3.1 RNA derived from exosome and platelet have different gene expression profiles
Comparison of transcriptomes in early lung cancer and normal groups identified 541 genes with differential expression (DEG; 208 increased and 333 decreased; p value < 0.05) in exosome group, and 10292 genes with differential expression (DEG; 4581 increased and 5711 decreased; p value < 0.05) in platelet group.Comparison of transcriptomes in the early lung cancer group and the normal group revealed 1177 genes with differential expression (DEG; 1023 increased and 154 decreased; p value < 0.05) in the exosome group, and 14393 genes with differential expression (DEG; 3703 increased and 10686 decreased; p value < 0.05) in the platelet group (Fig. 1A-D).
Gene functional enrichment analysis was performed on potential targets using GO, KEGG, DO Enrichment Analysis, and Reactome Enrichment Analysis to explore their function. Supplement Figure-1 shows that which pathways the up-regulated genes contributed to through the exosone group (early lung cancer vs. normal patient, and advanced lung cancer vs. the normal patient) through GO Enrichment Analysis. KEGG, DO, Reactome Enrichment Analysis showed the correlated pathways consistent with GO Enrichment Analysis. Futhermore, Venn intersection analysis on four sets of differentially expressed genes by regular method showed 44 common differential gene expression (Fig. 1E), and 37 upregulated candidate genes were selected to be conducted further analysis. 37 candidate genes, namely, AC093909.1, BSG, C9orf16, CALM3, CLDN5, CLU, CMTM5, CTSA, DDX11L10, DDX11L5, DOK2, FCER1G, GPX1, H2BC12, H4C9, HCFC1R1, HLA-C, HLA-H, IFI27L2, ITM2B, MCEMP1, MEA1, NDUFA6, NDUFAF3, PF4, POLR2E, PTCRA, RHOC, RUFY1, SAT1, SH3BGRL3, SPARC, SPX, TMEM106C, TREML1, YIF1B, YWHAZP2 were identified (Supplement Fig. 2). Venn intersection analysis by log2FoldChange showed no common differential gene expression (Fig. 1F). We obtained expression data from the TCGA and GTEx databases to analyze the mRNA levels of 37 potential genes in cancer and normal tissues. The findings revealed a marked increase in TREML1 expression in cancerous tissues compared to normal tissues in both the exosome and platelet groups (Fig. 1G, 1H, Supplement Fig. 3–4). Consistently, the clinical and molecular characteristics of TREML1 in lung cancer was validated in the later exploration.
3.2 Expression and prognosis profile of TREML1
Figure 2A shows a notable increase in TREML1 expression in lung cancer, specifically in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), compared to their corresponding normal samples. Figure 2B illustrates a significant difference in TREML1 expression among various pathological stages, suggesting a strong correlation between TREML1 and the clinical stage of lung cancer (p < 0.05).
Our findings suggested that increased TREML1 levels were associated with a poor outlook in terms of overall survival (OS) (Fig. 2C) and disease-free survival (DFS) (Fig. 2D) in lung cancer patients from the TCGA dataset.Immunohistochemistry analysis revealed that TREML1 exhibited decreased levels in lung cancer tissue samples (Fig. 2E).
3.3 TREML1 mutation analysis
Figure 3A, obtained from cBioPortal, shows the genetic changes in TREML1 for samples from patients. The highest alteration frequency of TREML1 occurs among patients with Esophageal adenocarcinoma (EAC), where the primary type of alteration was ‘amplification’ referring to copy number alteration (CNA). Six types of cancer with genetic mutations showed significant amplification of TREML1: stomach adenocarcinoma (STAD), ovarian serous cystadenocarcinoma (OVs), diffuse large B-Cell lymphoma (DLBCL), skin cutaneous melanoma (SKCM), cholangiocarcinoma, and lung adenocarcinoma. In Fig. 3B,C, the TCGA cohort displayed multiple mutation sites in TREML1, highlighting the site with the highest frequency of alteration (N290K) in the V-set within the 3D structure of TREML1. A single sample from the TCGA repository exhibited a mutation at this common location in a case of LUAC. Nevertheless, the N290K mutation in TREML1 had no impact on the overall survival of patients with LUAC (Fig. 3D).
3.4 The correlation between clinical characteristic and TREML1 expression
To improve comprehension of the relationship between TREML1 expression and clinical characteristics in various types of cancer. Sangerbox 3.0 online tools are utilized to analyze the relationship between important clinical features and TREML1 expression in TCGA dataset. Notable variances in TREML1 expression levels were noted among different groups based on proliferation, invasion, lymph node metastasis, distant metastases, total clinical stage, and gender in patients with LUAD, BRCA, ESCA, STES, KIPAN, STAD, PRAD, HNSC, LUSC, and LIHC. As shown in the Fig. 4A-4D, TREML1 expression was associated with through T status, N status, M status, and total clinical stage in LUAD. Morerover, there is lower correlation with LUSC, comparing with the LUAD. Additionally, TREML1 expression significantly higer in the male patients than the female patients (Fig. 4F).
Based on the aforementioned enrichment findings, it is hypothesized that TREML1 plays a role in controlling multiple biological functions including the progression of lung cancer, the regulation of EMT, and metabolic processes. These relevent processes all have been reported to be connected to stem cells. We will delve deeper into the cellular stemness of TREML1 in lung cancer to determine if TREML1 plays a significant regulatory role in stem cells. Figure 4E shows the standardized pan-cancer dataset obtained from 37 tumors. In particular, we collected the TREML1 (ENSG00000161911) expression data from every sample and calculated the RNA stemness scores for each tumor using mRNA characteristics. Next, we computed the Pearson correlation coefficients for each type of tumor and found significant positive correlations in 18 tumors, such as LUAD and LUSC, as well as negative correlations in 15 tumors.Thus, our initial results indicate that TREML1 could have a positive impact on the regulation of stem cells in lung cancer, however, additional experimental confirmation is required.
3.5 Genetic characteristics of TREML1 mutation in NSCLC
A large cohort of 995 patients with lung cancer and NGS genomic profiling were enrolled.Among these included patients, 508 were lung adenocarcinoma, of which 255 with low expression of TREML1 and 253 with high expression; 487 were lung squamous cell carcinoma, of which 244 with low expression of TREML1 and 243 with high expression.Lollipop map of hotspot mutations in TREML1 protein present that approximately 0.8% TREML1 mutation ocuurred in lung adenocarcinoma, 0.6% TREML1 mutation ocuurred in lung squamous cell carcinoma (Fig. 5A). The genomic profile of TREML1 mutation from the TCGA cohort was different between LUAD and LUSC.The most co-mutation of TREML1 was TTN (53.7%), and then RYR2 (42.8%), LRP1B (37.8%), USH2A (36.8%), ZFHX4 (35.9%), ZNF536 (23.5%), CSMD1 (22.8%), COL11A1 (22.8%)(Fig. 5B) for lung adenocarcinoma. APOB ranked at the top (20.7%) followed by CSMD (20.4%), CTNNA (16.1%), KCNH7 (12.9%), DCDC1 (12.4%), CTNND2 (12.1%), ADGRL3 (11.8%), UNC79 (10.9%) (Fig. 5C).