Using DNA sequencing data to quantify T cell fraction and therapy response

Robert Bentham; Kevin Litchfield; Thomas B.K. Watkins; Emilia L. Lim; Rachel Rosenthal; Carlos Martínez-Ruiz; Crispin T. Hiley; Maise Al Bakir; Roberto Salgado; David A. Moore; Mariam Jamal-Hanjani; Nicolai J. Birkbak; Mickael Escudero; Aengus Stewart; Andrew Rowan; Jacki Goldman; Peter Van Loo; Richard Kevin Stone; Tamara Denner; Emma Nye; Sophia Ward; Stefan Boeing; Maria Greco; Jerome Nicod; Clare Puttick; Katey Enfield; Emma Colliver; Brittany Campbell; Alexander M. Frankell; Daniel Cook; Mihaela Angelova; Alastair Magness; Chris Bailey; Antonia Toncheva; Krijn Dijkstra; Judit Kisistok; Mateo Sokac; Oriol Pich; Jonas Demeulemeester; Elizabeth Larose Cadieux; Carla Castignani; Krupa Thakkar; Hongchang Fu; Takahiro Karasaki; Othman Al-Sawaf; Mark S. Hill; Christopher Abbosh; Yin Wu; Selvaraju Veeriah; Robert E. Hynds; TRACERx Consortium; Hugo J.W.L. Aerts; Nicholas McGranahan

doi:10.1038/s41586-021-03894-5

Using DNA sequencing data to quantify T cell fraction and therapy response

Robert Bentham, Kevin Litchfield, Thomas B.K. Watkins, Emilia L. Lim, Rachel Rosenthal, Carlos Martínez-Ruiz, Crispin T. Hiley, Maise Al Bakir, Roberto Salgado, David A. Moore, Mariam Jamal-Hanjani, Nicolai J. Birkbak, Mickael Escudero, Aengus Stewart, Andrew Rowan, Jacki Goldman, Peter Van Loo, Richard Kevin Stone, Tamara Denner, Emma NyeSophia Ward, Stefan Boeing, Maria Greco, Jerome Nicod, Clare Puttick, Katey Enfield, Emma Colliver, Brittany Campbell, Alexander M. Frankell, Daniel Cook, Mihaela Angelova, Alastair Magness, Chris Bailey, Antonia Toncheva, Krijn Dijkstra, Judit Kisistok, Mateo Sokac, Oriol Pich, Jonas Demeulemeester, Elizabeth Larose Cadieux, Carla Castignani, Krupa Thakkar, Hongchang Fu, Takahiro Karasaki, Othman Al-Sawaf, Mark S. Hill, Christopher Abbosh, Yin Wu, Selvaraju Veeriah, Robert E. Hynds, TRACERx Consortium, Hugo J.W.L. Aerts, Nicholas McGranahan^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

Abstract

The immune microenvironment influences tumour evolution and can be both prognostic and predict response to immunotherapy ^1,2. However, measurements of tumour infiltrating lymphocytes (TILs) are limited by a shortage of appropriate data. Whole-exome sequencing (WES) of DNA is frequently performed to calculate tumour mutational burden and identify actionable mutations. Here we develop T cell exome TREC tool (T cell ExTRECT), a method for estimation of T cell fraction from WES samples using a signal from T cell receptor excision circle (TREC) loss during V(D)J recombination of the T cell receptor-α gene (TCRA (also known as TRA)). TCRA T cell fraction correlates with orthogonal TIL estimates and is agnostic to sample type. Blood TCRA T cell fraction is higher in females than in males and correlates with both tumour immune infiltrate and presence of bacterial sequencing reads. Tumour TCRA T cell fraction is prognostic in lung adenocarcinoma. Using a meta-analysis of tumours treated with immunotherapy, we show that tumour TCRA T cell fraction predicts immunotherapy response, providing value beyond measuring tumour mutational burden. Applying T cell ExTRECT to a multi-sample pan-cancer cohort reveals a high diversity of the degree of immune infiltration within tumours. Subclonal loss of 12q24.31–32, encompassing SPPL3, is associated with reduced TCRA T cell fraction. T cell ExTRECT provides a cost-effective technique to characterize immune infiltrate alongside somatic changes.

Original language	English
Pages (from-to)	555-560
Number of pages	6
Journal	Nature
Volume	597
Issue number	7877
DOIs	https://doi.org/10.1038/s41586-021-03894-5
Publication status	Published - 23 Sept 2021

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Bentham, R., Litchfield, K., Watkins, T. B. K., Lim, E. L., Rosenthal, R., Martínez-Ruiz, C., Hiley, C. T., Bakir, M. A., Salgado, R., Moore, D. A., Jamal-Hanjani, M., Birkbak, N. J., Escudero, M., Stewart, A., Rowan, A., Goldman, J., Van Loo, P., Stone, R. K., Denner, T., ... McGranahan, N. (2021). Using DNA sequencing data to quantify T cell fraction and therapy response. Nature, 597(7877), 555-560. https://doi.org/10.1038/s41586-021-03894-5

@article{722fd94de7434248ad3c473d25f2cc73,

title = "Using DNA sequencing data to quantify T cell fraction and therapy response",

abstract = "The immune microenvironment influences tumour evolution and can be both prognostic and predict response to immunotherapy 1,2. However, measurements of tumour infiltrating lymphocytes (TILs) are limited by a shortage of appropriate data. Whole-exome sequencing (WES) of DNA is frequently performed to calculate tumour mutational burden and identify actionable mutations. Here we develop T cell exome TREC tool (T cell ExTRECT), a method for estimation of T cell fraction from WES samples using a signal from T cell receptor excision circle (TREC) loss during V(D)J recombination of the T cell receptor-α gene (TCRA (also known as TRA)). TCRA T cell fraction correlates with orthogonal TIL estimates and is agnostic to sample type. Blood TCRA T cell fraction is higher in females than in males and correlates with both tumour immune infiltrate and presence of bacterial sequencing reads. Tumour TCRA T cell fraction is prognostic in lung adenocarcinoma. Using a meta-analysis of tumours treated with immunotherapy, we show that tumour TCRA T cell fraction predicts immunotherapy response, providing value beyond measuring tumour mutational burden. Applying T cell ExTRECT to a multi-sample pan-cancer cohort reveals a high diversity of the degree of immune infiltration within tumours. Subclonal loss of 12q24.31–32, encompassing SPPL3, is associated with reduced TCRA T cell fraction. T cell ExTRECT provides a cost-effective technique to characterize immune infiltrate alongside somatic changes.",

author = "Robert Bentham and Kevin Litchfield and Watkins, {Thomas B.K.} and Lim, {Emilia L.} and Rachel Rosenthal and Carlos Mart{\'i}nez-Ruiz and Hiley, {Crispin T.} and Bakir, {Maise Al} and Roberto Salgado and Moore, {David A.} and Mariam Jamal-Hanjani and Birkbak, {Nicolai J.} and Mickael Escudero and Aengus Stewart and Andrew Rowan and Jacki Goldman and {Van Loo}, Peter and Stone, {Richard Kevin} and Tamara Denner and Emma Nye and Sophia Ward and Stefan Boeing and Maria Greco and Jerome Nicod and Clare Puttick and Katey Enfield and Emma Colliver and Brittany Campbell and Frankell, {Alexander M.} and Daniel Cook and Mihaela Angelova and Alastair Magness and Chris Bailey and Antonia Toncheva and Krijn Dijkstra and Judit Kisistok and Mateo Sokac and Oriol Pich and Jonas Demeulemeester and Cadieux, {Elizabeth Larose} and Carla Castignani and Krupa Thakkar and Hongchang Fu and Takahiro Karasaki and Othman Al-Sawaf and Hill, {Mark S.} and Christopher Abbosh and Yin Wu and Selvaraju Veeriah and Hynds, {Robert E.} and {TRACERx Consortium} and Aerts, {Hugo J.W.L.} and Nicholas McGranahan",

note = "Funding Information: Competing interests D.A.M. reports speaker fees from AstraZeneca. M.A.B. has consulted for Achilles Therapeutics. R.R. has consulted for and has stock options in Achilles Therapeutics. K.L. has a patent on indel burden and CPI response pending and speaker fees from Roche tissue diagnostics, research funding from CRUK TDL/Ono/LifeArc alliance, and a consulting role with Monopteros Therapeutics. C.T.H. has received speaker fees from AstraZeneca. M.J.-H. is a member of the Scientific Advisory Board and Steering Committee for Achilles Therapeutics. N.M. has stock options in and has consulted for Achilles Therapeutics and holds a European patent in determining HLA LOH (PCT/GB2018/052004). C.S. acknowledges grant support from Pfizer, AstraZeneca, Bristol Myers Squibb, Roche-Ventana, Boehringer-Ingelheim, Archer Dx Inc. (collaboration in minimal residual disease sequencing technologies) and Ono Pharmaceutical; is an AstraZeneca Advisory Board Member and Chief Investigator for the MeRmaiD1 clinical trial; has consulted for Amgen, Pfizer, Novartis, GlaxoSmithKline, MSD, Bristol Myers Squibb, AstraZeneca, Illumina, Genentech, Roche-Ventana, GRAIL, Medicxi, Bicycle Therapeutics, Metabomed and the Sarah Cannon Research Institute; has stock options in Apogen Biotechnologies, Epic Bioscience and GRAIL; and has stock options and is co-founder of Achilles Therapeutics. C.S. holds patents relating to assay technology to detect tumour recurrence (PCT/GB2017/053289); to targeting neoantigens (PCT/EP2016/059401), identifying patent response to immune checkpoint blockade (PCT/EP2016/071471), determining HLA LOH (PCT/GB2018/052004), predicting survival rates of patients with cancer (PCT/GB2020/050221), to treating cancer by targeting Insertion/deletion mutations (PCT/GB2018/051893); identifying insertion/deletion mutation targets (PCT/GB2018/051892); methods for lung cancer detection (PCT/US2017/028013); and identifying responders to cancer treatment (PCT/GB2018/051912). Funding Information: Acknowledgements R.B. is supported by the NIHR BRC at University College London Hospitals. K.L. is funded by the UK Medical Research Council (MR/P014712/1 and MR/V033077/1), Rosetrees Trust and Cotswold Trust (A2437) and Cancer Research UK (C69256/A30194). T.B.K.W. is supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001169), the UK Medical Research Council (FC001169) and the Wellcome Trust (FC001169) as well as the Marie Curie ITN Project PLOIDYNET (FP7-PEOPLE-2013, 607722), Breast Cancer Research Foundation (BCRF), Royal Society Research Professorships Enhancement Award (RP/EA/180007) and the Foulkes Foundation. E.L.L. receives funding from NovoNordisk Foundation (ID 16584). R.R. is supported by Royal Society Research Professorships Enhancement Award (RP/EA/180007). C.M.-R. is supported by Rosetrees. C.T.H. is supported by the NIHR BRC at University College London Hospitals. M.J.-H. has received funding from Cancer Research UK, National Institute for Health Research, Rosetrees Trust, UKI NETs and NIHR University College London Hospitals Biomedical Research Centre. N.M. is a Sir Henry Dale Fellow, jointly funded by the Wellcome Trust and the Royal Society (Grant Number 211179/Z/18/Z) and also receives funding from Cancer Research UK, Rosetrees and the NIHR BRC at University College London Hospitals and the CRUK University College London Experimental Cancer Medicine Centre. C.S. is a Royal Society Napier Research Professor. His work was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001169), the UK Medical Research Council (FC001169) and the Wellcome Trust (FC001169). C.S. is funded by Cancer Research UK (TRACERx, PEACE and CRUK Cancer Immunotherapy Catalyst Network), Cancer Research UK Lung Cancer Centre of Excellence, the Rosetrees Trust, Butterfield and Stoneygate Trusts, NovoNordisk Foundation (ID16584), Royal Society Research Professorships Enhancement Award (RP/EA/180007), the NIHR BRC at University College London Hospitals, the CRUK-UCL Centre, Experimental Cancer Medicine Centre and the Breast Cancer Research Foundation (BCRF). This research is supported by a Stand Up To Cancer-LUNGevity-American Lung Association Lung Cancer Interception Dream Team Translational Research Grant (SU2C-AACR-DT23-17). Stand Up To Cancer is a program of the Entertainment Industry Foundation. Research grants are administered by the American Association for Cancer Research, the Scientific Partner of SU2C. C.S. also receives funding from the European Research Council (ERC) under the European Union{\textquoteright}s Seventh Framework Programme (FP7/2007-2013) Consolidator Grant (FP7-THESEUS-617844), European Commission ITN (FP7-PloidyNet 607722), an ERC Advanced Grant (PROTEUS) from the European Research Council under the European Union{\textquoteright}s Horizon 2020 research and innovation programme (835297) and Chromavision from the European Union{\textquoteright}s Horizon 2020 research and innovation programme (665233). The TRACERx study (Clinicaltrials.gov no: NCT01888601) is sponsored by University College London (UCL/12/0279) and has been approved by an independent Research Ethics Committee (13/LO/1546). TRACERx is funded by Cancer Research UK (C11496/A17786) and coordinated through the Cancer Research UK and UCL Cancer Trials Centre. The results published here are based in part on data generated by The Cancer Genome Atlas pilot project established by the NCI and the National Human Genome Research Institute. The data were Funding Information: retrieved through the database of Genotypes and Phenotypes (dbGaP) authorization (accession number phs000178.v9.p8). Information about TCGA and the constituent investigators and institutions of the TCGA research network can be found at http://cancergenome.nih.gov/. This project was enabled through access to the MRC eMedLab Medical Bioinformatics infrastructure, supported by the Medical Research Council (MR/L016311/1). In particular, we acknowledge the support of the High-Performance Computing at the Francis Crick Institute as well as the UCL Department of Computer Science Cluster and the support team. In addition, this work was supported by the CRUK City of London Centre Award (C7893/A26233). We thank all investigators, funders and industry partners that supported the generation of the data within this study, as well as patients for their participation. Specifically, we thank Merck & Co, Genentech and Bristol-Myers Squibb for generating the industry datasets used in this study, and E. Van Allen, L. Diaz, T. A. Chan, L. A. Garraway, R. S. Lo, D. F. Bajorin, D. Schadendorf, T. Powles, S.-H. Lee, A. Ribas and S. Ogawa for academic datasets. This work has been funded by Merck and Co. We gratefully acknowledge the patients and their families, the investigators and site personnel who participated in the KEYNOTE-001, -006, -012 and -028 studies. Publisher Copyright: {\textcopyright} 2021, The Author(s), under exclusive licence to Springer Nature Limited.",

year = "2021",

month = sep,

day = "23",

doi = "10.1038/s41586-021-03894-5",

language = "English",

volume = "597",

pages = "555--560",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Publishing Group",

number = "7877",

}

Bentham, R, Litchfield, K, Watkins, TBK, Lim, EL, Rosenthal, R, Martínez-Ruiz, C, Hiley, CT, Bakir, MA, Salgado, R, Moore, DA, Jamal-Hanjani, M, Birkbak, NJ, Escudero, M, Stewart, A, Rowan, A, Goldman, J, Van Loo, P, Stone, RK, Denner, T, Nye, E, Ward, S, Boeing, S, Greco, M, Nicod, J, Puttick, C, Enfield, K, Colliver, E, Campbell, B, Frankell, AM, Cook, D, Angelova, M, Magness, A, Bailey, C, Toncheva, A, Dijkstra, K, Kisistok, J, Sokac, M, Pich, O, Demeulemeester, J, Cadieux, EL, Castignani, C, Thakkar, K, Fu, H, Karasaki, T, Al-Sawaf, O, Hill, MS, Abbosh, C, Wu, Y, Veeriah, S, Hynds, RE, TRACERx Consortium, Aerts, HJWL & McGranahan, N 2021, 'Using DNA sequencing data to quantify T cell fraction and therapy response', Nature, vol. 597, no. 7877, pp. 555-560. https://doi.org/10.1038/s41586-021-03894-5

TY - JOUR

T1 - Using DNA sequencing data to quantify T cell fraction and therapy response

AU - Bentham, Robert

AU - Litchfield, Kevin

AU - Watkins, Thomas B.K.

AU - Lim, Emilia L.

AU - Rosenthal, Rachel

AU - Martínez-Ruiz, Carlos

AU - Hiley, Crispin T.

AU - Bakir, Maise Al

AU - Salgado, Roberto

AU - Moore, David A.

AU - Jamal-Hanjani, Mariam

AU - Birkbak, Nicolai J.

AU - Escudero, Mickael

AU - Stewart, Aengus

AU - Rowan, Andrew

AU - Goldman, Jacki

AU - Van Loo, Peter

AU - Stone, Richard Kevin

AU - Denner, Tamara

AU - Nye, Emma

AU - Ward, Sophia

AU - Boeing, Stefan

AU - Greco, Maria

AU - Nicod, Jerome

AU - Puttick, Clare

AU - Enfield, Katey

AU - Colliver, Emma

AU - Campbell, Brittany

AU - Frankell, Alexander M.

AU - Cook, Daniel

AU - Angelova, Mihaela

AU - Magness, Alastair

AU - Bailey, Chris

AU - Toncheva, Antonia

AU - Dijkstra, Krijn

AU - Kisistok, Judit

AU - Sokac, Mateo

AU - Pich, Oriol

AU - Demeulemeester, Jonas

AU - Cadieux, Elizabeth Larose

AU - Castignani, Carla

AU - Thakkar, Krupa

AU - Fu, Hongchang

AU - Karasaki, Takahiro

AU - Al-Sawaf, Othman

AU - Hill, Mark S.

AU - Abbosh, Christopher

AU - Wu, Yin

AU - Veeriah, Selvaraju

AU - Hynds, Robert E.

AU - TRACERx Consortium

AU - Aerts, Hugo J.W.L.

AU - McGranahan, Nicholas

N1 - Funding Information: Competing interests D.A.M. reports speaker fees from AstraZeneca. M.A.B. has consulted for Achilles Therapeutics. R.R. has consulted for and has stock options in Achilles Therapeutics. K.L. has a patent on indel burden and CPI response pending and speaker fees from Roche tissue diagnostics, research funding from CRUK TDL/Ono/LifeArc alliance, and a consulting role with Monopteros Therapeutics. C.T.H. has received speaker fees from AstraZeneca. M.J.-H. is a member of the Scientific Advisory Board and Steering Committee for Achilles Therapeutics. N.M. has stock options in and has consulted for Achilles Therapeutics and holds a European patent in determining HLA LOH (PCT/GB2018/052004). C.S. acknowledges grant support from Pfizer, AstraZeneca, Bristol Myers Squibb, Roche-Ventana, Boehringer-Ingelheim, Archer Dx Inc. (collaboration in minimal residual disease sequencing technologies) and Ono Pharmaceutical; is an AstraZeneca Advisory Board Member and Chief Investigator for the MeRmaiD1 clinical trial; has consulted for Amgen, Pfizer, Novartis, GlaxoSmithKline, MSD, Bristol Myers Squibb, AstraZeneca, Illumina, Genentech, Roche-Ventana, GRAIL, Medicxi, Bicycle Therapeutics, Metabomed and the Sarah Cannon Research Institute; has stock options in Apogen Biotechnologies, Epic Bioscience and GRAIL; and has stock options and is co-founder of Achilles Therapeutics. C.S. holds patents relating to assay technology to detect tumour recurrence (PCT/GB2017/053289); to targeting neoantigens (PCT/EP2016/059401), identifying patent response to immune checkpoint blockade (PCT/EP2016/071471), determining HLA LOH (PCT/GB2018/052004), predicting survival rates of patients with cancer (PCT/GB2020/050221), to treating cancer by targeting Insertion/deletion mutations (PCT/GB2018/051893); identifying insertion/deletion mutation targets (PCT/GB2018/051892); methods for lung cancer detection (PCT/US2017/028013); and identifying responders to cancer treatment (PCT/GB2018/051912). Funding Information: Acknowledgements R.B. is supported by the NIHR BRC at University College London Hospitals. K.L. is funded by the UK Medical Research Council (MR/P014712/1 and MR/V033077/1), Rosetrees Trust and Cotswold Trust (A2437) and Cancer Research UK (C69256/A30194). T.B.K.W. is supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001169), the UK Medical Research Council (FC001169) and the Wellcome Trust (FC001169) as well as the Marie Curie ITN Project PLOIDYNET (FP7-PEOPLE-2013, 607722), Breast Cancer Research Foundation (BCRF), Royal Society Research Professorships Enhancement Award (RP/EA/180007) and the Foulkes Foundation. E.L.L. receives funding from NovoNordisk Foundation (ID 16584). R.R. is supported by Royal Society Research Professorships Enhancement Award (RP/EA/180007). C.M.-R. is supported by Rosetrees. C.T.H. is supported by the NIHR BRC at University College London Hospitals. M.J.-H. has received funding from Cancer Research UK, National Institute for Health Research, Rosetrees Trust, UKI NETs and NIHR University College London Hospitals Biomedical Research Centre. N.M. is a Sir Henry Dale Fellow, jointly funded by the Wellcome Trust and the Royal Society (Grant Number 211179/Z/18/Z) and also receives funding from Cancer Research UK, Rosetrees and the NIHR BRC at University College London Hospitals and the CRUK University College London Experimental Cancer Medicine Centre. C.S. is a Royal Society Napier Research Professor. His work was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001169), the UK Medical Research Council (FC001169) and the Wellcome Trust (FC001169). C.S. is funded by Cancer Research UK (TRACERx, PEACE and CRUK Cancer Immunotherapy Catalyst Network), Cancer Research UK Lung Cancer Centre of Excellence, the Rosetrees Trust, Butterfield and Stoneygate Trusts, NovoNordisk Foundation (ID16584), Royal Society Research Professorships Enhancement Award (RP/EA/180007), the NIHR BRC at University College London Hospitals, the CRUK-UCL Centre, Experimental Cancer Medicine Centre and the Breast Cancer Research Foundation (BCRF). This research is supported by a Stand Up To Cancer-LUNGevity-American Lung Association Lung Cancer Interception Dream Team Translational Research Grant (SU2C-AACR-DT23-17). Stand Up To Cancer is a program of the Entertainment Industry Foundation. Research grants are administered by the American Association for Cancer Research, the Scientific Partner of SU2C. C.S. also receives funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP7/2007-2013) Consolidator Grant (FP7-THESEUS-617844), European Commission ITN (FP7-PloidyNet 607722), an ERC Advanced Grant (PROTEUS) from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (835297) and Chromavision from the European Union’s Horizon 2020 research and innovation programme (665233). The TRACERx study (Clinicaltrials.gov no: NCT01888601) is sponsored by University College London (UCL/12/0279) and has been approved by an independent Research Ethics Committee (13/LO/1546). TRACERx is funded by Cancer Research UK (C11496/A17786) and coordinated through the Cancer Research UK and UCL Cancer Trials Centre. The results published here are based in part on data generated by The Cancer Genome Atlas pilot project established by the NCI and the National Human Genome Research Institute. The data were Funding Information: retrieved through the database of Genotypes and Phenotypes (dbGaP) authorization (accession number phs000178.v9.p8). Information about TCGA and the constituent investigators and institutions of the TCGA research network can be found at http://cancergenome.nih.gov/. This project was enabled through access to the MRC eMedLab Medical Bioinformatics infrastructure, supported by the Medical Research Council (MR/L016311/1). In particular, we acknowledge the support of the High-Performance Computing at the Francis Crick Institute as well as the UCL Department of Computer Science Cluster and the support team. In addition, this work was supported by the CRUK City of London Centre Award (C7893/A26233). We thank all investigators, funders and industry partners that supported the generation of the data within this study, as well as patients for their participation. Specifically, we thank Merck & Co, Genentech and Bristol-Myers Squibb for generating the industry datasets used in this study, and E. Van Allen, L. Diaz, T. A. Chan, L. A. Garraway, R. S. Lo, D. F. Bajorin, D. Schadendorf, T. Powles, S.-H. Lee, A. Ribas and S. Ogawa for academic datasets. This work has been funded by Merck and Co. We gratefully acknowledge the patients and their families, the investigators and site personnel who participated in the KEYNOTE-001, -006, -012 and -028 studies. Publisher Copyright: © 2021, The Author(s), under exclusive licence to Springer Nature Limited.

PY - 2021/9/23

Y1 - 2021/9/23

N2 - The immune microenvironment influences tumour evolution and can be both prognostic and predict response to immunotherapy 1,2. However, measurements of tumour infiltrating lymphocytes (TILs) are limited by a shortage of appropriate data. Whole-exome sequencing (WES) of DNA is frequently performed to calculate tumour mutational burden and identify actionable mutations. Here we develop T cell exome TREC tool (T cell ExTRECT), a method for estimation of T cell fraction from WES samples using a signal from T cell receptor excision circle (TREC) loss during V(D)J recombination of the T cell receptor-α gene (TCRA (also known as TRA)). TCRA T cell fraction correlates with orthogonal TIL estimates and is agnostic to sample type. Blood TCRA T cell fraction is higher in females than in males and correlates with both tumour immune infiltrate and presence of bacterial sequencing reads. Tumour TCRA T cell fraction is prognostic in lung adenocarcinoma. Using a meta-analysis of tumours treated with immunotherapy, we show that tumour TCRA T cell fraction predicts immunotherapy response, providing value beyond measuring tumour mutational burden. Applying T cell ExTRECT to a multi-sample pan-cancer cohort reveals a high diversity of the degree of immune infiltration within tumours. Subclonal loss of 12q24.31–32, encompassing SPPL3, is associated with reduced TCRA T cell fraction. T cell ExTRECT provides a cost-effective technique to characterize immune infiltrate alongside somatic changes.

AB - The immune microenvironment influences tumour evolution and can be both prognostic and predict response to immunotherapy 1,2. However, measurements of tumour infiltrating lymphocytes (TILs) are limited by a shortage of appropriate data. Whole-exome sequencing (WES) of DNA is frequently performed to calculate tumour mutational burden and identify actionable mutations. Here we develop T cell exome TREC tool (T cell ExTRECT), a method for estimation of T cell fraction from WES samples using a signal from T cell receptor excision circle (TREC) loss during V(D)J recombination of the T cell receptor-α gene (TCRA (also known as TRA)). TCRA T cell fraction correlates with orthogonal TIL estimates and is agnostic to sample type. Blood TCRA T cell fraction is higher in females than in males and correlates with both tumour immune infiltrate and presence of bacterial sequencing reads. Tumour TCRA T cell fraction is prognostic in lung adenocarcinoma. Using a meta-analysis of tumours treated with immunotherapy, we show that tumour TCRA T cell fraction predicts immunotherapy response, providing value beyond measuring tumour mutational burden. Applying T cell ExTRECT to a multi-sample pan-cancer cohort reveals a high diversity of the degree of immune infiltration within tumours. Subclonal loss of 12q24.31–32, encompassing SPPL3, is associated with reduced TCRA T cell fraction. T cell ExTRECT provides a cost-effective technique to characterize immune infiltrate alongside somatic changes.

U2 - 10.1038/s41586-021-03894-5

DO - 10.1038/s41586-021-03894-5

M3 - Article

SN - 0028-0836

VL - 597

SP - 555

EP - 560

JO - Nature

JF - Nature

IS - 7877

ER -

Using DNA sequencing data to quantify T cell fraction and therapy response

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