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Lim C, Lee S, Shin Y, Cho S, Park C, Shin Y, Song EC, Kim WK, Ham C, Kim SB, Kwon YS, Oh KT. Development and application of novel peptide-formulated nanoparticles for treatment of atopic dermatitis. J Mater Chem B 2023; 11:10131-10146. [PMID: 37830254 DOI: 10.1039/d3tb01202f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Atopic dermatitis is a chronic inflammatory skin condition that is characterized by skin inflammation, itching, and redness. Although various treatments can alleviate symptoms, they often come with side effects, highlighting the need for new treatments. Here, we discovered a new peptide-based therapy using the intra-dermal delivery technology (IDDT) platform developed by Remedi Co., Ltd (REMEDI). The platform screens and identifies peptides derived from proteins in the human body that possess cell-penetrating peptide (CPP) properties. We screened over 1000-peptides and identified several derived from the Speckled protein (SP) family that have excellent CPP properties and have anti-inflammatory effects. We assessed these peptides for their potential as a treatment for atopic dermatitis. Among them, the RMSP1 peptide showed the most potent anti-inflammatory effects by inhibiting the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) and signal transducer and activator of transcription 3 (STAT3) signaling pathways while possessing CPP properties. To further improve efficacy and stability, we developed a palmitoylated version called Pal-RMSP1. Formulation studies using liposomes (Pal-RMSP1 LP) and micelles (Pal-RMSP1 DP) demonstrated improved anti-inflammatory effects in vitro and enhanced therapeutic effects in vivo. Our study indicates that nano-formulated Pal-RMSP1 could have the potential to become a new treatment option for atopic dermatitis.
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Affiliation(s)
- Chaemin Lim
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea.
- College of Pharmacy, CHA University, 335 Pangyo-ro, Bundang-gu, Seongnam-si, 13488 Gyeonggi-do, Republic of Korea
| | - Subin Lee
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea.
- Department of Global Innovative Drugs, The Graduate School of Chung-Ang University, Seoul 06974, Republic of Korea
| | - Yuseon Shin
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea.
- Department of Global Innovative Drugs, The Graduate School of Chung-Ang University, Seoul 06974, Republic of Korea
| | - Seongmin Cho
- Remedi Co., Ltd. Research Center, Songdo 21990, Republic of Korea
| | - Chanho Park
- Remedi Co., Ltd. Research Center, Songdo 21990, Republic of Korea
| | - Yungyeong Shin
- Remedi Co., Ltd. Research Center, Songdo 21990, Republic of Korea
| | - Ee Chan Song
- Remedi Co., Ltd. Research Center, Songdo 21990, Republic of Korea
| | - Wan Ki Kim
- Remedi Co., Ltd. Research Center, Songdo 21990, Republic of Korea
| | - Cheolmin Ham
- Rare Isotope Science Project, Institute for Basic Science, Daejeon 34000, Republic of Korea
| | - Sang Bum Kim
- College of Pharmacy, Sahmyook University, Seoul 01795, Republic of Korea
| | - Yong-Su Kwon
- Department of Ophthalmology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kyung Taek Oh
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea.
- Department of Global Innovative Drugs, The Graduate School of Chung-Ang University, Seoul 06974, Republic of Korea
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2
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Kanduc D. Epigenetics of Hypogonadotropic Hypogonadism: Molecular Mimicry between Severe Acute Respiratory Syndrome Coronavirus 2 and KISSR. Glob Med Genet 2023; 10:129-132. [PMID: 37360005 PMCID: PMC10289852 DOI: 10.1055/s-0043-1770767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023] Open
Abstract
This study analyzed KISS1 and its receptor KISSR for peptide sharing with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It was found that SARS-CoV-2 shares numerous minimal immune pentapeptide determinants with KISSR only. The peptide sharing has a high immunologic potential since almost all the common peptides are present in 101 SARS-CoV-2-derived immunoreactive epitopes. Data are in favor of configuring molecular mimicry as an epigenetic factor that can alter KISSR thus causing the hypogonadotropic hypogonadism syndrome with which altered KISSR associates.
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Affiliation(s)
- Darja Kanduc
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
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3
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Vijayakumar S. Harnessing Fuzzy Rule Based System for Screening Major Histocompatibility Complex Class I Peptide Epitopes from the Whole Proteome: An Implementation on the Proteome of Leishmania donovani. J Comput Biol 2022; 29:1045-1058. [PMID: 35404099 DOI: 10.1089/cmb.2021.0464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The development of peptide-based vaccines is enhanced by immunoinformatics, which predicts the patterns that B cells and T cells recognize. Although several tools are available for predicting the Major histocompatibility complex (MHC-I) binding peptides, the wide variants of human leucocyte antigen allele make it challenging to choose a peptide that will induce an immune response in a majority of people. In addition, for a peptide to be considered a potential vaccine candidate, factors such as T cell affinity, proteasome cleavage, and similarity to human proteins also play a major role. Identifying peptides that satisfy the earlier cited measures across the entire proteome is, therefore, challenging. Hence, the fuzzy inference system (FIS) is proposed to detect each peptide's potential as a vaccine candidate and assign it either a very high, high, moderate, or low ranking. The FIS includes input features from 6 modules (binding of 27 major alleles, T cell propensity, pro-inflammatory response, proteasome cleavage, transporter associated with antigen processing, and similarity with human peptide) and rules derived from an observation of features on positive samples. On validation of experimentally verified peptides, a balanced accuracy of ∼80% was achieved, with a Mathew's correlation coefficient score of 0.67 and an F-1 score of 0.74. In addition, the method was implemented on complete proteome of Leishmania donovani, which contains ∼4,800,000 peptides. Lastly, a searchable database of the ranked results of the L. donovani proteome was made and is available online (MHC-FIS-LdDB). It is hoped that this method will simplify the identification of potential MHC-I binding candidates from a large proteome.
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Affiliation(s)
- Saravanan Vijayakumar
- Department of Bioinformatics, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, India
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4
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Molecular mimicry between SARS-CoV-2 spike glycoprotein and mammalian proteomes: implications for the vaccine. Immunol Res 2020; 68:310-313. [PMID: 32946016 PMCID: PMC7499017 DOI: 10.1007/s12026-020-09152-6] [Citation(s) in RCA: 156] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 09/07/2020] [Indexed: 12/31/2022]
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5
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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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Bragazzi NL, Bridgewood C, Sharif K, Kamal M, Amital H, Watad A, Shoenfeld Y. HPV vaccines and lupus: current approaches towards preventing adverse immune cross-reactivity. Expert Rev Vaccines 2018; 18:31-42. [PMID: 30526148 DOI: 10.1080/14760584.2019.1557519] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
INTRODUCTION If not properly treated, human papillomavirus (HPV) infection may evolve from a common sexually transmitted disease to genital warts and cervical cancer. Various prophylactic HPV vaccines (HPVv), approved to reduce the incidence of the infection, have been found to be effective and safe; however, accounts of post-vaccination autoimmune phenomena, including systemic lupus erythematosus (SLE), have been reported in genetically susceptible individuals. AREAS COVERED Infectious agents play a role in breaking the immunologic tolerance to self-antigens, resulting in autoimmune events. There is molecular evidence supporting the involvement of HPV in SLE, with a high prevalence of L1 HPV peptide homology to proteins being associated with SLE. Therefore, approaches in vaccine preparations aiming to prevent adverse immune cross-reactivity are sought. Performing a broad search of the literature, we review the association between SLE, HPV, and HPVv, with a focus on the mechanisms of molecular mimicry and cross-reactivity, and the approaches currently being elaborated towards preventing such phenomena. EXPERT COMMENTARY The advantages of using low-similarity peptide antigens may be two-fold, abolishing the risk of cross-reactivity and eliminating the vaccine adjuvantation procedure. Vaccines based on pathogen unique sequences would provide effective vaccine preparation while curbing the risk for the human host.
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Affiliation(s)
- Nicola L Bragazzi
- a Postgraduate School of Public Health, Department of Health Sciences (DISSAL) , University of Genoa , Genoa , Italy
| | - Charlie Bridgewood
- b Section of Musculoskeletal Disease, Leeds Institute of Molecular Medicine , University of Leeds, NIHR Leeds Musculoskeletal Biomedical Research Unit, Chapel Allerton Hospital , Leeds , UK
| | - Kassem Sharif
- c Department of Medicine B and Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Ramat-Gan, Sackler Faculty of Medicine , Tel-Aviv University , Tel-Aviv , Israel
| | - Mohamad Kamal
- c Department of Medicine B and Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Ramat-Gan, Sackler Faculty of Medicine , Tel-Aviv University , Tel-Aviv , Israel
| | - Howard Amital
- c Department of Medicine B and Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Ramat-Gan, Sackler Faculty of Medicine , Tel-Aviv University , Tel-Aviv , Israel
| | - Abdulla Watad
- b Section of Musculoskeletal Disease, Leeds Institute of Molecular Medicine , University of Leeds, NIHR Leeds Musculoskeletal Biomedical Research Unit, Chapel Allerton Hospital , Leeds , UK.,c Department of Medicine B and Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Ramat-Gan, Sackler Faculty of Medicine , Tel-Aviv University , Tel-Aviv , Israel
| | - Yehuda Shoenfeld
- c Department of Medicine B and Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Ramat-Gan, Sackler Faculty of Medicine , Tel-Aviv University , Tel-Aviv , Israel
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Khairkhah N, Namvar A, Kardani K, Bolhassani A. Prediction of cross‐clade HIV‐1 T‐cell epitopes using immunoinformatics analysis. Proteins 2018; 86:1284-1293. [DOI: 10.1002/prot.25609] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 09/04/2018] [Accepted: 09/23/2018] [Indexed: 12/14/2022]
Affiliation(s)
| | - Ali Namvar
- Iranian Comprehensive Hemophilia Care Center Tehran Iran
| | - Kimia Kardani
- Iranian Comprehensive Hemophilia Care Center Tehran Iran
| | - Azam Bolhassani
- Department of Hepatitis and AIDSPasteur Institute of Iran Tehran Iran
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8
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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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Kawakami R, Nozato Y, Nakagami H, Ikeda Y, Shimamura M, Yoshida S, Sun J, Kawano T, Takami Y, Noma T, Rakugi H, Minamino T, Morishita R. Development of vaccine for dyslipidemia targeted to a proprotein convertase subtilisin/kexin type 9 (PCSK9) epitope in mice. PLoS One 2018; 13:e0191895. [PMID: 29438441 PMCID: PMC5811007 DOI: 10.1371/journal.pone.0191895] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 01/12/2018] [Indexed: 01/07/2023] Open
Abstract
Proprotein convertase subtilisin/kexin type 9 (PCSK9) regulates expression of low-density lipoprotein (LDL) receptors via receptor internalization and subsequent lysosomal degradation. Thus, an anti-PCSK9 antibody is well known as an anti-hyperlipidemia drug. Here, we aimed to develop vaccine for a long-term treatment of dyslipidemia targeted to PCSK9. In This study, we designed a peptide vaccine for mouse PCSK-9, which consisted of short peptides conjugated to keyhole limpet hemocyanin (KLH) as a carrier protein. Vaccines were administered to male apolipoprotein E (ApoE) deficient mice with adjuvants and significantly elicited an antibody response against PCSK9. The PCSK9 vaccines were administered to mice three times in 2-week intervals, and antibody titers and lipoprotein levels were evaluated up to 24 weeks after the first immunization to determine the therapeutic effect. Anti-PCSK9 antibody titers reached peak levels 6 weeks after the first immunization, and theses titers were maintained for up to 24 weeks. Decreased plasma levels of total cholesterol, very low-density lipoprotein (VLDL), and chylomicron (CM) were maintained for up to 24 weeks. Immunized mice exhibited a significant increase in cell-surface LDL receptor expression. Stimulation with KLH, but not PCSK9, induced the production of INF-gamma and interleukin-4 (IL-4), as determined with ELISPOT assays, thus indicating that PCSK9 vaccine did not elicit T-cell activation in our vaccine system. The present anti-PCSK9 vaccine induced long-lasting anti-PCSK9 antibody production and improved lipoprotein profiles. Thus, anti-PCSK9 vaccine could become a new option for the treatment of dyslipidemia as a long-acting therapy in future.
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Affiliation(s)
- Ryo Kawakami
- Department of Cardiorenal and Cerebrovascular Medicine, Faculty of Medicine, Kagawa University, Kagawa, Japan.,Department of Clinical Gene Therapy, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Yoichi Nozato
- Department of Geriatric and General Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Hironori Nakagami
- Department of Health Development and Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Yuka Ikeda
- Department of Clinical Gene Therapy, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Munehisa Shimamura
- Department of Health Development and Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Shota Yoshida
- Department of Health Development and Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Jiao Sun
- Department of Health Development and Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Tomohiro Kawano
- Department of Neurology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Yoichi Takami
- Department of Geriatric and General Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Takahisa Noma
- Department of Cardiorenal and Cerebrovascular Medicine, Faculty of Medicine, Kagawa University, Kagawa, Japan
| | - Hiromi Rakugi
- Department of Geriatric and General Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Tetsuo Minamino
- Department of Cardiorenal and Cerebrovascular Medicine, Faculty of Medicine, Kagawa University, Kagawa, Japan
| | - Ryuichi Morishita
- Department of Clinical Gene Therapy, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
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Pan Y, Zhou Y, Wu H, Chen X, Hu X, Zhang H, Zhou Z, Qiu Z, Liao Y. A Therapeutic Peptide Vaccine Against PCSK9. Sci Rep 2017; 7:12534. [PMID: 28970592 PMCID: PMC5624949 DOI: 10.1038/s41598-017-13069-w] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 09/13/2017] [Indexed: 02/05/2023] Open
Abstract
Vaccination provides a promising approach for treatment of hypercholesterolemia and improvement in compliance. In this study, the appropriate virus-like particle (VLP)-peptide vaccines targeting proprotein convertase subtilisin/kexin type 9 (PCSK9) were screened. The screening criteria of target peptides were as follows: (1) located in catalytic domain of PCSK9, or regulating the binding of PCSK9 and LDL receptors (LDLR); (2) having low/no-similarity when matched with the host proteome; (3) possessing ideal antigenicity and hydrophilicity; (4) including the functional mutation site of PCSK9. It was found that mice vaccinated with VLP -PCSK9 peptide vaccines, especially PCSK9Qβ-003 vaccine, developed high titer IgG antibodies against PCSK9. PCSK9Qβ-003 vaccine obviously decreased plasma total cholesterol in both Balb/c mice and LDLR+/- mice. Also, PCSK9Qβ-003 vaccine decreased plasma PCSK9 level and up-regulated LDLR expression in liver. Additionally, PCSK9Qβ-003 vaccine injection was associated with significant up-regulation of sterol-regulatory element-binding protein-2 (SREBP-2), hepatocyte nuclear factor 1α (HNF-1α), and 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase in LDLR+/- mice. No obvious immune injury was detected in vaccinated animals. The PCSK9Qβ-003 vaccine, therefore, may be an attractive treatment approach for hypercholesterolemia through decreasing cholesterol and regulating lipid homeostasis.
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Affiliation(s)
- Yajie Pan
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Institute of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Key Lab of Molecular Biological Targeted Therapies of the Ministry of Education, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yanzhao Zhou
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Institute of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Key Lab of Molecular Biological Targeted Therapies of the Ministry of Education, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Hailang Wu
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Institute of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Key Lab of Molecular Biological Targeted Therapies of the Ministry of Education, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Xiao Chen
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Institute of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Key Lab of Molecular Biological Targeted Therapies of the Ministry of Education, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Xiajun Hu
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Institute of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Key Lab of Molecular Biological Targeted Therapies of the Ministry of Education, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Hongrong Zhang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Institute of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Key Lab of Molecular Biological Targeted Therapies of the Ministry of Education, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Zihua Zhou
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Institute of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Key Lab of Molecular Biological Targeted Therapies of the Ministry of Education, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Zhihua Qiu
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China. .,Institute of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China. .,Key Lab of Molecular Biological Targeted Therapies of the Ministry of Education, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Yuhua Liao
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China. .,Institute of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China. .,Key Lab of Molecular Biological Targeted Therapies of the Ministry of Education, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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11
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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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12
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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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13
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Kanduc D. Measles virus hemagglutinin epitopes are potential hotspots for crossreactions with immunodeficiency-related proteins. Future Microbiol 2016; 10:503-15. [PMID: 25865190 DOI: 10.2217/fmb.14.137] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
AIMS Measles virus (MV) infection induces a protective immunity that is accompanied by a transient pathologic suppression of the immune system. This immunologic paradox remains unexplained in spite of the numerous hypotheses that have been advanced (i.e., cytokine production, soluble immunosuppressive factor, cell cycle block, signaling lymphocyte activation molecule receptor and MV infection of dendritic cells, among others). METHODS Searching for molecular link(s) between MV infection and host immunodeficiency, this study used the Immune Epitope DataBase to analyze the peptide sharing between the antigenic MV hemagglutinin (H) protein and human proteins associated with immunodeficiency. RESULTS It was found that the majority of MVH derived epitopes share several exact pentapeptide sequences with numerous human proteins involved in immune functions and immunodeficiency, such as B- and T-cell antigens, and complement components. CONCLUSION The data suggest that crossreactivity might contribute to our understanding of the link between MV immunogenicity and MV-induced immunosuppression, and highlight peptides unique to MV as a basis for developing effective and safe anti-MV vaccines.
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14
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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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15
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Lucchese G, Capone G, Kanduc D. Peptide sharing between influenza A H1N1 hemagglutinin and human axon guidance proteins. Schizophr Bull 2014; 40:362-75. [PMID: 23378012 PMCID: PMC3932078 DOI: 10.1093/schbul/sbs197] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Epidemiologic data suggest that maternal microbial infections may cause fetal neurodevelopmental disorders, potentially increasing susceptibility to heavy psychopathologies such as schizophrenia, schizophreniform disorder, autism, pervasive developmental disorders, bipolar disorders, psychosis, epilepsy, language and speech disorders, and cognitive impairment in adult offspring. However, the molecular pathomechanisms underlying such a relationship are not clear. Here we analyze the potential role of the maternal immune response to viral infection in determining fetal brain injuries that increase the risk of neurological disorders in the adult. We use influenza infection as a disease model and human axon guidance pathway, a key process in the formation of neural network during midgestation, as a potential fetal target of immune insults. Specifically, we examined influenza A H1N1 hemagglutinin (HA), an antigenic viral protein, for amino acid sequence similarity to a random library of 188 axon guidance proteins. We obtain the results that (1) contrary to any theoretical expectations, 45 viral pentapeptide matches are distributed throughout a subset of 36 guidance molecules; (2) in 24 guidance proteins, the peptide sharing with HA antigen involves already experimentally validated influenza HA epitopes; and (3) most of the axon guidance vs HA peptide overlap is conserved among influenza A viral strains and subsets. Taken together, our data indicate that immune cross-reactivity between influenza HA and axon guidance molecules is possible and may well represent a pathologic mechanism capable of determining neurodevelopmental disruption in the fetus.
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Affiliation(s)
- Guglielmo Lucchese
- To whom correspondence should be addressed; tel: +39.080.544.3321, fax: +39.080.544.3317, e-mail:
| | - Giovanni Capone
- Department of Biosciences, Biotechnologies and Pharmacological Sciences, University of Bari, Bari, Italy
| | - Darja Kanduc
- Department of Biosciences, Biotechnologies and Pharmacological Sciences, University of Bari, Bari, Italy,To whom correspondence should be addressed; tel: +39.080.544.3321, fax: +39.080.544.3317, e-mail:
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16
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Capone G, Kanduc D. Peptide sharing between Bordetella pertussis proteome and human sudden death proteins: a hypothesis for a causal link. Future Microbiol 2014; 8:1039-48. [PMID: 23902149 DOI: 10.2217/fmb.13.72] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
AIM To explore the molecular basis of the relationship between Bordetella pertussis infection and sudden death. METHODS B. pertussis proteins were analyzed for amino acid sequence identity to a set of 67 human proteins that, when altered, have been associated with sudden death. RESULTS More than 82,000 pentapeptides are shared between B. pertussis proteins and sudden death-associated antigens. CONCLUSION Results suggest that a possible link between B. pertussis infection and sudden death might be represented by potential immunological cross-reactions occurring between B. pertussis proteins and human proteins associated to sudden death.
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Affiliation(s)
- Giovanni Capone
- Department of Biosciences, Biotechnologies & Biopharmaceutics, University of Bari, Bari, Italy
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17
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Qiu Z, Chen X, Zhou Y, Lin J, Ding D, Yang S, Chen F, Wang M, Zhu F, Yu X, Zhou Z, Liao Y. Therapeutic vaccines against human and rat renin in spontaneously hypertensive rats. PLoS One 2013; 8:e66420. [PMID: 23825541 PMCID: PMC3692469 DOI: 10.1371/journal.pone.0066420] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 05/05/2013] [Indexed: 12/15/2022] Open
Abstract
Vaccination provides a promising approach for treatment of hypertension and improvement in compliance. As the initiation factor of renin-angiotensin system, renin plays a critical role in hypertension. In this study, we selected six peptides (rR32, rR72, rR215, hR32, hR72, and hR215) belonging to potential epitopes of rat and human renin. The main criteria were as follows: (1) include one of renin catalytic sites or the flap sequence; (2) low/no-similarity when matched with the host proteome; (3) ideal antigenicity and hydrophilicity. The peptides were coupled to keyhole limpet hemocyanin and injected into SpragueDawley (SD) rats, spontaneously hypertensive rats (SHRs) and Wistar-Kyoto rats. The antisera titers and the binding capacity with renin were detected. The effects of the anti-peptides antibodies on plasma renin activity (PRA) and blood pressure were also determined. All peptides elicited strong antibody responses. The antisera titers ranged from 1:32,000 to 1:80,000 in SD rats on day 63. All antisera could bind to renin in vitro. Compared with the control antibody, the antibodies against the rR32, hR32, rR72 and hR72 peptides inhibited PRA level by up to about 50%. Complete cross-reactivity of the anti-rR32 antibody and the anti-hR32 antibody was confirmed. The epitopes rR32 and hR32 vaccines significantly decreased systolic blood pressure (SBP) of SHRs up to 15mmHg (175±2 vesus 190±3 mmHg, P = 0.035; 180±2 vesus 195±3 mmHg, P = 0.039), while no obvious effect on SD rats. Additionally, no significant immune-mediated damage was detected in the vaccinated animals. In conclusion, the antigenic peptide hR32 vaccine mimicking the 32Asp catalytic site of human renin may constitute a novel tool for the development of a renin vaccine.
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Affiliation(s)
- Zhihua Qiu
- Laboratory of Cardiovascular Immunology, Key Laboratory of Molecular Targeted Therapies of the Ministry of Education, Institute of Cardiology, Union Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | - Xiao Chen
- Laboratory of Cardiovascular Immunology, Key Laboratory of Molecular Targeted Therapies of the Ministry of Education, Institute of Cardiology, Union Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | - Yanzhao Zhou
- Laboratory of Cardiovascular Immunology, Key Laboratory of Molecular Targeted Therapies of the Ministry of Education, Institute of Cardiology, Union Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | - Jibin Lin
- Laboratory of Cardiovascular Immunology, Key Laboratory of Molecular Targeted Therapies of the Ministry of Education, Institute of Cardiology, Union Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | - Dan Ding
- Laboratory of Cardiovascular Immunology, Key Laboratory of Molecular Targeted Therapies of the Ministry of Education, Institute of Cardiology, Union Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | - Shijun Yang
- Laboratory of Cardiovascular Immunology, Key Laboratory of Molecular Targeted Therapies of the Ministry of Education, Institute of Cardiology, Union Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | - Fen Chen
- Laboratory of Cardiovascular Immunology, Key Laboratory of Molecular Targeted Therapies of the Ministry of Education, Institute of Cardiology, Union Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | - Min Wang
- Laboratory of Cardiovascular Immunology, Key Laboratory of Molecular Targeted Therapies of the Ministry of Education, Institute of Cardiology, Union Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | - Feng Zhu
- Laboratory of Cardiovascular Immunology, Key Laboratory of Molecular Targeted Therapies of the Ministry of Education, Institute of Cardiology, Union Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | - Xian Yu
- Laboratory of Cardiovascular Immunology, Key Laboratory of Molecular Targeted Therapies of the Ministry of Education, Institute of Cardiology, Union Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | - Zihua Zhou
- Laboratory of Cardiovascular Immunology, Key Laboratory of Molecular Targeted Therapies of the Ministry of Education, Institute of Cardiology, Union Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
- * E-mail: (YL); (ZZ)
| | - Yuhua Liao
- Laboratory of Cardiovascular Immunology, Key Laboratory of Molecular Targeted Therapies of the Ministry of Education, Institute of Cardiology, Union Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
- * E-mail: (YL); (ZZ)
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18
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Flower DR, Perrie Y. Identification of Candidate Vaccine Antigens In Silico. IMMUNOMIC DISCOVERY OF ADJUVANTS AND CANDIDATE SUBUNIT VACCINES 2013. [PMCID: PMC7120937 DOI: 10.1007/978-1-4614-5070-2_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The identification of immunogenic whole-protein antigens is fundamental to the successful discovery of candidate subunit vaccines and their rapid, effective, and efficient transformation into clinically useful, commercially successful vaccine formulations. In the wider context of the experimental discovery of vaccine antigens, with particular reference to reverse vaccinology, this chapter adumbrates the principal computational approaches currently deployed in the hunt for novel antigens: genome-level prediction of antigens, antigen identification through the use of protein sequence alignment-based approaches, antigen detection through the use of subcellular location prediction, and the use of alignment-independent approaches to antigen discovery. Reference is also made to the recent emergence of various expert systems for protein antigen identification.
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Affiliation(s)
- Darren R. Flower
- Aston Pharmacy School, School of Life and Health Sciences, University of Aston, Aston Triangle, Birmingham, B4 7ET United Kingdom
| | - Yvonne Perrie
- Aston Pharmacy School, School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET United Kingdom
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19
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Minkiewicz P, Bucholska J, Darewicz M, Borawska J. Epitopic hexapeptide sequences from Baltic cod parvalbumin beta (allergen Gad c 1) are common in the universal proteome. Peptides 2012; 38:105-9. [PMID: 22940202 DOI: 10.1016/j.peptides.2012.08.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 08/14/2012] [Accepted: 08/14/2012] [Indexed: 01/25/2023]
Abstract
The aim of this study was to analyze the distribution of hexapeptide fragments considered as epitopes of Baltic cod parvalbumin beta (allergen Gad c 1) in the universal proteome. Cod (Gadus morhua subsp. callarias) parvalbumin hexapeptides cataloged in the Immune Epitope Database were used as query sequences. The UniProt database was screened using the WU-BLAST 2 program. The distribution of hexapeptide fragments was investigated in various protein families, classified according to the presence of the appropriate domains, and in proteins of plant, animal and microbial species. Hexapeptides from cod parvalbumin were found in the proteins of plants and animals which are food sources, microorganisms with various applications in food technology and biotechnology, microorganisms which are human symbionts and commensals as well as human pathogens. In the last case possible coverage between epitopes from pathogens and allergens should be avoided during vaccine design.
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Affiliation(s)
- Piotr Minkiewicz
- University of Warmia and Mazury in Olsztyn, Chair of Food Biochemistry, Olsztyn-Kortowo, Poland.
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20
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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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21
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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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22
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Harris F, Dennison SR, Singh J, Phoenix DA. On the selectivity and efficacy of defense peptides with respect to cancer cells. Med Res Rev 2011; 33:190-234. [PMID: 21922503 DOI: 10.1002/med.20252] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Here, we review potential determinants of the anticancer efficacy of innate immune peptides (ACPs) for cancer cells. These determinants include membrane-based factors, such as receptors, phosphatidylserine, sialic acid residues, and sulfated glycans, and peptide-based factors, such as residue composition, sequence length, net charge, hydrophobic arc size, hydrophobicity, and amphiphilicity. Each of these factors may contribute to the anticancer action of ACPs, but no single factor(s) makes an overriding contribution to their overall selectivity and toxicity. Differences between the anticancer actions of ACPs seem to relate to different levels of interplay between these peptide and membrane-based factors.
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Affiliation(s)
- Frederick Harris
- School of Forensic and Investigative Sciences, University of Central Lancashire, Preston, Lancashire, United Kingdom
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23
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Kanduc D. HCV: Written in our DNA. SELF NONSELF 2011; 2:108-113. [PMID: 22299062 DOI: 10.4161/self.2.2.15795] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 04/08/2011] [Accepted: 04/11/2011] [Indexed: 11/19/2022]
Abstract
An inspection of the sequence similarity between the hepatitis C virus (HCV) polyprotein and human proteins revealed a high level of peptide sharing, with a limited number of motifs unique to the virus (i.e., with no counterpart in the human proteome). Using pentapeptide matching, only 214 motifs out of a total of 3,007 (7.11%) identified HCV as nonself compared to the Homo sapiens proteome. However, this virus-versus-human phenetic difference disappeared at the genetic level. Indeed, a BLAST analysis of pentadecameric oligodeoxynucleotide sequences corresponding to the 214 pentapeptides unique to HCV revealed that almost all of them are present in the human genome, located in the non-coding strand, introns, and/or pseudogenes, thus being, as such, untranslatable. The present data warn against using DNA-based vaccines to fight HCV infection and emphasize peptide uniqueness as the molecular basis for designing effective anti-HCV immunotherapeutic approaches.
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Affiliation(s)
- Darja Kanduc
- Department of Biochemistry and Molecular Biology; University of Bari; Bari, Italy
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24
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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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25
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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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26
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Bavaro SL, Kanduc D. Pentapeptide commonality between Corynebacterium diphtheriae toxin and the Homo sapiens proteome. Immunotherapy 2010; 3:49-58. [PMID: 21174557 DOI: 10.2217/imt.10.83] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Cross-reactivity may affect diagnostic tests and cause harmful autoimmune reactions following immunotherapy. To predict potential cross-reactivity and search for safe immunotherapeutic approaches, we analyzed sequence identity between microbial antigens and the human proteome. Using diphtheria toxin (DT) as a model, we examined its patterns of identity with human proteins at the pentapeptide level. DT shares 503 pentapeptides with the human proteome, while only 31 pentapeptides are unique to the toxin. DT pentapeptide identity involves multiple/repeated matches in human proteins (a total of 4966 occurrences). Human proteins containing bacterial peptide matches include antigens linked to fundamental cellular functions, such as cell cycle control, proliferation, development and differentiation. The data presented in this article offer a rational basis for designing peptide-based vaccines that specifically target DT and thus eliminate the potential risk of cross-reactivity with human proteins. More generally, this study proposes a methodological approach for avoiding cross-reactivity in immune reactions.
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Affiliation(s)
- Simona Lucia Bavaro
- Department of Biochemistry & Molecular Biology, University of Bari, Bari 70126, Italy
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27
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Flower DR, Macdonald IK, Ramakrishnan K, Davies MN, Doytchinova IA. Computer aided selection of candidate vaccine antigens. Immunome Res 2010; 6 Suppl 2:S1. [PMID: 21067543 PMCID: PMC2981880 DOI: 10.1186/1745-7580-6-s2-s1] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Immunoinformatics is an emergent branch of informatics science that long ago pullulated from the tree of knowledge that is bioinformatics. It is a discipline which applies informatic techniques to problems of the immune system. To a great extent, immunoinformatics is typified by epitope prediction methods. It has found disappointingly limited use in the design and discovery of new vaccines, which is an area where proper computational support is generally lacking. Most extant vaccines are not based around isolated epitopes but rather correspond to chemically-treated or attenuated whole pathogens or correspond to individual proteins extract from whole pathogens or correspond to complex carbohydrate. In this chapter we attempt to review what progress there has been in an as-yet-underexplored area of immunoinformatics: the computational discovery of whole protein antigens. The effective development of antigen prediction methods would significantly reduce the laboratory resource required to identify pathogenic proteins as candidate subunit vaccines. We begin our review by placing antigen prediction firmly into context, exploring the role of reverse vaccinology in the design and discovery of vaccines. We also highlight several competing yet ultimately complementary methodological approaches: sub-cellular location prediction, identifying antigens using sequence similarity, and the use of sophisticated statistical approaches for predicting the probability of antigen characteristics. We end by exploring how a systems immunomics approach to the prediction of immunogenicity would prove helpful in the prediction of antigens.
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Affiliation(s)
- Darren R Flower
- School of Life and Health Sciences, University of Aston, Aston Triangle, Birmingham, B4 7ET, UK.
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28
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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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29
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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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30
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Proposing low-similarity peptide vaccines against Mycobacterium tuberculosis. J Biomed Biotechnol 2010; 2010:832341. [PMID: 20625421 PMCID: PMC2896900 DOI: 10.1155/2010/832341] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Revised: 12/02/2009] [Accepted: 03/24/2010] [Indexed: 12/03/2022] Open
Abstract
Using the currently available proteome databases and based on the concept that a rare sequence is a potential epitope, epitopic sequences derived from Mycobacterium tuberculosis were examined for similarity score to the proteins of the host in which the epitopes were defined. We found that: (i) most of the bacterial linear determinants had peptide fragment(s) that were rarely found in the host proteins and (ii) the relationship between low similarity and epitope definition appears potentially applicable to T-cell determinants. The data confirmed the hypothesis that low-sequence similarity shapes or determines the epitope definition at the molecular level and provides a potential tool for designing new approaches to prevent, diagnose, and treat tuberculosis and other infectious diseases.
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31
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Lucchese G, Stufano A, Kanduc D. Proteome-guided search for influenza A B-cell epitopes. ACTA ACUST UNITED AC 2009; 57:88-92. [PMID: 19659580 DOI: 10.1111/j.1574-695x.2009.00582.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The influenza A linear peptide epitopes recognized by murine antibodies, and currently cataloged at http://www.immuneepitope.org, were examined for the identity score to the host mouse proteome. It was found that almost all of the linear viral determinants are (or contain) regions formed by pentapeptide fragments with no or only very low similarity to the murine proteins. The present study adds to previous reports in suggesting a main role of amino acid sequence similarity in the modulation and definition of the B-cell epitope repertoire, inspiring innovative vaccine approaches able to avoid cross-reactive autoimmune collateral phenomena, and addressing future research in the study of immunity against the influenza A virus and infectious diseases in general.
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Affiliation(s)
- Guglielmo Lucchese
- Department of Biochemistry and Molecular Biology Ernesto Quagliariello, University of Bari, Bari, Italy
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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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