Enhancing immunogenicity in non-viral low mutation burden tumours

Lead Research Organisation: University College London
Department Name: Oncology

Abstract

Over the last decade, immunotherapy has become a new pillar of treatment in cancer, improving survival rates in over a dozen different tumour types. A key strength of immunotherapy is the duration of survival, with some patients experiencing long-term durable remission from cancer. While this leads to exceptionally positive outcome in some individuals, not all patients treated with immunotherapy experience benefit, and in fact most patients (~60-80%) do not respond to therapy. We now increasingly understand the reasons for therapeutic failure of immunotherapy, and a key factor is that some tumours are not mutated enough for the immune system to recognise and attack. The process of recognition involves tumour cells displaying their damaged contents for passing immune cells to recognize (a process called "neoantigen presentation"), and when the signal is strong enough immunotherapy can work. But when the extent of damage is low or moderate, immune recognition fails to activate.

This project aims to overcome this challenge using a novel approach, which is essentially blocking damage clean-up processes within cancer cells. The lack of clean-up allows damaged molecules to accumulate to higher levels in the cancer cell, and thus surpass the level of damage needed to activate immune recognition. A key benefit of this approach is that it serves to benefit patients whose tumours have insufficient damage for current immunotherapies to be effective (which is up to ~80% of all cases), as it doesn't require the underlying level of damage to be high. Instead by blocking damage clean-up, the level of mutated molecules can build up to higher levels even if the starting level of damage is low. The particular damage clean-up processes to be investigated in this project include the nonsense mediated decay, non-stop decay, no-go decay and unfolded protein response pathways. The choice of these pathways is based on prior evidence, where laboratory experiments and analysis of patient clinical trial data have validated their potential as novel candidates for immunotherapeutic development. In addition, cancer cells often rely heavily on these processes to deal with the burden of mutations within the cancer genome, so targeting these processes poses a lower risk of damage to normal (non-cancerous) cells.

The project has four distinct objectives, the first is to use advanced imaging techniques to look inside cancer cells to understand exactly how blocking damage clean-up impacts immune recognition. This objective will be critical in understanding the molecular workings of the these processes before therapeutic development work is undertaken. The second objective is study in detail how the processes of damage clean-up operate differently in cancerous and normal cells, and across different organ types. This is important in identifying a drug targeting strategy that has maximal impact on cancer cells but minimal toxicity to normal healthy tissue. The third objective is to induce anti-tumour immune response via tumour specific modulation of damage clean-up processes. The first three objectives are specifically focused on the most promising damage clean-up pathway, which is called nonsense mediated decay, so the fourth objective is to then broaden the work to the other damage clean-up pathways (non-stop decay, no-go decay and unfolded protein response).

The results from this work will firstly increase our biological understanding of how damage clean-up processes impact immune recognition of cancer cells. Secondly, this work aims to support the development of novel immunotherapies for patients whose tumours have insufficient damage for current immunotherapies to be effective.

Technical Summary

Background: Current cancer immunotherapies significantly extend survival in patients with high mutation load or oncogenic viral infection, however for the majority of patients (>80%) efficacy is limited. This limited efficacy is associated with poor immunogenicity, and novel strategies to enhance tumour antigen load are urgently required.

Aim: To induce anti-tumour immune response via inhibition of mRNA quality control pathways.

Rationale: I hypothesize that cellular processes engaged in mRNA and protein quality control can be inhibited to increase the abundance of mutated RNA/protein, and subsequently enhance the number of mutated peptides available for HLA presentation. This then serves to increase presentation of immunogenic neoantigens, thus driving anti-tumour immune response, even in the absence of a high mutation load or oncogenic viral infection. This hypothesis is supported by my published postdoctoral work, where I demonstrated that mutated mRNAs escaping from nonsense mediated decay (NMD) are strongly associated with improved patient response to immunotherapy. These results are further supported by preclinical data. Lastly, the NMD pathway is typically hyper-activated in tumour cells (due to the burden of somatic mutations), hence allowing cancer-specific targeting without normal cell toxicity.

Objectives: 1) To dissect the molecular underpinnings of NMD-escape and HLA presentation, 2) to characterise the differences in NMD pathway functionality between cancer and normal cell types, 3) to induce anti-tumour immune response via tumour specific modulation of NMD, 4) to identify other novel mRNA/protein quality control pathways associated anti-tumour immune response (e.g. UPR, no-go decay, etc).

Methods: Live cell imaging, bulk tissue/single cell sequencing analysis, in vitro CRISPR KO, ex vivo tumour organoids co-culture with T cells.

Publications

10 25 50
publication icon
Zhao Y (2021) Selection of metastasis competent subclones in the tumour interior. in Nature ecology & evolution

 
Description Immunology collaboration with Dr Sergio Quezada 
Organisation University College London
Department UCL Cancer Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution This is an academic collaboration with Dr Sergio Quezada, world expert in anti-tumour immunology. I have conducted bioinformatic analysis, related to Fc-gamma receptor (FCGR) function, and the influence of human germline FCGR polymorphisms in melanoma patient response to immunotherapy.
Collaborator Contribution Laboratory work related to Fc-gamma receptor (FCGR) function, and other tumor immunology projects.
Impact Paper accepted with Cancer Cell, titled: "Fc Effector Function Contributes to the Activity of Human Anti-CTLA-4 Antibodies".
Start Year 2017
 
Description Immunopeptidomics collaboration with Prof. Yardena Samuels 
Organisation Weizmann Institute of Science
Department Laboratory of Body and Mind Immunology Weizmann
Country Israel 
Sector Academic/University 
PI Contribution A collaboration has been initiated with Prof. Yardena Samuels at the Weizmann Institute in Israel. Through this collaboration I will be trained in a new technique called immunopeptidomics, a state of the art method for neoantigen identification. I will be spending a month in Israel in May-2019 training in the method. I am contributing tumour tissue samples from the TRACERx study.
Collaborator Contribution A collaboration has been initiated with Prof. Yardena Samuels at the Weizmann Institute in Israel. Through this collaboration I will be trained in a new technique called immunopeptidomics, a state of the art method for neoantigen identification. I will be spending a month in Israel in May-2019 training in the method. Weizmann is contributing methodological knowledge and expertise.
Impact Training skills will be the output, delivered in 2019
Start Year 2018
 
Description Inhibitor development with CRT/Ono/LifeArc 
Organisation Cancer Research Technology (CRT)
Country United Kingdom 
Sector Private 
PI Contribution We are conducting drug target identification work in the field of immune-oncology
Collaborator Contribution They are doing small molecule/antibody development, as well as further onward pharma development.
Impact Work is in progress - no outputs yet, but publications and drug development are planned.
Start Year 2022
 
Title EXTRECT 
Description Using DNA sequencing data to quantify T cell fraction and therapy response, as published in Betham, Litchfield et al. Nature (https://pubmed.ncbi.nlm.nih.gov/34497419/) 
Type Of Technology Software 
Year Produced 2021 
Open Source License? Yes  
Impact Allows T cell fraction to be inferred from DNA sequencing data 
URL https://pubmed.ncbi.nlm.nih.gov/34497419/
 
Description Podcast for Fifty Years 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact I recorded a podcast with a leading podcast company Fifty Years, which had >500 listens
Year(s) Of Engagement Activity 2021
URL https://fiftyyears.com/translation-podcast/tag/kevin+litchfield