High-Plex Spatial Profiling of Respiratory Epithelial Adenomatoid Hamartoma and Inflammatory Polyps
Emma Zou, Medical Student, University of NSW, Sydney, Australia
Authors List
Zou, E., University of New South Wales, Sydney, Australia
West, N., Central Facility for Genomics Mucosal Immunology Research Group Griffith University, Brisbane, Australia
Kalish, L., Rhinology and Skull Base Research Group, St Vincent’s Centre for Applied Medical Research, Sydney, Australia
Campbell, R., Rhinology and Skull Base Research Group, St Vincent’s Centre for Applied Medical Research, Sydney, Australia
Earls, P., St Vincent’s Pathology, Sydney, Australia
Harvey, R., Rhinology and Skull Base Research Group, St Vincent’s Centre for Applied Medical Research, Sydney, Australia
Introduction: Respiratory epithelial adenomatoid hamartoma (REAH) is a proliferative lesion of the nasal mucosa with unknown aetiology. Omics approaches have revealed allelic changes, altered protein expression and infiltration of a heterogeneous immune cell population within REAH. Spatial profiling techniques offer new opportunities to examine immune cell distribution and cell-cell communication within REAH that may assist the understanding of its pathogenesis. This study hypothesises that REAH will have distinct cellular patterns and gene expression to that of inflammatory nasal polyps.
Aims: This pilot study aims to employ spatial profiling techniques to better understand the biological processes driving the proliferative aspect of REAH by comparing it to inflammatory polyps.
Methods: Formalin-fixed paraffin embedded slides of sinonasal biopsies from patients with REAH and patients with inflammatory polyps were collected. The slides were analysed on the NanoString GeoMx™ DSP platform using the Cancer Transcriptome Atlas for interrogation of tumour and immune cell compartments. Sequencing was completed on a NovaSeq 2000. Data was normalised by TMM with edgeR (v3.36) and differential expression calculated with limma (v3.50.3). Significance was considered with adjusted and unadjusted p-values. Functional enrichment was calculated using a rank-based gene set enrichment approach (FGSEA) with the FGSEA R package (V1.20).
Results: Eight patients (50.75±15.4yrs,12.5% female, 50% REAH) were assessed. Cell abundance typing revealed distinct immune cell profiles between REAH and Inflammatory polyps. Proteomic analysis of differentially expressed genes in REAH demonstrated upregulation of proteins involved in cell cycle regulation and cell proliferation pathways such as RHOA, ERBB2, H3-5, CTNNB1, GSK3B and CXXC5. Inflammatory polyps demonstrated increased expression of proteins involved in inflammation and immune cell signaling (CCL18, JAK3, S100A8 and BTLA) as well as T cell surface glycoproteins and interleukin receptors.
Conclusions: Spatial profiling to examine REAH demonstrates distinct differences simple inflammatory polyps. Our study found dysregulation of canonical cancer pathways and cell proliferation pathways REAH, while inflammatory polyps had more expression of immune activation and general inflammatory pathways. REAH may represent a proliferative hyperplastic process.
Zou, E., University of New South Wales, Sydney, Australia
West, N., Central Facility for Genomics Mucosal Immunology Research Group Griffith University, Brisbane, Australia
Kalish, L., Rhinology and Skull Base Research Group, St Vincent’s Centre for Applied Medical Research, Sydney, Australia
Campbell, R., Rhinology and Skull Base Research Group, St Vincent’s Centre for Applied Medical Research, Sydney, Australia
Earls, P., St Vincent’s Pathology, Sydney, Australia
Harvey, R., Rhinology and Skull Base Research Group, St Vincent’s Centre for Applied Medical Research, Sydney, Australia
Introduction: Respiratory epithelial adenomatoid hamartoma (REAH) is a proliferative lesion of the nasal mucosa with unknown aetiology. Omics approaches have revealed allelic changes, altered protein expression and infiltration of a heterogeneous immune cell population within REAH. Spatial profiling techniques offer new opportunities to examine immune cell distribution and cell-cell communication within REAH that may assist the understanding of its pathogenesis. This study hypothesises that REAH will have distinct cellular patterns and gene expression to that of inflammatory nasal polyps.
Aims: This pilot study aims to employ spatial profiling techniques to better understand the biological processes driving the proliferative aspect of REAH by comparing it to inflammatory polyps.
Methods: Formalin-fixed paraffin embedded slides of sinonasal biopsies from patients with REAH and patients with inflammatory polyps were collected. The slides were analysed on the NanoString GeoMx™ DSP platform using the Cancer Transcriptome Atlas for interrogation of tumour and immune cell compartments. Sequencing was completed on a NovaSeq 2000. Data was normalised by TMM with edgeR (v3.36) and differential expression calculated with limma (v3.50.3). Significance was considered with adjusted and unadjusted p-values. Functional enrichment was calculated using a rank-based gene set enrichment approach (FGSEA) with the FGSEA R package (V1.20).
Results: Eight patients (50.75±15.4yrs,12.5% female, 50% REAH) were assessed. Cell abundance typing revealed distinct immune cell profiles between REAH and Inflammatory polyps. Proteomic analysis of differentially expressed genes in REAH demonstrated upregulation of proteins involved in cell cycle regulation and cell proliferation pathways such as RHOA, ERBB2, H3-5, CTNNB1, GSK3B and CXXC5. Inflammatory polyps demonstrated increased expression of proteins involved in inflammation and immune cell signaling (CCL18, JAK3, S100A8 and BTLA) as well as T cell surface glycoproteins and interleukin receptors.
Conclusions: Spatial profiling to examine REAH demonstrates distinct differences simple inflammatory polyps. Our study found dysregulation of canonical cancer pathways and cell proliferation pathways REAH, while inflammatory polyps had more expression of immune activation and general inflammatory pathways. REAH may represent a proliferative hyperplastic process.
