Summary

Langerhans cell histiocytosis (LCH) is a rare neoplasm predominantly affecting children. It occupies a hybrid position between cancers and inflammatory diseases, and it provides an attractive model for studying cancer development. To explore the molecular mechanisms underlying the pathophysiology of LCH and its characteristic clinical heterogeneity, we investigated the transcriptomic and epigenomic diversity in primary LCH lesions. Using single-cell RNA sequencing, we identified multiple recurrent types of LCH cells within these biopsies, including putative LCH progenitor cells and several subsets of differentiated LCH cells. We confirmed the presence of proliferative LCH cells in all analysed biopsies using immunohistochemistry, and we defined an epigenomic and gene regulatory basis of the different LCH cell subsets by chromatin accessibility profiling. In summary, our single-cell analysis of LCH un-covered an unexpected degree of cellular, transcriptomic, and epigenomic heterogeneity among LCH cells, indicative of complex developmental hierarchies in LCH lesions.

This study sketches a molecular portrait of LCH lesions by combining single-cell transcriptomics with epigenome profiling. We uncovered extensive cellular heterogeneity, explained in part by an intrinsic developmental hierarchy of LCH cells. Our findings provide new insights and hypotheses for advancing LCH research and a starting point for personalising therapy.

On this website we present additional supplementary materials accompanying the publication.

Data Tables

Data tables of processed single-cell RNA-seq and bulk ATAC-seq data for easy re-use.

Name Description and link
Single-cell RNA-seq
ATAC-seq

Marker Genes

Lists marker genes based on differential analysis between groups of cells in the single-cell RNA-seq data.

Name Description and link
LCH vs. non-LCH cells
LCH cell subsets

Genome Browser Tracks

Genome browser tracks for visualisation of the genomic alignments of ATAC-seq data from LCH cell subsets.

Name Description and link
Genome browser
Tutorials

Gene Regulatory Networks

Interactive visualisations of the gene regulatory networks underlying different LCH cell subsets.

Name Description and link
Network visualisations
Description Gene regulatory networks were inferred for three LCH cell subsets (LCH-S1, LCH-S12, LCH-S11), based on single-cell transcriptome and ATAC-seq data, and the key regulators identified by enrichment analysis. Nodes in the network correspond to the enriched transcription factors as well as their putative target genes (based on sequence proximity and chromatin 3D structure). Node size is proportional to both gene expression level and node out-degree (i.e., number of outgoing connections from the transcription factor) in the respective LCH subset. Edge colours indicate the module of the corresponding peak, and edge visibility is proportional to chromatin accessibility. Networks were implemented in R using igraph and converted into an interactive web version using visNetwork.

Data and Links

Links to raw data archives and related resources.

Name Description and link
GEO Processed single-cell RNA-seq and ATAC-seq data are openly available via Gene Expression Omnibus.
EGA Raw sequencing reads are available as controlled access via the European Genome-Phenome Archive.
Code Computer code used for the analysis of single-cell RNA-seq and ATAC-seq data in the paper are available via GitHub.
  • Via epigen organization: Code will be available shortly.
  • Via cancerbits organization: Code will be available shortly.
Research Groups

Citation

If you use this resource in your research, please cite:

Halbritter F*, Farlik M*, Schwentner R, Jug G, Fortelny N, Schnoeller T, Pisa H, Schuster LC, Reinprecht A, Czech T, Gojo J, Holter W, Minkov M, Bauer W, Simonitsch-Klupp I, Bock C#, Hutter C#. Epigenomics and Single-cell Sequencing Define a Developmental Hierarchy in Langerhans Cell Histiocytosis. Cancer Discovery (2019), doi: 10.1158/2159-8290.CD-19-0138