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Menditti D, Santagata M, Guida D, Magliulo R, D'Antonio GM, Staglianò S, Boschetti CE. State of the Art in the Diagnosis and Assessment of Oral Malignant and Potentially Malignant Disorders: Present Insights and Future Outlook-An Overview. Bioengineering (Basel) 2024; 11:228. [PMID: 38534502 DOI: 10.3390/bioengineering11030228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/28/2024] Open
Abstract
Oral Potentially Malignant Disorder (OPMD) is a significant concern for clinicians due to the risk of malignant transformation. Oral Squamous Cell Carcinoma (OSCC) is a common type of cancer with a low survival rate, causing over 200,000 new cases globally each year. Despite advancements in diagnosis and treatment, the five-year survival rate for OSCC patients remains under 50%. Early diagnosis can greatly improve the chances of survival. Therefore, understanding the development and transformation of OSCC and developing new diagnostic methods is crucial. The field of oral medicine has been advanced by technological and molecular innovations, leading to the integration of new medical technologies into dental practice. This study aims to outline the potential role of non-invasive imaging techniques and molecular signatures for the early detection of Oral Malignant and Potentially Malignant Disorders.
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Affiliation(s)
- Dardo Menditti
- Multidisciplinary Department of Medical-Surgical and Dental Specialties, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Mario Santagata
- Multidisciplinary Department of Medical-Surgical and Dental Specialties, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - David Guida
- Multidisciplinary Department of Medical-Surgical and Dental Specialties, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Roberta Magliulo
- Multidisciplinary Department of Medical-Surgical and Dental Specialties, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Giovanni Maria D'Antonio
- Division of Plastic and Reconstructive Surgery, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90128 Palermo, Italy
| | - Samuel Staglianò
- Multidisciplinary Department of Medical-Surgical and Dental Specialties, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Ciro Emiliano Boschetti
- Multidisciplinary Department of Medical-Surgical and Dental Specialties, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
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Correlation between Oral Lichen Planus and Viral Infections Other Than HCV: A Systematic Review. J Clin Med 2022; 11:jcm11185487. [PMID: 36143134 PMCID: PMC9501453 DOI: 10.3390/jcm11185487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVES This review aimed to evaluate the correlation between viral infections (HPV, EBV, HSV-1, CMV) other than HCV and oral lichen planus to assess if there is sufficient evidence to establish if these viruses can play a role in the etiopathogenesis of the disease. MATERIALS AND METHODS We reviewed the literature using different search engines (PubMed, ISI Web of Science, and the Cochrane Library), employing MeSH terms such as "oral lichen planus" and "OLP" in conjunction with other terms. We utilized the Population, Intervention, Comparison, Outcomes, and Study design (PICOS) method to define our study eligibility criteria. RESULTS A total of 43 articles of the 1219 results initially screened were included in the study. We allocated the 43 selected items into four groups, according to each related virus: HPV, EBV, HSV-1, and CMV. CONCLUSIONS Heterogeneous results neither confirm nor exclude a direct correlation between the investigated viral infections and oral lichen planus etiopathogenesis and its feasible malignant transformation. Many viral agents can cause oral lesions and act as cancerizing agents. Future studies could be desirable to produce comparable statistical analyses and enhance the quantity and quality of the outcomes to promote the translation of research into clinical practice.
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Kanduc D. SARS-CoV-2: The Self-Nonself Issue and Diagnostic Tests. J Lab Physicians 2022; 15:56-61. [PMID: 37064977 PMCID: PMC10104719 DOI: 10.1055/s-0042-1750078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022] Open
Abstract
Abstract
Objective At present, false negatives/positives have been reported in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostics. Searching for the molecular basis of such tests' unreliability, this study aimed at defining how specific are the sequences used in serological and polymerase chain reaction (PCR) tests to detect SARS-CoV-2.
Materials and Methods Analyses were performed on the leading SARS-CoV-2 biomarker spike glycoprotein (gp). Sharing of peptide sequences between the spike antigen and the human host was analyzed using the Peptide Search program from Uniprot database. Sharing of oligonucleotide sequences was investigated using the nucleotide Basic Local Alignment Search Tool (BLASTn) from National Center for Biotechnology Information (NCBI).
Results Two main points stand out: (1) a massive pentapeptide sharing exists between the spike gp and the human proteome, and only a limited number of pentapeptides (namely 107) identify SARS-CoV-2 spike gp as nonself when compared with the human proteome, and (2) the small phenetic difference practically disappears at the genetic level. Indeed, almost all of the 107 pentadecameric nucleotide sequences coding for the pentapeptides unique to SARS-CoV-2 spike gp are present in human nucleic acids too.
Conclusions The data are of immunological significance for defining the issue of the viral versus human specificity and likely explain the fact that false positives can occur in serological and PCR tests for SARS-CoV-2 detection.
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Affiliation(s)
- Darja Kanduc
- Department of Biosciences, Biotechnologies, and Biopharmaceutics, University of Bari, Bari, Italy
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Abstract
INTRODUCTION Proteomics, i.e. the study of the set of proteins produced in a cell, tissue, organism, or biological entity, has made possible analyses and contextual comparisons of proteomes/proteins and biological functions among the most disparate entities, from viruses to the human being. In this way, proteomic scrutiny of tumor-associated proteins, autoantigens, and pathogen antigens offers the tools for fighting cancer, autoimmunity, and infections. AREAS COVERED Comparative proteomics and immunoproteomics, the new scientific disciplines generated by proteomics, are the main themes of the present review that describes how comparative analyses of pathogen and human proteomes led to re-modulate the molecular mimicry concept of the pre-proteomic era. I.e. before proteomics, molecular mimicry - the sharing of peptide sequences between two biological entities - was considered as intrinsically endowed with immunologic properties and was related to cross-reactivity. Proteomics allowed to redefine such an assumption using physicochemical parameters according to which frequency and hydrophobicity preferentially confer an immunologic potential to shared peptide sequences. EXPERT OPINION Proteomics is outlining peptide platforms to be used for the diagnostics and management of human diseases. A Molecular Medicine targeted to obtain healing without paying the price for adverse events is on the horizon. The next step is to take up the challenge and operate the paradigm shift that the current proteomic era requires.
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Affiliation(s)
- Darja Kanduc
- Department of Biosciences, Biotechnologies, and Biopharmaceutics, University of Bari, Bari, Italy
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Kanduc D. Lack of Molecular Mimicry between Nonhuman Primates and Infectious Pathogens: The Possible Genetic Bases. Glob Med Genet 2021; 8:32-37. [PMID: 33748822 PMCID: PMC7964256 DOI: 10.1055/s-0041-1724106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Recently, it was found that proteomes from poliovirus, measles virus, dengue virus, and severe acute respiratory syndrome-related Coronavirus 2 (SARS-CoV-2) have high molecular mimicry at the heptapeptide level with the human proteome, while heptapeptide commonality is minimal or absent with proteomes from nonhuman primates, that is, gorilla, chimpanzee, and rhesus macaque. To acquire more data on the issue, analyses here have been expanded to Ebola virus,
Francisella tularensis
, human immunodeficiency virus-1 (HIV-1),
Toxoplasma gondii
, Variola virus, and
Yersinia pestis
. Results confirm that heptapeptide overlap is high between pathogens and
Homo sapiens
, but not between pathogens and primates. Data are discussed in light of the possible genetic bases that differently model primate phenomes, thus possibly underlying the zero/low level of molecular mimicry between infectious agents and primates. Notably, this study might help address preclinical vaccine tests that currently utilize primates as animal models, since autoimmune cross-reactions and the consequent adverse events cannot occur
in absentia
of shared sequences.
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Affiliation(s)
- Darja Kanduc
- Department of Biosciences, Biotechnologies, and Biopharmaceutics, University of Bari, Bari, Italy
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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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Kanduc D. The comparative biochemistry of viruses and humans: an evolutionary path towards autoimmunity. Biol Chem 2019; 400:629-638. [PMID: 30504522 DOI: 10.1515/hsz-2018-0271] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 11/07/2018] [Indexed: 11/15/2022]
Abstract
Analyses of the peptide sharing between five common human viruses (Borna disease virus, influenza A virus, measles virus, mumps virus and rubella virus) and the human proteome highlight a massive viral vs. human peptide overlap that is mathematically unexpected. Evolutionarily, the data underscore a strict relationship between viruses and the origin of eukaryotic cells. Indeed, according to the viral eukaryogenesis hypothesis and in light of the endosymbiotic theory, the first eukaryotic cell (our lineage) originated as a consortium consisting of an archaeal ancestor of the eukaryotic cytoplasm, a bacterial ancestor of the mitochondria and a viral ancestor of the nucleus. From a pathologic point of view, the peptide sequence similarity between viruses and humans may provide a molecular platform for autoimmune crossreactions during immune responses following viral infections/immunizations.
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Affiliation(s)
- Darja Kanduc
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, I-70124 Bari, Italy
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Morenikeji OB, Thomas BN. In silico analyses of CD14 molecule reveal significant evolutionary diversity, potentially associated with speciation and variable immune response in mammals. PeerJ 2019; 7:e7325. [PMID: 31338263 PMCID: PMC6628885 DOI: 10.7717/peerj.7325] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 06/19/2019] [Indexed: 12/23/2022] Open
Abstract
The cluster differentiation gene (CD14) is a family of monocyte differentiating genes that works in conjunction with lipopolysaccharide binding protein, forming a complex with TLR4 or LY96 to mediate innate immune response to pathogens. In this paper, we used different computational methods to elucidate the evolution of CD14 gene coding region in 14 mammalian species. Our analyses identified leucine-rich repeats as the only significant domain across the CD14 protein of the 14 species, presenting with frequencies ranging from one to four. Importantly, we found signal peptides located at mutational hotspots demonstrating that this gene is conserved across these species. Out of the 10 selected variants analyzed in this study, only six were predicted to possess significant deleterious effect. Our predicted protein interactome showed a significant varying protein–protein interaction with CD14 protein across the species. This may be important for drug target and therapeutic manipulation for the treatment of many diseases. We conclude that these results contribute to our understanding of the CD14 molecular evolution, which underlays varying species response to complex disease traits.
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Affiliation(s)
| | - Bolaji N Thomas
- Department of Biomedical Sciences, Rochester Institute of Technology, Rochester, NY, USA
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9
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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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11
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Lucchese A. Streptococcus mutans antigen I/II and autoimmunity in cardiovascular diseases. Autoimmun Rev 2017; 16:456-460. [PMID: 28286107 DOI: 10.1016/j.autrev.2017.03.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 02/05/2017] [Indexed: 12/12/2022]
Abstract
Infectious pathogens from the oral cavity cause oral diseases such as caries, gingivitis, periodontitis, endodontic infections, and alveolar osteitis, and often are also concomitant to systemic diseases, including cardiovascular disorders, stroke, preterm birth, diabetes, and pneumonia, among others. The relationship(s) between oral infections and systemic diseases are still unclear. Using the bacterial cell surface antigen I/II from S. mutans and cardiovascular diseases as a model, this study analyzes peptide commonalities that might underlie autoimmune crossreactions between the bacterial antigen and human proteins associated with cardiovascular disorders. The study outlines a vast peptide sharing that calls attention on autoimmune crossreactivity as a possible mechanism by which S. mutans infection might contribute to induce cardiovascular diseases, and, more in general, offers a new approach to investigate the still elusive molecular links between focal oral infections and human systemic diseases.
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Affiliation(s)
- Alberta Lucchese
- Multidisciplinary Department of Medical-Surgical and Odontostomatological Specialties, University of Campania 'Luigi Vanvitelli', Via de Crecchio 6, 80138 Naples, Italy.
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12
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Segal Y, Dahan S, Calabrò M, Kanduc D, Shoenfeld Y. HPV and systemic lupus erythematosus: a mosaic of potential crossreactions. Immunol Res 2017; 65:564-571. [DOI: 10.1007/s12026-016-8890-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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13
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Lucchese A, Guida A, Capone G, Donnarumma G, Laino L, Petruzzi M, Serpico R, Silvestre F, Gargari M. Proteomic peptide scan of porphyromonas gingivalis fima type ii for searching potential b-cell epitopes. ORAL & IMPLANTOLOGY 2017; 9:83-88. [PMID: 28042435 DOI: 10.11138/orl/2016.9.2.083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
PURPOSE To identify potential antigenic targets for Porphyromonas gingivalis vaccine development. MATERIALS AND METHODS In the present study, we analyzed the Porphyromonas gingivalis, fimA type II primary amino acid sequence and characterized the similarity to the human proteome at the pentapeptide level. RESULTS We found that exact peptide-peptide profiling of the fimbrial antigen versus the human proteome shows that only 19 out of 344 fimA type II pentapeptides are uniquely owned by the bacterial protein. CONCLUSIONS The concept that protein immunogenicity is allocated in rare peptide sequences and the search the Porphyromonas gingivalis fimA type II sequence for peptides unique to the bacterial protein and absent in the human host, might be used in new therapeutical approaches as a significant adjunct to current periodontal therapies.
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Affiliation(s)
- A Lucchese
- Multidisciplinary Department of Medical-Surgical and Odontostomatological Specialties, Second University of Naples SUN, Naples, Italy
| | - A Guida
- Postgraduate School in Oral Surgery, Department of Neurosciences, Reproductive and Odontostomatological Sciences, University of Naples "Federico II", Naples, Italy
| | - G Capone
- Department of Biosciences, Biotechnologies and Pharmacological Sciences, University of Bari, Bari, Italy
| | - G Donnarumma
- Department of Experimental Medicine, Section of Microbiology and Clinical Microbiology, Second University of Naples, Naples, Italy
| | - L Laino
- Multidisciplinary Department of Medical-Surgical and Odontostomatological Specialties, Second University of Naples SUN, Naples, Italy
| | - M Petruzzi
- Interdisciplinary Department of Medicine (DIM) - Section of Dentistry, University "Aldo Moro" of Bari, Bari, Italy
| | - R Serpico
- Multidisciplinary Department of Medical-Surgical and Odontostomatological Specialties, Second University of Naples SUN, Naples, Italy
| | - F Silvestre
- Departimento de Estomatologia, University of Valencia, Valencia, Spain
| | - M Gargari
- Department of Clinical Sciences And Translational Medicine, University of Rome "Tor Vergata", Rome, Italy; Department of dentistry "Fra G.B. Orsenigo - Ospedale San Pietro F.B.F.", Rome, Italy
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14
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Kanduc D, Shoenfeld Y. From HBV to HPV: Designing vaccines for extensive and intensive vaccination campaigns worldwide. Autoimmun Rev 2016; 15:1054-1061. [DOI: 10.1016/j.autrev.2016.07.030] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 07/12/2016] [Indexed: 12/12/2022]
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15
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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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16
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Kanduc D. Homology, similarity, and identity in peptide epitope immunodefinition. J Pept Sci 2012; 18:487-94. [PMID: 22696298 DOI: 10.1002/psc.2419] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2012] [Revised: 04/10/2012] [Accepted: 04/25/2012] [Indexed: 01/03/2023]
Abstract
The tendency to use the terms homology, similarity, and identity interchangeably persists in comparative biology. When translated to immunology, overlapping the concepts of homology, similarity, and identity complicates the exact definition of the self-nonself dichotomy and, in particular, affects immunopeptidomics, an emerging field aimed at cataloging and distinguishing immunoreactive peptide epitopes from silent nonreactive amino acid sequences. The definition of similar/dissimilar peptides in immunology is discussed with special attention to the analysis of immunological (dis)similarity between two or more protein sequences that equates to measuring sequence similarity with the use of a proper measurement unit such as a length determinant.
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Affiliation(s)
- Darja Kanduc
- Department of Biosciences, Biotechnologies and Pharmacological Sciences, University of Bari, Bari, Italy.
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17
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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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18
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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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19
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Adamczyk-Poplawska M, Markowicz S, Jagusztyn-Krynicka EK. Proteomics for development of vaccine. J Proteomics 2011; 74:2596-616. [PMID: 21310271 DOI: 10.1016/j.jprot.2011.01.019] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 01/26/2011] [Accepted: 01/31/2011] [Indexed: 12/20/2022]
Abstract
The success of genome projects has provided us with a vast amount of information on genes of many pathogenic species and has raised hopes for rapid progress in combating infectious diseases, both by construction of new effective vaccines and by creating a new generation of therapeutic drugs. Proteomics, a strategy complementary to the genomic-based approach, when combined with immunomics (looking for immunogenic proteins) and vaccinomics (characterization of host response to immunization), delivers valuable information on pathogen-host cell interaction. It also speeds the identification and detailed characterization of new antigens, which are potential candidates for vaccine development. This review begins with an overview of the global status of vaccinology based on WHO data. The main part of this review describes the impact of proteomic strategies on advancements in constructing effective antibacterial, antiviral and anticancer vaccines. Diverse aspects of disease mechanisms and disease preventions have been investigated by proteomics.
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Affiliation(s)
- Monika Adamczyk-Poplawska
- Department of Virology, Institute of Microbiology, Biology Faculty, Warsaw University, Warsaw, Poland
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20
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Abstract
Proteomics has been widely used in the last few years to look for new biomarkers and decipher the mechanism of HIV–host interaction. Herein, we review the recent developments of HIV/AIDS proteomic research, including the samples used in HIV/AIDS related research, the technologies used for proteomic study, the diagnosis biomarkers of HIV-associated disease especially HIV-associated neurocognitive impairment, the mechanisms of HIV–host interaction, HIV-associated dementia, substance abuse, and so on. In the end of this review, we also give some prospects about the limitation and future improvement of HIV/AIDS proteomic research.
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21
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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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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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