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.
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.
Organisations
- UNIVERSITY COLLEGE LONDON (Lead Research Organisation)
- Francis Crick Institute (Collaboration)
- University of Cambridge (Collaboration)
- Technical University of Denmark (Collaboration)
- University of Oxford (Collaboration)
- Royal Marsden Hospital (Collaboration)
- University College London (Collaboration)
- UNIVERSITY COLLEGE LONDON HOSPITALS NHS FOUNDATION TRUST (Collaboration)
- Herlev Hospital (Collaboration)
- International Alliance for Cancer Early Detection (Collaboration)
- ROYAL FREE LONDON NHS FOUNDATION TRUST (Collaboration)
Publications
Abbosh C
(2023)
Tracking early lung cancer metastatic dissemination in TRACERx using ctDNA
in Nature
Al Bakir M
(2023)
The evolution of non-small cell lung cancer metastases in TRACERx.
in Nature
Al Bakir M
(2025)
Clonal driver neoantigen loss under EGFR TKI and immune selection pressures
in Nature
Al-Sawaf O
(2023)
Body composition and lung cancer-associated cachexia in TRACERx.
in Nature medicine
Barnes JL
(2023)
Early human lung immune cell development and its role in epithelial cell fate.
in Science immunology
Bentham R
(2025)
ImmuneLENS characterizes systemic immune dysregulation in aging and cancer.
in Nature genetics
Black JRM
(2025)
Ultrasensitive ctDNA detection for preoperative disease stratification in early-stage lung adenocarcinoma.
in Nature medicine
Enfield KSS
(2024)
Spatial Architecture of Myeloid and T Cells Orchestrates Immune Evasion and Clinical Outcome in Lung Cancer.
in Cancer discovery
Fitzsimons E
(2024)
A pan-cancer single-cell RNA-seq atlas of intratumoral B cells.
in Cancer cell
| 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. 2024-25 Our team now comprises 19 researchers in total via awards of several new grants. I now lead the new Cancer Initiation and Interception theme at UCL, The new Cancer Interception theme in ACED and I am a member of the UK Cancer Prevention Trials Network Steering Group and CRUK prevention research committee. 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. 2025- We have completed large scale validation of our early detection work in several lung cohorts and extended this to several other cancer types. We have focused on Treg cells as a basis for detection and interception and have functional data showing that such approaches may be effective. We have also discovered several novel changes to the immune system during early lung cancer development leading to new avenues of research. 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. 2025 - impacts are listed in other outcome types. |
| Exploitation Route | Industry led development of our cancer early detection prototype biomarker, and a candidate immune interception drug, should results be further extended. 2025 - several patents now in development. We may be able to spin out a biotech in 2027 and hope to initiate a clinical trial by 2030. |
| 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. 2025 - we have shaped awareness, future investment and research strategy in cancer prevention via committees, workshops consortia and international presentations and I am now on the organising committee and co-chairing major scientific conferences (e.g. ESMO MAP 2025). |
| First Year Of Impact | 2023 |
| Sector | Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology |
| Description | CRUK PPI Panel discussion |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Impact | The feedback indicated that the group were now aware of this new form of cancer prevention and that they welcomed any approach to enable those at risk to be proactive in seeking an intervention. |
| Description | Education of MSc Students - lecturing |
| Geographic Reach | Local/Municipal/Regional |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Description | Lung cancer centre of excellence meeting and renewal |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| URL | https://news.cancerresearchuk.org/2024/11/19/powering-the-future-of-lung-cancer-research/#:~:text=Wh... |
| Description | Presentation to CRUK Trustees |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Description | UKTCPN Steering Committee |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| URL | https://www.ecmcnetwork.org.uk/groups/uk-therapeutic-cancer-prevention-network-group-uktcpn |
| 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 and Care 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 | Characterising Immune Surveillance and Dysfunction in Early Stage Pancreatic Cancer |
| Amount | £22,000 (GBP) |
| Organisation | Pancreatic Cancer Research Fund |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 04/2023 |
| End | 05/2026 |
| 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 and Care Research |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2022 |
| End | 04/2023 |
| Description | Decoding the Signs: Early Detection of High-risk Oral Pre-Malignant Lesions |
| Amount | £211,711 (GBP) |
| Funding ID | EDDAPA-2024/100013 |
| Organisation | Cancer Research UK |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 02/2025 |
| End | 02/2027 |
| Description | International Alliance for Cancer Early Detection (ACED) - Research Studentships - 2024 |
| Amount | £159,017 (GBP) |
| Funding ID | ACEDAS-2024/100001 |
| Organisation | Cancer Research UK |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 09/2024 |
| End | 09/2028 |
| Description | LungVax: Preventing lung cancer via targeting hotspot neoantigens with the ChAdOx vaccine platform |
| Amount | £1,452,871 (GBP) |
| Funding ID | PRCBTP-Nov23/100003 |
| Organisation | Cancer Research UK |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 03/2024 |
| End | 02/2026 |
| 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 | Precision immune interception patents |
| Description | Confidential: 4 patents in early stage development for novel methods of cancer interception using immune agents. |
| Type Of Material | Antibody |
| Year Produced | 2024 |
| Provided To Others? | No |
| Impact | None yet |
| Title | TreeLabel R package |
| Description | We work on single-cell RNA-seq data with gene expression profiles for thousands of cells. A common first step is to annotate each cell's cell type. The granularity of these cell type annotations can vary; one can classify cells broadly into immune cells or epithelial cells or one can be very detailed and distinguish within the immune cells CD4 positive T regulatory cells from CD4 positive T follicular helper cells. Choosing the best annotation level is difficult because one analysis may need broad cell types, whereas others require the highest possible resolution. The treelabel package provides an intuitive interface to store and work with these hierarchically related labels. Depending on the reference data and annotation method used for the cell typing, you often have multiple (partially) conflicting annotations. treelabel provides functions to build a consensus across different annotations and can integrate annotations at different resolutions. Furthermore, treelabel supports uncertainty scores associated with a label. For example, most automatic cell type scoring tools (like Azimuth or celltypist), return a confidence score in addition to the cell type label. These scores enable a more precise selection of cells where you have sufficient confidence in the cell type label. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2025 |
| Provided To Others? | Yes |
| Impact | The package, generated by an ACED funded postdoc in my team, Dr Constantin Ahlmann-Eltze, was posted on his GitHub, and users have reported implementing the tool in research and provided positive feedback. |
| URL | https://github.com/const-ae/treelabel |
| Title | Two patents filed - Contents remain confidential |
| Description | We have developed an immunological platform for early lung cancer detection Update 2024/5 - these have moved towards filing in the UK and EU |
| 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 | ACED |
| Organisation | International Alliance for Cancer Early Detection |
| Country | Global |
| Sector | Academic/University |
| PI Contribution | Led a work package for a successful international consortium bid |
| Collaborator Contribution | co-authored grant application |
| Impact | consortium bid, successful grant award, £0.5m to Reading lab |
| Start Year | 2022 |
| Description | ACED interception |
| Organisation | University of Cambridge |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | New ACED initiative; Interception theme, Phase 1. JR co-wrote grant application " Identifying and targeting obesity driven immune dysfunction for cancer interception". |
| Collaborator Contribution | Co-wrote application for ACED. |
| Impact | Application pending, team will include Immunologists, clinicians, bioinformaticians, systems biologists. |
| Start Year | 2024 |
| Description | Glioblastoma |
| Organisation | University College London |
| Department | UCL Cancer Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We tested our T cell driven early detection platform in spleens from mice with GBM using samples generated by the Parrinello Lab at UCL. Data were used in an application for an early detection grant to the Mark Foundation (submitted March 2025). |
| Collaborator Contribution | The SP lab generated the samples and provided the tissue. |
| Impact | New collaboration, none to report yet |
| Start Year | 2025 |
| 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 | LungVax |
| Organisation | University of Oxford |
| Department | Oxford Vaccine Group |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | we are screening T cell reactivity in a CRUK Biology to prevention grant to support development of a new universal vaccine for lung cancer |
| Collaborator Contribution | manufacture and immunogenicity testing and development of the Lungvax prototype vaccine. |
| Impact | Biology to prevention grant, CRUK Pending Clinical trial grant application with CRUK. |
| 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 | PDAC |
| Organisation | University College London Hospitals NHS Foundation Trust |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | we are profiling preinvasive and early invasive PDAC, then identifying and validating interception targets. |
| Collaborator Contribution | Prof Steve Pereira, has provided clinical specimens from a PDAC biorepository |
| Impact | PhD student in Reading lab, shared with Prof Pereira, PCRF grant. |
| Start Year | 2024 |
| 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 |
| Title | DETECTING CANCER |
| Description | A method for determining whether a subject is at risk for having a progressing or high-grade pre-invasive lesion, nodule or small mass, or having a solid malignant tumour is described. The method involves analysing the proportion of T cells in a sample of blood obtained from the subject which are activated and/or exhausted T cells by analysing a trait of the T cells, e.g., via analysing biomarker expression using cytometry. In some instances, a plurality of traits is analysed and combined, e.g., via analysing biomarker expression using cytometry in combination with analysing the diversity or clonality of the blood TCR repertoire using TCR-seq. |
| IP Reference | WO2024068614 |
| Protection | Patent / Patent application |
| Year Protection Granted | 2024 |
| Licensed | No |
| Title | TreeLabel R Package |
| Description | We work on single-cell RNA-seq data with gene expression profiles for thousands of cells. A common first step is to annotate each cell's cell type. The granularity of these cell type annotations can vary; one can classify cells broadly into immune cells or epithelial cells or one can be very detailed and distinguish within the immune cells CD4 positive T regulatory cells from CD4 positive T follicular helper cells. Choosing the best annotation level is difficult because one analysis may need broad cell types, whereas others require the highest possible resolution. The treelabel package provides an intuitive interface to store and work with these hierarchically related labels. Depending on the reference data and annotation method used for the cell typing, you often have multiple (partially) conflicting annotations. treelabel provides functions to build a consensus across different annotations and can integrate annotations at different resolutions. Furthermore, treelabel supports uncertainty scores associated with a label. For example, most automatic cell type scoring tools (like Azimuth or celltypist), return a confidence score in addition to the cell type label. These scores enable a more precise selection of cells where you have sufficient confidence in the cell type label. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2025 |
| Impact | Manuscript in preparation. |
| URL | https://github.com/const-ae/treelabel |
| 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 | ACED Interception Workshop - Boston, USA |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Led a CRUK ACED alliance workshop to scope opportunities in Cancer Interception, leading to the formation of a new research theme in ACED for the next 5 years. |
| Year(s) Of Engagement Activity | 2024 |
| 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 | CRUK Biology to Prevention Workshop |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | CRUK Biology to Prevention Workshop held at the Francis Crick Institute to attract applications and engagement of the cancer research community |
| Year(s) Of Engagement Activity | 2024 |
| Description | CRUK Donor Event |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Supporters |
| Results and Impact | Recorded video content to promote our research which was used at a donor event by CRUK |
| Year(s) Of Engagement Activity | 2024 |
| Description | CRUK Presentation to board of senior trustees |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation to CRUK board of trustees to discuss cancer prevention research |
| Year(s) Of Engagement Activity | 2025 |
| Description | CRUK Prevention Research Committee |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | I am a newly appointed member of the Prevention Research Committee at CRUK, we meet twice annually to review funding applications and decide awards. |
| Year(s) Of Engagement Activity | 2024,2025 |
| URL | https://www.cancerresearchuk.org/funding-for-researchers/applying-for-funding/funding-committees/pre... |
| 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 Cancer Institute Faculty Annual Meeting |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation of new research theme in Cancer Initiation and Interception at UCL, for which I am Co-lead |
| Year(s) Of Engagement Activity | 2025 |
| 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 | UK Cancer Prevention Trials Network, Steering Committee |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Recurring monthly meetings to shape the UK Cancer prevention landscape and trial design |
| Year(s) Of Engagement Activity | 2024,2025 |
| URL | https://www.ecmcnetwork.org.uk/groups/uk-therapeutic-cancer-prevention-network-group-uktcpn |
| 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 |
