Using MHC class I peptides to modulate NK cell activity, as a basis for immunotherapy

Lead Research Organisation: University of Southampton
Department Name: Clinical and Experimental Sciences

Abstract

Natural killer (NK) cells are cells of the immune system that can fight infections and cancer. Their responses are controlled by a number of cell surface receptors including the killer cell immunoglobulin-like receptors (KIR). There are many different KIR but extensive studies have shown that NK cells and specific KIR genes can be important factors in determining the outcome of both infections, such as HIV and hepatitis C, and also of cancers, including leukaemia and liver cancer. To date harnessing specific sub-populations of NK cells for therapeutic benefit has been difficult because of a lack of understanding of NK cell biology. This has meant that NK cell based therapies are relatively crude and do not take account of the fact that different NK cells express different cell-surface receptors that may be relevant only in specific diseases. For instance the gene KIR2DL3 is associated with protection against hepatitis C, and the gene KIR2DS2 is associated with a better response to treatment in non-small cell lung cancer.
Work in our group has pioneered how NK cell reactivity can be altered by small peptides expressed on the surface of cells. The aim of this project is to develop our ideas so that a therapeutic reagent can be obtained. We will do this by targeting both the KIR2DL3 and KIR2DS2 genes, and identifying peptides that specifically bind these receptors to activate NK cells. We will also look for peptides that can activate KIR3DS1-positive NK cells. This is important because KIR3DS1 is associated with protection against HIV infection and also against the development of liver cancer. Whilst much activity has been focused on HIV, liver cancer continues to be a major health problem worldwide (it is the 6th commonest cancer), and alarmingly is on the increase in the UK. Importantly it is difficult to treat, and there is only one chemotherapeutic reagent currently licensed for this condition.
Having identified key peptides that we can use to activate NK cell, we will then use them in vitro to activate NK cells. We will devise optimal strategies for expressing the identified peptides and then optimising the culture conditions necessary for growing large numbers of NK cells expressing the relevant receptor. By the end of the project we hope to have a reagent suitable for therapeutic use, which depending on the results of the investigation maybe directly suitable for phase I studies.

Technical Summary

We will use transporter associated with antigen processing (TAP) deficient cell lines for peptide loading experiments to identify specific peptides that bind HLA and also either bind the activating receptor KIR2DS2 or function as peptide antagonists for KIR2DL2/3. Peptides will be designed based on our on-going experiments and the current literature.
We have identified an HCV derived peptide involved in the direct recognition of virus-expressing cells by KIR2DS2. We have used this to synthesize related peptides that induce KIR2DS2-binding and these experiments will inform the design of additional peptides that will engage KIR2DS2 to stimulate NK cells in vitro.
KIR3DS1 is a receptor associated with protective responses to HIV and hepatocellular carcinoma. We have identified that KIR3DS1 is also protective against chronic HCV infection. We will use HLA-B*2705 as an allele with which to perform a screen for peptides that may bind KIR3DS1, taking a motif-based approach and going on to perform a large scale screen if the initial approach is unsuccessful.
To investigate inhibitory receptors, we will make use of our published and pilot data to identify antagonist peptides for KIR2DL2/3. This will inform the design and testing of peptides that may antagonize inhibition by other HLA-C alleles.
To translate these into a potential therapeutic reagent we will set up assays of endogenous peptide presentation using minigenes and vector constructs to express the peptide with or without its cognate MHC class I ligands on the cell surface. Cell lines expressing these constructs, and exosomes derived from these cell lines, will be tested for their potential to activate and proliferate NK cells expressing specific KIR. We will also express our peptides transiently in monocyte derived dendritic cells in cultures with autologous NK cells so that HLA class I is completely matched as would be the case for in vivo therapy.

Planned Impact

We anticipate that the work will impact academia, patients, the pharmaceutical industry, charities and could have wider global health implications.

Academia
Immunotherapy was highlighted by Science magazine as one of the breakthroughs of 2013. Therefore we feel that the work has an opportunity to benefit the academic community including researchers in immunology, NK cell biology, cancer medicine and infectious diseases.

Patients
The work proposed has a strong translational component with a broad aim to develop new NK cell based therapeutics. Therefore there is potential for a large clinical community to benefit. These could include patients with a variety of different malignancies and patients with viral infection. Given the expertise at Southampton in cancer immunotherapy we feel that there is a potential for a rapid translation into phase I studies through collaboration with the Experimental Cancer Medicine Centre at Southampton, which has experience of DNA vaccines. Thuse there is an opportunity for patient benefit within the timespan of 3-5 years.

Pharmaceutical industry
The work should also generate patentable materials eg peptides that specifically activate NK cells. As NK cell therapy is in its infancy and these ideas are novel they could from the basis for a first-in-class therapeutic, which could be attractive to the pharmaceutical industry. We would anticipate commercializing any reagent in partnership with pharma, giving them the opportunity to benefit from this research in collaboration with the University of Southampton. If developed as a first-in-class therapy this would have the benefit that the UK could be world-leading in targeted NK cell therapy.

Charities
We feel that our work will be of value to cancer and liver charities. Such organisations will include CRUK, Leukemia and Lymphoma Research, The British Liver Trust and The Brian Mercer Charitable Trust, which has a specific interest in treatment and prevention of primary liver cancer. These may stimulate an interest in the charities in developing NK cell based therapeutics. Particularly important is the need to highlight the difficulties and lack of therapeutic options that patients with liver cancer currently have, and so it is anticipated that this work will improve this.

Global opportunities
With the recent knowledge that NK cells have memory properties one long-term goal could be the use of an NK cell vaccine as a prophylaxis against cancer or viral infections. Such infections could include both hepatitis C and HIV, both of which have protective associations with KIR genes. Therefore there is a potential for this work to have a global benefit. If a DNA vaccine could be produced this could be a low cost therapeutic or prophylactic vaccine for use in developing countries. This type of therapy would require additional studies to demonstrate in vivo generation of memory type NK cells but anticipate it would be possible within 5 years.
 
Description NIH R01 scheme
Amount $1,559,969 (USD)
Funding ID 1R01AI143740 
Organisation National Institutes of Health (NIH) 
Sector Public
Country United States
Start 03/2020 
End 02/2025
 
Description Targeting natural killer cell receptors for immunotherapeutic benefit
Amount £489,999 (GBP)
Funding ID MR/S009388/1 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 04/2019 
End 03/2022
 
Description University of Southampton - Confidence in Concept 2017
Amount £236,000 (GBP)
Funding ID MC_PC_17177 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 03/2018 
End 02/2020
 
Title Developing a strategy to active NK cells in vitro 
Description We are using DNA vaccination to activate natural killer cells in vitro 
Type Of Material Model of mechanisms or symptoms - mammalian in vivo 
Provided To Others? No  
Impact None as yet 
 
Description CRUK accelerator application "HUNTER" 
Organisation Miltenyi Biotec GmBH
Country Germany 
Sector Private 
PI Contribution We are part of a UK wide bid to address hepatocellular carcinoma: in the immunology stream. We will study natural killer cell responses and develop new natural killler cell therapeutics for this bid. We have an industrial partner (Miltneyi) on our part of the application. It has also enabled me to link with Professor Marcel Utz on this project. He is a chemist at Southampton who I brought into the application in order to bring a new magnetic resonance strand to the application. This links the UK with his Horizon2020 program on liver imaging (TISuMR). To date we have helped write and organise the bid.
Collaborator Contribution They have set up the bid and included us as partners.
Impact We have been selected for a full application following a preliminary application
Start Year 2017
 
Description CRUK accelerator application "HUNTER" 
Organisation Newcastle University
Country United Kingdom 
Sector Academic/University 
PI Contribution We are part of a UK wide bid to address hepatocellular carcinoma: in the immunology stream. We will study natural killer cell responses and develop new natural killler cell therapeutics for this bid. We have an industrial partner (Miltneyi) on our part of the application. It has also enabled me to link with Professor Marcel Utz on this project. He is a chemist at Southampton who I brought into the application in order to bring a new magnetic resonance strand to the application. This links the UK with his Horizon2020 program on liver imaging (TISuMR). To date we have helped write and organise the bid.
Collaborator Contribution They have set up the bid and included us as partners.
Impact We have been selected for a full application following a preliminary application
Start Year 2017
 
Description Collaboration on infectious diseases in the population 
Organisation Federal University of Minas Gerais
Country Brazil 
Sector Academic/University 
PI Contribution We have worked together to understand how natural killer cells are involved int he outcome of viral infection. We have published jointly In Science Immunology (Centre for Virus Research and University of Bristol) on mechanisms of recognition of viruses by natural killer cells. We led this research (I am senior author). This has allowed us to put in further funding applications (to MRC at present).
Collaborator Contribution Centre for Virus Research and University of Bristol, have performed experiments to help us to publish our paper in Science Immunology.
Impact Major publication in Science Immunology: Naiyer MM, Cassidy SA, Magri A, Cowton V, Chen K, Mansour S, Kranidioti H, Mbirbindi B, Rettman P, Harris S, Fanning LJ, Mulder A, Claas FHJ, Davidson AD, Patel AH, Purbhoo MA, Khakoo SI. KIR2DS2 recognizes conserved peptides derived from viral helicases in the context of HLA-C. Sci Immunol. 2017 Sep 15;2(15). pii: eaal5296. doi: 10.1126/sciimmunol.aal5296. PubMed PMID: 28916719.
Start Year 2015
 
Description Collaboration on infectious diseases in the population 
Organisation University of Bristol
Department Faculty of Life Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution We have worked together to understand how natural killer cells are involved int he outcome of viral infection. We have published jointly In Science Immunology (Centre for Virus Research and University of Bristol) on mechanisms of recognition of viruses by natural killer cells. We led this research (I am senior author). This has allowed us to put in further funding applications (to MRC at present).
Collaborator Contribution Centre for Virus Research and University of Bristol, have performed experiments to help us to publish our paper in Science Immunology.
Impact Major publication in Science Immunology: Naiyer MM, Cassidy SA, Magri A, Cowton V, Chen K, Mansour S, Kranidioti H, Mbirbindi B, Rettman P, Harris S, Fanning LJ, Mulder A, Claas FHJ, Davidson AD, Patel AH, Purbhoo MA, Khakoo SI. KIR2DS2 recognizes conserved peptides derived from viral helicases in the context of HLA-C. Sci Immunol. 2017 Sep 15;2(15). pii: eaal5296. doi: 10.1126/sciimmunol.aal5296. PubMed PMID: 28916719.
Start Year 2015
 
Description Collaboration on infectious diseases in the population 
Organisation University of Glasgow
Department MRC - University of Glasgow Centre for Virus Research
Country United Kingdom 
Sector Academic/University 
PI Contribution We have worked together to understand how natural killer cells are involved int he outcome of viral infection. We have published jointly In Science Immunology (Centre for Virus Research and University of Bristol) on mechanisms of recognition of viruses by natural killer cells. We led this research (I am senior author). This has allowed us to put in further funding applications (to MRC at present).
Collaborator Contribution Centre for Virus Research and University of Bristol, have performed experiments to help us to publish our paper in Science Immunology.
Impact Major publication in Science Immunology: Naiyer MM, Cassidy SA, Magri A, Cowton V, Chen K, Mansour S, Kranidioti H, Mbirbindi B, Rettman P, Harris S, Fanning LJ, Mulder A, Claas FHJ, Davidson AD, Patel AH, Purbhoo MA, Khakoo SI. KIR2DS2 recognizes conserved peptides derived from viral helicases in the context of HLA-C. Sci Immunol. 2017 Sep 15;2(15). pii: eaal5296. doi: 10.1126/sciimmunol.aal5296. PubMed PMID: 28916719.
Start Year 2015
 
Description Dengue replicon cell lines 
Organisation University of Bristol
Department School of Cellular and Molecular Medicine
Country United Kingdom 
Sector Academic/University 
PI Contribution We are currently transfecting cell lines expressing the Dengue replicon provided to us by Dr Andrew Davidson with HLA-C constructs
Collaborator Contribution He sent us the Dengue replicon cell line to test in NK cell assays. If successful this will further collaborative experiments
Impact none
Start Year 2015
 
Description Discussion with CRUK Centre for Drug Development 
Organisation Cancer Research UK
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution We have started discussions with the CRUK drug discovery unit to determine if our putative cancer vaccine would be suitable for the programme
Collaborator Contribution They are assisting us with the application process at the moment
Impact none as yet
Start Year 2018
 
Description GCRF application to MRC 
Organisation Federal University of Minas Gerais
Country Brazil 
Sector Academic/University 
PI Contribution We have started a collaboration to apply for funding to understand the role of NK cells in Flavivirus infection. At present we ahem not secured funding for this, but it has allowed some on-going discussion and applications in UK and Brazil.
Collaborator Contribution they have partnered us on research grant applications
Impact No outcomes as yet
Start Year 2016
 
Description NK cell vaccination 
Organisation Defence Science & Technology Laboratory (DSTL)
Country United Kingdom 
Sector Public 
PI Contribution We are currently discussing opportunities for NK cell vaccination strategies with DSTL for this
Collaborator Contribution This is in the discussion phase at present
Impact No outcomes at present we are still in discussion phase
Start Year 2017
 
Title PEPTIDE-INDUCED NK CELL ACTIVATION 
Description The invention relates to a peptide capable of activating NK cell-mediated immunity, the peptide comprising or consisting of the amino acid sequence XnAX2X1, Wherein Xn is an amino acid sequence of between 5 and 12 residues, and X1 is any amino acid; or leucine or phenylalanine; and X2 is alanine, threonine or serine. The invention further relates to an MHC class I molecule and the peptide, nucleic acids encoding the peptide, activated NK cells, and related compositions and methods, including use in methods of treatment. 
IP Reference US2018325979 
Protection Patent application published
Year Protection Granted 2018
Licensed No
Impact None as yet, but is part of discussions with industry
 
Title PEPTIDE-INDUCED NK CELL ACTIVATION 
Description priority filing of a cancer ligands for NK cells 
IP Reference EP3374375 
Protection Patent granted
Year Protection Granted 2018
Licensed No
Impact none as yet, but has facilitated engagement with industyr
 
Title DNA vaccine for immunotherapy 
Description we have created a DNA vaccine that activates natural killer cells. We are seeking support for this through industry or grant funding. We have called this initiative Vaxinc and created a video associated with this: https://futureworlds.com/discover-vaxinc/ 
Type Therapeutic Intervention - Vaccines
Current Stage Of Development Refinement. Non-clinical
Year Development Stage Completed 2017
Development Status Actively seeking support
Impact none as yet 
URL https://futureworlds.com/discover-vaxinc/
 
Description A talk at Bioseed 2019 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact I presented our opportunity to a group of Biotech funders including venture capitalists and big pharma
Year(s) Of Engagement Activity 2019
URL https://bioseed.eu/
 
Description A talk at the British Society for Immunology 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I gave a seminar on our current research to the audience
Year(s) Of Engagement Activity 2017
URL https://www.immunology.org/events/bsi-congress
 
Description A talk at the German NK cell meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I gave a presentation on our research
Year(s) Of Engagement Activity 2018
URL https://nk-symposium.org/
 
Description BSI liver immunology 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact This was a talk on the immunology of liver disease
Year(s) Of Engagement Activity 2017
URL https://www.immunology.org/events/basic-translational-current-concepts-liver-immunology
 
Description CAR NK meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact This was a presentation to at the CAR-NK cell meeting in London 2020. I gave a talk on our new NK cell immunotheraoy
Year(s) Of Engagement Activity 2020
 
Description EASL basic science symposium, invited speaker 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This was an invited talk on our work to The European Society for the Study of the liver. The work is a training event for post-graduate students and post-doctoral fellows. the work sparked discussions and the opportunity for further international collabroation
Year(s) Of Engagement Activity 2016
URL http://www.easl.eu/discover/events/detail/2016/t-cell-responses-in-viral-hepatitis-and-hepatocellula...
 
Description Invited speaker to the British Association for the Study of the Liver annual general meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact I was an invited speaker at The BASL meeting in Manchester, UK. I discussed my work on natural killer cells in a disease context
Year(s) Of Engagement Activity 2016
 
Description NK cell workshop 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact We had a presentation a poster presentation at the NK2017 meeting for the work.
Year(s) Of Engagement Activity 2016
URL https://www.nk2016.it
 
Description Pitch of potential new immunotherapeutic to audience of students and academics 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact I gave a pitch for a new immunotherapeutic based on our research to an audience at Future Worlds which is our University business incubator. It received the highest support for any pitch given at these seminars
Year(s) Of Engagement Activity 2018
URL https://futureworlds.com/
 
Description Speaker seminar Karolinska Institute 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I have a seminar encompassing our work on peptides and natural killer cells
Year(s) Of Engagement Activity 2017
 
Description Two talks at the UK NK cell meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact My student and post-doctoral fellow both gave talks at this meetinghttps://www.immunology.org/civicrm/event/info?reset=1&id=540
Year(s) Of Engagement Activity 2019
URL https://www.immunology.org/civicrm/event/info?reset=1&id=540
 
Description interview for The Scientist magazine 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact I gave an interview to the Scientist Magazine. this was published as an "Editors Choice" article
Year(s) Of Engagement Activity 2017
URL https://www.the-scientist.com/?articles.view/articleNo/50953/title/Immune-System-Targets-Diverse-Vir...