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TNF-α released by melanoma liver metastasis activates AKT and NFKβ1 pathways to promote collagen type I secretion by hepatocytes

ABSTRACT: A total of four human melanoma liver metastasis (MLiM) formalin-fixed paraffin-embedded (FFPE) sections were analyzed using Nanostring GeoMx digital spatial profiling (NGDSP). The FFPE tissues were obtained from patients who underwent surgery and were pathological diagnosed with MLiM. Patients who had received any preoperative therapy were excluded. In each region of interest (ROI), two areas of interest (AOI)s were defined by HepPar1+ (hepatocytes); HMB45+ (melanoma cells) staining. A total of 43 AOIs were carefully reviewed for segments with sequencing saturation < 25%, nuclei fewer than 80, negative probe counts <3, or a surface area of <12,000 squared microns. Background correction and scaling were performed using geometric means and normalization was performed using Q3 averages of housekeeping genes. Genes with expression levels at or lower than limit of quantification (LOQ) in at least 5% of segments were filtered out. A total of 1,811 genes passed quality control and were analyzed. A total of seven ROIs with tumor margin (TM) and 13 ROIs with tumor center (TC) were selected, respectively. TM was defined as the areas on the border of malignant tumor cells close to normal tissue based on pathological features. TC was defined as central tumor tissue further inside from TM. In addition, 14 ROIs were selected at ANH. The ANH areas were defined as an area within 1,200 µm from the TM. Furthermore, nine ROIs were selected at the DNH areas. DNH was defined as an area at least 6 mm away from TM. Differential expressed genes (DEGs, Log2 fold-change >1.5, <-1.5, p < 0.05) were calculated on AOIs selected from MLiM comparing TC vs. TM; ANH vs. DNH; and ANH vs. Melanoma cells (TC+TM).

ORGANISM(S): Homo sapiens

PROVIDER: GSE255328 | GEO | 2024/11/13

REPOSITORIES: GEO

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			Action	DRS
		Other
	GSE255328_Annotation_43_AOIs.xlsx	Xlsx
	GSE255328_Processed_data_file_43_AOIs.xlsx	Xlsx

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Project description:BACKGROUND: Competitive endogenous RNA (ceRNA) reveals new mechanisms for interactions between RNAs. However, knowledge of ceRNA regulatory networks in macrophages infected with Talaromyces marneffei (T. marneffei, TM) is still limited. This study aims to explore the expression profiles of lncRNA, miRNA and mRNA, and the changes of ceRNA network related to immunity, inflammation, metabolism in TM-infected macrophage. METHODS: Next-generation sequencing technology (NGS) was used to obtain mRNA, miRNA and lncRNA expression profiles in TM-infected macrophages and normal macrophages. Cuffdiff and DESeq2 software packages are used to identify differentially expressed lncRNA, miRNA and mRNA. The function enrichment analysis was performed by GOseq package in R platform, and the lncRNA–miRNA–mRNA interaction ceRNA network was established in Cytoscape. Functional enrichment analysis was performed on genes contained in the ceRNA network, and genes significantly enriched in functional pathways were selected for qRT-PCR verification. RESULTS: A total of 119 lncRNAs, 28 miRNAs and 208 mRNAs were identified as differentially expressed RNAs in TM-infected macrophages. Among them, 38 lncRNAs, 10 miRNAs and 109 mRNAs are contained in the ceRNA regulatory network. GO analysis and KEGG pathway of mRNA in the ceRNA network showed that macrophages infected with TM activated pathways and functions related to immune response, metabolic response and inflammatory response. Select genes that are significantly abundant in GO analysis and KEGG pathway. The core genes were selected for quantitative real-time PCR (qRT-PCR) to verify consistency with the sequencing results. Eight groups of ceRNAs consisting of 3 mRNAs, 5 lncRNAs, and 2 miRNAs were verified. They are mRNA CSF3, IL24, LIF. lncRNA IL6R-AS1, LINC02009, AC068831.1, AC006252.1, LINC02466. These genes may be involved in immune response and inflammatory response-related pathways and functions in TM-infected macrophages. CONCLUSIONS: The CeRNA network plays an important role in understanding the mechanism of TM infection in macrophages. This study may provide effective and novel insights for further understanding the underlying mechanism of Talaromyces marneffei.

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TNF-α released by melanoma liver metastasis activates AKT and NFKβ1 pathways to promote collagen type I secretion by hepatocytes

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