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| Status |
Public on May 20, 2024 |
| Title |
Neoantigen identification for 1956 and F244 murine MCA-sarcomas |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
This study was to predict neoantigens in 1956 and F244 murine MCA-sarcomas (female C57BL/6N and male 129S6 lines, respectively). Mutations were called by comparing tumor versus normal whole exome sequencing (WES) data, and filtered for expressing mutations using RNA-seq data. Out of expressing mutations, MHC class I or II neoantigens were predicted and screened by T cell reactivities (IFN-gamma ELISPOT and tetramer staining). Therapeutic vaccine confirmed an M50I mutation in Psmd6 and an R144S mutation in Cs to be the major MHC class I (H-2Kb) and II (I-Ab) neoantigens for 1956; and a G122A in Pex14 and a D2944Y mutation in Plec to be the major class I (H-2Kb) and class II (I-Ab) neoantigens for F244.
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| Overall design |
WES was performed for DNA extracted from in vitro cultured 1956 or F244 cells (n=1 per line); or a tail of a female C57BL/6N or male 129S6 mouse (normal controls for 1956 and F244, respectively; n=1 per strain). RNA-seq was performed for RNA extracted from in vitro cultured 1956 or F244 cells (n=1 per line).
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| Web link |
https://aacrjournals.org/cancerimmunolres/article/doi/10.1158/2326-6066.CIR-23-0900/745442/Improvement-of-tumor-neoantigen-detection-by-high
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| Contributor(s) |
Yoshiko T, Jeffrey WP, Wei M, Hussein S, Cora AD, Elaine MR, Maxim AN, Cheryl LF, Robert SD |
| Citation(s) |
38768391 |
| Submission date |
May 20, 2024 |
| Last update date |
May 21, 2024 |
| Contact name |
Robert D Schreiber |
| Organization name |
Washington University in St. Louis
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| Department |
Department of Pathology and Immunology
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| Street address |
425 South Euclid
|
| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA1113588 |
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