Clonal TCR-engineered T cells as a new strategy for adoptive T cell therapy

Primary Supervisor: Sergio A. Quezada, UCL

Secondary supervisor: Charles Swanton, Francis Crick Institute

Project

Tumour neoantigens induce T cell responses against cancer and positively associate with responses to checkpoint blockade in Non-Small Cell Lung Cancer (NSCLC) (1). Work from our laboratory has shown that clonal neoantigens (expressed in all tumour cells) are more powerful drivers of T cell priming and patient survival than sub-clonal neoantigens (expressed in a subset of tumour cells) which associate with poorer responses and disease progression (2). Adoptive cell therapies using clonal neoantigen reactive T cells holds promise for their use in the clinic. However, to the date, this approach has only been attempted using expanded tumour infiltrating lymphocytes which already harbour a dysfunctional state (3).
The objective of this proposal is to develop a new approach using non-dysfunctional T cells obtained from blood, engineered to express the T cell receptor of clonal neoantigen reactive T cells (clonal TCRs). In collaboration with the Chain (UCL, Royal Free Hospital), Swanton (Francis Crick Institute) and Pule (UCL Cancer Institute) labs, the student will develop a bioinformatic and wet-lab pipeline to identify clonal TCRs, engineer blood T cells and subsequently test their activity against tumour cells using NSCLC organoids and patient-derived xenografts (PDXs).

Aims:

1. Generation of a bioinformatic and wet-lab pipeline for the identification of clonal TCRs, cloning and transduction of blood T cells. The student will build on current bioinformatics pipeline (Chain lab. (4)) to identify and clone clonal TCRs into T cells obtained from peripheral blood (Pule lab.) and assess reactivity against the tumour. It is expected that the student will identify a set of clonal TCR that will be subsequently tested in in vitro and in vivo models.
2. Assess reactivity and understand the interaction between TCR transduced T cells and tumour cells using NSCLC organoids and PDXs. The student will use co-cultures between organoids (Swanton lab.) and TCR transduced T cells as well as PDXs where T cells are inoculated and then analysed inside the tumours. It is expected that this aim will lead to the validation of tumour reactive clonal TCRs and the identification of negative regulators of T cell activity as potential targets for immunotherapy using single cell technologies.
3. Modulate the interactions between TCR transduced T cells and tumour cells using gene-editing techniques to enhance their activity. From aim 2 the student will have identified novel negative regulators of T cell activity that will be knocked out using CRISPR/Cas9 on T cells and their function tested in co-culture with organoids and in PDXs. Our laboratory has already established protocols to perform gene-editing on T cells and we are currently validating other targets.

Candidate background

Enthusiastic about cancer immunology and keen to develop models for systematic evaluation of targets in the setting of NSCLC-reactive T cells. The ideal candidate must hold a BSc or MSc in a related field with previous experience in molecular biology and primary cell culturing.

Potential Research Placements

1. Benny Chain, Division of Infection and Immunity, UCL
2. Martin Pule, UCL Cancer Institute
3. Charles Swanton, Francis Crick Institute

References

1. Ghorani E, Reading JL, Henry JY, de Massy MR, Rosenthal R, Turati V, Joshi K, Furness AJS, Aissa AB, Saini SK, Ramskov S, Georgiou A, Sunderland MW, Wong YNS, De Mucha MV, Day W, Galvez- Cancino F, Becker PD, Uddin I, Ismail M, Ronel T, Woolston A, Jamal-Hanjani M, Veeriah S, Birkbak NJ, Wilson GA, Litchfield K, Conde L, Guerra-Assunc?a?o JA, Blighe K, Biswas D, Salgado R, Lund T, Al Bakir M, Moore DA, Hiley CT, Loi S, Sun Y, Yuan Y, AbdulJabbar K, Turajilic S, Herrero J, Enver T, Hadrup SR, Hackshaw A, Peggs KS, McGranahan N, Chain B, Swanton C, Quezada SA. The T cell differentiation landscape is shaped by tumour mutations in lung cancer. Nat Cancer. 2020 May;1(5):546- 561
2. McGranahan N, Furness AJ, Rosenthal R, Ramskov S, Lyngaa R, Saini SK, Jamal-Hanjani M, Wilson GA, Birkbak NJ, Hiley CT, Watkins TB, Shafi S, Murugaesu N, Mitter R, Akarca AU, Linares J, Marafioti T, Henry JY, Van Allen EM, Miao D, Schilling B, Schadendorf D, Garraway LA, Makarov V, Rizvi NA, Snyder A, Hellmann MD, Merghoub T, Wolchok JD, Shukla SA, Wu CJ, Peggs KS, Chan TA, Hadrup SR, Quezada SA, Swanton C. Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade. Science. 2016 Mar 25;351(6280):1463-9.
3. Reading JL, Galvez-Cancino F, Swanton C, Lladser A, Peggs KS, Quezada SA. 2018. The function and dysfunction of memory CD8(+) T cells in tumor immunity. Immunol Rev 283: 194-212
4. Joshi K, Robert de Massy M, Ismail M, Reading JL, Uddin I, Woolston A, Hatipoglu E, Oakes T, Rosenthal R, Peacock T, Ronel T, Noursadeghi M, Turati V, Furness AJS, Georgiou A, Wong YNS, Ben Aissa A, Werner Sunderland M, Jamal-Hanjani M, Veeriah S, Birkbak NJ, Wilson GA, Hiley CT, Ghorani E, Guerra-Assunc?a?o JA, Herrero J, Enver T, Hadrup SR, Hackshaw A, Peggs KS, McGranahan N, Swanton C; TRACERx Consortium, Quezada SA*, Chain B*. Spatial heterogeneity of the T cell receptor repertoire reflects the mutational landscape in lung cancer. Nat Med. 2019; 25(10):1549-1559. Co- Corresponding author.