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Updated: Feb 27, 2026
Oncogenic Gene Fusion Detection Using Anchored Multiplex Polymerase Chain Reaction Followed by Next Generation Sequencing
Published on: July 5, 2019
RNA sequencing of esophageal adenocarcinomas identifies novel fusion transcripts, including NPC1-MELK, arising from a
Zhixiong Wang1,2, Yulan Cheng2,3, John M Abraham2,3
1Department of Gastrointestinal Surgery, First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China.
Background:
Studies of chromosomal rearrangements and fusion transcripts have elucidated mechanisms of tumorigenesis and led to targeted cancer therapies. This study was aimed at identifying novel fusion transcripts in esophageal adenocarcinoma (EAC).
Methods:
To identify new fusion transcripts associated with EAC, targeted RNA sequencing and polymerase chain reaction (PCR) verification were performed in 40 EACs and matched nonmalignant specimens from the same patients. Genomic PCR and Sanger sequencing were performed to find the breakpoint of fusion genes.
Results:
Five novel in-frame fusion transcripts were identified and verified in 40 EACs and in a validation cohort of 15 additional EACs (55 patients in all): fibroblast growth factor receptor 2 (FGFR2)-GRB2-associated binding protein 2 (GAB2) in 2 of 55 or 3.6%, Niemann-Pick C1 (NPC1)-maternal embryonic leucine zipper kinase (MELK) in 2 of 55 or 3.6%, ubiquitin-specific peptidase 54 (USP54)-calcium/calmodulin dependent protein kinase II γ (CAMK2G) in 2 of 55 or 3.6%, megakaryoblastic leukemia (translocation) 1 (MKL1)-fibulin 1 (FBLN1) in 1 of 55 or 1.8%, and CCR4-NOT transcription complex subunit 2 (CNOT2)-chromosome 12 open reading frame 49 (C12orf49) in 1 of 55 or 1.8%. A genomic analysis indicated that NPC1-MELK arose from a complex interchromosomal translocation event involving chromosomes 18, 3, and 9 with 3 rearrangement points, and this was consistent with chromoplexy.
Conclusions:
These data indicate that fusion transcripts occur at a stable frequency in EAC. Furthermore, our results indicate that chromoplexy is an underlying mechanism that generates fusion transcripts in EAC. These and other fusion transcripts merit further study as diagnostic markers and potential therapeutic targets in EAC. Cancer 2017;123:3916-24. © 2017 American Cancer Society.
Insights
Novel fusion transcripts were identified in esophageal adenocarcinoma (EAC), revealing chromoplexy as a mechanism driving these genetic alterations. These findings highlight potential new diagnostic markers and therapeutic targets for EAC.
Area of Science:
- Oncology
- Genetics
- Molecular Biology
Background:
- Chromosomal rearrangements and fusion transcripts are key drivers of tumorigenesis and targets for cancer therapy.
- Esophageal adenocarcinoma (EAC) is a significant malignancy where understanding genetic alterations is crucial.
Purpose of the Study:
- To identify novel fusion transcripts in esophageal adenocarcinoma (EAC).
- To investigate the underlying genomic mechanisms generating these fusion transcripts.
Main Methods:
- Targeted RNA sequencing and polymerase chain reaction (PCR) were used to identify fusion transcripts in 40 EAC samples.
- Genomic PCR and Sanger sequencing were employed to determine fusion gene breakpoints.
Main Results:
- Five novel in-frame fusion transcripts were identified in 55 EAC patients.
- FGFR2-GAB2, NPC1-MELK, and USP54-CAMK2G fusions were found in 3.6% of cases each.
- The NPC1-MELK fusion resulted from a complex chromoplexy event involving chromosomes 18, 3, and 9.
Conclusions:
- Fusion transcripts occur at a consistent frequency in EAC.
- Chromoplexy is identified as a mechanism responsible for generating fusion transcripts in EAC.
- These novel fusion transcripts warrant further investigation as potential diagnostic markers and therapeutic targets for EAC.
