Article
Biochemical Research Methods
Raphael Trevizani, Zhen Yan, Jason A. Greenbaum, Alessandro Sette, Morten Nielsen, Bjoern Peters
Summary: An approach to assess the reliability of different metrics for evaluating the performance of MHC class I binding predictors was developed. The study found that using percentile-ranked results improved the stability of the ranks and identified the top-performing tools in the benchmark.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Cell Biology
Maria C. Tovar Fernandez, Ewa M. Sroka, Mathilde Lavigne, Aikaterini Thermou, Chrysoula Daskalogianni, Benedicte Manoury, Rodrigo Prado Martins, Robin Fahraeus
Summary: The accumulation of protein aggregates is toxic and its relation to diseases is still unclear. This study reveals that certain antigenic peptides can be presented to the MHC class I pathway via autophagy. The presentation of peptides derived from the viral EBNA1 protein was not affected by autophagy suppression, while the presentation of ovalbumin was suppressed. The study also suggests that the relative levels of protein expression do not affect autophagy-mediated antigen presentation.
CELLULAR IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Lauren E. Stopfer, Nicholas J. Rettko, Owen Leddy, Joshua M. Mesfin, Eric Brown, Shannon Winski, Bryan Bryson, James A. Wells, Forest M. White
Summary: Combining multiple therapeutic strategies may improve survival benefits for NRAS/BRAF mutant melanoma patients. This study utilized immunopeptidomics to measure the impact of MEK inhibition on anti-tumor immunity and identified enhanced expression of specific tumor antigens following therapy. Targeting these upregulated tumor antigens can enhance cell killing.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Immunology
Yang Liu, Baozeng Sun, Jiawei Wang, Hao Sun, Zhenhua Lu, Longyu Chen, Mingfu Lan, Jiahao Xu, Jingyu Pan, Jingqi Shi, Yuanjie Sun, Xiyang Zhang, Jing Wang, Dongbo Jiang, Kun Yang
Summary: This study used computational approaches to predict the MHC class-I restricted epitopes of Ebola virus glycoprotein, and validated their conservation and immunogenicity. These results contribute to a better understanding of the immune response to Ebola virus and provide potential strategies for epitope-based immunotherapy.
INTERNATIONAL IMMUNOLOGY
(2022)
Review
Immunology
Karthik Dhatchinamoorthy, Jeff D. Colbert, Kenneth L. Rock
Summary: Loss of MHC I antigen presentation is common in many cancers, which may impair immune responses and affect the efficacy of immunotherapy. Studies have discussed underlying mechanisms through which some cancers evade immune killing by shutting down the MHC I pathway, and proposed potential strategies to overcome this limitation.
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Immunology
Karolina D. Witt
Summary: MHC class I antigen processing is a less recognized area in nonviral host-pathogen interactions, involving immunology and cell biology. This review focuses on the MHC-I antigen processing pathway and alternative sources of antigens, particularly in the context of Mycobacterium tuberculosis (Mtb) as an intracellular pathogen. It explores how Mtb manipulates host immunity for survival and proposes directions for MHC-I-focused approaches in developing vaccines against tuberculosis.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Immunology
Saskia V. Vijver, Sarah Danklmaier, Lisa Pipperger, Raphael Gronauer, Gabriel Floriani, Hubert Hackl, Krishna Das, Guido Wollmann
Summary: This study aimed to identify the anti-viral T cells raised by VSV-GP virotherapy in C57BL/6J mice using a multi-level adapted bioinformatics approach. The top-ranked viral epitopes triggering IFN-gamma secretion due to T cell activation were identified and validated. Overall, this identification of VSV-GP T cell epitopes enables comprehensive monitoring of anti-viral T cell responses and supports the development of novel VSV-GP variants.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Oncology
Lei Zhan, Junhui Zhang, Jing Zhang, Xiaojing Liu, Suding Zhu, Yuchuan Shi, Yu He, Wenyan Wang, Yijing Wei, Zhenhai Tang, Guo Chen, Bing Wei, Yunxia Cao
Summary: In this study, the researchers found that upregulated autophagy and decreased expression of MHC-I and NLRC5 were associated with endometrial cancer (EC). Inhibition of autophagy was found to suppress MHC-I gene expression. They also discovered that LC3 interacted with NLRC5 to inhibit the NLRC5-mediated MHC-I antigen presentation pathway. These findings suggest that inhibiting LC3 and promoting NLRC5 may be a promising immunotherapy strategy for EC management.
Article
Immunology
Mark N. Lee, Matthew Meyerson
Summary: This study introduces a high-throughput epitope identification system that combines T cell-secreted cytokines capture, cell sorting, and next-generation sequencing to identify new class I- and class II-restricted epitopes. The technology successfully validated known viral, neoepitope, and autoimmune epitope-specific TCR targets, as well as discovered new epitopes encoded by the human cytomegalovirus genome. This cytokine capture-based assay enables pooled screening of thousands of encoded peptides for epitope discovery and may lead to identification of HLA-epitope-TCR complexes relevant to disease control, etiology, or treatment.
SCIENCE IMMUNOLOGY
(2021)
Article
Medicine, Research & Experimental
Yingying Shi, Yu Liu, Jiaxin Huang, Zhenyu Luo, Xuemeng Guo, Mengshi Jiang, Xiang Li, Yichao Lu, Xu Liu, Xinyu Shan, Lihua Luo, Jian You
Summary: This study indicates that a simultaneous and coordinated mobilization of MHC-restricted immunity may enhance cancer therapy, providing new insights for cancer treatment.
Review
Oncology
Edyta Wieczorek, Malgorzata A. Garstka
Summary: This study focuses on the relationship between MHC class I and BC, discussing the importance and application of MHC class I in BC treatment. The paper suggests that loss of MHC class I expression in BC may affect treatment outcomes, and explores methods to enhance MHC class I antigen presentation to CD8+ T cells, emphasizing the significance of immune status in predicting treatment outcomes for BC patients.
INTERNATIONAL JOURNAL OF CANCER
(2021)
Article
Computer Science, Artificial Intelligence
Benjamin Alexander Albert, Yunxiao Yang, Xiaoshan M. M. Shao, Dipika Singh, Kellie N. N. Smith, Valsamo Anagnostou, Rachel Karchin
Summary: Researchers propose a method based on long short-term memory ensembles and transfer learning to predict effective neoepitopes that elicit an immune response. This method can help address the challenge of predicting immunogenicity of neoepitopes in developing personalized cancer vaccines. Compared to other state-of-the-art classifiers, this method significantly improves the prediction of epitope presentation.
NATURE MACHINE INTELLIGENCE
(2023)
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
Computer Science, Artificial Intelligence
Yanyi Chu, Yan Zhang, Qiankun Wang, Lingfeng Zhang, Xuhong Wang, Yanjing Wang, Dennis Russell Salahub, Qin Xu, Jianmin Wang, Xue Jiang, Yi Xiong, Dong-Qing Wei
Summary: The study presents the TransMut framework, which automatically optimizes mutated peptides with higher affinity to the target HLA allele. This framework provides an automated approach for screening immunogenic peptides and vaccine design.
NATURE MACHINE INTELLIGENCE
(2022)
Article
Biochemistry & Molecular Biology
Jieru Deng, Chunni Lu, Chuanxin Liu, Sara Oveissi, W. Douglas Fairlie, Erinna F. Lee, Pamuk Bilsel, Hamsa Puthalakath, Weisan Chen
Summary: The study demonstrates that IAV infection induces endogenous presentation of a viral epitope by MHC-II to CD4(+) T cells, dependent on de novo protein synthesis and the ER-Golgi network. Some antigenic peptides are of cytosolic origin in this process. Additionally, autophagy inhibitors and deletion of autophagy-related genes block most of the MHC-II-restricted endogenous IAV antigen presentation.
Editorial Material
Biochemistry & Molecular Biology
Ye-Guang Chen, Elena Ezhkova, Marina Ostankovitch
JOURNAL OF MOLECULAR BIOLOGY
(2016)
Article
Biochemical Research Methods
Stacy A. Malaker, Michael J. Ferracane, Florence R. Depontieu, Angela L. Zarling, Jeffrey Shabanowitz, Dina L. Bai, Suzanne L. Topalian, Victor H. Engelhard, Donald F. Hunt
JOURNAL OF PROTEOME RESEARCH
(2017)
Editorial Material
Biochemistry & Molecular Biology
Tatiana G. Kutateladze, Or Gozani, Mariann Bienz, Marina Ostankovitch
JOURNAL OF MOLECULAR BIOLOGY
(2017)
Article
Oncology
Fiyaz Mohammed, Daniel H. Stones, Angela L. Zarling, Carrie R. Willcox, Jeffrey Shabanowitz, Kara L. Cummings, Donald F. Hunt, Mark Cobbold, Victor H. Engelhard, Benjamin E. Willcox
Article
Oncology
Amber N. Woods, Ashley L. Wilson, Nithya Srivinisan, Jianhao Zeng, Arun B. Dutta, J. David Peske, Eric F. Tewalt, Randal K. Gregg, Andrew R. Ferguson, Victor H. Engelhard
CANCER IMMUNOLOGY RESEARCH
(2017)
Article
Medicine, Research & Experimental
Yared Hailemichael, Amber Woods, Tihui Fu, Qiuming He, Michael C. Nielsen, Farah Hasan, Jason Roszik, Zhilan Xiao, Christina Vianden, Hiep Khong, Manisha Singh, Meenu Sharma, Faisal Faak, Derek Moore, Zhimin Dai, Scott M. Anthony, Kimberly S. Schluns, Padmanee Sharma, Victor H. Engelhard, Willem W. Overwijk
JOURNAL OF CLINICAL INVESTIGATION
(2018)
Review
Immunology
Victor H. Engelhard, Anthony B. Rodriguez, Ileana S. Mauldin, Amber N. Woods, J. David Peske, Craig L. Slingluff
JOURNAL OF IMMUNOLOGY
(2018)
Article
Oncology
Marit M. Melssen, Walter Olson, Nolan A. Wages, Brian J. Capaldo, Ileana S. Mauldin, Adela Mahmutovic, Ciara Hutchison, Cornelis J. M. Melief, Timothy N. Bullock, Victor H. Engelhard, Craig L. Slingluff
Article
Oncology
Katie M. Leick, Joel Pinczewski, Ileana S. Mauldin, Samuel J. Young, Donna H. Deacon, Amber N. Woods, Marcus W. Bosenberg, Victor H. Engelhard, Craig L. Slingluff
CANCER IMMUNOLOGY IMMUNOTHERAPY
(2019)
Article
Immunology
Stella J. Berendam, Alexander F. Koeppel, Nicole R. Godfrey, Sherin J. Rouhani, Amber N. Woods, Anthony B. Rodriguez, J. David Peske, Kara L. Cummings, Stephen D. Turner, Victor H. Engelhard
FRONTIERS IN IMMUNOLOGY
(2019)
Review
Immunology
Laura Santambrogio, Stella J. Berendam, Victor H. Engelhard
FRONTIERS IN IMMUNOLOGY
(2019)
Article
Dermatology
Emilia R. Dellacecca, Cormac Cosgrove, Zhussipbek Mukhatayev, Suhail Akhtar, Victor H. Engelhard, Alfred W. Rademaker, Katherine L. Knight, I. Caroline Le Poole
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2020)
Article
Oncology
Victor H. Engelhard, Rebecca C. Obeng, Kara L. Cummings, Gina R. Petroni, Angela L. Ambakhutwala, Kimberly A. Chianese-Bullock, Kelly T. Smith, Amanda Lulu, Nikole Varhegyi, Mark E. Smolkin, Paisley Myers, Keira E. Mahoney, Jeffrey Shabanowitz, Nico Buettner, Emily H. Hall, Kathleen Haden, Mark Cobbold, Donald F. Hunt, Geoffrey Weiss, Elizabeth Gaughan, Craig L. Slingluff
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2020)
Article
Oncology
Amanda M. Lulu, Kara L. Cummings, Erin D. Jeffery, Paisley T. Myers, Dennis Underwood, Rachel M. Lacy, Kimberly A. Chianese-Bullock, Craig L. Slingluff, Susan C. Modesitt, Victor H. Engelhard
Summary: A study found preexisting immune memory to cancer-expressed phosphopeptides in most healthy donors, indicating exposure to common microbial agents, but with significant variability. The research suggests that the immunogens generating phosphopeptide-specific immune memory are rare infectious agents or early cancer cells with distinct phosphoproteome dysregulations, and repetitive immunogenic exposures occur in individual donors. Overall, enhancing phosphopeptide-specific T-cell responses could be a useful approach to improve tumor immunotherapy.
CANCER IMMUNOLOGY RESEARCH
(2021)
Article
Oncology
Kevin T. Lynch, Samuel J. Young, Max O. Meneveau, Nolan A. Wages, Victor H. Engelhard, Craig L. Slingluff, Ileana S. Mauldin
Summary: The presence of TLS in cutaneous melanoma metastases is associated with increased intratumoral lymphocyte infiltration and improved overall survival in patients. Different types of TLS have varying effects on patient survival, indicating potential regulatory or antigen-driven immune responses.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2021)