Gene-drug interactions in the melanocyte lineage and melanoma

Lead Research Organisation: University of Edinburgh

Abstract

The aim of our work is to discover new therapeutic approaches and drug targets for melanoma. Melanoma is the most deadly form of skin cancer, and incidence continues to rise rapidly in the UK and Europe.
Recent advances in melanoma therapy often lead to regression of the cancer, but for most patients, the melanoma comes back. This suggests that while therapies can kill most of the cancer, there are some cells in the melanoma that are resistant to therapy. Our goal is to identify these different cells within melanoma, and develop new therapeutic approaches that can be used in combination with current therapy to eradicate the tumour.
We have developed a model system that enables us to genetically engineer zebrafish to develop melanomas that are similar to human melanomas. We use these animals to image the different cell types within melanoma, to screen for new drugs, and follow how the different cell populations within the cancers respond to new drugs at the single cell level. There are no other animal systems that allow us to do these studies at this resolution. We hope that these studies will help us to better understand how melanoma responds to drug treatment, and identify new vulnerabilities that we can use to target melanoma.

Technical Summary

My research goal is to develop new therapeutic approaches to treat melanoma. Our strategy is to interrogate the melanocyte lineage in zebrafish as a novel source of therapeutic targets and drug-leads that can target the diverse, heterogeneous subpopulations in melanoma.
As supported by an ERC Consolidator Award and a BBSRC funded screening facility, we perform phenotype-based small molecule screens on the zebrafish melanocyte lineage to identify new drugs that can target lineage specific vulnerabilities in melanoma.
Within the context of my core MRC Programme research, I now propose to translate one of the hit classes from our screen, the 5-NFNs, to target ALDHHigh subpopulations in cancer. In parallel, we will use zebrafish genetic technologies to discover and dissect the melanoma lineages that underpin the cancer cell subpopulations that drive disease progression and treatment failure. These efforts are further supported by a Melanoma Research Alliance-L’Oreal Team Award for Women in Science to identify and target dormant melanoma subpopulations.
The two main experimental aims of my MRC programme are:
Aim 1: To develop the potential of the 5-NFNs to target melanoma subpopulations and to reveal new 5-NFN synthetic lethal interactions.
Aim 2: To discover new melanocyte lineage and melanoma subpopulations in zebrafish and to test their role in melanoma progression and therapy.
We will use single cell sequencing, transcriptomics, and fluorescent reporter lines to identify and label heterogeneous cell populations in melanocyte development and in our melanoma models. Select chemical compounds from our screens will be tested in the context of targeting melanoma cell populations, and developed in pre-clinical models for drug-development.

Publications

10 25 50
 
Title CFC-zebrafish 
Description We have developed an assay to test the activity of cardio-facio-cutaneous alleles, and to test the effects of specific clinically active drugs on restoring their "normal" activity 
Type Of Material Model of mechanisms or symptoms - mammalian in vivo 
Year Produced 2009 
Provided To Others? Yes  
Impact Publication -- Kinase-activating and kinase-impaired cardio-facio-cutaneous syndrome alleles have activity during zebrafish development and are sensitive to small molecule inhibitors. Anastasaki C, Estep AL, Marais R, Rauen KA, Patton EE. Hum Mol Genet. 2009 Jul 15;18(14):2543-54. Epub 2009 Apr 17. PMID: 19376813 [PubMed - indexed for MEDLINE] Anastasaki C, Rauen KA, Patton EE. Continual low-level MEK inhibition ameliorates cardio-facio-cutaneous phenotypes in zebrafish. Dis Model Mech. 2012 Jul;5(4):546-52. 
URL http://europepmc.org/abstract/MED/19376813
 
Title CRISPR-Cas9 zebrafish 
Description Developing gene editing techniques in zebrafish 
Type Of Material Model of mechanisms or symptoms - non-mammalian in vivo 
Year Produced 2019 
Provided To Others? No  
Impact It helps us look at genetic mutations in zebrafish 
 
Title PRL3 mutant 
Description We have developed an important mutant line for our research in a gene called PRL3 in zebrafish 
Type Of Material Model of mechanisms or symptoms - non-mammalian in vivo 
Provided To Others? No  
Impact This will be critical to understand the role of PRL3 in an animal system, especially in melanocyte regeneration. It is currently unpublished. 
 
Title Small molecule 
Description a small molecule that causes a specific developmental phenotype (kills developing and differentiated melanocytes) 
Type Of Material Technology assay or reagent 
Provided To Others? No  
Impact n/a considering for patent 
 
Description CP/TC 
Organisation Medical Research Council (MRC)
Department MRC Human Genetics Unit
Country United Kingdom 
Sector Public 
PI Contribution We are using single cell analysis to study the melanocyte stem cell lineage
Collaborator Contribution Concepts and helping with analysis
Impact An eLIFE paper
Start Year 2017
 
Description CS/ALDH 
Organisation University of Manchester
Country United Kingdom 
Sector Academic/University 
PI Contribution New collaboration with team in UK to examine function of ALDH in cells
Collaborator Contribution We are sharing chemical compounds and sturctures
Impact It is too early, but we are starting by testing some of their pre-drug leads in our models.
Start Year 2018
 
Description MS/NFN 
Organisation Spanish National Cancer Research Center
Country Spain 
Sector Academic/University 
PI Contribution We are part of a team science award for women in science. We are studying metastasis and tumour cell dormancy.
Collaborator Contribution We submitted a joint proposal that was successfully funded. We are currently sharing resources and ideas about tumour cell dormancy in melanoma.
Impact £1million grant for women in science, with 5 partners - 3 in the USA, 1 Spain and 1 UK In addition to our science, we are trying bring awareness to women in science and to help shape the culture surrounding these issues.
Start Year 2016
 
Description MT Drop out screen 
Organisation University of Montreal
Country Canada 
Sector Academic/University 
PI Contribution This is a new collaboration to do a gene-drug screen (drop out screen) to determine drug mechanism of action.
Collaborator Contribution This is a new collaboration - we will be sending our MRC postdoc to Montreal to learn how to do the technique, and hopefully bring some of the technology back to the UK.
Impact This is a new collaboration and we do not have outputs at this stage.
Start Year 2016
 
Description MT/Small molecule screening 
Organisation Wellcome Trust
Department Wellcome Trust Centre for Cell Biology
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Mike Tyers: Small molecules of interest that are identified in zebrafish are screened in yeast to identify target pathways.
Collaborator Contribution Publications (please see list attached)
Impact Three manuscripts (one in review; two published, below) Differentiated melanocyte cell division occurs in vivo and is promoted by mutations in Mitf. Taylor KL, Lister JA, Zeng Z, Ishizaki H, Anderson C, Kelsh RN, Jackson IJ, Patton EE. Development. 2011 Aug;138(16):3579-89. Epub 2011 Jul 19. Combined zebrafish-yeast chemical-genetic screens reveal gene-copper-nutrition interactions that modulate melanocyte pigmentation. Ishizaki H, Spitzer M, Wildenhain J, Anastasaki C, Zeng Z, Dolma S, Shaw M, Madsen E, Gitlin J, Marais R, Tyers M, Patton EE. Dis Model Mech. 2010 Sep-Oct;3(9-10):639-51. Epub 2010 Aug 16.
Start Year 2006
 
Description VK Mosaic syndromes 
Organisation London College (UCK)
Country United Kingdom 
Sector Academic/University 
PI Contribution We developed a zebrafish model to validate a new disease gene found in children with giant congenital nevi.
Collaborator Contribution They identified new disease genes in children that cause giant congenital nevi.
Impact Mosaic Activating Mutations in GNA11 and GNAQ Are Associated with Phakomatosis Pigmentovascularis and Extensive Dermal Melanocytosis. Thomas AC, Zeng Z, Rivière JB, O'Shaughnessy R, Al-Olabi L, St-Onge J, Atherton DJ, Aubert H, Bagazgoitia L, Barbarot S, Bourrat E, Chiaverini C, Chong WK, Duffourd Y, Glover M, Groesser L, Hadj-Rabia S, Hamm H, Happle R, Mushtaq I, Lacour JP, Waelchli R, Wobser M, Vabres P, Patton EE, Kinsler VA.
Start Year 2014
 
Description Conference Organizer 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Conference Organising Committee Strategic Conference for Zebrafish Investigators, Asilomar, California. 01-2019
Conference Organizing committee Society for Melanoma Research Conference, Manchester 10-2018
Conference Organizing committee NCRI Cancer Conference, Glasgow 10-2018
Year(s) Of Engagement Activity 2018,2019
 
Description Invited Speaker Royal Society of Biology: 23rd Annual Meeting for Biology Teachers, Edinburgh Scottish High School Teachers 05-2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Presentation to school teachers about my science, very good response (informally)
Year(s) Of Engagement Activity 2018
 
Description 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 Invited Speaker The European Melanoma Workshop, Sestri Levente, Italy 06-2017
Invited Speaker The Wistar Institute, Philadelphia, USA 06-2017
Invited Speaker Human Giant Nevus session, International Pigment Cell Conference, Colorado, USA 08-2017
Invited Speaker The Boston Zebrafish Workshop, Harvard Medical School, USA 10-2017
Invited Speaker International Melanoma Working Group, Edinburgh 03-2018
Invited Speaker Non-Mammalian Models Session, International Pigment Cell Conference, Colorado, USA 08-2017
Invited Speaker University of Toronto, Careers for PhD and postdoc conference 06-2018
Invited Speaker University College London Autumn 2018
Invited Speaker Blizard Institute, London 07-2018
Invited Speaker European Melanoma Workshop, Israel 04-2018
Invited Speaker Montagna Symposium of the Biology of Skin and Pan-American Society for Pigment Cell Research, Gleneden Beach, Oregon, USA 10-2018

Selected Speaker 11th Zebrafish Disease Models Conference, Leiden, July 2018 07-2018
Selected Speaker Society for Melanoma Research, Brisbane, Australia November 2017 11-2017
Year(s) Of Engagement Activity 2017,2018,2019
 
Description Open day IGMM talk 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Open Day lecture on our science (melanoma genetics)
Year(s) Of Engagement Activity 2018
 
Description Workshop organizer 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Organizer and Leader Drug Discovery Research Interest Group, 10th Zebrafish Disease Models Conference, San Diego, USA 07-2017
Organizer and Leader Women in Science Session, 10th Zebrafish Disease Models Conference, San Diego, USA 07-2017
Organizer and Leader Mentoring workshop Women in Science Workshop 11th Zebrafish Disease Models Conference, Leiden 07-2018
Year(s) Of Engagement Activity 2018
 
Description invited session chair 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited Session Chair Melanoma Session, NCRI Cancer Conference, Glasgow 10-2018
Invited Session Chair 10th Zebrafish Disease Models Conference, San Diego, USA 07-2017
Invited Session Chair Non-Mammalian Models Session, International Pigment Cell Conference, Colorado, USA 08-2017
Year(s) Of Engagement Activity 2018,2019