Surgical Sciences & Biotechnology, University "La Sapienza", Latina, Italy
| | - Alessio Cortellini
- Department of Biotechnological & Applied Clinical Sciences, St Salvatore Hospital, University of L'Aquila, L'Aquila, Italy
| | - Cristian Lolli
- Medical Oncology, Scientific Institute of Romagna for the Study & Treatment of Tumors (IRST) IRCCS, Meldola, Italy
| | - Raffaele Ratta
- Genito-Urinary Oncology Unit, Fondazione IRCCS Istituto Nazionale Tumori of Milan, Milano, Italy
| | - Maria Michiara
- Medical Oncology Unit, University Hospital of Parma, Parma, Italy
| | - Michele Milella
- Oncology Unit 1, Regina Elena National Cancer Institute, Rome, Italy
| | - Emmanuele De Luca
- Medical Oncology, Ordine Mauriziano Hospital, University of Turin, Torino, Italy
| | | | | | - Francesco Atzori
- Department of Medical Sciences "M. Aresu", Medical Oncology, University Hospital & University of Cagliari, Cagliari, Italy
| | | | - Leonardo La Torre
- Medical Oncology Department, Santa Maria della Scaletta Hospital, Imola, Italy
| | | | | | - Sara Elena Rebuzzi
- Medical Oncology Unit 1, IRCCS Policlinico San Martino Hospital, Genova, Italy
| | - Gaetano Facchini
- SSD Oncologia Clinica Sperimentale Uro-Andrologica, Dipartimento Corp-S Assistenziale dei Percorsi Oncologici Uro-Genitale, Istituto Nazionale Tumori "Fondazione G. Pascale", IRCCS, Napoli, Italy
| | | | - Silverio Tomao
- Department of Medical & Surgical Sciences & Biotechnology, University "La Sapienza", Latina, Italy
| | - Simona Bui
- Medical Oncology Unit, University Hospital of Parma, Parma, Italy
| | - Vanja Vaccaro
- Oncology Unit 1, Regina Elena National Cancer Institute, Rome, Italy
| | - Giuseppe Procopio
- Genito-Urinary Oncology Unit, Fondazione IRCCS Istituto Nazionale Tumori of Milan, Milano, Italy
| | - Ugo De Giorgi
- Medical Oncology, Scientific Institute of Romagna for the Study & Treatment of Tumors (IRST) IRCCS, Meldola, Italy
| | | | - Corrado Ficorella
- Department of Biotechnological & Applied Clinical Sciences, St Salvatore Hospital, University of L'Aquila, L'Aquila, Italy
| | | | - Antonio Maestri
- Medical Oncology Department, Santa Maria della Scaletta Hospital, Imola, Italy
| | - Clara Natoli
- Department of Medical, Oral & Biotechnological Sciences & CeSI-MeT, University G. D'Annunzio, Chieti-Pescara, Italy
| | - Michele De Tursi
- Department of Medical, Oral & Biotechnological Sciences & CeSI-MeT, University G. D'Annunzio, Chieti-Pescara, Italy
| | - Massimo Di Maio
- Medical Oncology, Ordine Mauriziano Hospital, University of Turin, Torino, Italy
| | - Elena Rapacchi
- Medical Oncology Unit, University Hospital of Parma, Parma, Italy
| | - Annagrazia Pireddu
- Department of Medical Sciences "M. Aresu", Medical Oncology, University Hospital & University of Cagliari, Cagliari, Italy
| | - Teodoro Sava
- Medical Oncology, Camposampiero Hospital, Padova, Italy
| | - Helga Lipari
- Medical Oncology, Cannizzaro Hospital, Catania, Italy
| | - Francesca Comito
- Division of Oncology, Sant'Orsola-Malpighi Hospital, Bologna, Italy
| | - Elena Verzoni
- Genito-Urinary Oncology Unit, Fondazione IRCCS Istituto Nazionale Tumori of Milan, Milano, Italy
| | | | - Sebastiano Buti
- Medical Oncology Unit, University Hospital of Parma, Parma, Italy
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6
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From influenza infection to anti-ADAMTS13 autoantibodies via cross-reactivity. INFECTION INTERNATIONAL 2018. [DOI: 10.2478/ii-2019-0002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Abstract
Autoantibodies (AAbs) against von Willebrand factor (vWF)-cleaving protease ADAMTS13 causally relate to thrombotic thrombocytopenic purpura (TTP). How anti-ADAMTS13 AAbs are generated is unknown. Starting from reports according to which influenza infection can trigger TTP by the production of ADAMTS13 AAbs, this study explores influenza viruses and ADAMTS13 protein for common peptide sequences that might underlie anti-influenza immune responses able to cross-react with ADAMTS13. Results document that numerous peptides are shared between influenza A and B viruses and ADAMTS13, thus supporting the hypothesis of cross-reactivity as a mechanism driving the generation of anti-ADAMTS13 AAbs.
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Kanduc D, Shoenfeld Y. Inter-Pathogen Peptide Sharing and the Original Antigenic Sin: Solving a Paradox. ACTA ACUST UNITED AC 2018. [DOI: 10.2174/1874226201808010016] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Aims:To analyse the peptide commonality among viral, bacterial, and protozoan pathogens, and the immunopathologic consequences in the human host.Methods:HPV16, HCMV,C. diphtheriae, B. pertussis, C. tetani, T. gondii,andT. cruziwere analysed for common amino acid sequences that are additionally shared with the human host. The pentapeptide, a minimal immune determinant in humoral and cellular immune recognition, was used as a measurement unit of the peptide similarity level. Molecular modeling was applied to compare the amino acid contexts containing common minimal determinants.Results:Twenty-nine pentapeptides were found to occur, even hundreds of times, throughout the analyzed pathogen proteomes as well as in the human proteome. Such vast peptide commonalities together with molecular modeling data support the possibility that a pre-existing immune response to a first pathogen can be boosted by a successive exposure to a second different pathogen,i.e., the primary response to a pathogen can be transformed into a secondary response to a previously encountered different pathogen. Two possible consequences emerge. Firstly, no responses might be elicited against the pathogen lastly encountered either by infection or active immunization, but reactions could occur only with the early sensitizing pathogen, which is no more present in the organism. Secondly, the immune response boosted by the pathogen lastly encountered will find a way out by cross-reacting with human proteins.Conclusion:This study might explain the “original antigenic sin” phenomenon described seven decades ago [Francis T. Jr. Ann Intern Med 1953;39:203], thus providing explanations for vaccine failures and offering possible clues for designing successful vaccines.
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8
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Capone G, Fasano C, Lucchese G, Calabrò M, Kanduc D. EBV-Associated Cancer and Autoimmunity: Searching for Therapies. Vaccines (Basel) 2015; 3:74-89. [PMID: 26344947 PMCID: PMC4494242 DOI: 10.3390/vaccines3010074] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 12/12/2014] [Accepted: 01/27/2015] [Indexed: 12/26/2022] Open
Abstract
Epstein-Barr virus (EBV) infects B-, T-, and NK cells and has been associated not only with a wide range of lymphoid malignancies but also with autoimmune diseases such as lupus erythematosus, rheumatoid arthritis and, in particular, multiple sclerosis. Hence, effective immunotherapeutic approaches to eradicate EBV infection might overthrow cancer and autoimmunity incidence. However, currently no effective anti-EBV immunotherapy is available. Here we use the concept that protein immunogenicity is allocated in rare peptide sequences and search the Epstein-Barr nuclear antigen 1 (EBNA1) sequence for peptides unique to the viral protein and absent in the human host. We report on a set of unique EBV EBNA1 peptides that might be used in designing peptide-based therapies able to specifically hitting the virus or neutralizing pathogenic autoantibodies.
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Affiliation(s)
- Giovanni Capone
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari 70126, Italy.
| | - Candida Fasano
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari 70126, Italy.
| | - Guglielmo Lucchese
- Brain and Language Laboratory, Free University of Berlin, 14195 Berlin, Germany.
| | - Michele Calabrò
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari 70126, Italy.
| | - Darja Kanduc
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari 70126, Italy.
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9
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Wei Y, Xu J, Zhang L, Fu Y, Xu X. Development of novel small peptide ligands for antibody purification. RSC Adv 2015. [DOI: 10.1039/c5ra07829f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Small peptide ligands which were designed based on the interactions with human immunoglobulin G (IgG) using the molecular simulations, can offer a potential alternative for mAb purification with elution condition at pH 9 and pH 3.
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Affiliation(s)
- Yuping Wei
- State
- Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
| | - Jiandong Xu
- State
- Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
| | - Liang Zhang
- State
- Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
| | - Yankai Fu
- State
- Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
| | - Xia Xu
- State
- Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
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10
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Impact of Residual Impurities and Contaminants on Protein Stability. J Pharm Sci 2014; 103:1315-30. [DOI: 10.1002/jps.23931] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 02/17/2014] [Accepted: 02/18/2014] [Indexed: 02/03/2023]
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11
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Kanduc D, Fasano C, Bavaro SL, Novello G, Lucchese G, Capone G. Peptide profiling of the route from Mahoney to Sabin, and return. J Basic Microbiol 2014; 54:369-77. [DOI: 10.1002/jobm.201200642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 02/07/2013] [Indexed: 11/05/2022]
Affiliation(s)
- Darja Kanduc
- Department of Biosciences, Biotechnologies and Pharmacological Sciences; University of Bari; Bari Italy
| | - Candida Fasano
- Department of Biosciences, Biotechnologies and Pharmacological Sciences; University of Bari; Bari Italy
| | - Simona Lucia Bavaro
- Department of Biosciences, Biotechnologies and Pharmacological Sciences; University of Bari; Bari Italy
| | - Giuseppe Novello
- Department of Biosciences, Biotechnologies and Pharmacological Sciences; University of Bari; Bari Italy
| | - Guglielmo Lucchese
- Department of Biosciences, Biotechnologies and Pharmacological Sciences; University of Bari; Bari Italy
| | - Giovanni Capone
- Department of Biosciences, Biotechnologies and Pharmacological Sciences; University of Bari; Bari Italy
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12
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Pharmacokinetics and pharmacokinetic-pharmacodynamic correlations of therapeutic peptides. Clin Pharmacokinet 2014; 52:855-68. [PMID: 23719681 DOI: 10.1007/s40262-013-0079-0] [Citation(s) in RCA: 209] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Peptides, defined as polymers of less than 50 amino acids with a molecular weight of less than 10 kDa, represent a fast-growing class of new therapeutics which has unique pharmacokinetic characteristics compared to large proteins or small molecule drugs. Unmodified peptides usually undergo extensive proteolytic cleavage, resulting in short plasma half-lives. As a result of their low permeability and susceptibility to catabolic degradation, therapeutic peptides usually have very limited oral bioavailability and are administered either by the intravenous, subcutaneous, or intramuscular route, although other routes such as nasal delivery are utilized as well. Distribution processes are mainly driven by a combination of diffusion and to a lesser degree convective extravasation dependent on the size of the peptide, with volumes of distribution frequently not larger than the volume of the extracellular body fluid. Owing to the ubiquitous availability of proteases and peptidases throughout the body, proteolytic degradation is not limited to classic elimination organs. Since peptides are generally freely filtered by the kidneys, glomerular filtration and subsequent renal metabolism by proteolysis contribute to the elimination of many therapeutic peptides. Although small peptides have usually limited immunogenicity, formation of anti-drug antibodies with subsequent hypersensitivity reactions has been described for some peptide therapeutics. Numerous strategies have been applied to improve the pharmacokinetic properties of therapeutic peptides, especially to overcome their metabolic instability, low permeability, and limited tissue residence time. Applied techniques include amino acid substitutions, modification of the peptide terminus, inclusion of disulfide bonds, and conjugation with polymers or macromolecules such as antibody fragments or albumin. Application of model-based pharmacokinetic-pharmacodynamic correlations has been widely used for therapeutic peptides in support of drug development and dosage regimen design, especially because their targets are often well-described endogenous regulatory pathways and processes.
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13
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Spinosa JP, Kanduc D. Ovarian cancer: designing effective vaccines and specific diagnostic tools. Immunotherapy 2014; 6:35-41. [DOI: 10.2217/imt.13.144] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Aim: Notwithstanding a renewed interest in the application of immunotherapy as an alternative to chemotherapy and radiotherapy for the treatment of ovarian cancer (OC), and in spite of the available knowledge about ovarian tumor-associated-antigens, the search for a vaccine against OC remains a scientific and clinical challenge. Likewise, immunodiagnostics can detect only a late stage of the disease. Thus, the development of new therapeutic and diagnostic options is highly desirable. Methods: Based on the low-similarity hypothesis, which supports the concept that immunogenicity is preferentially associated to sequences with no/low-similarity to the host proteome, and using Protein Information Resource peptide match program, we searched the ovarian tumor antigen CA125 for amino acid sequences unique to CA125 and absent in the remaining human proteins. Results & conclusion: We identified a set of 159 pentapeptides unique to CA125 that might be used to design specific and effective immunological tools for diagnosis and treatment of OC.
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Affiliation(s)
- Jean Pierre Spinosa
- Department Biosciences, Biotechnologies & Biopharmaceutics, University of Bari, Bari, Italy
- Faculty of Biology & Medicine, University of Lausanne, Lausanne, Switzerland
| | - Darja Kanduc
- Department Biosciences, Biotechnologies & Biopharmaceutics, University of Bari, Bari, Italy
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14
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Capone G, Lucchese G, Calabrò M, Kanduc D. West Nile virus diagnosis and vaccination: using unique viral peptide sequences to evoke specific immune responses. Immunopharmacol Immunotoxicol 2012; 35:64-70. [DOI: 10.3109/08923973.2012.736521] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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15
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Capone G, Pagoni M, Delfino AP, Kanduc D. Evidence for a vast peptide overlap between West Nile virus and human proteomes. J Basic Microbiol 2012; 53:800-7. [PMID: 22961336 DOI: 10.1002/jobm.201200204] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 06/15/2012] [Indexed: 11/08/2022]
Abstract
The primary amino acid sequence of West Nile virus (WNV) polyprotein, GenBank accession number M12294, was analyzed by computional biology. WNV is a mosquito-borne neurotropic flavivirus that has emerged globally as a significant cause of viral encephalitis in humans. Using pentapeptides as scanning units and the perfect peptide match program from PIR International Protein Sequence Database, we compared the WNV polyprotein and the human proteome. WNV polyprotein showed significant sequence similarities to a number of human proteins. Several of these proteins are involved in embryogenesis, neurite outgrowth, cortical neuron branching, formation of mature synapses, semaphorin interactions, and voltage dependent L-type calcium channel subunits. The biocomputional study suggest that common amino acid segments might represent a potential platform for further studies on the neurological pathophysiology of WNV infections.
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Affiliation(s)
- Giovanni Capone
- Department of Biosciences, Biotechnologies and Pharmacological Sciences, University of Bari, Bari, Italy
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16
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Pentamers not found in the universal proteome can enhance antigen specific immune responses and adjuvant vaccines. PLoS One 2012; 7:e43802. [PMID: 22937099 PMCID: PMC3427150 DOI: 10.1371/journal.pone.0043802] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 07/26/2012] [Indexed: 12/22/2022] Open
Abstract
Certain short peptides do not occur in humans and are rare or non-existent in the universal proteome. Antigens that contain rare amino acid sequences are in general highly immunogenic and may activate different arms of the immune system. We first generated a list of rare, semi-common, and common 5-mer peptides using bioinformatics tools to analyze the UniProtKB database. Experimental observations indicated that rare and semi-common 5-mers generated stronger cellular responses in comparison with common-occurring sequences. We hypothesized that the biological process responsible for this enhanced immunogenicity could be used to positively modulate immune responses with potential application for vaccine development. Initially, twelve rare 5-mers, 9-mers, and 13-mers were incorporated in frame at the end of an H5N1 hemagglutinin (HA) antigen and expressed from a DNA vaccine. The presence of some 5-mer peptides induced improved immune responses. Adding one 5-mer peptide exogenously also offered improved clinical outcome and/or survival against a lethal H5N1 or H1N1 influenza virus challenge in BALB/c mice and ferrets, respectively. Interestingly, enhanced anti-HBsAg antibody production by up to 25-fold in combination with a commercial Hepatitis B vaccine (Engerix-B, GSK) was also observed in BALB/c mice. Mechanistically, NK cell activation and dependency was observed with enhancing peptides ex vivo and in NK-depleted mice. Overall, the data suggest that rare or non-existent oligopeptides can be developed as immunomodulators and supports the further evaluation of some 5-mer peptides as potential vaccine adjuvants.
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Manikwar P, Kiptoo P, Badawi AH, Büyüktimkin B, Siahaan TJ. Antigen-specific blocking of CD4-specific immunological synapse formation using BPI and current therapies for autoimmune diseases. Med Res Rev 2012; 32:727-64. [PMID: 21433035 PMCID: PMC4441537 DOI: 10.1002/med.20243] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In this review, we discuss T-cell activation, etiology, and the current therapies of autoimmune diseases (i.e., MS, T1D, and RA). T-cells are activated upon interaction with antigen-presenting cells (APC) followed by a "bull's eye"-like formation of the immunological synapse (IS) at the T-cell-APC interface. Although the various disease-modifying therapies developed so far have been shown to modulate the IS and thus help in the management of these diseases, they are also known to present some undesirable side effects. In this study, we describe a novel and selective way to suppress autoimmunity by using a bifunctional peptide inhibitor (BPI). BPI uses an intercellular adhesion molecule-1 (ICAM-1)-binding peptide to target antigenic peptides (e.g., proteolipid peptide, glutamic acid decarboxylase, and type II collagen) to the APC and therefore modulate the immune response. The central hypothesis is that BPI blocks the IS formation by simultaneously binding to major histocompatibility complex-II and ICAM-1 on the APC and selectively alters the activation of T cells from T(H)1 to T(reg) and/or T(H)2 phenotypes, leading to tolerance.
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Affiliation(s)
- Prakash Manikwar
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KA 66047, USA
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18
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Lucchese G, Pesce Delfino A. Developing an anti-Campylobacter jejunivaccine. Immunopharmacol Immunotoxicol 2012; 34:385-90. [DOI: 10.3109/08923973.2011.608685] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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19
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Capone G, Novello G, Bavaro SL, Fasano C, Pesce Delfino A, Polito AN, Kanduc D. A qualitative description of the peptide sharing between poliovirus and Homo sapiens. Immunopharmacol Immunotoxicol 2012; 34:779-85. [PMID: 22303874 DOI: 10.3109/08923973.2012.654610] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In a companion paper, we reported that pentapeptides from human poliovirus 1, Mahoney strain, occur repeatedly in human proteins for a total of more than 18,000 overlaps. In the present study, we describe the distribution of the polio pentapeptides throughout biochemical pathways and networks characterizing functions and tissues in the human host. The present study might be of help to better define the poliovirus-host relationships as well as for designing peptide modules with anti-polio activity.
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Affiliation(s)
- Giovanni Capone
- Department of Biochemistry and Molecular Biology, Universityof Bari, Bari, Italy
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20
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Novello G, Capone G, Fasano C, Bavaro SL, Polito AN, Kanduc D. A quantitative description of the peptide sharing between poliovirus and Homo sapiens. Immunopharmacol Immunotoxicol 2011; 34:373-8. [PMID: 22145926 DOI: 10.3109/08923973.2011.608360] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In the present study, we analyze the peptide commonality between poliovirus polyprotein and the human proteins. We report on the following findings: (1) the extent of polio peptide overlap on the human proteome is high, and involves the entire viral polyprotein; (2) viral peptide matching affects human proteins linked to fundamental cellular functions. The data may help to further our understanding of the relationships between poliovirus and the human host.
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Affiliation(s)
- Giuseppe Novello
- Department of Biochemistry and Molecular Biology, University of Bari, Italy
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21
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Ackerman ME, Lai JI, Pastan I, Wittrup KD. Exploiting bias in a non-immune human antibody library to predict antigenicity. Protein Eng Des Sel 2011; 24:845-53. [PMID: 21908549 DOI: 10.1093/protein/gzr046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Non-immune human antibody fragment libraries have generated antigen-binding proteins useful as prospective research, imaging, diagnostic and therapeutic agents. However, because the generation of such libraries relies on cloning antibody sequences from the circulating immune repertoire rather than truly naïve, germline sequences, their composition may reflect the deletion of autoreactive sequences, making them less suited for isolating binding clones to human antigens, but perhaps useful in applications where an in vitro handle on representative circulating antibody diversity is desired. Here we demonstrate that a large non-immune human scFv library is relatively depleted of sequences capable of recognizing human antigens as compared with orthologs antigens. Additionally, because this non-naïve, non-immune library may capture a representative section of antibody diversity, we explore its possible utility in conducting early pre-screens to predict the antigenicity of prospective therapeutics and find a correlation between the clinical immunogenicity of a small panel of protein therapeutics with their propensity for interacting with the library.
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22
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Fasano C, Kanduc D. Selfness-nonselfness in designing an anti-B19 erythrovirus vaccine. SELF/NONSELF 2011; 2:114-119. [PMID: 22299063 PMCID: PMC3268997 DOI: 10.4161/self.2.2.16190] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 06/14/2011] [Accepted: 06/15/2011] [Indexed: 11/19/2022]
Abstract
Although B19 erythrovirus infection may be associated with severe clinical outcomes, especially in early infancy, pregnancy and in immunocompromised or hemolytic subjects, no vaccine is currently available. Using the concept that effective immune responses to an infectious agent may be restricted to the specific peptidome unique to that agent, we analyzed primary amino acid sequence of B19 erythrovirus, searching for peptide motifs to be used in vaccine formulations. Here, we identify and describe a set of unique viral peptides that may guarantee both high efficacy and practically no cross-reactive autoimmune responses in anti-B19 immunotherapeutic approaches.
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Affiliation(s)
- Candida Fasano
- Department of Biochemistry and Molecular Biology; University of Bari; Bari, Italy
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23
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Lucchese G, Stufano A, Kanduc D. Searching for an effective, safe and universal anti-HIV vaccine: Finding the answer in just one short peptide. SELF/NONSELF 2011; 2:49-54. [PMID: 21776335 PMCID: PMC3136904 DOI: 10.4161/self.2.1.14762] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 01/06/2011] [Accepted: 01/07/2011] [Indexed: 01/17/2023]
Abstract
We explore the pentapeptide overlapping between human immunodeficiency virus (HIV) proteins and the human proteome. Our intent was to define viral peptides to be used in vaccines effective against different HIV strains, vaccines that are able to overcome the difficulties posed by the tendency of HIV to mutate, and that are also exempt from harmful collateral cross-reactions, as well as being repeatedly administrable to the global population. Analysis of HIV-1 envelope glycoprotein 160 (Env gp160) sequences revealed a set of 15 pentapeptides highly conserved among a number of retroviral sequences, and absent in the human proteome, thus representing unique molecular retroviral signatures. Use of these short viral peptide modules may represent the first concrete step toward the goal of a universal, safe and effective anti-HIV vaccine.
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Affiliation(s)
- Guglielmo Lucchese
- Department of Biochemistry and Molecular Biology; University of Bari; Bari, Italy
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24
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Kanduc D. Describing the hexapeptide identity platform between the influenza A H5N1 and Homo sapiens proteomes. Biologics 2010; 4:245-61. [PMID: 20859452 PMCID: PMC2943197 DOI: 10.2147/btt.s12097] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Indexed: 11/23/2022]
Abstract
We searched the primary sequence of influenza A H5N1 polyprotein for hexamer amino acid sequences shared with human proteins using the Protein International Resource database and the exact peptide matching analysis program. We find that the viral polyprotein shares numerous hexapeptides with the human proteome. The human proteins involved in the viral overlap are represented by antigens associated with basic cell functions such as proliferation, development, and differentiation. Of special importance, many human proteins that share peptide sequences with influenza A polyprotein are antigens such as reelin, neurexin I-α, myosin-IXa, Bardet–Biedl syndrome 10 protein, Williams syndrome transcription factor, disrupted in schizophrenia 1 protein, amyotrophic lateral sclerosis 2 chromosomal region candidate gene 17 protein, fragile X mental retardation 2 protein, and jouberin. That is, the viral-vs-human overlap involves human proteins that, when altered, have been reported to be potentially associated with multiple neurological disorders that can include autism, epilepsy, obesity, dystonia, ataxia–telangiectasia, amyotrophic lateral sclerosis, sensorineural deafness, sudden infant death syndrome, Charcot-Marie-Tooth disease, and myelination. The present data are discussed as a possible molecular basis for understanding influenza A viral escape from immunosurveillance and for defining anti-influenza immune-therapeutic approaches devoid of collateral adverse events.
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Affiliation(s)
- Darja Kanduc
- Department of Biochemistry and Molecular Biology, University of Bari, Italy
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25
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Capone G, Novello G, Fasano C, Trost B, Bickis M, Kusalik A, Kanduc D. The oligodeoxynucleotide sequences corresponding to never-expressed peptide motifs are mainly located in the non-coding strand. BMC Bioinformatics 2010; 11:383. [PMID: 20646284 PMCID: PMC2919516 DOI: 10.1186/1471-2105-11-383] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Accepted: 07/20/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We study the usage of specific peptide platforms in protein composition. Using the pentapeptide as a unit of length, we find that in the universal proteome many pentapeptides are heavily repeated (even thousands of times), whereas some are quite rare, and a small number do not appear at all. To understand the physico-chemical-biological basis underlying peptide usage at the proteomic level, in this study we analyse the energetic costs for the synthesis of rare and never-expressed versus frequent pentapeptides. In addition, we explore residue bulkiness, hydrophobicity, and codon number as factors able to modulate specific peptide frequencies. Then, the possible influence of amino acid composition is investigated in zero- and high-frequency pentapeptide sets by analysing the frequencies of the corresponding inverse-sequence pentapeptides. As a final step, we analyse the pentadecamer oligodeoxynucleotide sequences corresponding to the never-expressed pentapeptides. RESULTS We find that only DNA context-dependent constraints (such as oligodeoxynucleotide sequence location in the minus strand, introns, pseudogenes, frameshifts, etc.) provide a coherent mechanistic platform to explain the occurrence of never-expressed versus frequent pentapeptides in the protein world. CONCLUSIONS This study is of importance in cell biology. Indeed, the rarity (or lack of expression) of specific 5-mer peptide modules implies the rarity (or lack of expression) of the corresponding n-mer peptide sequences (with n < 5), so possibly modulating protein compositional trends. Moreover the data might further our understanding of the role exerted by rare pentapeptide modules as critical biological effectors in protein-protein interactions.
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Affiliation(s)
- Giovanni Capone
- Department of Biochemistry and Molecular Biology "Ernesto Quagliariello", University of Bari, Bari, Italy
| | - Giuseppe Novello
- Department of Biochemistry and Molecular Biology "Ernesto Quagliariello", University of Bari, Bari, Italy
| | - Candida Fasano
- Department of Biochemistry and Molecular Biology "Ernesto Quagliariello", University of Bari, Bari, Italy
| | - Brett Trost
- Department of Computer Science, University of Saskatchewan, Saskatoon, Canada
| | - Mik Bickis
- Department of Mathematics and Statistics, University of Saskatchewan, Saskatoon, Canada
| | - Anthony Kusalik
- Department of Computer Science, University of Saskatchewan, Saskatoon, Canada
| | - Darja Kanduc
- Department of Biochemistry and Molecular Biology "Ernesto Quagliariello", University of Bari, Bari, Italy
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26
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Kanduc D. Protein information content resides in rare peptide segments. Peptides 2010; 31:983-8. [PMID: 20153390 DOI: 10.1016/j.peptides.2010.02.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Revised: 02/03/2010] [Accepted: 02/03/2010] [Indexed: 01/01/2023]
Abstract
Discovering the informational rule(s) underlying structure-function relationships in the protein language is at the core of biology. Current theories have proven inadequate to explain the origins of biological information such as that found in nucleotide and amino acid sequences. Here, we demonstrate that the information content of an amino acid motif correlates with the motif rarity. A structured analysis of the scientific literature supports the theory that rare pentapeptide words have higher significance than more common pentapeptides in biological cell 'talk'. This study expands on our previous research showing that the immunological information contained in an amino acid sequence is inversely related to the sequence frequency in the host proteome.
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Affiliation(s)
- Darja Kanduc
- Department of Biochemistry and Molecular Biology, University of Bari, Italy.
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27
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Stufano A, Capone G, Pesetti B, Polimeno L, Kanduc D. Clustering of rare peptide segments in the HCV immunome. SELF/NONSELF 2010; 1:154-162. [PMID: 21487517 PMCID: PMC3065674 DOI: 10.4161/self.1.2.11391] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Revised: 02/01/2010] [Accepted: 02/03/2010] [Indexed: 01/01/2023]
Abstract
Our previous research and a comprehensive meta-analysis of data from the literature on epitope mapping has revealed that the B cell epitope repertoire is allocated to rare peptide motifs, i.e., antigenic peptide sequences endowed with a low level of similarity to the host proteome. From a clinical point of view, low-similarity peptides able to evoke an immune response appear to be of special interest for the rational design of vaccines for poorly treatable diseases such as hepatitis-C virus (HCV) infection. Indeed, low similarity peptides would guarantee the highest specificity and lowest cross-reactivity, i.e., effectiveness without adverse side-effects. In this study, aimed at gaining further information for the development of effective anti-HCV peptide-based vaccines, the HCV epitopes recognized by human antibodies and currently catalogued in the Immune Epitope Data Base (IEDB) were examined for pentamer sequence similarities to the human proteome. We report that the analyzed HCV determinants are characterized by the presence of fragment absent from (or scarcely represented in) human proteins. These data confirm the low-similarity hypothesis, according to which a low-similarity to the host proteome defines the nonself character of microbial antigens and modulates peptide immunogenicity. Moreover, this study indicates a concrete and safe immunotherapeutic approach which might be used in a universal anti-HCV vaccine.
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Affiliation(s)
- Angela Stufano
- Department of Biochemistry and Molecular Biology; University of Bari; Bari, Italy
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28
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Removal of B cell epitopes as a practical approach for reducing the immunogenicity of foreign protein-based therapeutics. Adv Drug Deliv Rev 2009; 61:977-85. [PMID: 19679153 DOI: 10.1016/j.addr.2009.07.014] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Revised: 07/09/2009] [Accepted: 07/14/2009] [Indexed: 11/23/2022]
Abstract
Immunogenicity of non-human proteins with useful therapeutic properties has prevented their development for use in the therapy of disease. However, this class of proteins could be very useful, if their immunogenicity could be markedly reduced so that many treatment cycles could be administered. One approach to reduce the immunogenicity of foreign proteins is to identify B cell epitopes on the protein and eliminate them by mutagenesis. In this article, theoretical aspects and experimental evidence for the feasibility of B cell epitope removal is reviewed. A special focus is given to our results with deimmunization of recombinant immunotoxins in which Fvs are fused to a 38kDa portion of the bacterial protein, Pseudomonas exotoxin A (PE38). Immunotoxins targeting CD22 and CD25 have produced complete remissions in many patients with drug resistant Hairy Cell Leukemia and are being evaluated in other malignancies. Experimental data summarized in this review indicates that removal of B cell epitopes is a practical approach for making less immunogenic protein therapeutics from non-human functional proteins. This approach requires grouping of the epitopes to identify targets for deimmunization followed by quantitative analysis of the decrease in affinity produced by the mutations in B cell epitopes.
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29
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Lucchese A, Serpico R, Crincoli V, Shoenfeld Y, Kanduc D. Sequence Uniqueness as a Molecular Signature of HIV-1-Derived B-Cell Epitopes. Int J Immunopathol Pharmacol 2009; 22:639-46. [DOI: 10.1177/039463200902200309] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The complex pathophysiology of human immunodeficiency virus (HIV) infection and the relatively high mutation rate of the retrovirus make it challenging to design effective anti-HIV vaccines. Several attempts have been made during the last decades to elucidate the enigmatic immunology of HIV infection and to predict potential immunogenic peptides for active vaccination using bioinformatic analysis methods. The results obtained to date to address this important problem are scarce. In this study, we exploit available HIV databases and analyse previously characterized HIV-encoded linear B-cell epitopes for their amino acid sequence similarity to the human or murine host proteome. We obtained further documentation that the HIV-derived antibody-targeted sequences mostly coincide with peptide areas rarely shared with the host proteins. In toto, our past and present data give clear-cut support to the statement that low-similarity to the host proteome is a major mechanism in defining viral peptide immunogenicity and indicate a possible way for inducing effective, high-titer, and non-cross-reactive antibodies to be used in anti-HIV vaccine therapy.
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Affiliation(s)
| | | | - V. Crincoli
- Department of Odontostomatology and Surgery, University of Bari, Italy
| | - Y. Shoenfeld
- Center for Autoimmune Diseases, Department of Medicine ‘B’, Sheba Medical Center, Israel and Sackler Faculty of Medicine, Tel-Aviv University, Israel
| | - D. Kanduc
- Department of Biochemistry and Molecular Biology, University of Bari, Italy
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30
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Kanduc D. Epitopic peptides with low similarity to the host proteome: towards biological therapies without side effects. Expert Opin Biol Ther 2008; 9:45-53. [DOI: 10.1517/14712590802614041] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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31
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Kanduc D, Stufano A, Lucchese G, Kusalik A. Massive peptide sharing between viral and human proteomes. Peptides 2008; 29:1755-66. [PMID: 18582510 PMCID: PMC7115663 DOI: 10.1016/j.peptides.2008.05.022] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Revised: 05/28/2008] [Accepted: 05/30/2008] [Indexed: 11/10/2022]
Abstract
Thirty viral proteomes were examined for amino acid sequence similarity to the human proteome, and, in parallel, a control of 30 sets of human proteins was analyzed for internal human overlapping. We find that all of the analyzed 30 viral proteomes, independently of their structural or pathogenic characteristics, present a high number of pentapeptide overlaps to the human proteome. Among the examined viruses, human T-lymphotropic virus 1, Rubella virus, and hepatitis C virus present the highest number of viral overlaps to the human proteome. The widespread and ample distribution of viral amino acid sequences through the human proteome indicates that viral and human proteins are formed of common peptide backbone units and suggests a fluid compositional chimerism in phylogenetic entities canonically classified distantly as viruses and Homo sapiens. Importantly, the massive viral to human peptide overlapping calls into question the possibility of a direct causal association between virus-host sharing of amino acid sequences and incitement to autoimmune reactions through molecular recognition of common motifs.
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Affiliation(s)
- Darja Kanduc
- Department of Biochemistry and Molecular Biology, University of Bari, Bari 70126, Italy.
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