Identification and targeting of early T cell dysfunction in pulmonary preinvasive neoplasia

Lead Research Organisation: University College London
Department Name: Haematology

Abstract

Cancer is initiated by mutations that often arise from exposure to environmental factors, such as UV light or cigarette smoke. The immune system eliminates the vast majority of mutant cells that develop as we age but dysfunction of this defence allows some mutant cells to break through into cancer. If we could detect pre-cancerous growths at an early stage and rapidly repair this underlying immune dysfunction, we could reawaken mutation-specific immunity to destroy small tumours before they advance or prevent tumour formation altogether. However, we lack robust methods to detect pre-cancerous growth for many cancer types and the identity of these crucial defects in the immune system remains a mystery. This presents two urgent scientific challenges:

1. How can we detect tumours in early or pre-cancerous stages?

2. How can we identify and repair the early defects in our immune system that allow mutant cells to progress to cancer?

This UKRI FLF application sets out an innovative research programme that will be the first to study the immune response to mutant cells in pre-cancerous lesions of the lungs at never-before-seen scale and depth. Using a globally unique set of clinical samples from patients with 'preinvasive' lung lesions I will study key killer 'T cells' which recognise pre-cancerous growths. Using experimental, cutting-edge technology I have developed over the last 5 years I aim to pinpoint defects in mutation-specific T cells to refine a portfolio of precision, prototype drugs to resurrect their killer functions. At the same time, I will attempt to hi-jack the dysfunction of killer T cells as a method of early lung cancer detection, thus weaponising the failing immune system in pre-cancerous disease into a clinical strategy to track and target dangerous lesions to stop cancer in its nascent form.

My own research, and that of others has shown that both of these approaches may be potent clinical strategies with the potential to save a significant number of lives. Firstly, early detection of lung cancer reduces deaths by approximately 25%, because we can deploy treatment before tumours have a chance to spread. Secondly fixing tumour-associated T cell dysfunction at an earlier stage in animals and humans is more effective than doing so later and can generate long-lived potentially, curative immune responses that destroy tumours and may protect patients from mutated cells that arise in the future. Whilst my laboratory are focussing this series of experiments in preinvasive lung disease, it has much wider ranging impact. For example, we know that T cell dysfunction in later stages is similar across multiple cancers and that current 'immunotherapies' have an effect on several types of cancer. Moreover, we have preliminary results suggesting that tracking tumours via dysfunctional T cells in the blood is feasible. To conduct this study in preinvasive lung disease I will test three hypotheses:

1. Early T cell dysfunction can be used as a blood-based method of detecting pre-cancerous growths in the lung

2. Killer T cells recognise the mutated cells that give rise to cancer

3. Defects in mutation-specific killer T cells can be identified and repaired to restore their function.

This work will develop novel tests for early cancer detection and prototype drugs to pioneer future clinical strategies, paving the way for a new era of cancer medicines I have coined Early Intervention Immunotherapy and Cancer Immunoprevention.
 
Description Group development

2022-23
I have established a fully-fledged research group at my host institute, currently 7 staff, rising to 10 by the end of the year.
My staff have been trained in computational courses and/or cutting edge in vitro T cell immunology technology and are embedded in peer to peer learning fora and have now each presented at internal, department and/or national conferences. I have undergone training and development at UCL and have started to develop a new theme of carcinogesis research and an immuno-oncology programme whilst consolidating my position as theme lead of Immunology in the CRUK lung cancer centre of excellence.

2023-24
Building on my first year I have successfully applied for several additional grants (see awards) to continue to expand the group. We now have 10 members in the research team,
rising to 12 by the end of the year. My staff have developed significant wet and dry lab skills, attended international symposia, worked closely with FLF collaborator Prof Sam Janes and my first PhD student has successfully upgraded. I have also co-supervised a PhD student through graduation and recruited additional MSc students who are currently enrolling or completed last year with a distinction. We have appointed a Postdoc from the Francis Crick institute with significant Immunology expertise under the UKRI FLF award, who is leading the wet lab work. I have used national and international conferences, editorials, primary research articles and internal presentations to establish the group's reputation and niche in Pre-Cancer Immunology. I have initiated and now lead a new transatlantic consortium for cancer interception, who will be competing for several large scale collaborative awards. All of this work is complimentary to the research proposal of the FLF and consistent with the plans outlined for field leadership.

Research progress
2022-23
Our research has progressed significantly since the award started in June 2022.
Consistent with Aim 1 (objectives 1.1-1.2) we have discovered and integrated two types of immune derived signals in the blood of patients with progressive pre-malignant lesions of the lung. These signals have now formed the back bone of a prototype biomarker, the IP for which has been filed (see relevant section). Validation of this biomarker is ongoing as per objective 1.3.

Our work in Aim 2 thus far has led to the discover that mutated, but non-cancerous cells of the airways may evoke an immune response. This work, if further substantiated, will lead to a paradigm shift in our fundamental understanding of how and when the immune system first recognises cancer.

2023-24
Aim 1: We have now completed Objectives 1.1 and 1.2 using a combination of cross sectional analysis in patients with premalignant airway lesions, and longitudinal samples from the SUMMIT cohort. Objective 1.3 is ongoing, with collection of >250 biospecimens now complete.

Aim 2: Given advances in T cell antigen specific profiling technology within the group, we have now established a streamlined platform to assess neoantigen specificity of TCRs.
In parallel we have conducted scRNAseq analysis on CIS lesions and are running large scale reactivity profiling across a cohort of 3 UCLH bronch patients initially.

Aim 3: We are optimising the ATACseq protocol following a successful pilot assay and have completed scRNAseq analysis of candidate Tneo cells.

Aim 4: We have optimised a cutting edge tumour fragment platform to interrogate funcitonal targets and have cryopreserved samples from over 10 patients with stage 1-2 NSCLC.

We have been invited by a world leading journal to submit a manuscript in April 2024 on this work.
We have a related paper under review at Nature and Cell press with our collaborators and we are preparing an in silico manuscript for submission in summer 2024.

Societal impact
2023: I have taken on the position of co-lead in a new program of widening participation for STEM research for disadvantaged youths, the first event of the ATOMIC programme will occur in July 2023.
2024: I delivered this activity in July 2023 and have since conducted PPI activities via CRUK to discuss cancer prevention via immune therapies. I have given talks at several levels and promoted the concept of immune-interception.
Exploitation Route Industry led development of our cancer early detection prototype biomarker, and a candidate immune interception drug, should results be further extended.
Sectors Communities and Social Services/Policy

Healthcare

Pharmaceuticals and Medical Biotechnology

 
Description The presentation of our work at international conferences (CICON 2022; http://www.cancerimmunotherapyconference.org/s/Meeting-Agenda-092922_CICON22.pdf ) has galvanised research efforts in this space and contributed to the emergence of Immune cancer early detection (ICEdx) as a field. We have engaged with Astra-Zeneca, who have written a letter of support for our forthcoming consortia application on cancer interception.
First Year Of Impact 2023
Sector Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology
 
Description Education of MSc Students - lecturing
Geographic Reach Local/Municipal/Regional 
Policy Influence Type Influenced training of practitioners or researchers
 
Description 2022CRUK City of London Centre 4 Year PhD studentship
Amount £151,306 (GBP)
Organisation Cancer Research UK 
Sector Charity/Non Profit
Country United Kingdom
Start 08/2022 
End 08/2026
 
Description A multiomic T cell differentiation index (TEDI) for non-invasive early detection of lung and renal cancer (CRUK early detection project award)
Amount £513,339 (GBP)
Funding ID EDDPJT-Nov22/100042 
Organisation Cancer Research UK 
Sector Charity/Non Profit
Country United Kingdom
Start 05/2023 
End 06/2026
 
Description BRC Funding for Project ID - 6766671 Reading BC and Tech Student
Amount £230,000 (GBP)
Funding ID BRC907/CN/JR/101330 
Organisation National Institute for Health Research 
Sector Public
Country United Kingdom
Start 12/2022 
End 12/2026
 
Description CRUK City of London Centre 2023 Development Fund Award
Amount £24,800 (GBP)
Organisation Cancer Research UK 
Sector Charity/Non Profit
Country United Kingdom
Start 04/2023 
End 05/2024
 
Description Clinical Research and Development Committee Research Funding from the BRC and UCLH Charities - Fast Track Grant
Amount £39,593 (GBP)
Funding ID CRDC Reference: F226 
Organisation National Institute for Health Research 
Sector Public
Country United Kingdom
Start 03/2022 
End 04/2023
 
Description MRC DTP PhD
Amount £67,842 (GBP)
Funding ID 170890 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 09/2022 
End 09/2025
 
Description Targeting early T cell regulation to intercept lung squamous carcinogenesis
Amount £572,000 (GBP)
Funding ID PRCBTP-Nov23/100012 
Organisation Cancer Research UK 
Sector Charity/Non Profit
Country United Kingdom
Start 05/2024 
End 06/2028
 
Description UCL ACED PhD Studentship Programme
Amount £15,901,700 (GBP)
Funding ID RRDCANSING01 
Organisation Cancer Research UK 
Sector Charity/Non Profit
Country United Kingdom
Start 09/2024 
End 09/2028
 
Title Two patents filed - Contents remain confidential 
Description We have developed an immunological platform for early lung cancer detection 
Type Of Material Physiological assessment or outcome measure 
Year Produced 2023 
Provided To Others? No  
Impact Work with these tools is ongoing. 
 
Title HCC early detection pilot sample collection 
Description PBMCs collected from 30 cirrhotic controls and 30 patients with HCC 
Type Of Material Database/Collection of data 
Year Produced 2024 
Provided To Others? No  
Impact NA 
 
Title Patient Derived Tumour Fragment Collection - Early stage lung cancer 
Description n=20 Curated cryopreserved bio specimens to study TME interactions under perturbation in early stage lung cancer 
Type Of Material Database/Collection of data 
Year Produced 2024 
Provided To Others? No  
Impact na 
 
Description HCC early detection project 
Organisation Royal Free London NHS Foundation Trust
Country United Kingdom 
Sector Public 
PI Contribution Immunology expertise and analysis of T cell multi-omics
Collaborator Contribution Clinical expertise and patient cohort biobanks to study HCC
Impact Multi-disciplinary: Clinical oncology and T cell immunology. £24800 CRUK CoL Development Award for T cell driven early HCC detection
Start Year 2023
 
Description International research collaboration - Dr Marco Donia 
Organisation Herlev Hospital
Country Denmark 
Sector Hospitals 
PI Contribution JR Academic partnership around CD4 T cells in solid tumours JR is co supervisor for a PhD student in the Donia laboratory.
Collaborator Contribution MD Academic partnership around CD4 T cells in solid tumours MD is primary supervisor of a PhD student co-supervised by JR
Impact NA
Start Year 2024
 
Description NIMBLE 
Organisation Royal Marsden Hospital
Country United Kingdom 
Sector Hospitals 
PI Contribution Immunological analysis of blood samples
Collaborator Contribution Provision of samples
Impact None yet
Start Year 2022
 
Description Prof Sam Janes - lung neoplasia 
Organisation University College London
Department Lungs for Living Research Centre
Country United Kingdom 
Sector Academic/University 
PI Contribution 1. High dimensional flow cytometry profiling of blood samples from patients with preinvasive pulmonary neoplasia 2. TCRseq profiling of blood samples from patients with preinvasive pulmonary neoplasia 3. TCRseq profiling of pre-malignant lesion samples from patients with preinvasive pulmonary neoplasia 4. Single cell RNAseq analysis of lesion biopsies from patients with preinvasive pulmonary neoplasia 5. Joint laboratory meetings once every 2 months 6. Generation and initial filing of IP 7. Led a successful bid for a CRUK early detection project award 8. Co-ordinated a bid for a successful consortium grant for ACED 9. Guidance and supervision on Immunology
Collaborator Contribution 1. Provision of biospecimens including PBMCs, bronchial biopsies 2. Provision of human and mouse scRNAseq data 3. Provision of spatial transcriptomics data 4. Provision of whole exome sequencing data 5. Joint laboratory meetings once every 2 months 6. Guidance and supervision on respiratory medicine
Impact Cancer Research UK Early Detection Project Award Lead Investigator JR, CO-Is Sam Janes and Maxine Tran: https://www.cancerresearchuk.org/funding-for-researchers/how-we-deliver-research/recently-funded-awards#Population%20Research%20Committee: £0.5m. ACED consortium award: Exploiting the immune system for cancer early detection; £1.5m for UCL, £0.5m for JR lab Generation of IP: The T cell Early Detection Index (TEDI) created by my group has undergone provisional filing via UCLBusiness All are multidisciplinary - combining Respiratory Medicine, Immunology, Oncology, Informatics
Start Year 2022
 
Description Sine Hadrup 
Organisation Technical University of Denmark
Country Denmark 
Sector Academic/University 
PI Contribution Supervision of T cell biology
Collaborator Contribution Reagents and technical guidance
Impact Publication https://www.nature.com/articles/s41467-022-29342-0
Start Year 2022
 
Description TRACERx - Charles Swanton 
Organisation Francis Crick Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution Analysis of circulating T cells during lung cancer progression
Collaborator Contribution Provision of samples
Impact BRC Fast track award £40'000
Start Year 2022
 
Description 2023 HOT TOPIC IN BASIC & TRANSLATIONAL SCIENCE: RESISTANCE TO IO IN NSCLC 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Oral presentation, invited speaker: Title "Weaponising preinvasive T cell differentiation to intercept lung cancer".
Year(s) Of Engagement Activity 2023
URL https://www.iaslc.org/2023-hot-topic-basic-translational-science-resistance-io-nsclc
 
Description CRICK Open day 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Patients, carers and/or patient groups
Results and Impact PhD student Amber Rogers (CRUK COL program) presented work which is overlapping with the laboratory's main aims, supported by the UKRI award.
This was a poster presented to patient groups and the public at the Francis Crick institute.
Year(s) Of Engagement Activity 2023
 
Description Cambridge Conference for Interception of Cancer 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Invited speaker. 30 group leaders gathered for presentations and discussion on cancer interception
Year(s) Of Engagement Activity 2023
URL https://talks.ox.ac.uk/talks/id/555f58dc-1b57-437d-b012-0a458db834c6/
 
Description Opportunities Meeting in Ovarian Cancer - GSK/ Open Health 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Oral presentation and panel discussion on OC hosted by GSK, attended by approx 100 academics, clinicians industry staff
Year(s) Of Engagement Activity 2023
 
Description Oxford Cancer Precision Prevention Symposium 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Invited oral presentation at a new national symposia on Cancer Prevention
Year(s) Of Engagement Activity 2023
URL https://talks.ox.ac.uk/talks/id/555f58dc-1b57-437d-b012-0a458db834c6/
 
Description SITC (Society for the Immunotherapy of Cancer) 2023 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Awarded Young Investigator Abstract Travel Award and Bursary.
Presented an oral presentation in San Diego convention centre (audience capacity 7000), participated in panel discussion, presented a poster and attended the awards ceremony.
Oral presentation Concurrent Session 106c: Immunoprevention of Cancer.
Year(s) Of Engagement Activity 2023
URL https://www.sitcancer.org/2023/schedule/sitc23-annualmeeting#tab1
 
Description UCL Career Pathways Talk 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact Oral presentation providing career advice at UCL
Year(s) Of Engagement Activity 2023
 
Description Widening Participation to Medical Students (WAMS) Taster Day - EDI eveny 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Taster day for college students with strong academic performances from underprivileged boroughs in London.
Gave an oral presentation discussing Cancer Biomedicine and career opportunities
Year(s) Of Engagement Activity 2023