Article
Immunology
Rodrigo Ochoa, Victoria Alves Santos Lunardelli, Daniela Santoro Rosa, Alessandro Laio, Pilar Cossio
Summary: In this study, researchers developed a method called PanMHC-PARCE for engineering multiple-allele binders by optimizing epitope sequence through mutations and simulations. They successfully improved the binding affinity of a Plasmodium vivax epitope for multiple human MHC II alleles. Additionally, in vivo experiments showed that immunization with the engineered peptides induced interferon-gamma cellular immune response in mice. This method contributes to the design of new immunotherapies.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Immunology
Yanan Wu, Nianzhi Zhang, Keiichiro Hashimoto, Chun Xia, Johannes M. Dijkstra
Summary: The structures of peptide-loaded major histocompatibility complex class I (pMHC-I) and class II (pMHC-II) complexes are similar, but there are differences in the components. Comparative analysis of primitive vertebrate species' pMHC-I and pMHC-II structures sheds light on the evolution of MHC structures. The establishment of pMHC-I involved the development of important new functions that have been well conserved since their early inception.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemical Research Methods
Siyuan Liu, Yusong Wang, Yifan Deng, Liang He, Bin Shao, Jian Yin, Nanning Zheng, Tie-Yan Liu, Tong Wang
Summary: This study proposes a novel approach called IGT that improves the prediction performance of active binding drugs in virtual screening. Compared to existing methods, IGT achieves better results in binding activity and binding pose prediction, and demonstrates superior generalization ability to unseen receptor proteins. Furthermore, IGT shows promising accuracy in drug screening against severe acute respiratory syndrome coronavirus 2.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biotechnology & Applied Microbiology
Kenji Sugata, Yukiko Matsunaga, Yuki Yamashita, Munehide Nakatsugawa, Tingxi Guo, Levon Halabelian, Yota Ohashi, Kayoko Saso, Muhammed A. Rahman, Mark Anczurowski, Chung-Hsi Wang, Kenji Murata, Hiroshi Saijo, Yuki Kagoya, Dalam Ly, Brian D. Burt, Marcus O. Butler, Tak W. Mak, Naoto Hirano
Summary: By combining molecular biological and immunological techniques, this study successfully cloned sequences encoding HLA-DP, HLA-DQ, and HLA-DR molecules with enhanced CD4 binding affinity and produced affinity-matured class II dimers that stain antigen-specific T cells better than conventional multimers. These affinity-matured class II dimers will aid in the investigation of human CD4(+) T-cell responses, providing a comprehensive library of dimers for HLA-DP, HLA-DQ, and HLA-DR alleles. The readily detectable CD4(+) T cells with class II MHC dimers are crucial for studying human immune responses.
NATURE BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Josef Laimer, Peter Lackner
Summary: MHCII3D is a method based on structural scaffolds of MHC II-peptide complexes and statistical scoring functions, showing strong predictive power compared to sequence-based machine learning methods. It can help identify problematic entries in the IEDB.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Immunology
Yuri Poluektov, Marybeth George, Pirouz Daftarian, Marc C. Delcommenne
Summary: The study focuses on evaluating the binding affinities of SARS-CoV-2 peptides to different MHC alleles using the QuickSwitchTM platform, identifying multiple MHC binders with high promiscuity. These results provide important data for further research on the SARS-CoV-2 virus and its antigenic epitopes.
Article
Biochemistry & Molecular Biology
Chunyu Wang, Yuanlong Chen, Lingling Zhao, Junjie Wang, Naifeng Wen
Summary: In this paper, the authors propose a method to predict drug-target interactions using a multi-instance learning approach. They organize drug and target sequences into instances using a private-public mechanism and combine the predicted scores to generate the final output. The results show that the proposed method outperforms other state-of-the-art methods on three benchmark datasets.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Arne Claeys, Peter Merseburger, Jasper Staut, Kathleen Marchal, Jimmy van den Eynden
Summary: This study evaluated the performance of 13 HLA genotyping tools on Whole Exome Sequencing (WES) and RNA sequencing data. The results showed that Optitype and arcasHLA had the highest accuracies for MHC-I genotyping on WES and RNA sequencing data respectively, while HLA-HD was the most accurate tool for MHC-II genotyping on both data types. Therefore, depending on the available data type and computational resources, we recommend using Optitype and HLA-HD for MHC-I and MHC-II genotyping.
Article
Multidisciplinary Sciences
Binkai Chi, Muhammet M. Oeztuerk, Christina L. Paraggio, Claudia E. Leonard, Maria E. Sanita, Mahtab Dastpak, Jeremy D. O'Connell, Jordan A. Coady, Jiuchun Zhang, Steven P. Gygi, Rodrigo Lopez-Gonzalez, Shanye Yin, Robin Reed
Summary: Mutations in RNA/DNA-binding proteins can cause ALS, but the exact disease mechanisms are still unclear. This study found that a group of ALS-associated proteins can affect the expression of genes involved in the MHC II antigen presentation pathway. Additionally, hematopoietic progenitor cells with mutations also exhibit disrupted MHC II expression. These findings suggest that the loss of the MHC II pathway may result in the immune system's failure to protect motor neurons from ALS-related damage.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemical Research Methods
Fuxu Wang, Haoyan Wang, Lizhuang Wang, Haoyu Lu, Shizheng Qiu, Tianyi Zang, Xinjun Zhang, Yang Hu
Summary: This study introduces the MHCRoBERTa method, which uses RoBERTa pre-training approach to predict the binding affinity between type I MHC and peptides. Experimental results show that MHCRoBERTa outperforms other prediction methods, with a significant improvement on IC50 value, demonstrating its potential in cancer immunotherapy.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Peicong Lin, Yumeng Yan, Sheng-You Huang
Summary: Protein-protein interactions are important in biological processes, but predicting the structure of protein-protein complexes remains a challenge. DeepHomo2.0 is a deep learning-based model that uses direct-coupling analysis (DCA) and Transformer features to predict protein-protein interactions of homodimeric complexes. It outperforms other methods in terms of precision, even without using structural information. Integrating the predicted contacts into protein docking improves structure prediction. DeepHomo2.0 and DeepHomoSeq are available at http://huanglab.phys.hust.edu.cn/DeepHomo2/.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Peicong Lin, Yumeng Yan, Sheng-You Huang
Summary: Protein-protein interactions are crucial for biological processes, but predicting the structure of protein-protein complexes remains challenging. Researchers have developed DeepHomo2.0 and DeepHomoSeq, deep learning models that utilize sequence and structure features to predict protein-protein interactions in homodimeric complexes. Experimental results show that DeepHomo2.0 outperforms eight other methods in predicting contact points, and even DeepHomoSeq achieves good accuracy without using structure information.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Genetics & Heredity
Diego Ordonez, Michel David Bohorquez, Catalina Avendano, Manuel Alfonso Patarroyo
Summary: The MHC polymorphism plays a crucial role in cattle evolution and immune response. This study provides insights into the genetic diversity of different cattle breeds and their response to diseases and vaccines.
FRONTIERS IN GENETICS
(2022)
Article
Genetics & Heredity
Lichao Zhang, Haojin Li, Zhenjiu Zhang, Jinjin Wang, Gang Chen, Dong Chen, Wentao Shi, Gaozhi Jia, Mingjun Liu
Summary: Understanding the interaction between T-cell receptors (TCRs) and major histocompatibility-peptide (MHC-peptide) complexes is crucial for human immunotherapy and vaccine development. However, existing models for predicting this interaction have yielded unsatisfactory results due to limited data availability. In this study, we propose a gMLP model combined with attention mechanism to accurately predict TCR-peptide interactions, addressing the issues caused by varying TCR lengths. Our results demonstrate that models trained with paired CDR3 beta-chain and CDR3 alpha-chain data outperform those trained with only one chain, and the hybrid model shows greater potential than the traditional convolutional neural network.
FRONTIERS IN GENETICS
(2023)
Article
Engineering, Biomedical
Chengyang Gao, Qiule Sun, Wen Zhu, Lizhi Zhang, Jianxin Zhang, Bin Liu, Junxing Zhang
Summary: Computer-aided diagnosis based on deep learning improves the efficiency of pathologists. This study explores the effectiveness of Transformers in classifying breast cancer tissues in WSIs and proposes a hybrid multiple instance learning method called HTransMIL. The method selects informative instances and strengthens their correlation to achieve accurate classification, while visualization analysis helps understand the weakly supervised classification model.
BIOMEDICAL SIGNAL PROCESSING AND CONTROL
(2024)
Article
Biochemistry & Molecular Biology
Jun Cheng, Kerstin C. Maier, Ziga Avsec, Petra Rus, Julien Gagneur
Article
Biotechnology & Applied Microbiology
Christelle Remy-Ziller, Christine Thioudellet, Julie Hortelano, Murielle Gantzer, Virginie Nourtier, Marie-Christine Claudepierre, Benoit Sansas, Xavier Preville, Kaidre Bendjama, Eric Quemeneur, Karola Rittner
HUMAN VACCINES & IMMUNOTHERAPEUTICS
(2018)
Meeting Abstract
Oncology
Alan Anthoney, Adel Samson, Emma West, Samantha Jane Turnbull, Karen Scott, Emma Tidswell, Jennifer Kingston, Michelle Johnpulle, Samantha Noutch, Kaidre Bendjama, Michel Homerin, Nicolas Stojkowitz, Giles Toogood, Chris Twelves, Christy Ralph, Alan Melcher, Fiona Jane Collinson
JOURNAL OF CLINICAL ONCOLOGY
(2018)
Article
Genetics & Heredity
Jun Cheng, Muhammed Hasan Celik, Thi Yen Duong Nguyen, Ziga Avsec, Julien Gagneur
Letter
Biotechnology & Applied Microbiology
Ziga Avsec, Roman Kreuzhuber, Johnny Israeli, Nancy Xu, Jun Cheng, Avanti Shrikumar, Abhimanyu Banerjee, Daniel S. Kim, Thorsten Beier, Lara Urban, Anshul Kundaje, Oliver Stegle, Julien Gagneur
NATURE BIOTECHNOLOGY
(2019)
Article
Genetics & Heredity
Stephen M. Mount, Ziga Avsec, Liran Carmel, Rita Casadio, Muhammed Hasan Celik, Ken Chen, Jun Cheng, Noa E. Cohen, William G. Fairbrother, Tzila Fenesh, Julien Gagneur, Valer Gotea, Tamar Holzer, Chiao-Feng Lin, Pier Luigi Martelli, Tatsuhiko Naito, Thi Yen Duong Nguyen, Castrense Savojardo, Ron Unger, Robert Warig, Yuedong Yang, Huiying Zhao
Article
Biotechnology & Applied Microbiology
Fabien Zoulim, Claire Fournier, Francois Habersetzer, Martin Sprinzl, Stanislas Pol, Carla S. Coffin, Vincent Leroy, Mang Ma, Heiner Wedemeyer, Ansgar W. Lohse, Robert Thimme, Karine Lugardon, Perrine Martin, Berangere Bastien, Benoit Sansas, Nathalie Adda, Celine Halluard, Kaidre Bendjama, Maud Brandely, Genevieve Inchauspe
HUMAN VACCINES & IMMUNOTHERAPEUTICS
(2020)
Article
Oncology
Adrian von Witzleben, Eve Currall, Oliver Wood, Lindsey Chudley, Oluyemisi Akinyegun, Jaya Thomas, Kaidre Bendjama, Gareth J. Thomas, Peter S. Friedmann, Emma V. King, Simon Laban, Christian H. Ottensmeier
Summary: This study investigated the relationship between HPV16 gene expression and adaptive immune responses, revealing that the expression of the E7 gene was correlated with antibody levels in the blood. Patients with high levels of anti-E2 IgG antibodies demonstrated better overall survival.
FRONTIERS IN ONCOLOGY
(2021)
Article
Oncology
Katy McCann, Adrian von Witzleben, Jaya Thomas, Chuan Wang, Oliver Wood, Divya Singh, Konstantinos Boukas, Kaidre Bendjama, Nathalie Silvestre, Finn Cilius Nielsen, Gareth Thomas, Tilman Sanchez-Elsner, Jason Greenbaum, Stephen Schoenberger, Bjoern Peters, Pandurangan Vijayanand, Natalia Savelyeva, Christian Ottensmeier
Summary: This study demonstrates the feasibility of efficiently identifying tumor-specific neoantigens and targeting them with vaccination in tumors with a low mutational burden, showing promising potential for successful clinical exploitation.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2022)
Article
Immunology
Rodrigo Nalio Ramos, Caroline Tosch, Fiorella Kotsias, Marie-Christine Claudepierre, Doris Schmitt, Christelle Remy-Ziller, Chantal Hoffmann, Marine Ricordel, Virginie Nourtier, Isabelle Farine, Laurence Laruelle, Julie Hortelano, Clementine Spring-Giusti, Christine Sedlik, Christophe Le Tourneau, Caroline Hoffmann, Nathalie Silvestre, Philippe Erbs, Kaidre Bendjama, Christine Thioudellet, Eric Quemeneur, Eliane Piaggio, Karola Rittner
Summary: This study identifies bovine pseudocowpox virus (PCPV) as a viral vector with strong immune stimulating abilities, capable of activating immune cells and reversing tumor-induced T-cell suppression. Using PCPV encoding the HPV16 E7 protein as a vaccine, significant antigen-specific T-cell responses were induced in experimental tumor-bearing mice, resulting in complete tumor regression. From a translational perspective, PCPV-E7 effectively stimulated IFN-γ production by T cells from tumor-draining lymph nodes of HPV+-infected cancer patients.
CLINICAL & TRANSLATIONAL IMMUNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Jun Cheng, Muhammed Hasan Celik, Anshul Kundaje, Julien Gagneur
Summary: MTSplice is a free and open-source model developed to predict the effects of genetic variants on splicing of cassette exons in 56 human tissues. It outperforms existing models in predicting tissue-specific variations, especially in brain tissues. Furthermore, MTSplice predicts enrichment of autism-associated de novo mutations for variants affecting splicing specifically in the brain.
Article
Biotechnology & Applied Microbiology
Jun Cheng, Thi Yen Duong Nguyen, Kamil J. Cygan, Muhammed Hasan Celik, William G. Fairbrother, Ziga Avsec, Julien Gagneur
Article
Biochemical Research Methods
Ziga Avsec, Mohammadamin Barekatain, Jun Cheng, Julien Gagneur