Identifying the drivers and vulnerabilities of acral lentiginous melanoma through the study of PDX models from Latin American patients

Lead Research Organisation: The Wellcome Trust Sanger Institute
Department Name: Cancer Genetics and Genomics

Abstract

Melanoma is the common cancer that has increased its worldwide incidence the most in the last decades. Survival rates for cutaneous melanoma have increased dramatically in the last decades due in part to the development of drugs that specifically target disease subtypes and agents that stimulate the immune response against tumours. These breakthroughs have been possible thanks to the study of mutations in melanoma genomes and the use of pre-clinical models that faithfully resemble human tumours. However, this success has not been realised yet for patients with acral lentiginous melanoma (ALM), which constitutes the most common subtype of this disease in some Latin American countries. ALM has remained poorly studied to date due to its rarity in European-descent populations, and its causes and genetic and environmental drivers remain mostly unknown; thus survival rates and response to therapy are still poor in these patients. The long-term aim of this project is to develop novel therapies for ALM patients. In this context, we have two specific aims:

1. Generate and characterise a comprehensive collection of faithful ALM pre-clinical models in the form of patient-derived xenografts (PDX). PDX are human tumours implanted into immunodeficient mice. This collection will include tumours from a variety of body locations and will come from Brazil and Mexico to account for the large variability observed within the disease. We will sequence each PDX's protein-coding genome, and determine gene and protein expression levels to understand what biological pathways are altered in ALM tumours. We will also analyse genetic ancestry, which has been hypothesised to increase risk to develop some tumour types, such as breast cancer. An enrichment of certain genome variants in cases when compared to their population of origin might indicate regions of the genome that modify risk to develop ALM.

2. Use the PDX collection in order to explore new targets for therapy and biomarkers of ALM. The molecular characterisation of ALMs will allow us to identify potential drug targets, biomarkers useful to determine responders to a specific treatment, and potential resistance mechanisms. We plan to explore this at first by focusing on CDK4 pathway dependencies via direct treatment of PDX-carrying mice with CDK4 inhibitors followed by assessment of tumour growth, as well as the study of gene and protein profiles of responder and non-responders.

We expect that the results from this project will identify genetic risk factors and suggest therapeutic alternatives for ALM patients, and that it will establish a valuable resource, in the form of a PDX collection, that can be shared with the research community.

Technical Summary

Although cutaneous melanoma survival rates have increased dramatically over the last decades, this success has not been realised for acral lentiginous melanoma (ALM), the most common form of the disease in some Latin American countries. This subtype of melanoma has been poorly studied due to its rarity in European-descent populations, and as a result there is a lack of pre-clinical models of the disease and a relatively low number of available ALM genomes. As a result, survival rates and response to therapy are still poor in these patients.
Our long-term objective is to develop novel therapies for ALM patients. We have two Specific Aims:
1. To establish and characterise a genetically diverse patient-derived xenograft (PDX) collection from ALMs from Brazil and Mexico. We expect to establish 50 PDX models during the first year, which we will exome-sequence to determine genomic drivers and copy number alterations. We will also perform RNA-seq of all tumours and determine protein expression levels via reverse-phase protein arrays (RPPA). To search for ALM-predisposing haplotypes, we will genotype all patients with arrays specialised for admixed populations.
2. To use the PDX collection to identify and explore potential therapeutically targetable alterations and disease biomarkers. We will characterise gain of function alterations and validate their expression in ALM to identify potential drug targets. We will focus on CCND1/CDK4 dependencies. PDXs will be analysed for sensitivity to CDK4 inhibitors in vivo, and RNA and protein expression profiles of responders and non-responders will be compared.
By bringing together a multi-disciplinary group with synergistic expertise, this project has the potential to identify risk factors and biomarkers to rationalise treatment for ALM patients, and will establish a valuable resource that can be shared with the research community.

Planned Impact

This project has the potential to identify targeted therapies for a subtype of melanoma that has been poorly studied due to its rarity in European-descent populations, but that is the most common form of the disease in many Latin American, African and Asian countries. As such, it can benefit individuals and institutions at different levels:

1. Scientists and clinicians around the world investigating treatment for ALM patients. ALM is the most common subtype of melanoma in many developing countries. By creating an ALM PDX collection resource and making it publicly available, researchers in Latin America and in other countries can study this genomic data and contribute to identifying possible therapeutic options for these patients.

2. Pharmaceutical companies. Companies interested in manufacturing targeted drugs for this subtype of cancer will obtain candidates to work on. Additionally, the biological alterations found in ALM may inform about novel biological pathways dysregulated in cancer.

3. Clinicians treating ALM patients. Clinicians do not have many options when treating advanced ALM, the best alternative currently is immunotherapy but it is seldom used in developing countries due to its cost. If suitable targets are identified, this can potentially translate into cheaper targeted options to treat ALM patients.

4. ALM patients. Potentially, by identifying suitable targets, treatment options will increase and contribute to improve survival of ALM patients.

This research not only has the potential to improve the quality of life of a large number of patients in developing countries, especially Latin America, but also will help close the diversity gap in cancer genomic studies, where less than ~3% of samples in repositories are of Hispanic origin (Ethnicity data from the TCGA-SKCM project). Additionally, researchers working on this project, who will be based in Latin America, will become proficient in a set of skills ranging from cell biology techniques and use of animal models, to bioinformatic techniques for analysis of cancer genomes.

This project is ODA-compliant (Brazil and Mexico, co-applicants in this proposal, are ODA countries). Benefits to these countries are many: This will constitute a large research project that will make use of modern analysis techniques, which will be led by the UK and these ODA countries, which will contribute to build homegrown expertise and to the formation of human resources. It will also stimulate organisation and cooperation across sectors (scientific, health, and potentially pharmaceutical), which often do not communicate efficiently in these countries. Also, it will constitute a novel angle to study cancer development considering genetic ancestry (a majority of the Brazilian and Mexican populations are genetically admixed).

Publications

10 25 50
 
Description "Genomics of acral lentiginous melanoma in Mexico" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Talk to a group of domain experts.
Year(s) Of Engagement Activity 2019
 
Description "Genomics of acral lentiginous melanoma in Mexico" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Major international think tank group
Year(s) Of Engagement Activity 2019
 
Description Genetics and genomics of acral lentiginous melanoma 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Latin American Contributions to Global Oncology Research, Latin American School of Oncology, webinar
Year(s) Of Engagement Activity 2019
 
Description Genomic studies of tumour samples: What can we learn about the origins of cancer? 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Science talk at a major conference
Year(s) Of Engagement Activity 2019
 
Description Identifying the drivers and vulnerabilities of Acral Lentiginous Melanoma through the study of PDX models from Latina American patients 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk at the Genomel virtual meeting in 2020 - mainly clinical people and scientists.
Year(s) Of Engagement Activity 2020