Exploring the role of T cells in the immune surveillance of early renal cancer

Lead Research Organisation: University College London
Department Name: Surgical Biotechnology

Abstract

Context: The immune system is important at defending the body against cancer. When the immune system does not work as it should, cancer is more likely to occur.
Cancer is able to trick the immune system's defence. When this happens, cancer grows and can spread to other body parts. We still do not know what happens in the immune system in the first stages of cancer growth.
We have never been better at diagnosing kidney cancer early. Now, up to half of diagnosed kidney cancer cases are in early stages (i.e. small tumour in the kidney that hasn't spread to other body parts). We do not know why some early kidney cancers grow and spread through the body but others do not. Knowing why this difference exists can help inform how patients are treated and what the best course of treatment might be.

Aims and objectives: The main goal of this study is to understand the role of the immune cells in early kidney cancer growth. There are hints that a specific type of immune system cell, called T cell, plays an important role in the way cancer and the immune system work. I will be looking at these T cells. I will use tumour and blood samples donated by patients, and obtain the T cells. I will study how many T cells are in the tumour, what they look like, and how they work.
The second goal is to study how kidney cancer metabolism (i.e. the food it uses to grow) affects the way T cells work. Cancer cells use the nutrients (i.e. food) available around them. This leads to T cells not having enough nutrients and not being able to work properly. There are hints that this may be one of the reasons why cancer overcomes the immune system's defence and grows. A new non-invasive technique, called hyperpolarised magnetic resonance imaging (MRI), measures the level of nutrients eaten by the cancer. In patients who were tested with this new type of MRI prior to surgery, I will study what T cells look like and how they work.

Potential applications and benefits: This study will help show how the immune system and kidney cancer work together. When patients are diagnosed with early kidney cancer, we are not able to tell the difference between who can just be monitored and who will need a lot of treatment. Looking closely at the relationship between the immune system and early kidney cancer might help guide treatment and improve patient care. The findings of this study could also be applied to kidney cancer at later stages or other cancers.

Note: public and patients have been involved in writing this summary - patient representatives known to the Specialist Centre for Kidney Cancer (Royal Free London NHS Foundation Trust) have contributed, as well as patients and public through an activity promoted with the support of the UCL Joint Research Office.

Technical Summary

Context: The immune system has an important role in the recognition and elimination of malignant cells. There is clinical evidence of cancer immune surveillance in the kidney but the phenotype and functional profile of the immune cells controlling early cancer development remains unknown. Half of renal cell carcinomas (RCC) are diagnosed at early stage but the biology of early RCC is understudied. I want to improve the knowledge on immune-related disease progression events associated with early RCC.

Aims: The primary aim is to explore the T cell profiles associated with progression in early RCC. The secondary aim is to investigate the impact of environmental nutrient deprivation in kidney cancer on T cell function.

Methodology: Patient blood and tissue samples will be used. Primary aim: phenotypical and functional characterisation of T cell subsets associated with shift to escape in early RCC will be done using flow cytometry, immunohistochemistry (IHC), and transcriptomics. Progression-related changes in intratumoural clonal distribution of T cells will be sought after with TCR repertoire analysis. Secondary aim: phenotypic and functional characterisation of tumour T cell subsets using flow cytometry, IHC, and transcriptomics will be done on a cohort of patients that underwent non-invasive tumour metabolic assessment using hyperpolarised MRI.

Scientific and medical opportunities: Innovative experimental and analytic pipelines will generate high quality outputs, contributing to one of the world's leading efforts in applied early cancer research. Elucidating T cell immune mechanisms associated with early RCC progression will lead to biomarker development, improved risk stratification, and ultimately the adoption of more personalised management decisions. While the project focuses on early RCC, a high level of translatability of methods and outputs to other disease stages, cancers, and study designs (i.e. longitudinal monitoring) is expected.

Planned Impact

The immune system has an important role in the recognition and elimination of cancer cells. When immune defence is altered, the likelihood of cancer arising in the kidney increases. Likewise, cancer can avoid the killing action of the immune system, a process thought to be essential for cancer growth. T cells appear to play a significant role in the interaction with cancer cells. However, we still don't know exactly what is the nature of this interaction.

Early cancer and specially the mechanisms that govern early cancer development are understudied. Improvement in health service provision and increased use of imaging techniques have led to a high rate of diagnosis of asymptomatic early kidney cancer. While some of the early kidney cancers do grow and spread through the body, others remain stable over time, and do not limit life or quality of life. Currently, our discriminating ability between these two subgroups of early disease is poor. Thus, there is an unmet need to understand early kidney cancer development.

The main aim of this project is to investigate the role of T cells in early kidney cancer growth using clinical samples. The impact goals of the project are:

1) To generate world leading research and knowledge into the immunological basis of early kidney cancer.
This research will lead to high quality outputs that will be disseminated, including published results and data made publicly available that can extend scientific discoveries beyond the scope of this project. This will contribute to academic advancement, to increased international competitiveness of UCL and the UK, and will place the collaboration between the Specialist Centre for Kidney Cancer and the Institute of Immunology and Transplantation as one the world's leading efforts for this kind of research. The outputs of this project are cross disciplinary and will be of interest to immunology, cancer biology, urology, other surgical specialties, oncology, pathology, and bioinformatics.

2) To encourage research into the events behind early kidney cancer development.
I will contribute towards the development of other ventures and collaborations by curating the UCL-RFH biobank kidney cancer repository and encouraging other groups at national and international forums to make use of the samples stored (pending ethical approval). In addition, letters/comments will be published in high-impact factor journals to raise awareness for the need to invest intellectual and financial resources into understanding early cancer development.

3) To define public and patient driven standards in basic and translational kidney cancer research.
Public and patients stand to benefit from well conducted, high impact research. Likewise, service users can greatly impact research in a number of ways. This project will foster the creation of a Patient Advisory Panel following NIHR INVOLVE guidelines to define strategies to increase patient participation in research, identify research priorities in kidney cancer, assist in the dissemination output of challenges and results of the current project, and support the development of future research projects.

4) To generate hypotheses for further validating translational research.
The outputs of this project can contribute to biomarker development, improved risk stratification, and ultimately the adoption of more personalised management decisions. This has the potential to positively impact society and the NHS by upgrading the service provided to kidney cancer patients, improving patient quality of life, and potentially reducing cost. The Specialist Centre for Kidney Cancer is perfectly positioned to lead following validating studies, contributing towards UCL's and UK's international competitiveness. In addition, the research outputs can also generate commercial interest from companies investing in immunotherapy for example, and attract more research partnership initiatives to UCL and the UK.

Publications

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Title SDH def RCC 
Description DNA and RNA sequencing data from patients with SDH deficient RCC Sequence data reported in this paper is European Genome-Phenome Archive: EGAD00001008469 for whole-genome sequencing data, and EGAD00001008470 for the RNA sequencing data. Raw RNA count data is deposited on Mendeley at 10.17632/ysmbcgyscx.1. All original code has been deposited at zenodo and is publicly available as of the date of publication. DOIs are listed in the key resources table. Any additional information required to reanalyse the data reported in this work paper is available from the lead contact upon request. 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? Yes  
Impact Succinate dehydrogenase (SDH)-deficient renal cell carcinoma represents a rare subtype of hereditary kidney cancer. Clinical diagnosis can be challenging and there is little evidence to guide systemic therapeutic options. We performed genomic profiling of a cohort of tumors through the analysis of whole genomes, transcriptomes, as well as flow cytometry and immunohistochemistry in order to gain a deeper understanding of their molecular biology. We find neutral evolution after early tumor activation with a lack of secondary driver events. We show that these tumors have epithelial derivation, possibly from the macula densa, a specialized paracrine cell of the renal juxtaglomerular apparatus. They subsequently develop into immune excluded tumors. We provide transcriptomic and protein expression evidence of a highly specific tumor marker, PAPPA2. These translational findings have implications for the diagnosis and treatment for this rare tumor subtype. 
URL https://ega-archive.org/
 
Description Genetic profiling and the immune compartment of SDHB deficient tumours (Dr Tom Mitchell) 
Organisation The Wellcome Trust Sanger Institute
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Me and my supervisor, Maxine Tran, have provided all human samples for sequencing under this project. I performed immunohistochemical stainings and generated flow cytometry data. I co-analysed the sequencing data under Tom Mitchell's supervision.
Collaborator Contribution Tom Mitchell has sequenced the samples. He provided me training in bioinformatics and supervised data analysis.
Impact Output: - one publication http://doi.org/10.1016/j.isci.2022.105389 Other outcomes: - potential clinical biomarker to be validated - increased my knowledge in bioinformatics, genetics, and translational research
Start Year 2019
 
Description Genetic profiling of Oncocytomas (Dr Tom Mitchell) 
Organisation The Wellcome Trust Sanger Institute
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Me and my supervisor, Maxine Tran, are collaborating with Tom Mitchell on a project involving genetic profiling of oncocytomas. We have provided human samples.
Collaborator Contribution Tom Mitchell will process and analyse the data.
Impact No outputs/outcomes yet.
Start Year 2019
 
Description Genetic profiling of Small Renal Masses (Drs Samra Turajlic and Scott Shepherd) 
Organisation Francis Crick Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution Me and my supervisor, Maxine Tran, are collaborating with Samra Turajlic and Scott Shepherd in a project aimed at profiling the genetic landscape of small renal masses. We have provided multi-regional samples from 46 relevant tumours. Some of these samples are directly related to my MRC funded project as they represent cases that have been on active surveillance prior to surgery. We will then be able to match the T cell microenvironment to tumour genetic events, and correlate this with clinical outcome.
Collaborator Contribution Samra Turajlic and Scott Shepherd will sequence the samples and analyse the data.
Impact No outputs or outcomes have yet to be generated from this collaboration. This collaboration involves surgeons, oncologists, pathologists, scientists and bioinformaticians.
Start Year 2019
 
Description 2019 UCL Immunity and Transplantation Summer Challenge 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact I collaborated on one lecture on the UCL Immunity and Transplantation Summer Challenge in 2019. This is a six-week programme run at UCL for Year 12 students attending state schools to have a first contact with subject-specific higher education experiences. The aim of the Immunity and Transplantation Summer Challenge is to introduce Year 12 students to immunology. The course is particularly focused on immunotherapy for the treatment of cancer, which is in line with my research focus. I guided the students while they prepared a small presentation on the ethics of therapies using gene editing.
Year(s) Of Engagement Activity 2019
 
Description Clinical Research Training Fellowship - Invited talk at Virtual Academic Surgery Conference 2021 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact I delivered a talk in conference format on the subject of, Clinical Research Training Fellowship, at the Virtual Academic Surgery Conference (VASC) 2021 on Saturday 27th March 2021. The talk generated a lot of questions
The aims of the conference were to increase medical student awareness about a career in academics, the potential career pathway, and opportunities for students to get involved with research.
The conference was attended by 495 delegates from 58 countries, and 6 continents.
The talk was recorded and the recording was shared to amplify the audience reach.
Year(s) Of Engagement Activity 2021
 
Description Kidney Cancer Patient Support Group 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Patients, carers and/or patient groups
Results and Impact In 2019 I gave a presentation on my team's kidney cancer research portfolio on a Kidney Cancer Patient Support Group at the Royal Free London NHS Foundation Trust. This was aimed at introducing patients/carers to the various projects currently ongoing at the unit and was also an opportunity to show previous research participants some of the outcomes/outputs obtained thus far.
Year(s) Of Engagement Activity 2019
 
Description London Urology Specialty Registrar Kidney Cancer teaching session 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact I was invited to lecture at the London Urology Specialty Registrar Kidney Cancer teaching session, an educational event for junior doctors training in urology. I gave a lecture on immunological aspects in kidney cancer.
Year(s) Of Engagement Activity 2018
 
Description London Urology Specialty Registrar Kidney Cancer teaching session 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact I was again invited to lecture at the London Urology Specialty Registrar Kidney Cancer teaching session, an educational event for junior doctors training in urology. I gave 3 lectures: on immunological aspects in kidney cancer, active surveillance in kidney cancer and hereditary kidney cancer syndromes.
Year(s) Of Engagement Activity 2019
 
Description Specialist Centre for Kidney Cancer Educational Sessions 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Since 2019 I have been organising and occasionally lecturing on monthly educational sessions focused on evidence-based kidney cancer diagnosis and management. These sessions are aimed at educating junior doctors, nurses, health allied professionals and research team members involved in kidney cancer care and research at Royal Free Hospital.
Year(s) Of Engagement Activity 2019,2020
 
Description Specialist Centre for Kidney Cancer Journal Club 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Since 2018 I organise a monthly journal club for a multidisciplinary team of doctors, nurses, health allied professionals and research team members involved in kidney cancer care and research at Royal Free Hospital. This activity contributes to their professional development by exposing them to novel and up-to-date clinical and translational studies. In addition, I have presented on 3 papers at the journal club.
Year(s) Of Engagement Activity 2018,2019