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Noncoding regions are the main source of targetable tumor-specific antigens

ABSTRACT: Noncoding regions are the main source of targetable tumor-specific antigens

PROVIDER: PRJNA525590 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8668620_1.fastq.gz	Fastqsanger.gz
	SRR8668620_2.fastq.gz	Fastqsanger.gz
	SRR8668630_1.fastq.gz	Fastqsanger.gz
	SRR8668630_2.fastq.gz	Fastqsanger.gz
	SRR8668611_1.fastq.gz	Fastqsanger.gz

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Noncoding regions are the main source of targetable tumor-specific antigens

Project description:Purpose: Tumor-specific antigens (TSAs) represent ideal targets for cancer immunotherapy, but very few of them have been identified. Therefore, the goal of this study was to develop a novel approach, combining RNA-Sequencing and mass spectrometry, to enlarge the landscape of actionable TSAs in seven human primary samples, namely 4 B-ALL and 3 lung tumor biopsies. Methods: We performed RNA-Sequencing on each primary tumor sample (unreplicated) with the Illumina HiSeq200. Using those RNA-Sequencing data to build a global cancer database for each sample, we performed a transcriptomic-informed mass spectrometry analysis of their MHC I-associated peptides to identify TSAs. Results: We identified a total of 30 TSAs, 90% of which derived from allegedly non-coding regions and would have been missed by standard approaches. Moreover, most of these TSAs derived from non-mutated yet cancer-restricted transcripts that can be shared by multiple tumors. Conclusions: In conclusion, the strategy reported herein is readily applicable to human tumors and should considerably enlarge the landscape of actionable TSAs.

2019-11-20 | GSE127825 | GEO

Non-coding regions are the main source of tumor-specific antigens

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Non-coding regions are the main source of tumor-specific antigens [mouse]

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Non-coding regions are the main source of tumor-specific antigens [human]

Project description:Non-coding regions are the main source of tumor-specific antigens [human]

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Non-coding regions are the main source of tumor-specific antigens [human]

Project description:Purpose: Tumor-specific antigens (TSAs) represent ideal targets for cancer immunotherapy, but very few of them have been identified. Therefore, the goal of this study was to develop a novel approach, combining RNA-Sequencing and mass spectrometry, to enlarge the landscape of actionable TSAs in seven human primary samples, namely 4 B-ALL and 3 lung tumor biopsies. Methods: We performed RNA-Sequencing on each primary tumor sample (unreplicated) with the Illumina HiSeq2000. Using those RNA-Sequencing data to build a global cancer database for each sample, we performed a transcriptomic-informed mass spectrometry analysis of their MHC I-associated peptides to identify TSAs. Results: We identified a total of 30 TSAs, 90% of which derived from allegedly non-coding regions and would have been missed by standard approaches. Moreover, most of these TSAs derived from non-mutated yet cancer-restricted transcripts that can be shared by multiple tumors. Conclusions: In conclusion, the strategy reported herein is readily applicable to human tumors and should considerably enlarge the landscape of actionable TSAs.

2018-10-18 | GSE113972 | GEO

Non-coding regions are the main source of tumor-specific antigens [mouse]

Project description:Purpose: Tumor-specific antigens (TSAs) represent ideal targets for cancer immunotherapy, but very few of them have been identified. Therefore, the goal of this study was to develop a novel approach, combining RNA-Sequencing and mass spectrometry, to enlarge the landscape of actionable TSAs in two murine cell lines, namely EL4 and CT26 cells. Methods: We performed RNA-Sequencing on both tumor cell lines (unreplicated) as well as on the syngeneic mature medullary thymic epithelial cells (mTEChi, in triplicate), using either the Illumina HiSeq200 or the Illumina NextSeq 500. Using those RNA-Sequencing data to build a global cancer database for each tumor cell line, we performed a transcriptomic-informed mass spectrometry analysis of their MHC I-associated peptides to identify TSAs. Results: We identified a total of 21 TSAs, 90% of which derived from allegedly non-coding regions and would have been missed by standard approaches. Moreover, about 70% of these TSAs derived from non-mutated yet cancer-restricted transcripts (e.g., endogenous retroelements) that can be shared by multiple tumors. Conclusions: In conclusion, the strategy reported herein is readily applicable to human tumors and should considerably enlarge the landscape of actionable TSAs.

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Non-coding regions are the main source of tumor-specific antigens

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2018-10-18 | GSE113992 | GEO

MEK inhibition enhances presentation of targetable MHC-I tumor antigens in mutant melanomas

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Bronchioalveolar stem cells are a main source for regeneration of distal lung epithelia

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MEK inhibition enhances presentation of targetable MHC-I tumor antigens in mutant melanomas [RNA-seq]

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