Understanding the role of the chromatin insulator CTCF in human papillomavirus gene expression and disease progression
Lead Research Organisation:
University of Birmingham
Department Name: Cancer Sciences
Abstract
Viral infections are estimated to cause over 1 in 10 of all cancers, resulting in over 1.3 million deaths a year, worldwide. Human papillomavirus (HPV) infections cause almost half of these cancers, including cancer of the uterine cervix, genitals and in the mouth and throat. While this causal link between HPV and the development of cancer is well established, the specific changes that occur in HPV infections that drive the formation of HPV tumours are not well understood. Thus, it is important to understand these changes so that new therapies to treat HPV infections and cancer, and diagnostic tools for early disease detection, can be developed. Our work has shown that a host cell protein, CTCF, binds to the HPV genome and limits production of viral proteins that cause increased host cell growth and cancer development. Therefore, we hypothesize that in normal HPV infections CTCF is a key regulator of viral gene expression and works to allow the virus to complete the infectious cycle and produce new virus. We predict that the control of HPV-induced cell growth by CTCF is lost in HPV-driven cancers. The experiments described in this proposal are designed to answer long-standing questions about how the virus behaves in a normal infection and how this novel virus-host interaction contributes to virus productivity. Using clinical samples of HPV-associated disease, we will also explore how this virus-host interaction is disrupted in HPV-driven cancer.
Technical Summary
Infection with high-risk human papillomavirus (HR-HPV) is the cause of cancers within the anogenital and oropharyngeal tracts. The fundamental link between HR-HPV infection and neoplastic progression is well established, but the molecular changes are poorly defined. The HPV life cycle is dependent on the differentiation of the infected cell. Infection is established in the undifferentiated basal layer of the epithelium where early gene expression is initiated. Terminal differentiation of the cell results in late promoter activation and expression of late transcripts. This switch in gene expression is essential for life cycle completion, but how it is controlled has not been elucidated. We have recently demonstrated that the host cell transcriptional insulator protein CTCF binds to the HPV genome and regulates early gene expression. Our preliminary data provide strong evidence that CTCF function is essential for the transcriptional regulation of HPV gene expression by influencing transcriptional boundary formation and through the control of RNA polymerase II programming and gene splicing. Loss of CTCF binding not only enhances early gene expression but also prevents late gene expression, suggesting that CTCF function is important in the early to late switch in transcription control. We will study the function of CTCF in the differentiation-dependent control of virus gene expression using physiologically relevant models of the HPV life cycle at different body sites (anogenital and oropharyngeal) using innovative and quantitative methods. These experiments will be underpinned by the study of CTCF-HPV association in cervical cancer specimens to determine whether loss of CTCF binding contributes to cancer development. Consolidation of our findings will provide important insight into the function of CTCF in the HPV life cycle and HPV-driven disease progression and will impact on our understanding of CTCF function in gene expression control in healthy and disease states.
Planned Impact
Impact Summary 4000 characters
The work in this proposal focuses on fundamental pathways that regulate virus gene expression and their involvement in HPV-driven carcinogenesis. The results will contribute to our knowledge of HPV biology and HPV-driven disease progression, but more broadly to our understanding of the host cell transcription and gene splicing regulation. The main beneficiaries will be:
THE ACADEMIC COMMUNITY
To our knowledge we are the only grouping addressing the specific questions raised in our proposal and, with our combined expertise, we are ideally placed to answer these long-standing and important questions. Therefore, the results obtained will benefit those interested in the HPV life cycle and the molecular control of viral gene expression. Our study will also be beneficial to those interested in CTCF-mediated regulation of the life cycles of other DNA viruses and host cell gene expression. CTCF is mutated and dysregulated in many cancers and human disease and therefore our study will also benefit those interested in CTCF function in healthy and disease states.
Establishment of state-of-the-art methods (e.g. PAT-ChIP) will benefit our local academic community, as these methods will be shared with our colleagues at the University of Birmingham and further afield. The academic community will also benefit from the training of a postdoctoral scientist in the use of such methods to study the HPV life cycle, gene expression and chromatin structure, as well as more general training in project management and communication skills.
CLINICIANS
By identifying molecular events that contribute to HPV-driven carcinogenesis, we will benefit clinicians interested in HPV-associated disease. The proposed work will facilitate immediate engagement with clinicians (Nick Coleman, University of Cambridge and Hisham Mehanna, University of Birmingham) and future studies will take advantage of the highly integrated clinical academic environment at the University of Birmingham and within Birmingham Health Partners (BHP).
STAFF WORKING ON THE PROJECT
The postdoctoral scientist working on this project will develop a skill set highly desirable for future employment. With guidance from Parish and Roberts, the researcher will gain project management skills, obtained from running a research project, which are transferrable to many other disciplines in addition to the scientific employment sector. The researcher will also develop her communication and supervision/teaching skills that will be transferable to any management discipline.
SOCIETY
The immediate impact on society will be in the development of a highly skilled academic researcher. The proposed work could also have an economic impact in the long term through the development of novel biomarkers and therapies for HPV-driven disease.
The work in this proposal focuses on fundamental pathways that regulate virus gene expression and their involvement in HPV-driven carcinogenesis. The results will contribute to our knowledge of HPV biology and HPV-driven disease progression, but more broadly to our understanding of the host cell transcription and gene splicing regulation. The main beneficiaries will be:
THE ACADEMIC COMMUNITY
To our knowledge we are the only grouping addressing the specific questions raised in our proposal and, with our combined expertise, we are ideally placed to answer these long-standing and important questions. Therefore, the results obtained will benefit those interested in the HPV life cycle and the molecular control of viral gene expression. Our study will also be beneficial to those interested in CTCF-mediated regulation of the life cycles of other DNA viruses and host cell gene expression. CTCF is mutated and dysregulated in many cancers and human disease and therefore our study will also benefit those interested in CTCF function in healthy and disease states.
Establishment of state-of-the-art methods (e.g. PAT-ChIP) will benefit our local academic community, as these methods will be shared with our colleagues at the University of Birmingham and further afield. The academic community will also benefit from the training of a postdoctoral scientist in the use of such methods to study the HPV life cycle, gene expression and chromatin structure, as well as more general training in project management and communication skills.
CLINICIANS
By identifying molecular events that contribute to HPV-driven carcinogenesis, we will benefit clinicians interested in HPV-associated disease. The proposed work will facilitate immediate engagement with clinicians (Nick Coleman, University of Cambridge and Hisham Mehanna, University of Birmingham) and future studies will take advantage of the highly integrated clinical academic environment at the University of Birmingham and within Birmingham Health Partners (BHP).
STAFF WORKING ON THE PROJECT
The postdoctoral scientist working on this project will develop a skill set highly desirable for future employment. With guidance from Parish and Roberts, the researcher will gain project management skills, obtained from running a research project, which are transferrable to many other disciplines in addition to the scientific employment sector. The researcher will also develop her communication and supervision/teaching skills that will be transferable to any management discipline.
SOCIETY
The immediate impact on society will be in the development of a highly skilled academic researcher. The proposed work could also have an economic impact in the long term through the development of novel biomarkers and therapies for HPV-driven disease.
Publications
Burley M
(2020)
Epigenetic regulation of human papillomavirus transcription in the productive virus life cycle.
in Seminars in immunopathology
Califano J
(2023)
Lead Time to Recurrence After Posttreatment Plasma and Saliva HPV DNA Testing in Patients With Low-Risk HPV Oropharynx Cancer
in JAMA Otolaryngology-Head & Neck Surgery
Campos-León K
(2017)
Association of Human Papillomavirus 16 E2 with Rad50-Interacting Protein 1 Enhances Viral DNA Replication.
in Journal of virology
D'Arienzo V
(2021)
The CCCTC-binding factor CTCF represses hepatitis B virus enhancer I and regulates viral transcription.
in Cellular microbiology
Dobrica MO
(2024)
CTCF regulates hepatitis B virus cccDNA chromatin topology.
in The Journal of general virology
Description | Cancer Research UK PhD Non-Clinical Studentship |
Amount | £140,000 (GBP) |
Organisation | Cancer Research UK |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 09/2018 |
End | 09/2022 |
Description | Host cell reprogramming by oncogenic human papillomavirus |
Amount | £459,193 (GBP) |
Funding ID | MR/T015985/1 |
Organisation | Medical Research Council (MRC) |
Sector | Public |
Country | United Kingdom |
Start | 11/2020 |
End | 10/2024 |
Description | MRC DTP - IMPACT (Awarded to Universities of Birmingham, Leicester and Nottingham) |
Amount | £80,000 (GBP) |
Organisation | Medical Research Council (MRC) |
Sector | Public |
Country | United Kingdom |
Start | 09/2018 |
End | 03/2022 |
Description | MRC Project Grant |
Amount | £765,000 (GBP) |
Funding ID | MR/R022011/1 |
Organisation | Medical Research Council (MRC) |
Sector | Public |
Country | United Kingdom |
Start | 05/2018 |
End | 03/2021 |
Description | Wellcome Trust ISSF Award |
Amount | £17,629 (GBP) |
Organisation | Wellcome Trust |
Department | Wellcome Trust Strategic Award |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 08/2017 |
End | 09/2018 |
Description | Adam Grundhoff |
Organisation | Leibniz Association |
Department | Heinrich Pette Institute, Leibniz Institute for Experimental Virology |
Country | Germany |
Sector | Academic/University |
PI Contribution | Providing primary cell culture model system to study the influence of HPV infection on host cell gene expression changes |
Collaborator Contribution | Initiation of ChIP-Seq experiments and bioinformatic analysis of data |
Impact | Isolation of CTCF redeployment in host cell genome following HPV infection; currently under investigation. |
Start Year | 2016 |
Description | Analysis of 3D chromatin topology of HPV episomes |
Organisation | University of Sussex |
Department | School of Life Sciences Sussex |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | This collaboration with Michelle West and her research team was initiated to study 3D looping with HPV episomes and how these structure regulate HPV gene expression |
Collaborator Contribution | Experiments were designed by the West group using their expertise in chromatin topology methods and experiments were carried out in the Parish group. |
Impact | Pentland I., Campos-Leon K., Cotic M., Davies K-J., Wood C.D., Groves I., Burley M., Coleman N., Stockton J., Noyvert B., Beggs A., West M.J., Roberts S., Parish J.L. (2018) Disruption of CTCF-YY1 dependent looping of the human papillomavirus genome activates differentiation-induced viral oncogene transcription. PLoS Biology, 16(10): e2005752. |
Start Year | 2017 |
Description | CTCF regulation of HBV gene expression |
Organisation | University of Oxford |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Using the techniques we have developed in my laboratory to study epigenetic control of gene expression, DNA topology and virus gene expression, we are now studying the role of CTCF in the transcription control of HBV. My contribution is in the execution of molecular biology experiments |
Collaborator Contribution | The McKeating lab are contributing expertise in HBV culture techniques. Both research groups are intellectually contributing to the project. |
Impact | None as yet |
Start Year | 2016 |
Description | Professor Nick Coleman |
Organisation | University of Cambridge |
Department | Department of Chemistry |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | The Parish lab aims to understand the function of CTCF in papillomavirus gene expression control. Our studies have focused on HPV type 18. Our findings have been solidified by the study of HPV type 16 by the Coleman lab. We are continuing this combined research to study the mechanism of CTCF-mediated HPV gene expression control |
Collaborator Contribution | The study of a second oncogenic HPV type (16) to underpin our mechanistic studies. The Coleman lab have also contributed significant technical expertise to our study. |
Impact | Paris, C., Pentland, I., Groves, I., Roberts, D.C., Coleman, N., Roberts, S. and Parish J.L. CCCTC-Binding Factor Recruitment to the Early Region of the Human Papillomavirus Type 18 Genome Regulates Viral Oncogene Expression. (2015) Journal of Virology. 89(9):4770-85. |
Start Year | 2014 |
Description | Cancer prevention and healthy living workshop |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Other audiences |
Results and Impact | Workshop at local scout group to discuss health living and cancer prevention. |
Year(s) Of Engagement Activity | 2020 |
Description | Frontiers Science Presentation ay Association for Science Teachers Conference |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Schools |
Results and Impact | Delivered a presentation of my research area to a 'lay audience' of science teachers at an International conference in the Fronteirs Science lecture series |
Year(s) Of Engagement Activity | 2018 |
Description | Judge at the national science and engineering competition (Big Bang) |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Schools |
Results and Impact | Judge for the intermediate (15-16 year olds) science and maths category at the national final of the science and engineering competition. The event encourages school children to design and carry out experiments and showcase their research findings at the competition. The event inspires participants to continue with science and engineering subjects and also encourages other attendees at the event to become involved with school science projects. I discussed the research projects with school groups and judged the best projects for science concept, execution and explanations. |
Year(s) Of Engagement Activity | 2016 |
URL | https://www.thebigbangfair.co.uk |
Description | Laboratory Tours (CRUK) |
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 | Supporters |
Results and Impact | I host Laboratory tours for CRUK donors and patient groups so showcase my research area and explain the techniques we use to study oncogenic viruses. |
Year(s) Of Engagement Activity | 2015,2016,2017 |
Description | Life Sciences in Six |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | Presentation of Life Sciences in Six at the Birmingham Rep to an audience of approximately 250. Discussion afterwards was very lively and audience reported increased interest and changed perceptions. |
Year(s) Of Engagement Activity | 2018 |
URL | https://www.birmingham.ac.uk/university/colleges/mds/events/2017/11/life-sciences-six-2017/index.asp... |
Description | Life Sciences in Six |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Other audiences |
Results and Impact | Presentation of 'Viruses and Cancer' in Pecha Kucha style to School students, University staff (including professional), Alumni and undergraduate/postgraduate students |
Year(s) Of Engagement Activity | 2016 |
URL | https://www.youtube.com/watch?v=FZPMwcvJCZs |
Description | Presentation to lay audience |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Other audiences |
Results and Impact | 80 students and staff attended a day of talks called UBeEnlightened from across the University to showcase the breadth of our research. |
Year(s) Of Engagement Activity | 2020 |
Description | School Visit (Bromsgrove) |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Schools |
Results and Impact | 55 pupils and teachers attended a series of workshops designed to explain cell structure and function and DNA. I facilitated hands-on demonstrations, provided short talks and held a workshop to extract DNA from strawberries. |
Year(s) Of Engagement Activity | 2017 |
Description | School Visit (Bromsgrove, Worcestershire) |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | Ran a science workshop focussed on genetics with school children aged 10-13 |
Year(s) Of Engagement Activity | 2018 |
Description | School Visit (Redditch, Worcestershire) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | School Science day including judging science competion, careers talk and hands on demonstrations. |
Year(s) Of Engagement Activity | 2018 |
Description | School Visit (Redditch, Worcestershire) |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | Science workshop based on DNA extraction and genetics for school children aged 10-13 |
Year(s) Of Engagement Activity | 2018 |
Description | School visit |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | Visited a local secondary school in Birmingham to give a talk on life as a postgraduate student and the possible career paths for life sciences graduates. Inspired year 12 pupils to consider pursuing life science subjects at university and gave insight in to working as a PhD student. The talk sparked discussions between the class members about university options and future careers and aspirations. |
Year(s) Of Engagement Activity | 2016 |
Description | Schools visit for Science workshop |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Schools |
Results and Impact | Schools visit to Woodfield Academy, Redditch, Worcestershire to run science workshop focused on DNA with children aged 10-11. 120+ children attended. Very postitive feedback from students and teachers was received. This is part of a long term initiative to work with this school to develop a STEM club supported by academics at the University of Birmingham. |
Year(s) Of Engagement Activity | 2018 |
Description | Smoking and Cancer Workshop |
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 | Workshop with Bromsgrove Scout group to discuss smoking and cancer/health. Scouts were very engaged with many questions. There was much discussion. Scouts reported increased awareness of health impact of smoking. |
Year(s) Of Engagement Activity | 2018 |
Description | Smoking, alcohol and cancer workshop - Scout group |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Third sector organisations |
Results and Impact | ran a workshop and talks and activities to explain the health consequences of smoking and alcohol use to local scout group. |
Year(s) Of Engagement Activity | 2012,2013,2014,2015,2016,2017,2018,2019,2020,2021,2022,2023 |
Description | Student committee |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Undergraduate students |
Results and Impact | Women's Association UoB: as part of Women's History Month a lecture series of Women in Academia took place on 3rd March. Female academics from the Medical School talked about their journey in a science career and about the science we perform. This was followed by an interesting debate. |
Year(s) Of Engagement Activity | 2017 |
URL | https://en-gb.facebook.com/WomensUoB/ |