Title: Deciphering the molecular rules that govern CD4+ T cell responses to tumour associated antigen peptides to enhance anti-tumour immunity
Funder: Health and Care Research Wales (Welsh Government)

Abstract: Unlike T cell immunity to viruses, immunity towards tumour associated antigens (TAAs) is silenced by the expression of these proteins in the thymus resulting in deletion of high-affinity and high-sensitivity T cells which could otherwise respond to and eliminate cancer cell outgrowth. Consequently, anti- tumour immunity is inherently different from anti-viral immunity and therapies to generate potent anti- tumour immune memory through vaccination is currently limited by this fundamental property of T cell development. Yet, tipping the balance towards increased immune reactivity to tumours through cancer immunotherapies, such as checkpoint inhibition, vaccination with altered antigens or adoptive cell therapy, has been transformative to healthcare and for cancer patients. The profound influence of immune-tolerance on anti-tumour immunity is exemplified by the activity of T cells which recognise somatic mutations of tumour proteins i.e. “neoepitopes”, which break tolerance. Such T cells can be highly effective at clearing tumours, yet these somatic mutations are patient specific meaning vaccination against these antigens would require personalisation. Nevertheless, this demonstrates that breaking tolerance through even single amino-acid changes can drastically alter the perception of self-proteins to the T cell repertoire. As a result, a strategy whereby cancer vaccines carrying modified TAA-derived T cell antigens (“neo-modified”) which universally expand and generate immunity to TAAs would be highly attractive and less patient specific. Importantly, T cell memory driven by neo-modified antigens/vaccines would require the maintenance of specificity for the native germline TAA sequence expressed by the tumour. A potential pathway to achieve these two key aims is to alter away from self the peptide flanking residues (PFRs) of CD4+ T cell epitopes which are a unique property of HLA-II restricted epitopes. I, and others, have previously shown that alteration of PFRs are an attractive target to manipulate the T cell response to an antigen as (i) PFR modifications can be introduced to stimulate and alter the cognate CD4+ T cell repertoire whilst (ii) maintaining specificity and reactivity to wild type epitopes. To this end, the programme of work proposed herein, enabled by a HCRW HRF, would allow me to utilise my established molecular, structural and cellular immunology expertise to further understanding of fundamental features of tumour-derived epitopes in the context of self-derived proteins and build pipeline methodologies for the selection of candidate TAA-derived epitopes and their enhancement through PFR neo-modification for improved anti-cancer vaccination strategies. Overarching hypotheses: The molecular rules that govern CD4+ T cell immunity to tumour associated antigens are inherently different to that of anti-viral immunity due to thymic selection against self-proteins. Breaking this tolerance through modification of peptide flanking residues may lead to enhanced immunity against such antigens. Outcomes: This proposal will create fundamental understanding of a pivotal process in cancer immunology; specifically, by defining the constituents of tumour-derived epitopes in the context of CD4+ T cells. Furthermore, a universal platform methodology to identify, characterise, optimise and enhance tumour epitope immunogenicity will be established with exciting therapeutic implications in future vaccination development.

Lay abstract: Harnessing the power of the immune system to fight cancer has resulted in a new era of cancer treatments. Our own body’s immune system was first thought to only fight off invading foreign bugs such as viruses and bacteria, however, it is now appreciated that the immune system is able detect cancer during an individual’s lifetime. In fact, for cancer to develop in a patient, the cancer must progress in such a way that it is able to avoid the action of watching immune system. Understanding this process has led to treatments, termed cancer immunotherapies, which aim to make the immune system better at recognising cancer so that a patient’s own body can find back stronger against the cancer. These therapies have proven incredibly powerful; however, much work is still needed to make these therapies work in everyone as well as financially viable and practically achievable to be delivered on wide scale for everyone by healthcare systems like the NHS. An important arm of the immune response against cancer are T helper cells, named because of their development in the Thymus and their function to help and orchestrate the entire immune response towards a target. T helper cells recognise cancer by monitoring the body for small signs of cancer occurring. These small signposts – called peptides – are scanned by T cells to determine whether or not an immune response should be enacted. T helper cells hold the power to license and instruct the immune response towards the destruction of a cancerous cell. Whilst this is a very power function, these immune cells must be very strictly trained by our bodies on what they should target – as if the immune system is directed towards normal healthy tissues, T cells can cause disease (known as autoimmunity). For this reason, before T helper cells are released from the thymus to patrol the body, they are trained not to respond to our own body (termed “self”). This has important consequences on how well T helper cells recognise signpost peptides of cancer, as cancer peptides are also derived from “self”. It is for this reason that fewer cancer “signpost” peptides are seen by T helper cells and those that are seen are seen less well. As a result, it is important to explore ways to better train T helper cells to see and target cancer. One of the ways to try and achieve this is to re-train the immune system to better recognise cancer through vaccination – just like vaccines protect people from viruses. There are challenges, however, to achieving this goal. Firstly, it is important to identify the cancer peptide “signposts” that T helper cells can recognise and understand why these peptide “signposts” are seen out of the thousands of others that are not seen – this is Aim 1 & 2 of this project. Having identified which peptide signposts are seen it will be possible to explore whether these peptides can be subtly altered so that they are seen better by T helper cells – Aim 3. Finally, having identified ways to optimise the cancer signpost peptides that are seen, it will be explored whether this tactic can be applied to parts of cancer which are not normally seen – Aim 4. Together, it is hoped that increasing the magnitude of the immune response to cancer peptides and broadening the number of cancer signpost peptides the immune system can see may identify a way that cancer vaccines can be designed in the future to stimulate a better immune response against cancer.

Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS;INFLAMMATORY AND IMMUNE SYSTEM