Decoding a gene expression program that accompanies the phenotype of sporadic and basal cell nevus syndrome‐associated odontogenic keratocyst

Abstract

Background: Odontogenic keratocyst is characterized by local aggressive behavior and a high recurrence rate, as well as its potential to develop in association with the basal cell nevus syndrome. The aim of this study was to decode the gene expression program accompanying odontogenic keratocyst phenotype.Methods: 150-bp paired-end RNA-sequencing was applied on six sporadic and six basal cell nevus syndrome-associated whole-tissue odontogenic keratocyst samples in comparison to six dental follicles, coupled with bioinformatics and complemented by immunohistochemistry.Results: 2654 and 2427 differentially expressed genes were captured to characterize the transcriptome of sporadic and basal cell nevus syndrome-associated odontogenic keratocysts, respectively. Gene ontologies related to "epidermis/skin development" and "keratinocyte/epidermal cell differentiation" were enriched among the upregulated genes (KRT10, NCCRP1, TP63, GRHL3, SOX21), while "extracellular matrix organization" (ITGA5, LOXL2) and "odontogenesis" (MSX1, LHX8) gene ontologies were overrepresented among the downregulated genes in odontogenic keratocyst. Interestingly, upregulation of various embryonic stem cells markers (EPHA1, SCNN1A) and genes committed in cellular reprogramming (SOX2, KLF4, OVOL1, IRF6, TACSTD2, CDH1) was found in odontogenic keratocyst. These findings were highly shared between sporadic and basal cell nevus syndrome-associated odontogenic keratocysts. Immunohistochemistry verified SOX2, KLF4, OVOL1, IRF6, TACSTD2/TROP2, CDH1/E-cadherin, and p63 expression predominantly in the odontogenic keratocyst suprabasal epithelial layers. Conclusion:The odontogenic keratocyst transcriptomic profile is characterized by a prominent epidermal and dental epithelial fate, a repressed dental mesenchyme fate combined with deregulated extracellular matrix organization, and enhanced stemness gene signatures. Thus, we propose a developed epidermis-like phenotype in the odontogenic keratocyst suprabasal epithelial cells, established in parallel to a Marios Agelopoulos and Konstantinos I. Tosios have contributed equally to this work.

The Stem Cell Expression Profile of Odontogenic Tumors and Cysts: A Systematic Review and Meta-Analysis

“…The vast majority of studies (24 out of 29) reported experiments on FFPE tissue samples ( Table S3 ), two studies included both fresh-frozen and FFPE samples [ 6 , 39 ], one study reviewed only fresh-frozen samples [ 42 ], and in vitro analysis of human odontogenic lesion-derived cells was performed in two studies [ 43 , 47 ]. A minority of studies (10 out of 29) documented the microscopic diagnosis of included odontogenic entities, either by providing a detailed microscopic description [ 6 , 11 , 12 , 29 , 35 ] or by mentioning an appropriate reference [ 13 , 32 , 36 , 37 , 39 ], e.g., the WHO 2017 [ 1 ] or 2005 [ 51 ] editions for odontogenic tumors and cysts.…”

“…All but one of the retrieved studies reported the expression of stem cell markers in odontogenic tumors and cysts based on immunohistochemical or immunofluorescence analyses ( Table 1 ). One study used flow cytometry to compare the expression of stem cell markers in cells derived from odontogenic cysts and dental pulp stem cells [ 43 ], two studies confirmed the expression of stem cell markers via reverse transcription-PCR (RT-PCR) and immunohistochemistry [ 13 , 47 ], and two studies employed advanced molecular biology methods, i.e., microarrays on fresh-frozen samples [ 42 ] and RNA-seq on FFPE tissues [ 37 ], and validated their results via RT-PCR and/or immunohistochemistry/immunofluorescence. Tables S4 and S5 present detailed information regarding the immunohistochemistry/immunofluorescence experiments and the other techniques, respectively.…”

“…OKC expressed ALDH1 [ 34 ], CD166 [ 41 ], CD44 [ 31 , 46 , 48 ], c-Myc [ 45 ], and KLF4 [ 37 ] in the cystic lining, predominantly in the basal and/or intermediate layers, and CD34 and NANOG in cells of the cystic capsule [ 10 ]. OCT4 was negative [ 28 ] or focally expressed in the superficial epithelial layer [ 32 ] or in a few stromal cells of OKC [ 10 ], whereas one study employing a polyclonal anti-OCT4 antibody reported 100% positivity in OKC [ 31 ].…”

Digital pathology-based artificial intelligence models for differential diagnosis and prognosis of sporadic odontogenic keratocysts

“…5 , 6 However, there was no significant difference between sporadic OKC and GS among mutations in the PTCH1 , proliferating markers such as proliferating cell nuclear antigen (PCNA), Ki-67, and p53 expression, as well as broad-spectrum transcriptomic features. 33 – 36 And so far, there is no clear method of identification when there was no clinical manifestations except OKC at the early stage of GS. OOC is a relatively uncommon odontogenic developmental cyst, and was previously classified as belonging to OKC.…”

“…The relationship between OKC and GS is strengthened by numerous correlations, such as similar PTCH1 mutations and gene expression profiles, resulting in the confusion tendency. 34 , 36 , 47

Fig. 6 The workflow of artificial intelligence models development.

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