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Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy

ABSTRACT: Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy

PROVIDER: PRJNA826110 | ENA |

REPOSITORIES: ENA

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Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy

Project description:Oesophageal adenocarcinoma (OAC) is a poor prognosis cancer and the molecular features underpinning response to treatment remain unclear. We investigated whole genome, and where possible transcriptomic and methylation data from 115 OAC patients mostly from the DOCTOR phase II clinical trial (ANZCTR-ACTRN12609000665235). We identified genomic features associated with poorer overall survival, such as the APOBEC mutational and RS3-like rearrangement signatures. We also showed that positron emission tomography non-responders have more sub-clonal genomic copy number alterations. Transcriptomic analysis categorised patients into four immune clusters correlated with survival. The immune suppressed cluster was associated with worse survival, enriched with myeloid-derived cells, and an epithelial-mesenchymal transition signature. The immune hot cluster was associated with better survival, enriched with lymphocytes, myeloid-derived cells, and an immune signature including CCL5, CD8A, and NKG7. The immune clusters highlight patients who may respond to immunotherapy and thus may guide future clinical trials.

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Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy.

Project description:Oesophageal adenocarcinoma is a poor prognosis cancer and the molecular features underpinning response to treatment remain unclear. We investigate whole genome, transcriptomic and methylation data from 115 oesophageal adenocarcinoma patients mostly from the DOCTOR phase II clinical trial (Australian New Zealand Clinical Trials Registry-ACTRN12609000665235), with exploratory analysis pre-specified in the study protocol of the trial. We report genomic features associated with poorer overall survival, such as the APOBEC mutational and RS3-like rearrangement signatures. We also show that positron emission tomography non-responders have more sub-clonal genomic copy number alterations. Transcriptomic analysis categorises patients into four immune clusters correlated with survival. The immune suppressed cluster is associated with worse survival, enriched with myeloid-derived cells, and an epithelial-mesenchymal transition signature. The immune hot cluster is associated with better survival, enriched with lymphocytes, myeloid-derived cells, and an immune signature including CCL5, CD8A, and NKG7. The immune clusters highlight patients who may respond to immunotherapy and thus may guide future clinical trials.

| S-EPMC10232490 | biostudies-literature

Transcription profiling of human squamous cell carcinomas to predict response to neoadjuvant chemoradiotherapy in oesophageal cancer patients

Project description:To use gene expression profiles to predict response to neoadjuvant chemoradiotherapy in oesophageal cancer patients.

2008-02-08 | E-MEXP-426 | biostudies-arrayexpress

b095bbad-6e3a-480c-927d-ad443b93a000 - samples

Project description:WGS data for manuscript titled: Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy

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84607b0c-7bf2-4076-a4bc-2bebac5d224a - samples

Project description:RNA-Seq data for manuscript titled: Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy

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RNAseq of Oesophageal Adenocarcinoma Cell Lines

Project description:rna sequencing of Oesophageal Adenocarcinoma Cell lines: OACP4, OE19, FLO-1, SK-GT-4, ESO26, OE33, ESO51, OACM5.1 C, JH-EsoAd1

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Circulating serum miRNAs as potential diagnostic biomarkers for oesophageal adenocarcinoma

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Project description:We present data from tissues of seven oesophageal adenocarcinomas of CD4 and CD8 T cell epitopes eluted from the cell surface using mass spectrometry (immunopeptidomics) of presented HLA bound peptides.This dataset forms part of the publication:Nicholas, B., Bailey, A., McCann, K.J., Wood, O., Walker, R.C., Parker, R., Ternette, N., Elliott, T., Underwood, T.J., Johnson, P. and Skipp, P. (2022), Identification of neoantigens in esophageal adenocarcinoma. Immunology. Accepted Author Manuscript. https://doi.org/10.1111/imm.13578

2022-09-27 | PXD031108 | Pride

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