SPECIAL: Dissecting the melanoma ecosystem one cell at the time during immunotherapy

The aim of this study was to identify potential biomarkers of response to immunotherapy (anti-PD1-based) as well as gain understanding of the biological mechanism of therapy resistance (either intrinsic or acquired) in melanoma patients. Single cell RNA sequencing was performed from pre- and on-treatment (2-3 weeks after immunotherapy) metastatic biopsies from stage III and IV melanoma patients.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

2 Datasets 4 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001009291	Tumour biopsies were collected from twenty-three patients (46 samples) (of which 20 were matched) with locally advanced or metastatic melanoma (stage IIIB – stage IV). Library construction was done either with the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (n = 16; 10x genomics, Cat#1000092) or the Chromium Single Cell A Chip Kit and 5’ Library & Gel Bead Kit (10x genomics, Cat#1000014). All libraries were sequenced on Illumina NextSeq, HiSeq4000 or NovaSeq6000 until sufficient saturation was reached (60% on average). The reference genome used in this study was GRCh38.	unspecified	46
EGAD00001010921	This dataset contains the Visium Spatial Transcriptomics data from treatment naive melanoma lymph node metastatic samples.	unspecified	6

Publications	Citations
CD4<sup>+</sup> T cell-induced inflammatory cell death controls immune-evasive tumours. Kruse B, Buzzai AC, Shridhar N, Braun AD, Gellert S, Knauth K, Pozniak J, Peters J, Dittmann P, Mengoni M, van der Sluis TC, Höhn S, Antoranz A, Krone A, Fu Y, Yu D, Essand M, Geffers R, Mougiakakos D, Kahlfuß S, Kashkar H, Gaffal E, Bosisio FM, Bechter O, Rambow F, Marine JC, Kastenmüller W, Müller AJ, Tüting T. Nature 618: 2023 1033-1040	64
The CD58-CD2 axis is co-regulated with PD-L1 via CMTM6 and shapes anti-tumor immunity. Ho P, Melms JC, Rogava M, Frangieh CJ, Poźniak J, Shah SB, Walsh Z, Kyrysyuk O, Amin AD, Caprio L, Fullerton BT, Soni RK, Ager CR, Biermann J, Wang Y, Khosravi-Maharlooei M, Zanetti G, Mu M, Fatima H, Moore EK, Vasan N, Bakhoum SF, Reiner SL, Bernatchez C, Sykes M, Mace EM, Wucherpfennig KW, Schadendorf D, Bechter O, Shah P, Schwartz GK, Marine JC, Izar B. Cancer Cell 41: 2023 1207-1221.e12	19
STmut: a framework for visualizing somatic alterations in spatial transcriptomics data of cancer. Chen L, Chang D, Tandukar B, Deivendran D, Pozniak J, Cruz-Pacheco N, Cho RJ, Cheng J, Yeh I, Marine C, Bastian BC, Ji AL, Shain AH. Genome Biol 24: 2023 273	3
ALDH1A3-acetaldehyde metabolism potentiates transcriptional heterogeneity in melanoma. Lu Y, Travnickova J, Badonyi M, Rambow F, Coates A, Khan Z, Marques J, Murphy LC, Garcia-Martinez P, Marais R, Louphrasitthiphol P, Chan AHY, Schofield CJ, von Kriegsheim A, Marsh JA, Pavet V, Sansom OJ, Illingworth RS, Patton EE. Cell Rep 43: 2024 114406	2