Defining the clonality of peripheral T cell lymphomas using RNA-seq.

Abstract

Motivation:

In T-cell lymphoma, malignant T cells arising from a founding clone share an identical T cell receptor (TCR) and can be identified by the over-representation of this TCR relative to TCRs from the patient's repertoire of normal T cells. Here, we demonstrate that TCR information extracted from RNA-seq data can provide a higher resolution view of peripheral T cell lymphomas (PTCLs) than that provided by conventional methods.

Results:

For 60 subjects with PTCL, flow cytometry/FACS was used to identify and sort aberrant T cell populations from diagnostic lymph node cell suspensions. For samples that did not appear to contain aberrant T cell populations, T helper (T H ), T follicular helper (T FH ) and cytotoxic T lymphocyte (CTL) subsets were sorted. RNA-seq was performed on sorted T cell populations, and TCR alpha and beta chain sequences were extracted and quantified directly from the RNA-seq data. 96% of the immunophenotypically aberrant samples had a dominant T cell clone readily identifiable by RNA-seq. Of the samples where no aberrant population was found by flow cytometry, 80% had a dominant clone by RNA-seq. This demonstrates the increased sensitivity and diagnostic ability of RNA-seq over flow cytometry and shows that the presence of a normal immunophenotype does not exclude clonality.

Availability and Implementation:

R scripts used in the processing of the data are available online at https://www.github.com/scottdbrown/RNAseq-TcellClonality.

Contacts:

[email protected] or [email protected].

Supplementary information:

Supplementary data are available at Bioinformatics online.

• Authors: Scott D Brown, Greg Hapgood, Christian Steidl, Andrew P Weng, Kerry J Savage, Robert A Holt
• Journal: Bioinformatics (Oxford, England) (Bioinformatics) Vol. 33 Issue 8 Pg. 1111-1115 (04 15 2017) ISSN: 1367-4811 [Electronic] England
• PMID: 28003262 (Publication Type: Journal Article)
• Copyright: © The Author 2016. Published by Oxford University Press.

Chemical References

• Receptors, Antigen, T-Cell, alpha-beta

Topics

• Base Sequence
• Cell Line, Tumor
• Clone Cells
• Flow Cytometry
• Humans
• Immunophenotyping
• Lymphoma, T-Cell, Peripheral (genetics, pathology)
• Receptors, Antigen, T-Cell, alpha-beta (genetics, metabolism)
• Sequence Analysis, RNA (methods)
• T-Lymphocytes (immunology)