2 74 | Nature | Vol 579 | 12 March 2020
Article
Peripheral T cell expansion predicts tumour
infiltration and clinical response
Thomas D. Wu^1 ✉, Shravan Madireddi^2 , Patricia E. de Almeida^2 , Romain Banchereau^3 ,
Ying-Jiun J. Chen^4 , Avantika S. Chitre^2 , Eugene Y. Chiang^2 , Hina Iftikhar^2 ,
William E. O’Gorman^5 , Amelia Au-Yeung^5 , Chikara Takahashi^5 , Leonard D. Goldstein^1 ,
Chungkee Poon^6 , Shilpa Keerthivasan^2 , Denise E. de Almeida Nagata^2 , Xiangnan Du^2 ,
Hyang-Mi Lee^2 , Karl L. Banta^2 , Sanjeev Mariathasan^3 , Meghna Das Thakur^7 ,
Mahrukh A. Huseni^7 , Marcus Ballinger^7 , Ivette Estay^7 , Patrick Caplazi^8 , Zora Modrusan^4 ,
Lélia Delamarre^2 , Ira Mellman^2 , Richard Bourgon^1 & Jane L. Grogan2,9 ✉Despite the resounding clinical success in cancer treatment of antibodies that block
the interaction of PD1 with its ligand PDL1^1 , the mechanisms involved remain
unknown. A major limitation to understanding the origin and fate of T cells in tumour
immunity is the lack of quantitative information on the distribution of individual
clonotypes of T cells in patients with cancer. Here, by performing deep single-cell
sequencing of RNA and T cell receptors in patients with different types of cancer, we
survey the profiles of various populations of T cells and T cell receptors in tumours,
normal adjacent tissue, and peripheral blood. We find clear evidence of clonotypic
expansion of effector-like T cells not only within the tumour but also in normal
adjacent tissue. Patients with gene signatures of such clonotypic expansion respond
best to anti-PDL1 therapy. Notably, expanded clonotypes found in the tumour and
normal adjacent tissue can also typically be detected in peripheral blood, which
suggests a convenient approach to patient identification. Analyses of our data
together with several external datasets suggest that intratumoural T cells, especially
in responsive patients, are replenished with fresh, non-exhausted replacement cells
from sites outside the tumour, suggesting continued activity of the cancer immunity
cycle in these patients, the acceleration of which may be associated with clinical
response.We sequenced 330 million mRNA transcripts in 141,623 T cells from 14
treatment-naive patients across four different types of cancer (Extended
Data Fig. 1a–i, Supplementary Tables 1, 2). For each patient, samples were
obtained from surgically resected tumour and histologically normal
adjacent tissue (NAT), and, in four patients, from peripheral blood.
Single-cell T cell receptor (TCR) sequencing (scTCR-seq) yielded one or
more complementarity-determining region 3 (CDR3) regions of α- or
β-chains in 99,788 cells. T cells were grouped into 56,975 distinct clono-
types by matching CDR3 regions, which allowed us to measure clonal
expansion and track clonal lineages across tissues. Although individual
clonotypes were rarely shared across patients (Supplementary Table 3),
many clonotypes resided in both the tumour and the corresponding NAT
from a given patient (Extended Data Fig. 2a). Such dual-expanded clones
contrasted with expanded clones that resided solely in one compart-
ment (termed tumour or NAT multiplets), and with clones having only
one observed cell in either compartment (singletons).
Although most clonotypes were singletons (Extended Data Fig. 2b),
representing a diverse repertoire of T cells, 9–18% of clonotypes in each
patient were clonally expanded multiplets or dual-expanded clones.
Dual-expanded clonotypes constituted substantial fractions of observed
cells, sometimes the majority of T cells in a given compartment (Extended
Data Fig. 2c). Analysing clones by their cell counts in NAT and tumour
samples revealed diverse clonal expansion behaviours across patients
(Extended Data Fig. 2d). In some patients—for example, Colon1—
dual-expanded clones aligned along the main diagonal, reflecting
approximately equal cell counts in the two compartments and suggest-
ing coordinate or parallel processes in tumour and NAT, brought about
by multiple clonotypes acting similarly. Conversely, in other patients,
dual-expanded clones were scattered from the main diagonal, indicating
that each clone had an independent, divergent pattern of expansion,
migration or attrition in the tumour and NAT compartments.
We hypothesized that parallel expansion in tumour and NAT might
represent infiltration of T cells from the periphery, extravasating
into both tissues equally from inflamed blood vessels^2. We found
supporting evidence from matched blood samples, in which clones
highly expanded in blood showed evidence of parallel expansion inhttps://doi.org/10.1038/s41586-020-2056-8
Received: 27 September 2018
Accepted: 8 January 2020
Published online: 26 February 2020
Check for updates(^1) Department of Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, CA, USA. (^2) Department of Cancer Immunology, Genentech, Inc., South San Francisco, CA,
USA.^3 Department of Oncology Biomarker Development, Genentech, Inc., South San Francisco, CA, USA.^4 Department of Microchemistry, Proteomics, Lipidomics and Next Generation
Sequencing, Genentech, Inc., South San Francisco, CA, USA.^5 Department of OMNI Biomarker Development, Genentech, Inc., South San Francisco, CA, USA.^6 Department of Research Biology,
Genentech, Inc., South San Francisco, CA, USA.^7 Department of Development Sciences, Genentech, Inc., South San Francisco, CA, USA.^8 Department of Pathology, Genentech, Inc., South San
Francisco, CA, USA.^9 Present address: ArsenalBio, South San Francisco, CA, USA. ✉e-mail: [email protected]; [email protected]