Epigenomics and Single-Cell Sequencing Define a Developmental Hierarchy in Langerhans Cell Histiocytosis

Abstract

Langerhans cell histiocytosis (LCH) is a rare neoplasm predominantly affecting children. It occupies a hybrid position between cancers and inflammatory diseases, which makes it 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 analyzed biopsies using IHC, and we defined an epigenomic and generegulatory basis of the different LCH-cell subsets by chromatin-accessibility profiling. In summary, our single-cell analysis of LCH uncovered an unexpected degree of cellular, transcriptomic, and epigenomic heterogeneity among LCH cells, indicative of complex developmental hierarchies in LCH lesions. SIGNIFICANCE: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 personalizing therapy.

Knowledge-primed neural networks enable biologically interpretable deep learning on single-cell sequencing data

“…Second, we explored the utility of the GEN KPNN for analyzing disease-associated cell states in Langerhans cell histiocytosis (LCH), a rare developmental disorder that combines relevant aspects of a cancer and of an autoinflammatory disease [ 78 ]. Based on a recently published single-cell RNA-seq analysis of LCH [ 51 ], we trained the GEN KPNN to distinguish between progenitor-like and mature LCH cell populations described previously. We obtained separate KPNN models for (i) bone-derived LCH cells from patients with relatively benign single-system disease and (ii) skin-derived LCH cells from patients with aggressive multi-system disease.…”

“…The LCH dataset [ 51 ] was downloaded from GEO (GSE133704). Single-cell annotations were downloaded from http://www.medical-epigenomics.org/papers/LCH_hierarchy/data/lch_10x_meta.csv.gz as of 1 October 2019.…”

“…We validate KPNNs for interpretable deep learning using simulated data with known ground truth, we compare them to other machine learning algorithms including the ex post biological interpretation of feature weights, and we demonstrate the practical use of KPNNs in five biological applications with publicly available single-cell RNA-seq datasets: T cell receptor signaling [ 49 ], immune cells in the Human Cell Atlas [ 50 ], clinical subtypes of Langerhans cell histiocytosis [ 51 ], cancer cell development in acute myeloid leukemia [ 52 ], and cancer cell subtypes in glioblastoma [ 53 ]. Overall, our results establish KPNNs as a new form of interpretable deep learning that may be broadly useful for biological discovery based on large-scale datasets.…”

“…The HCA dataset [ 50 ] was downloaded from the “Census of Immune Cells” that is part of the Human Cell Atlas ( https://preview.data.humancellatlas.org/ ), as of 31 July 2018. The LCH dataset [ 51 ] was downloaded from GEO (GSE133704). The AML dataset [ 52 ] was downloaded from GEO (GSE116256).…”

Apparent Lack of BRAFV600E Derived HLA Class I Presented Neoantigens Hampers Neoplastic Cell Targeting by CD8+ T Cells in Langerhans Cell Histiocytosis

“…Previous studies have already demonstrated that LCH-cells express the co-stimulatory receptors CD40 (10)(11)(12), CD80 (3, [11][12][13], ICOS ligand (ICOSL) (14) and, although variably, CD86 (3, 11,12) in situ. Moreover, transcriptome analyses revealed that LCH-cells express similar levels of CD40, CD80, and CD86 messenger RNA when compared to normal epidermal CD207 + Langerhans cells (15,16), and that they confer high expression of genes relevant for antigen presentation (including CD1E) and genes encoding members of the HLA (class II) complex (17). Thus, LCH-cells do not appear to have an intrinsic defect in their capacity to elicit a T cell immune response (12).…”