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Wang A, Lin X, Chau KN, Onuchic JN, Levine H, George JT. RACER-m leverages structural features for sparse T cell specificity prediction. SCIENCE ADVANCES 2024; 10:eadl0161. [PMID: 38748791 PMCID: PMC11095454 DOI: 10.1126/sciadv.adl0161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 04/10/2024] [Indexed: 05/19/2024]
Abstract
Reliable prediction of T cell specificity against antigenic signatures is a formidable task, complicated by the immense diversity of T cell receptor and antigen sequence space and the resulting limited availability of training sets for inferential models. Recent modeling efforts have demonstrated the advantage of incorporating structural information to overcome the need for extensive training sequence data, yet disentangling the heterogeneous TCR-antigen interface to accurately predict MHC-allele-restricted TCR-peptide interactions has remained challenging. Here, we present RACER-m, a coarse-grained structural model leveraging key biophysical information from the diversity of publicly available TCR-antigen crystal structures. Explicit inclusion of structural content substantially reduces the required number of training examples and maintains reliable predictions of TCR-recognition specificity and sensitivity across diverse biological contexts. Our model capably identifies biophysically meaningful point-mutant peptides that affect binding affinity, distinguishing its ability in predicting TCR specificity of point-mutants from alternative sequence-based methods. Its application is broadly applicable to studies involving both closely related and structurally diverse TCR-peptide pairs.
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Affiliation(s)
- Ailun Wang
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, USA
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Xingcheng Lin
- Department of Physics, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Kevin Ng Chau
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, USA
- Department of Physics, Northeastern University, Boston, MA, USA
| | - José N. Onuchic
- Departments of Physics and Astronomy, Chemistry, and Biosciences, Rice University, Houston, TX, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | - Herbert Levine
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, USA
- Department of Physics, Northeastern University, Boston, MA, USA
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Jason T. George
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- Department of Biomedical Engineering, Texas A&M University, Houston, TX, USA
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Yang J, Shu L, Han M, Pan J, Chen L, Yuan T, Tan L, Shu Q, Duan H, Li H. RDmaster: A novel phenotype-oriented dialogue system supporting differential diagnosis of rare disease. Comput Biol Med 2024; 169:107924. [PMID: 38181610 DOI: 10.1016/j.compbiomed.2024.107924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/18/2023] [Accepted: 01/01/2024] [Indexed: 01/07/2024]
Abstract
BACKGROUND Clinicians often lack the necessary expertise to differentially diagnose multiple underlying rare diseases (RDs) due to their complex and overlapping clinical features, leading to misdiagnoses and delayed treatments. The aim of this study is to develop a novel electronic differential diagnostic support system for RDs. METHOD Through integrating two Bayesian diagnostic methods, a candidate list was generated with enhance clinical interpretability for the further Q&A based differential diagnosis (DDX). To achieve an efficient Q&A dialogue strategy, we introduce a novel metric named the adaptive information gain and Gini index (AIGGI) to evaluate the expected gain of interrogated phenotypes within real-time diagnostic states. RESULTS This DDX tool called RDmaster has been implemented as a web-based platform (http://rdmaster.nbscn.org/). A diagnostic trial involving 238 published RD patients revealed that RDmaster outperformed existing RD diagnostic tools, as well as ChatGPT, and was shown to enhance the diagnostic accuracy through its Q&A system. CONCLUSIONS The RDmaster offers an effective multi-omics differential diagnostic technique and outperforms existing tools and popular large language models, particularly enhancing differential diagnosis in collecting diagnostically beneficial phenotypes.
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Affiliation(s)
- Jian Yang
- Clinical Data Center, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Zhejiang, China; The College of Biomedical Engineering and Instrument Science, Zhejiang University, Zhejiang, China
| | - Liqi Shu
- Rhode Island Hospital, Warren Alpert Medical School of Brown University, Rhode Island, USA
| | - Mingyu Han
- Neonatal Department, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Zhejiang, China
| | - Jiarong Pan
- Neonatal Department, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Zhejiang, China
| | - Lihua Chen
- Neonatal Department, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Zhejiang, China
| | - Tianming Yuan
- Neonatal Department, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Zhejiang, China
| | - Linhua Tan
- Surgical Intensive Care Unit, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Zhejiang, China
| | - Qiang Shu
- Clinical Data Center, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Zhejiang, China
| | - Huilong Duan
- The College of Biomedical Engineering and Instrument Science, Zhejiang University, Zhejiang, China
| | - Haomin Li
- Clinical Data Center, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Zhejiang, China.
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