Review
Immunology
Peter M. Kloetzel
Summary: Proteasome generates spliced peptides through a reverse proteolysis reaction, potentially holding therapeutic and immune relevance. However, there is controversy surrounding the frequency, abundance, and therapeutic applicability of spliced peptides. Nevertheless, the search for tumor and patient-specific neosplicetopes still seems valuable.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Immunology
Patrik D'haeseleer, Nicole M. Collette, Victoria Lao, Brent W. Segelke, Steven S. Branda, Magdalena Franco
Summary: Peptide-based subunit vaccines offer safety and cost-effective production, with linear epitopes having advantages of simple structure, ease of synthesis, and immune response stimulation, but lower accuracy in prediction, necessitating experimental verification.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Multidisciplinary Sciences
Giacomo Oliveira, Kari Stromhaug, Susan Klaeger, Tomasz Kula, Dennie T. Frederick, Phuong M. Le, Juliet Forman, Teddy Huang, Shuqiang Li, Wandi Zhang, Qikai Xu, Nicoletta Cieri, Karl R. Clauser, Sachet A. Shukla, Donna Neuberg, Sune Justesen, Gavin MacBeath, Steven A. Carr, Edward F. Fritsch, Nir Hacohen, Moshe Sade-Feldman, Kenneth J. Livak, Genevieve M. Boland, Patrick A. Ott, Derin B. Keskin, Catherine J. Wu
Summary: The authors demonstrate through single-cell profiling and T cell receptor specificity screening that tumour antigen recognition influences the phenotypes of CD8(+) T cells and antitumour immune responses. Non-tumour-reactive T cells show a non-exhausted memory phenotype, while melanoma-reactive lymphocytes exhibit an exhausted state, providing insights into the properties of the anti-melanoma TCR repertoire.
Article
Immunology
Ning Ma, Huihui Liu, Yang Zhang, Wei Liu, Zeyin Liang, Qian Wang, Yuhua Sun, Lihong Wang, Yuan Li, Hanyun Ren, Yujun Dong
Summary: This study identifies the testis-cancer antigen AKAP4 as a potential target for multiple myeloma (MM) and demonstrates the efficacy of cytotoxic T lymphocytes (CTLs) targeting AKAP4 in lysis of MM cells.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Farzana Hossain, Shruthi Kandalai, Xiaozhuang Zhou, Nan Zhang, Qingfei Zheng
Summary: In this review, synthetic approaches for antigen-based cancer vaccines are highlighted, along with the discussion of various bioconjugation strategies. The progress of genetically modified cancer vaccines in clinical research is also summarized. Additionally, the synthesis of adjuvants and utilization of biomaterial scaffolds for enhancing immune responses are mentioned.
Article
Immunology
Tresa Rani Sarraf, Malini Sen
Summary: This study demonstrates the crucial role of Wnt5A signaling in antigen processing and CD8 T cell activation. The results show that Wnt5A signaling regulates actin and proteasome dynamics to support antigen processing and presentation, and depletion of Wnt5A leads to impaired antigen processing and reduced CD8 T cell activation. These findings highlight the importance of Wnt5A in cell-mediated immunity.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biology
Manaswini Jagadeb, Kali Prasad Pattanaik, Surya Narayan Rath, Avinash Sonawane
Summary: The study identified potential peptide-based vaccine targets against tuberculosis using an immune-informatics approach. By analyzing the Mtb proteome, two potential vaccine candidates were selected, showing the ability to induce protective immune responses. The peptides exhibited strong binding affinity and antigenic properties, suggesting their potential as vaccine candidates against TB.
COMPUTERS IN BIOLOGY AND MEDICINE
(2021)
Article
Immunology
Davide Cavazzini, Gloria Spagnoli, Filipe Colaco Mariz, Filippo Reggiani, Stefano Maggi, Valentina Franceschi, Gaetano Donofrio, Martin Mueller, Angelo Bolchi, Simone Ottonello
Summary: In this study, a positively supercharged protein was constructed and characterized as a promising carrier for intracellular antigen delivery. The protein showed different intracellular localization and cell-penetrating ability. Fusion of peptide epitopes to the protein enhanced its immunogenicity and induced a faster immune response.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biology
Thais Cristina Vilela Rodrigues, Arun Kumar Jaiswal, Marcela Rezende Lemes, Marcos Vinicius da Silva, Helioswilton Sales-Campos, Luiz Carlos Junior Alcantara, Sthephane Fraga de Oliveira Tosta, Rodrigo Bentes Kato, Khalid J. Alzahrani, Debmalya Barh, Vasco Ariston de Carvalho Azevedo, Sandeep Tiwari, Siomar de Castro Soares
Summary: A multi-epitope vaccine against Mycoplasma pneumoniae was designed using immunoinformatics approach, selecting epitopes based on immunogenicity and other criteria from core proteins. Docking and simulation showed potential efficacy, and in vitro cloning in expression vectors yielded positive results, suggesting the vaccine's safety and effectiveness, pending further experimental and clinical validations.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Immunology
Vishnu Raman, Lars M. Howell, Shoshana M. K. Bloom, Christopher L. Hall, Victoria E. Wetherby, Lisa M. Minter, Ashish A. Kulkarni, Neil S. Forbes
Summary: This study genetically engineered Salmonella to deliver exogenous antigens into tumor cells, aiming to activate antigen-specific CD8 T cells for immunotherapy. The results showed that intracellular delivery of the antigen reduced tumor growth and triggered a cytotoxic T cell response. In mice, intracellular delivery of the antigen cleared established tumors and increased survival.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Immunology
Artem Mansurkhodzhaev, Camila R. R. Barbosa, Michele Mishto, Juliane Liepe
Summary: This study investigates the effect of proteasome-generated cis-spliced peptides on the anti-viral response of CD8(+) T cells. Despite their high frequency, the cis-spliced peptides we studied are suggested to only marginally impact the variety of functional CD8(+) cytotoxic T cells involved in the response against viruses.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Immunology
Yoshihiro Watanabe, Natsuko Hosokawa, Misaki Yoshida, Tomoyuki Miura, Mitsuhiro Kawano
Summary: The study found that different variants of SARS-CoV-2 can infect through the human ACE2 pathway, and effective antibody responses are needed. By identifying specific peptide epitopes of the SARS-CoV-2 Spike molecule, antibodies can be induced to inhibit pseudo-virus infections mediated by the ACE2 pathway. These epitopes include #7, #11, and #111 in S1-RBD and S2-HR2. The results indicate that immunization with multiple epitopes can enhance the protective effect of neutralizing antibodies.
Review
Infectious Diseases
Gabriela Silva Cruz, Ariane Teixeira dos Santos, Erika Helena Salles de Brito, Gandhi Radis-Baptista
Summary: This review presents the antibacterial, antiparasitic, and antiviral effects of cell-penetrating antimicrobial peptides and highlights their potential for treating intracellular infections.
Article
Biochemistry & Molecular Biology
Alicia Mas, Clara Hurtado-Morillas, Abel Martinez-Rodrigo, Jose A. Orden, Ricardo de la Fuente, Gustavo Dominguez-Bernal, Javier Carrion
Summary: The DNA vaccine pHisAK70 and the peptide HisDTC have shown potential in inducing immune response against Leishmania infection, suggesting their effectiveness as vaccine candidates for leishmaniases control.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Wenqi Sun, Panpan Ji, Tian Zhou, Zhelong Li, Changyang Xing, Liang Zhang, Mengying Wei, Guodong Yang, Lijun Yuan
Summary: This article introduces a nanoscale cancer vaccine based on PLGA, which can efficiently induce anti-tumor immune response and provide neoantigens of metastatic cancer.
Article
Immunology
Kathrin Textoris-Taube, Clemens Cammann, Petra Henklein, Eylin Topfstedt, Frederic Ebstein, Sarah Henze, Juliane Liepe, Fang Zhao, Dirk Schadendorf, Burkhardt Dahlmann, Wolfgang Uckert, Annette Paschen, Michele Mishto, Ulrike Seifert
EUROPEAN JOURNAL OF IMMUNOLOGY
(2020)
Article
Immunology
Robin H. G. A. van den Biggelaar, Willem van Eden, Victor P. M. G. Rutten, Christine A. Jansen
Article
Biochemistry & Molecular Biology
Qingkang Lyu, Magdalena Wawrzyniuk, Victor P. M. G. Rutten, Willem van Eden, Alice J. A. M. Sijts, Femke Broere
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Article
Immunology
Artem Mansurkhodzhaev, Camila R. R. Barbosa, Michele Mishto, Juliane Liepe
Summary: This study investigates the effect of proteasome-generated cis-spliced peptides on the anti-viral response of CD8(+) T cells. Despite their high frequency, the cis-spliced peptides we studied are suggested to only marginally impact the variety of functional CD8(+) cytotoxic T cells involved in the response against viruses.
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Nutrition & Dietetics
Josep Bassaganya-Riera, Elliot M. Berry, Ellen E. Blaak, Barbara Burlingame, Johannes le Coutre, Willem van Eden, Ahmed El-Sohemy, J. Bruce German, Dietrich Knorr, Christophe Lacroix, Maurizio Muscaritoli, David C. Nieman, Michael Rychlik, Andrew Scholey, Mauro Serafini
Summary: In the past five years, significant progress has been made in nutrition science, such as the integration of Sustainable Development Goals and nutritional science, as well as research on the Human Microbiome. Looking ahead to the next five years, emphasis on health and sustainability will be the main focus of nutrition science.
FRONTIERS IN NUTRITION
(2021)
Article
Immunology
Michele Mishto, Artem Mansurkhodzhaev, Teresa Rodriguez-Calvo, Juliane Liepe
Summary: Increasing evidence indicates that post-translational peptide splicing can affect immune responses, especially in Type 1 Diabetes. Spliced peptides have variable sequences, increasing the risk of viral-human zwitter peptides. Some viral-human zwitter peptides may be produced by proteasome-catalyzed peptide splicing, enhancing the destruction of pancreatic beta cells by virus-specific CD8(+) T cells.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Cell Biology
Alessia Melacarne, Valentina Ferrari, Luca Tiraboschi, Michele Mishto, Juliane Liepe, Marina Aralla, Laura Marconato, Michela Lizier, Chiara Pozzi, Offer Zeira, Giuseppe Penna, Maria Rescigno
Summary: Infection of tumor cells with Salmonella induces the release of peptides that promote an antitumor response, applicable to both melanoma and osteosarcoma. Mass spectrometry analysis revealed a class of shared tumor antigens generated in ER-stressed cells, which do not induce tolerance and are effective in promoting the immune response against cancer cells.
Editorial Material
Immunology
Michele Mishto, Guillermo Rodriguez-Hernandez, Jacques Neefjes, Henning Urlaub, Juliane Liepe
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Camila R. R. Barbosa, Justin Barton, Adrian J. Shepherd, Michele Mishto
Summary: The human immune system has evolved multiple strategies to diversify the CD8(+) T cell response against pathogens and aberrations of self, by presenting a variety of antigenic peptide sequences through MHC class I complexes. Recent progress in evaluating the prevalence and immunological relevance of unconventional antigen peptides, as well as the cross-recognition of antigenic peptides by CD8(+) T cell T cell receptors, has been a controversial but important area of study.
BIOCHEMICAL JOURNAL
(2021)
Article
Biochemical Research Methods
Michele Mishto, Yehor Horokhovskyi, John A. Cormican, Xiaoping Yang, Steven Lynham, Henning Urlaub, Juliane Liepe
Summary: Unconventional epitopes are emerging targets for T cell immunotherapy, and mass spectrometry is commonly used for their identification. This study compared the performance of three database search engines and found that PEAKS DB showed better performance in identifying cis-spliced peptides and HLA class I immunopeptidomes.
Article
Chemistry, Multidisciplinary
Ilanit Gutman, Ron Gutman, John Sidney, Leila Chihab, Michele Mishto, Juliane Liepe, Anthony Chiem, Jason Greenbaum, Zhen Yan, Alessandro Sette, Zeynep Kosaloglu-Yalcin, Bjoern Peters
Summary: Synthetic peptides are widely used in biomedical science for research purposes. However, the synthesis of certain peptide sequences can be challenging due to the chemical nature of some amino acids and the complexity of the synthesis process. This study analyzed a dataset of synthesized peptides and developed a computational tool to predict the likelihood of successful synthesis based on the peptide sequence.
Article
Biochemical Research Methods
John A. Cormican, Yehor Horokhovskyi, Wai Tuck Soh, Michele Mishto, Juliane Liepe
Summary: This article introduces a method of rescoring mass spectrometry search results using spectral predictors, which can increase the identification rate of peptide spectrum matches. This method is particularly effective in immunopeptidomics and has potential benefits for the identification of noncanonical peptides.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Biochemical Research Methods
John A. Cormican, Wai Tuck Soh, Michele Mishto, Juliane Liepe
Summary: The discovery of noncanonical peptides using mass spectrometry has led to the development of new methods for their identification, often without proper benchmarking. This article presents iBench, a bioinformatic tool that can construct proteomics datasets and databases, allowing for testing and performance estimation of various methods and strategies. iBench can be used with database search engines, offers customizable features, provides benchmarking outputs, and is open source. In a proof-of-concept application, iBench was used to analyze the impact of noncanonical peptides on the identification of canonical peptides using Mascot search with rescoring via Percolator (Mascot+Percolator).
Article
Multidisciplinary Sciences
Hanna P. Roetschke, Guillermo Rodriguez-Hernandez, John A. Cormican, Xiaoping Yang, Steven Lynham, Michele Mishto, Juliane Liepe
Summary: Noncanonical epitopes presented by HLA-I complexes have gained attention in the research of immunotherapies. Proteasomes can catalyze peptide hydrolysis and splicing, and here, we provide a comprehensive database of proteasome-generated spliced and non-spliced peptides. The database contains a variety of peptide products and substrate sequences, which can be valuable for predicting proteasome-catalyzed peptide hydrolysis and splicing.
Article
Immunology
Robin H. G. A. van den Biggelaar, Willem van Eden, Victor P. M. G. Rutten, Christine A. Jansen