hum0294-v2Release info

Single cell analysis of tumor-infiltrating T cells

Aims

The objective is to analyze tumor and normal cell whole exome sequencing (WES) of esophageal cancer patients participating in the TENERGY-TR before treatment and RNA-seq specimens of tumor biopsy specimens at three points before treatment, after radiation chemotherapy, and after Atezolizumab administration, to search for biomarkers to predict treatment response.
The objective is to perform single-cell RNA sequencing (scRNA-seq) and single-cell T-cell receptor sequencing (scTCR-seq) of tumor samples collected before treatment, during treatment, and at disease progression from patients with gastric or gastroesophageal junction cancer participating in “A Phase Ib/II study of regorafenib and nivolumab plus chemotherapy in patients with unresectable advanced/recurrent gastric/gastroesophageal junction/esophageal adenocarcinoma” (REGONIVOCTx). These analyses aim to characterize longitudinal changes in the tumor microenvironment during treatment, identify biomarkers predictive of treatment response, and elucidate mechanisms of treatment resistance.

Methods

DNA/RNA was extracted from frozen tumor or blood samples using an AllPrep DNA/RNA Mini kit (Qiagen) at each time point. Whole exome sequencing and RNA sequencing analyses were performed.
Chromium Single Cell 5' Reagent Kit v2 (10x Genomics) was used to generate scRNA-seq and scTCR-seq libraries and sequenced on an Illumina NovaSeq 6000.

Participants/materials

esophageal cancer patients participating in the Tenergy trial
- WES: tumor tissue (27 samples) and normal tissue (27 samples) from esophageal cancer patients
- RNA-seq: tumor biopsy specimens at three-time points before treatment (28 samples), after radiation chemotherapy (25 samples) and after Atezolizumab administration (25 samples)
advanced gastric or gastroesophageal junction (GEJ) cancer patients participating in the REGONIVOCTx trial (EPOC2104)
- scRNA-seq/scTCR-seq: tumor specimens from 14 patients with advanced gastric or GEJ cancer at three time points (12 gastric, 2 GEJ): before treatment (14 samples: 12 gastric, 2 GEJ), during treatment (12 samples: 10 gastric, 2 GEJ), and at disease progression (9 samples: 7 gastric, 2 GEJ)

URL

• https://doi.org/10.1186/s12885-020-06716-5 (opens in a new tab)

Principal investigator

Shogo Kumagai

Affiliation

Division of Cancer Immunology, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center

Principal investigator

Kota Itahashi

Affiliation

Division of Cancer Immunology, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center