Article
Multidisciplinary Sciences
Angela R. Smith, Jesus A. Alonso, Cory M. Ayres, Nishant K. Singh, Lance M. Hellman, Brian M. Baker
Summary: This study shows that modifications at primary anchors, even without structural impact, can significantly affect T cell recognition depending on the TCR. The impact of peptide anchor modification can be sensed by a TCR at regions distant from the modification site, indicating a through-protein mechanism. These findings have implications for the use of anchor-modified peptides and predicting the immunogenicity of tumor neoantigens.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Immunology
Zeynep Kosaloglu-Yalcin, John Sidney, William Chronister, Bjoern Peters, Alessandro Sette
Summary: Binding prediction tools are commonly used in identifying peptides presented on MHC class II molecules, but discrepancies between ligand elution data and binding predictions have been reported. While most MHC class II eluted ligands are predicted to bind with high affinity, there are instances where an increased number of ligands not predicted to bind were found due to ambiguous MHC restrictions. Additional analyses also showed that ligands predicted to not bind may bind other co-expressed MHC class II molecules.
Article
Chemistry, Applied
Wei Wang, Yuran Huang, Wenhong Zhao, Hao Dong, Juan Yang, Weidong Bai
Summary: This study identified and compared umami peptides from eight commercial dry-cured Spanish mackerels via molecular simulation. The results showed that the sequence of peptides varied in different samples, with only ten sequences being repeated across multiple samples. Four peptides were found to exhibit umami taste and umami-enhancing effects, forming hydrogen bonds and hydrophobic bonds in ligand-receptor interactions.
Article
Immunology
Pengbo Hu, Liang Xu, Yongqing Liu, Xiuyuan Zhang, Zhou Li, Yiming Li, Hong Qiu
Summary: By analyzing the tumor microenvironment of hepatocellular carcinoma using single-cell technology, we constructed molecular typing and risk models for LRs, and investigated their association with prognosis, drug sensitivity, and mutations. We also studied the role of SLC1A5 in liver cancer cells. Our findings provide valuable insights for clinical treatment and prognosis.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Multidisciplinary Sciences
Ke Pan, Yulun Chiu, Eric Huang, Michelle Chen, Junmei Wang, Ivy Lai, Shailbala Singh, Rebecca M. Shaw, Michael J. MacCoss, Cassian Yee
Summary: T cell responses are crucial for recovery and immune protection from SARS-CoV-2 infections, with epitopes best defined by analyzing peptides eluted from the naturally processed peptide-MHC. Traditional in silico methods for predicting immunogenic epitopes may not always be effective in eliciting T cell responses, highlighting the importance of empirical analysis for identifying immunogenic epitopes. T cell receptor-engineered T cell technology for targeting and killing SARS-CoV-2 target cells is currently unavailable, but mass spectrometric analysis of MHC-eluted peptides shows promise in identifying immunogenic epitopes and enabling engineered TCR-redirected killing.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Gastroenterology & Hepatology
June -Young Koh, Min-Seok Rha, Seong Jin Choi, Ha Seok Lee, Ji Won Han, Heejin Nam, Dong-Uk Kim, Jae Geun Lee, Myoung Soo Kim, Jun Yong Park, Su-Hyung Park, Dong Jin Joo, Eui-Cheol Shin
Summary: The study identified a distinct population of CD56hiCD161-CD8+ T cells in the liver sinusoids that exhibited NK-like activation via TCR-independent NKG2C ligation. This population was expanded in patients with chronic liver disease and may have pathogenic relevance.
JOURNAL OF HEPATOLOGY
(2022)
Article
Materials Science, Multidisciplinary
Sunil Rawat, Alankar Alankar
Summary: Molecular dynamics simulations were used to investigate crack growth behavior and microstructural evolution in different Ti single crystals. It was found that crack growth in alpha-Ti was independent of initial crack length, while it depended on initial crack length in beta-Ti and lamellar-Ti. Structural changes were observed in beta-Ti and lamellar-Ti, where the beta-phase transformed into variants of the alpha-phase. The critical strain energy release rate was largest in beta-Ti and lowest in alpha-Ti, and it showed a strong dependence on initial crack length in beta-Ti and lamellar-Ti.
JOURNAL OF THE MECHANICS AND PHYSICS OF SOLIDS
(2023)
Article
Oncology
Miranda H. Meeuwsen, Anne K. Wouters, Tassilo L. A. Wachsmann, Renate S. Hagedoorn, Michel G. D. Kester, Dennis F. G. Remst, Dirk M. van der Steen, Arnoud H. de Ru, Els P. van Hees, Martijn Kremer, Marieke Griffioen, Peter A. van Veelen, J. H. Frederik Falkenburg, Mirjam H. M. Heemskerk
Summary: Jchain is highly expressed in multiple myeloma (MM) and Jchain-derived peptides presented in HLA molecules may be suitable antigens for T-cell therapy of MM. Using immunopeptidomics, Jchain-derived epitopes presented by MM cells were identified, and Jchain-specific T-cell clones were isolated using pHLA tetramer technology. TCRs targeting Jchain-derived peptides presented in four common HLA alleles demonstrated potent preclinical anti-myeloma activity, encouraging further preclinical testing and ultimately clinical development.
JOURNAL OF HEMATOLOGY & ONCOLOGY
(2023)
Article
Oncology
Xueyan Xi, Yang Guo, Min Zhu, Fen Qiu, Feifei Lei, Gang Li, Boyu Du
Summary: The research team identified a new peptide and protein antigen recognized by gamma delta T cells in hepatocellular carcinoma, providing a new potential therapeutic target for immunotherapy.
CANCER IMMUNOLOGY IMMUNOTHERAPY
(2021)
Article
Immunology
Nadezhda Logunova, Marina Kapina, Elena Kondratieva, Alexander Apt
Summary: By analyzing the role of MHC-II genes in the control of tuberculosis infection, it was found that the H2-Ab gene plays a major role. Further research revealed that regular genetic recombination within the MHC-II recombination hot spot region can severely impair immune system functioning.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Domingo Mendez-Alvarez, Maria F. Torres-Rojas, Edgar E. Lara-Ramirez, Laurence A. Marchat, Gildardo Rivera
Summary: Obesity is a global health issue, and this study aimed to predict new small molecules as potential ER beta activators for obesity control. Ligand-based virtual screening and molecular docking were used to identify potential compounds. Molecular dynamic simulations and ADMET evaluation showed that the selected compounds had good stability, safety, and potential for obesity control.
Review
Cell Biology
Inbar Arman, Maya Haus-Cohen, Yoram Reiter
Summary: The search for new targets in cancer immunotherapy has focused on the intracellular proteome, particularly peptides presented by MHC class I molecules on malignant cells. TCR or TCRL antibodies can specifically target these disease-specific class I HLA-peptide complexes. Preclinical and clinical trials are testing TCR-engineered T cells, TCR-like CAR-T cells, and other TCRL- and TCR-based agents for their therapeutic potential in cancer. The success of the anti-gp100/HLA-A2 TCR-based T cell engager has demonstrated the promising results of targeting the intracellular proteome in cancer immunotherapy.
Article
Biochemical Research Methods
Zhaochun Xu, Meng Luo, Weizhong Lin, Guangfu Xue, Pingping Wang, Xiyun Jin, Chang Xu, Wenyang Zhou, Yideng Cai, Wenyi Yang, Huan Nie, Qinghua Jiang
Summary: Accurate prediction of immunogenic peptides recognized by T cell receptor (TCR) is crucial for vaccine development and cancer immunotherapy, but current methods face challenges. DLpTCR, a multimodal ensemble deep learning framework, demonstrates high predictive power in accurately predicting peptide-TCR interactions, offering a promising approach for improving accuracy in immunogenic peptide prediction.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Rene Platzer, Joschka Hellmeier, Janett Gohring, Iago Doel Perez, Philipp Schatzlmaier, Clara Bodner, Margarete Focke-Tejkl, Gerhard J. Schuetz, Eva Sevcsik, Hannes Stockinger, Mario Brameshuber, Johannes B. Huppa
Summary: This study demonstrates that single freely diffusing agonist pMHC II can autonomously elicit a full T-cell response in a peptide-specific manner, while endogenous pMHC II has minimal impact on TCR engagement.
Article
Health Care Sciences & Services
Josephine G. M. Strijker, Ronja Pscheid, Esther Drent, Jessica J. F. van der Hoek, Bianca Koopmans, Kimberley Ober, Sander R. van Hooff, Waleed M. Kholosy, Annelisa M. Cornel, Chris Coomans, Andrea Bisso, Marleen M. van Loenen, Jan J. Molenaar, Judith Wienke
Summary: A novel T cell-based immunotherapy approach for neuroblastoma, utilizing TEG002, showed promising results in recognizing and killing target cells independent of MHC-I expression. The efficacy of TEG002 treatment was superior to untransduced alpha beta-T cells or endogenous gamma delta-T cells in killing neuroblastoma organoids, indicating its potential as a new treatment option for a subset of patients.
JOURNAL OF PERSONALIZED MEDICINE
(2021)
Article
Oncology
Qiong J. Wang, Zhiya Yu, Kayla Griffith, Ken-ichi Hanada, Nicholas P. Restifo, James C. Yang
CANCER IMMUNOLOGY RESEARCH
(2016)
Meeting Abstract
Oncology
Qiong J. Wang, Zhiya Yu, Kenichi Hanada, Nicholas P. Restifo, James C. Yang
Article
Oncology
Qiong J. Wang, Zhiya Yu, Ken-Ichi Hanada, Krishna Patel, David Kleiner, Nicholas P. Restifo, James C. Yang
CLINICAL CANCER RESEARCH
(2017)
Meeting Abstract
Oncology
Romi Biswas, Shaojian Gao, Contance Cultraro, Xu Zhang, Tapan Maity, Corey Carter, Anish Thomas, Arun Rajan, Ken-Ichi Hanada, Young Song, Zied Abdullaev, Paul Meltzer, James Yang, Svetlana Pack, Giuseppe Giaccone, Javed Khan, Udayan Guha
JOURNAL OF THORACIC ONCOLOGY
(2017)
Article
Hematology
Daniel Abate-Daga, Ken-ichi Hanada, Jeremy L. Davis, James C. Yang, Steven A. Rosenberg, Richard A. Morgan
Article
Oncology
Joseph G. Crompton, Madhusudhanan Sukumar, Rahul Roychoudhuri, David Clever, Alena Gros, Robert L. Eil, Eric Tran, Ken-ichi Hanada, Zhiya Yu, Douglas C. Palmer, Sid P. Kerkar, Ryan D. Michalek, Trevor Upham, Anthony Leonardi, Nicolas Acquavella, Ena Wang, Francesco M. Marincola, Luca Gattinoni, Pawel Muranski, Mark S. Sundrud, Christopher A. Klebanoff, Steven A. Rosenberg, Douglas T. Fearon, Nicholas P. Restifo
Editorial Material
Biotechnology & Applied Microbiology
Ken-ichi Hanada, Nicholas P. Restifo
NATURE BIOTECHNOLOGY
(2013)
Article
Oncology
Nicolas Acquavella, David Clever, Zhiya Yu, Melody Roelke-Parker, Douglas C. Palmer, Liqiang Xi, Holger Pflicke, Yun Ji, Alena Gros, Ken-ichi Hanada, Ian S. Goldlust, Gautam U. Mehta, Christopher A. Klebanoff, Joseph G. Crompton, Madhusudhanan Sukumar, James J. Morrow, Zulmarie Franco, Luca Gattinoni, Hui Liu, Ena Wang, Francesco Marincola, David F. Stroncek, Chyi-Chia R. Lee, Mark Raffeld, Marcus W. Bosenberg, Rahul Roychoudhuri, Nicholas P. Restifo
CANCER IMMUNOLOGY RESEARCH
(2015)
Article
Dermatology
Takashi Inozume, Ken-ichi Hanada, Kazuyo Takeda, Tatsuo Maeda, Kazutoshi Harada, Tatsuyoshi Kawamura
JOURNAL OF DERMATOLOGY
(2019)
Article
Oncology
Ken-ichi Hanada, Chihao Zhao, Raul Gil-Hoyos, Jared J. Gartner, Christopher Chow-Parmer, Frank J. Lowery, Sri Krishna, Todd D. Prickett, Scott Kivitz, Maria R. Parkhurst, Nathan Wong, Zachary Rae, Michael C. Kelly, Stephanie L. Goff, Paul F. Robbins, Steven A. Rosenberg, James C. Yang
Summary: This study proposes a signature to identify neoantigen-reactive T cells and demonstrates a successful rate of identifying such T cells using the signature. It provides a potential method for quick identification and engineering of personalized neoantigen-reactive T cells for therapy.
Article
Oncology
Catherine M. Ade, Matthew J. Sporn, Sudipto Das, Zhiya Yu, Ken-ichi Hanada, Yue A. Qi, Tapan Maity, Xu Zhang, Udayan Guha, Thorkell Andresson, James C. Yang
Summary: This article introduces a method of using mass spectrometry to identify common tumor-specific neoepitopes derived from mutated oncogenes, and develop TCRs based on these data. The results of the study show that this method successfully identified precise neoepitopes derived from KRAS, EGFR, BRAF, and PIK3CA presented by HLA-A*03:01 and/or HLA-A*11:01 across multiple biological replicates.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2023)
Article
Oncology
Jared J. Gartner, Maria R. Parkhurst, Alena Gros, Eric Tran, Mohammad S. Jafferji, Amy Copeland, Ken-Ichi Hanada, Nikolaos Zacharakis, Almin Lalani, Sri Krishna, Abraham Sachs, Todd D. Prickett, Yong F. Li, Maria Florentin, Scott Kivitz, Samuel C. Chatmon, Steven A. Rosenberg, Paul F. Robbins
Summary: Robbins and colleagues developed and tested a machine learning model for ranking tumor neoantigens, aiding in the identification of potential therapeutic targets for future immunotherapies. The model showed improved sensitivity and specificity by incorporating multiple factors impacting epitope presentation and recognition, compared to using predicted HLA binding alone. The ranked output provides a list of potential neoantigens for further in vitro and in vivo studies, facilitating the development of more effective immunotherapies.
Article
Medicine, Research & Experimental
Ken-ichi Hanada, Zhiya Yu, Gabrielle R. Chappell, Adam S. Park, Nicholas P. Restifo
Meeting Abstract
Oncology
M. L. Good, N. Tamaoki, T. Maeda, S. Islam, M. Bosch-Marce, M. Kruhlak, S. Pack, N. Bedanova, P. Malckzadeh, D. C. Deniger, R. Yoseph, C. Liu, K. Hanada, R. Robbins, S. A. Rosenberg, R. Vizcardo, N. P. Restifo
ANNALS OF SURGICAL ONCOLOGY
(2019)
Article
Medicine, Research & Experimental
Alena Gros, Paul F. Robbins, Xin Yao, Yong F. Li, Simon Turcotte, Eric Tran, John R. Wunderlich, Arnold Mixon, Shawn Farid, Mark E. Dudley, Ken-ichi Hanada, Jorge R. Almeida, Sam Darko, Daniel C. Douek, James C. Yang, Steven A. Rosenberg
JOURNAL OF CLINICAL INVESTIGATION
(2014)