Comparison of whole exome sequencing in circulating tumor cells of primitive and metastatic nasopharyngeal carcinoma

Abstract

Background Nasopharyngeal carcinoma (NPC) is one of the most common cancers. To investigate the gene mutation profile of NPC patients, we performed whole exome sequencing (WES) in tumor cells, peripheral blood cells, and circulating tumor cells (CTCs) of primitive and metastatic NPC patients, and explored its clinical significance. Methods Primitive tumor cells, white blood cells, and CTCs of patients were collected and hybridized with probes targeting whole exons. Mutational signatures, signaling pathways, and cancer associated genes from CTCs cells of two primitive and two metastatic patients were analyzed using gene ontology (GO) method. Results The mutational landscape of four primitive tumors showed that there were more MSH2 alterations in more non-silent mutation number patients Additionally, BAP1 gene mutation only occurred in metastatic patients. The most frequently mutated genes among the primitive tumor and CTC samples were CFAP74, MOB3C , PDE4DIP , IGFN1 , CYFIP2 , NOP16 , SLC22A1 , ZNF117 , and SSPO . Interestingly, only PMS1 , BRIP1 , DEE , OR2T12 , CPN2 , MLXIPL , BAIAP3 , IGSF3 , SIN3B , and ZNF880 alterations occurred in primary tumors of metastatic patients. Primitive and metastatic NPC had significantly distinct mutational signatures. GO analysis revealed that each patient had his own mutational signaling pathways. Non-silent single nucleotide variations (non-silent SNVs) and insertion-deletion mutations (INDELs) in CTCs were more dramatic than in primitive tumor cells. Conclusions These changes are strongly relevant to their clinical characteristics and therapeutic strategy.

Epithelial-mesenchymal transition classification of circulating tumor cells predicts clinical outcomes in progressive nasopharyngeal carcinoma

“…Owing to its highly efficient design, this system successfully isolated single CTCs and captured CTC clusters in our earlier study ( 12 ). The quality and integrity of the isolated CTCs were found to be adequate for nucleic acid extraction and subsequent whole-exome sequencing in a later study ( 19 ), indicating that the CanPatrol™ CTC enrichment system is suitable for CTC isolation and in-depth analyses. Furthermore, our previous whole-exome sequencing showed that various genes are frequently mutated in primary tumors and CTCs ( 19 ).…”

“…The quality and integrity of the isolated CTCs were found to be adequate for nucleic acid extraction and subsequent whole-exome sequencing in a later study ( 19 ), indicating that the CanPatrol™ CTC enrichment system is suitable for CTC isolation and in-depth analyses. Furthermore, our previous whole-exome sequencing showed that various genes are frequently mutated in primary tumors and CTCs ( 19 ). Of these mutated genes, some are well-characterized functional oncogenes, such as CYFIP2 , NOP16 , and ZNF117 ( 28 – 30 ), and genetic variations in others are closely associated with other cancers, such as MOB3C and SSPO ( 31 , 32 ).…”

“…The protocol used in the present study was optimized with slight modifications for CTC detection in NPC as described in our previous study ( 12 ). Briefly, 5 mL of peripheral blood was collected from patients and stored in anticoagulant tubes for CTC detection within 4 h. The CanPatrol™ CTC enrichment system was used to efficiently isolate CTCs by size as previously described ( 12 , 16 , 19 ). Red blood cell lysis buffer (154 mmol/L NH 4 Cl, 10 mmol/L KHCO 3 , and 0.1 mmol/L EDTA) was administered to eliminate erythrocytes in blood samples.…”

“…Of the epithelial, mesenchymal, and epithelial/mesenchymal (E/M) hybrid CTCs, we found that the E/M hybrid CTCs were closely associated with EBV infection, with the highest levels of EBV DNA, EBV-specific viral capsid antigen (VCA)-IgA, and early antigen (EA)-IgA detected in this CTC subpopulation ( 12 ). In a later study, we further investigated distinct mutational signatures among primary tumors and CTCs using whole-exome sequencing ( 19 ). However, the significance of the distribution of E/M hybrid CTCs in predicting prognosis in patients with NPC, especially in evaluating the risk of locoregional and metastatic relapses after standard first-line treatment, remains poorly understood.…”

Nasopharyngeal Carcinoma Progression: Accumulating Genomic Instability and Persistent Epstein–Barr Virus Infection

“…In addition, mutations in EP300 , PIK3CA , and splicing factor 3b subunit 1 ( SF3B1 ) also contribute to metastasis in NPC [ 7 , 47 ]. Specifically, mutations in the BRCA1-associated protein 1 ( BAP1 ) are found only in NPC patients with metastatic disease [ 48 ].…”