Whole exome sequencing study of adamantinomatous craniopharyngioma reveals the mutational characteristics of recurrent cases

Abstract

Purpose: Adamantinomatous craniopharyngioma (ACP) is a benign but surgically challenging intracranial tumor, and its high postoperative recurrence rate poses a threat to patient prognosis. In this study, whole exome sequencing (WES) was performed to comprehensively understand the genomic alterations in ACP.

Methods: First, the gene mutation profile of ACP was acquired through an overview of the WES data. The somatic single nucleotide variants (SNV) mutational spectrum and signature of ACP were analyzed. Subsequently, somatic mutation data were used to identify the characteristic SNV of recurrent ACP to further explore the mechanism underlying recurrence, and the effect of these mutations on protein expression was verified through immunohistochemical and immunofluorescence analyses.

Results: We obtained the overall mutational landscape of ACP and identified four key mutated genes in recurrent samples: Procollagen-Lysine,2-Oxoglutarate 5-Dioxygenase 3 (PLOD3), Collagen Type XVII Alpha 1 chain (COL17A1), Fibronectin 1 (FN1), and Laminin Subunit Beta 3 (LAMB3). Among these, we verified that COL17A1, FN1, and LAMB3 expression was mainly located in the keratin nodule structures in tumors and was elevated in recurrent cases.

Conclusion: PLOD3, COL17A1, FN1, and LAMB3 were identified as the key mutated genes in recurrent samples. These findings could provide a new perspective for understanding the tumorigenesis and recurrence mechanisms of ACP. A deeper exploration is needed to determine whether these key mutated genes promote ACP recurrence and drive the overproduction of keratin nodules in recurrent cases.

Keywords: Adamantinomatous craniopharyngioma; Mutation; Recurrent tumor; Whole exome sequencing.

Fig. 1

Overview of whole exome sequencing data in ACP and RCC. (A) The total number and proportion of germline and somatic mutations in all samples. (B) Different types of mutations detected in primary (n = 5) and recurrent ACP (n = 5) samples. (C) The distribution of different types of somatic SNVs in genome regions and (D) in coding regions. (E) The distribution of different types of somatic InDels in genome regions and (F) in coding regions. The results are shown as mean ± SD; n.s., no significance; two-tailed Student t-test. ACP, Adamantinomatous craniopharyngioma; RCC, Rathke’s cleft cyst

Fig. 2

Somatic SNV mutational spectrum and signature in ACP and RCC. (A) Bar plot of somatic SNV mutation spectrum of each sample. (B) Heatmap of somatic SNV mutation spectrum of each sample. (C) Different point mutations in all samples were factorized into multiple mutational signatures. (D) Contributions of different mutational signatures in each sample. (E) Cosine similarity heatmap of the mutational signature. SNV, single nucleotide variation; ACP, Adamantinomatous craniopharyngioma; RCC, Rathke’s cleft cyst

Fig. 3

Screening of somatic SNVs characteristic of recurrent ACP. (A) TMB value of RCC (n = 1), primary ACP (n = 5) and recurrent ACP (n = 5). (B) Flow chart of recurrent ACP-characteristic somatic SNV screening. (C) STRING PPI network of genes unique to ACP_R. (D) Top 10 hub nodes of PPI network calculated using 12 algorithms in Cytoscape. The results are shown as mean ± SD; n.s., no significance; two-tailed Student t-test. SNV, single nucleotide variation; ACP, Adamantinomatous craniopharyngioma; RCC, Rathke’s cleft cyst; TMB, tumor mutational burden; PPI, protein-protein interaction

Fig. 4

Mutation frequency, correlated gene, and overall survival analysis of recurrent ACP-characteristic somatic SNVs. (A) The mutation condition of recurrent ACP-characteristic somatic SNVs in each sample; blue refers to the mutation while grey refers to the wild type. (B) Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment of genes correlated with COL17A1. (C) KEGG pathway enrichment of genes correlated to FN1. (D) KEGG pathway enrichment of genes correlated to LAMB3. Only genes involved in enriched pathways were listed. Kaplan- Meier plot of overall survival in pan-cancer (E) or CNS/brain tumor (F) patients with or without PLOD3, COL17A1, FN1, and LAMB3 mutations. ACP, Adamantinomatous craniopharyngioma; RCC, Rathke’s cleft cyst; SNV, single nucleotide variation; KEGG, Kyoto Encyclopedia of Genes and Genomes

Fig. 5

Immunohistochemical and immunofluorescence staining to evaluate the expression level of characteristic mutations in paired primary and recurrent ACP samples. (A) Immunohistochemical staining of COL17A1, (B) immunofluorescence staining of FN1 in paired primary and recurrent ACP samples, two views were captured for each sample. (C) Immunofluorescence staining of LAMB3 in paired primary and recurrent ACP samples. (1), (3), (5) show primary samples while (2), (4), and (6) show the corresponding paired recurrent samples. ACP, Adamantinomatous craniopharyngioma