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Lang F, Sorn P, Suchan M, Henrich A, Albrecht C, Köhl N, Beicht A, Riesgo-Ferreiro P, Holtsträter C, Schrörs B, Weber D, Löwer M, Sahin U, Ibn-Salem J. Prediction of tumor-specific splicing from somatic mutations as a source of neoantigen candidates. BIOINFORMATICS ADVANCES 2024; 4:vbae080. [PMID: 38863673 PMCID: PMC11165244 DOI: 10.1093/bioadv/vbae080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/26/2024] [Accepted: 05/28/2024] [Indexed: 06/13/2024]
Abstract
Motivation Neoantigens are promising targets for cancer immunotherapies and might arise from alternative splicing. However, detecting tumor-specific splicing is challenging because many non-canonical splice junctions identified in tumors also appear in healthy tissues. To increase tumor-specificity, we focused on splicing caused by somatic mutations as a source for neoantigen candidates in individual patients. Results We developed the tool splice2neo with multiple functionalities to integrate predicted splice effects from somatic mutations with splice junctions detected in tumor RNA-seq and to annotate the resulting transcript and peptide sequences. Additionally, we provide the tool EasyQuant for targeted RNA-seq read mapping to candidate splice junctions. Using a stringent detection rule, we predicted 1.7 splice junctions per patient as splice targets with a false discovery rate below 5% in a melanoma cohort. We confirmed tumor-specificity using independent, healthy tissue samples. Furthermore, using tumor-derived RNA, we confirmed individual exon-skipping events experimentally. Most target splice junctions encoded neoepitope candidates with predicted major histocompatibility complex (MHC)-I or MHC-II binding. Compared to neoepitope candidates from non-synonymous point mutations, the splicing-derived MHC-I neoepitope candidates had lower self-similarity to corresponding wild-type peptides. In conclusion, we demonstrate that identifying mutation-derived, tumor-specific splice junctions can lead to additional neoantigen candidates to expand the target repertoire for cancer immunotherapies. Availability and implementation The R package splice2neo and the python package EasyQuant are available at https://github.com/TRON-Bioinformatics/splice2neo and https://github.com/TRON-Bioinformatics/easyquant, respectively.
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Affiliation(s)
- Franziska Lang
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
- Faculty of Biology, Johannes Gutenberg University Mainz, Mainz 55128, Germany
| | - Patrick Sorn
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Martin Suchan
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Alina Henrich
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Christian Albrecht
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Nina Köhl
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Aline Beicht
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Pablo Riesgo-Ferreiro
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Christoph Holtsträter
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Barbara Schrörs
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - David Weber
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Martin Löwer
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Ugur Sahin
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
- BioNTech SE, Mainz 55131, Germany
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz 55131, Germany
| | - Jonas Ibn-Salem
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
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Paolino J, Tsai HK, Harris MH, Pikman Y. IKZF1 Alterations and Therapeutic Targeting in B-Cell Acute Lymphoblastic Leukemia. Biomedicines 2024; 12:89. [PMID: 38255194 PMCID: PMC10813044 DOI: 10.3390/biomedicines12010089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
IKZF1 encodes the transcription factor IKAROS, a zinc finger DNA-binding protein with a key role in lymphoid lineage development. IKAROS plays a critical role in the development of lineage-restricted mature lymphocytes. Deletions within IKZF1 in B-cell acute lymphoblastic leukemia (B-ALL) lead to a loss of normal IKAROS function, conferring leukemic stem cell properties, including self-renewal and subsequent uncontrolled growth. IKZF1 deletions are associated with treatment resistance and inferior outcomes. Early identification of IKZF1 deletions in B-ALL may inform the intensification of therapy and other potential treatment strategies to improve outcomes in this high-risk leukemia.
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Affiliation(s)
- Jonathan Paolino
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Harrison K. Tsai
- Department of Pathology, Boston Children’s Hospital, Boston, MA 02115, USA (M.H.H.)
| | - Marian H. Harris
- Department of Pathology, Boston Children’s Hospital, Boston, MA 02115, USA (M.H.H.)
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA
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