title: Ultra-deep T cell receptor sequencing reveals the complexity and intratumour heterogeneity of T cell clones in renal cell carcinomas.
abstract: The recognition of cancer cells by T cells can impact upon prognosis and be exploited for immunotherapeutic approaches. This recognition depends on the specific interaction between antigens displayed on the surface of cancer cells and the T cell receptor (TCR), which is generated by somatic rearrangements of TCR α- and β-chains (TCRb). Our aim was to assess whether ultra-deep sequencing of the rearranged TCRb in DNA extracted from unfractionated clear cell renal cell carcinoma (ccRCC) samples can provide insights into the clonality and heterogeneity of intratumoural T cells in ccRCCs, a tumour type that can display extensive genetic intratumour heterogeneity (ITH). For this purpose, DNA was extracted from two to four tumour regions from each of four primary ccRCCs and was analysed by ultra-deep TCR sequencing. In parallel, tumour infiltration by CD4, CD8 and Foxp3 regulatory T cells was evaluated by immunohistochemistry and correlated with TCR-sequencing data. A polyclonal T cell repertoire with 367-16 289 (median 2394) unique TCRb sequences was identified per tumour region. The frequencies of the 100 most abundant T cell clones/tumour were poorly correlated between most regions (Pearson correlation coefficient, -0.218 to 0.465). 3-93% of these T cell clones were not detectable across all regions. Thus, the clonal composition of T cell populations can be heterogeneous across different regions of the same ccRCC. T cell ITH was higher in tumours pretreated with an mTOR inhibitor, which could suggest that therapy can influence adaptive tumour immunity. These data show that ultra-deep TCR-sequencing technology can be applied directly to DNA extracted from unfractionated tumour samples, allowing novel insights into the clonality of T cell populations in cancers. These were polyclonal and displayed ITH in ccRCC. TCRb sequencing may shed light on mechanisms of cancer immunity and the efficacy of immunotherapy approaches.
authors.affiliation: Cancer Research UK, London Research Institute, UK; Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, London, UK.
authors.forename: Marco
authors.initials: M
authors.lastname: Gerlinger
authors.forename: Sergio A
authors.initials: SA
authors.lastname: Quezada
authors.forename: Karl S
authors.initials: KS
authors.lastname: Peggs
authors.forename: Andrew J S
authors.initials: AJ
authors.lastname: Furness
authors.forename: Rosalie
authors.initials: R
authors.lastname: Fisher
authors.forename: Teresa
authors.initials: T
authors.lastname: Marafioti
authors.forename: Vishvesh H
authors.initials: VH
authors.lastname: Shende
authors.forename: Nicholas
authors.initials: N
authors.lastname: McGranahan
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Rowan
authors.forename: Steven
authors.initials: S
authors.lastname: Hazell
authors.forename: David
authors.initials: D
authors.lastname: Hamm
authors.forename: Harlan S
authors.initials: HS
authors.lastname: Robins
authors.forename: Lisa
authors.initials: L
authors.lastname: Pickering
authors.forename: Martin
authors.initials: M
authors.lastname: Gore
authors.forename: David L
authors.initials: DL
authors.lastname: Nicol
authors.forename: James
authors.initials: J
authors.lastname: Larkin
authors.forename: Charles
authors.initials: C
authors.lastname: Swanton
mesh_terms: D002292:Carcinoma, Renal Cell / Q000235:genetics / Q000276:immunology* / Q000473:pathology; D002999:Clone Cells / Q000276:immunology; D004273:DNA, Neoplasm / Q000235:genetics; D005260:Female; D015333:Gene Rearrangement, beta-Chain T-Cell Antigen Receptor / Q000276:immunology; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D007111:Immunity, Cellular; D007680:Kidney Neoplasms / Q000235:genetics / Q000276:immunology* / Q000473:pathology; D016246:Lymphocytes, Tumor-Infiltrating / Q000276:immunology*; D008297:Male; D008875:Middle Aged; D009367:Neoplasm Staging; D016693:Receptors, Antigen, T-Cell, alpha-beta / Q000235:genetics*; D016176:T-Lymphocyte Subsets / Q000276:immunology*
chemical_list: D004273:DNA, Neoplasm; D016693:Receptors, Antigen, T-Cell, alpha-beta
keywords: T cell; biomarker; cancer immunity; immunotherapy; intratumour heterogeneity