NYU Dataset

RNA and TCR Sequencing Characterized Cytotoxic T Cells and TCR Clonality in Organ Transplant Recipients with Squamous Cell Carcinoma

UID: 10456
* Corresponding Author
Description

This dataset was collected to show that there is a decline in cytotoxic T cells and TCR clonality in organ transplant recipients (OTRs) with squamous cell carcinoma (SCC). In this study, 5 SCC tumor samples and 6 transplant-associated SCC (TSCC) tumor samples were analyzed. Among SCC samples, the male to female ratio was 3 to 2 and the mean patient age was 81 years. Among TSCC samples, the male to female ratio was 1 to 5 (TSCC2 and TSCC3 were obtained from the same patient) and the mean patient age was 65 years. OTRs had either a liver or kidney transplant and they were on 2 or 3 immunosuppression drugs, which included combinations of mycophenolate, tacrolimus, sirolimus, cyclosporine, azathioprine and/or prednisone.

The dataset includes RNA and TCR sequencing data as well as supplementary data tied to the publication. Supplementary data contains data on patient and tumor characteristics, total clonotypes and total VDJ sequencing reads in cutaneous SCC tumors from immunocompetent and immunocompromised patients, percentage of known antigen versus neoantigen among the top 10 clonotypes in cutaneous SCC tumors from immunocompetent and immunocompromised patients, and putative antigens of the top 10 clonotypes in cutaneous SCC tumors from immunocompetent and immunocompromised patients based on McPAS analysis.

Subject of Study
Subject Domain
Population Age
Adult (19 years - 64 years)
Senior (65 years - 79 years)
Aged (80 years and over)
Keywords

Access

Restrictions
Free to All
Instructions
Sequencing data are available on Gene Expression Omnibus (GEO). All other data are available within the article on PubMed Central (PMC) under Supplementary Materials.
Access via GEO

Sequencing data
Accession #: GSE145328

Access via PMC

Supplementary data
Accession #: PMC7270180

Associated Publications
Data Type
Equipment Used
10× Genomics Chromium
BD FACSAria II
Illumina NovaSeq 6000
Software Used
Cell Ranger
iCellR
Study Type
Observational
Grant Support
Regeneron Pharmaceuticals/Regeneron Pharmaceuticals