A single-cell atlas of Schwannoma across genetic backgrounds and anatomic locations

Abstract

Background: Schwannomas are nerve sheath tumors arising at cranial and peripheral nerves, either sporadically or in patients with a schwannomatosis-predisposition syndrome. There is limited understanding of the transcriptional heterogeneity of schwannomas across genetic backgrounds and anatomic locations.

Methods: Here, we prospectively profile by single-cell full-length transcriptomics tumors from 22 patients with NF2-related schwannomatosis, non-NF2-related schwannomatosis, and sporadic schwannomas, resected from cranial and peripheral nerves. We profiled 11,373 cells (after QC), including neoplastic cells, fibroblasts, T cells, endothelial cells, myeloid cells, and pericytes.

Results: We characterize the intra-tumoral genetic and transcriptional heterogeneity of schwannoma, identifying six distinct transcriptional metaprograms, with gene signatures related to stress, myelin production, antigen presentation, interferon signaling, glycolysis, and extracellular matrix. We demonstrate the robustness of our findings with analysis of an independent cohort.

Conclusions: Overall, our atlas describes the spectrum of gene expression across schwannoma entities at the single-cell level and will serve as an important resource for the community.

Keywords: NF2; Neurofibromatosis type 2; Schwannoma; Schwannomatosis.

Fig. 1

Comprehensive atlas of schwannoma. a Scheme depicting the anatomical location and etiology of the analyzed samples. b UMAP annotating cells by the sample of origin and cell type. See Table S1 for the upregulated genes that defined the annotations. c Percentage of cells per cell type per sample. Values were clustered as described in text (using percentages for the upper 2 heatmaps and binary 0 or 1 for the etiology and location)

Fig. 2

Chromosome 22 deletion in neoplastic and TME cells. a CNA plot for all neoplastic (SCHW) cells, using fibroblasts, pericytes, and endothelial cells as reference cells. Neoplastic cells were sorted within each sample by mean CNA on chromosome 22. Reference cells were sorted similarly. Interestingly, 22 deletion was seen in some fibroblasts and pericytes. See Additional file 3: Fig. S1 for computational validation that the fibroblasts and pericytes harboring chromosome 22 deletion are unlikely to represent doublets. b UMAP (same coordinates as in Fig. 1) colored by mean CNA on chromosome 22. Inferred deletion is observed also in the fibroblast and pericyte clusters

Fig. 3

Inter-tumor transcriptional variability is mainly driven by factors other than etiology or location. a Top 7000 genes were averaged across cancer cells in each sample and then clustered. Black broken rectangles demarcate 3 clusters. Cluster 2 is mostly composed of NF2 mutant tumors. b Volcano plots comparing differentially expressed genes between clusters. See Table S2 for the full list of differentially expressed genes. P-values were calculated using a two-sided t-test and corrected for multiple comparisons using FDR. Volcano plots that were similarly obtained by comparing samples in different locations or with different etiologies did now show any significantly differentiated genes after correction for multiple comparisons

Fig. 4

Schwannoma patterns of intra-tumor heterogeneity and decoupling of Interferon and MHC-II signaling. a Gene expression metaprograms (MPs) were derived using NMF with ranks 2–10 and subsequent extraction of robust programs and clustering, as previously described. Six heterogeneity MPs were recovered (highlighted). b UMAP (same coordinates as in Fig. 1) colored by expression of the myelin marker PRX provides further evidence that myelination varies across SCHW cells. c Decoupling of MHC-I from Interferon signaling in SCHW. Cells were scored to selected MHC-II genes (shown to the upper left) in samples that participated in the major published MHC-II MP in the pan-cancer study and in the SCHW samples. Gene expression was then compared per sample between cells that scored > 1 and cells that scored < 0. MHC-I and MHC-II showed weaker coupling in SCHW samples compared to other cancer types. Interestingly, decoupling of MHC-I (and also complement) and interferon was especially apparent in vestibular samples