1. Fibroblast-related genes are the major difference between PA and PC
To comprehensively investigate the TME alternations, we first explored the expression pattern of the TME compartment-dominant genes in 39 parathyroid tumors pooling BJCY.1, BJCY.2 and GSE83421 cohort. The expression heatmap showed that TME genes were highly distinct between PA and PC samples, especially the stromal cell compartment (Fig.1A). More importantly, among the top 10 ranked genes based on AUC value, 6 genes, namely SERPINA1, INSR, FN1, CXCL14, CFD and CD9, were fibroblast associated genes (Fig. 1A). Next, we evaluated the TME infiltration level. We found that immune cells including NK cells, CD8T cells, T cells, and B lineages were significantly enriched in PAs. Fibroblasts were the only cells that upregulated in PCs despite the P-value being 0.071 (Fig. 1B). We also illustrated PCs expressed a high level of fibroblast-related genes (Fig. 1C) and GO biological process enrichment analysis revealed that PCs upregulated genes were mainly associated with extracellular matrix/structure organization and cell-substrate adhesion (Fig.1D). These results indicated that fibroblast related genes are major contribution in PC diagnosis.
2. FN1 and CFD contribute to PC identification
Because fibroblast cells were highly heterogeneous with distinct cell clusters[18, 26, 27], we next focus on their functional status in parathyroid tumors. The expression level of these DEGs and fibroblast-related genes identified 2 distinct gene clusters (Fig. 2A). It is worth noting that iCAF markers like CFD, CXCL12, DPT, AGTR1 and IGF1 were enriched in PA tumors, while mCAF or vCAF markers like MMP11, POSTN, GJA4, and RGS5 and pan-CAF markers COL1A1 and FAP were upregulated in PCs (Fig.2B) [18, 28]. To identify representative genes of the above 2 gene clusters, we integrated the AUC and fold change values and finally, FN1 and CFD were selected as representative markers (Fig.2C). As expected, FN1 was mainly expressed by CAF and CFD was enriched in adipogenic CAF and NF cluster according to the pan-cancer scRNA-seq data (https://gist-fgl.github.io/sc-caf-atlas/). The expression pattern of FN1 and CFD showed significant exclusive and FC score marked a big difference between PA and PC (Fig. 2D). The exclusive pattern between FN1 and CFD was also validated in the fibroblasts from the pan-cancer scRNA-seq data (Fig. 2E). FN1 exhibited high expression level in cancers; on the contrary, CFD was enriched in normal or cancer adjacent tissue (Fig. 2E). We also examine the distinguish capacity of FC score in pan-cancer using RNA-seq data in TCGA. Among the identified 15 cancers, the FC score in 10 cancers including thyroid carcinoma is obvious (Fig. S2A). However, the FC score did not show a diagnosis role in kidney clear cell carcinoma, kidney papillary cell carcinoma, liver hepatocellular carcinoma, etc., which might be because of low infiltration level (Fig. S2B, Fig.S2C). Taken together, these data suggested that FN1 and CFD were highly exclusive in distinct fibroblast states, which also played an important role in cancer diagnosis.
3. FC score highly correlated with the EMT process
The TME compartments were closely related through soluble factors or direct contact, we then next focused on cytokine and ligand-receptor (LR) interactions to assess the influence of FC score on the PC microenvironment. We have identified multiple FN1/CFD-related LR links in PC but failed in PA samples. Many FN1-related ligand-receptor interactions were links associated with angiogenesis, and metastasis like TGFB2:TGFBR1[29, 30], and FN1:ITGAV [31]. While CFD-associated LR pairs were concerned with CCR5 and LPAR1. The widely reported ligand of CCR5 was CCL5, and functions in recruiting cDC1, Treg, and CD8T cells and mediating tumor-TAM interactions[32, 33]. LPAR1 was positively correlated with immune infiltration level in prostate cancer[34] (Fig. 3A). In the cytokines and cytokine receptors analysis, we have found chemokines (INHBA, TGFB2, VEGFA) associated with EMT showed a positive relation with FC score. Similarly, enrichment analysis of the cancer hallmark gene set indicated that EMT, NOTCH signaling, and inflammatory response related signature was enriched in patients with high FC score (Fig. 3C). Next, we implemented the immune cell infiltration correlation analysis and revealed the proportions of CD8+T, fibroblast and endothelial cells were increased in high FC score patients (Fig. 3D). And the EMT canonical like TWIST1, SNAI2 and cytotoxic CD8B, PRF1 were positively correlated with FC score, although these marker genes did not reach the significant level (Fig. S3).
4. Relevance of FC score to clinical metrics
PHPT was first discovered by hypercalcemia and increased levels of PTH. Therefore, we examine whether the FC score was associated with these clinical parameters. Correlation analysis indicated that FC score did not relate with the level of serum calcium, PTH level, 25-dihydroxyvitamin D (25OHD), phosphorus (P), alkaline phosphatase (ALP) and creatinine (CREA) in blood before surgery (Fig. 4).