Periodic Reporting for period 1 - cellsIMPACT (Understanding resistance to immune checkpoint inhibitors by mapping the tumor-host ecosystem at single-cell resolution)
Période du rapport: 2020-05-01 au 2022-04-30
The trend for tanned skin (in western countries) goes hand in hand with a high risk of getting melanoma: the most dangerous skin cancer. The recent development of novel classes of immunotherapies such as immune checkpoint blockade (ICB) for oncology has brought up hopes for the treatment of advanced-stage melanoma patients. Targeting immune checkpoints has reached remarkable clinical benefit in multiple cancers (especially in melanoma), enabling life extension and even complete remission in some cases. However, up to the present time, one of the major limitations of ICB is that they cause durable clinical responses only in a relatively small number of patients and the reason behind this is still poorly understood. The central goal of this project was to discover novel biomarkers predicting response to ICB as well as to understand the biological basis of mechanism of the therapy resistance (either intrinsic or acquired) in melanoma patients.
Drug-naive patients with advanced melanoma were prospectively recruited to undergo serial biopsy before initiation of therapy and right before administration of the second Immune Checkpoint Blockade (ICB) cycle. Single-cell RNA sequencing (scRNA-seq) was performed using the Chromium 10X platform. In addition, embedded material was kept for multiplex immune histochemistry and where possible, spatial transcriptomics. Baseline demographic, clinical, histopathological and genetic information was collected and patients were stratified as responders (complete remission, partial remission) and non-responders (stable disease, progressive disease) according to RECIST1.1.
Applying various bioinformatic and statistical approaches to scRNA-seq data we established a comprehensive view of the cellular architecture of the melanoma ecosystem, and defined 6 evolutionarily conserved melanoma transcriptional metaprograms (Melanocytic, Mesenchymal-like, Neural Crest-like, Antigen Presentation, Stress (hypoxia response) and Stress (p53 response). Our results suggest that these metaprograms are not solely driven by genetic makeup. Instead, we postulate that they are partly driven by specific cell-cell interactions with the tumour microenvironment. This was consistent with a non-random geographical distribution of the melanoma cell states as revealed by spatial transcriptomic analyses. Importantly, two of the metaprograms were associated with divergent clinical responses to ICB. While the Antigen Presentation cell population was more abundant in tumours from patients who exhibited a clinical response to ICB, Mesenchymal-like cells were significantly enriched in early on-treatment biopsies from non-responders, and their presence significantly predicted lack of response. Critically, we identified TCF4 (E2-2) as a master regulator of the Mesenchymal-like program. Targeting TCF4 expression in Mesenchymal-like cells either genetically or pharmacologically using a bromodomain inhibitor increased immunogenicity and sensitivity to targeted therapy.
Applying various bioinformatic and statistical approaches to scRNA-seq data we established a comprehensive view of the cellular architecture of the melanoma ecosystem, and defined 6 evolutionarily conserved melanoma transcriptional metaprograms (Melanocytic, Mesenchymal-like, Neural Crest-like, Antigen Presentation, Stress (hypoxia response) and Stress (p53 response). Our results suggest that these metaprograms are not solely driven by genetic makeup. Instead, we postulate that they are partly driven by specific cell-cell interactions with the tumour microenvironment. This was consistent with a non-random geographical distribution of the melanoma cell states as revealed by spatial transcriptomic analyses. Importantly, two of the metaprograms were associated with divergent clinical responses to ICB. While the Antigen Presentation cell population was more abundant in tumours from patients who exhibited a clinical response to ICB, Mesenchymal-like cells were significantly enriched in early on-treatment biopsies from non-responders, and their presence significantly predicted lack of response. Critically, we identified TCF4 (E2-2) as a master regulator of the Mesenchymal-like program. Targeting TCF4 expression in Mesenchymal-like cells either genetically or pharmacologically using a bromodomain inhibitor increased immunogenicity and sensitivity to targeted therapy.
Analyses of our unique scRNA-seq data from melanoma lesions unravelled previously undescribed melanoma cell states and their molecular identity and further emphasized the critical role of the tumour microenvironment as a driver of intra-tumoural heterogeneity and its association with responses to ICB. Importantly, our results might lead to the new robust biomarkers of the response to the ICB applied in clinical routine or new strategies of ICB treatment in combination with other drugs.
*No website has been developed for the project.
*No website has been developed for the project.