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The fusion landscape of hepatocellular carcinoma
Most cases of hepatocellular carcinoma (HCC) are already advanced at the time of diagnosis, which limits treatment options. Challenges in early‐stage diagnosis may be due to the genetic complexity of HCC. Gene fusion plays a critical function in tumorigenesis and cancer progression in multiple cance...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6487730/ https://www.ncbi.nlm.nih.gov/pubmed/30903738 http://dx.doi.org/10.1002/1878-0261.12479 |
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author | Zhu, Chengpei Wu, Liangcai Lv, Yanling Guan, Jinxia Bai, Xue Lin, Jianzhen Liu, Tingting Yang, Xiaobo Robson, Simon C. Sang, Xinting Xue, Chenghai Zhao, Haitao |
author_facet | Zhu, Chengpei Wu, Liangcai Lv, Yanling Guan, Jinxia Bai, Xue Lin, Jianzhen Liu, Tingting Yang, Xiaobo Robson, Simon C. Sang, Xinting Xue, Chenghai Zhao, Haitao |
author_sort | Zhu, Chengpei |
collection | PubMed |
description | Most cases of hepatocellular carcinoma (HCC) are already advanced at the time of diagnosis, which limits treatment options. Challenges in early‐stage diagnosis may be due to the genetic complexity of HCC. Gene fusion plays a critical function in tumorigenesis and cancer progression in multiple cancers, yet the identities of fusion genes as potential diagnostic markers in HCC have not been investigated. Here, we employed STAR‐Fusion and identified 43 recurrent fusion events in our own and four public RNA‐seq datasets. We identified 2354 different gene fusions in two hepatitis B virus (HBV)‐HCC patients. Validation analysis against the four RNA‐seq datasets revealed that only 1.8% (43/2354) were recurrent fusions. Comparison with the four fusion databases demonstrated that 19 recurrent fusions were not previously annotated to diseases and three were annotated as disease‐related fusion events. Finally, we validated six of the novel fusion events, including RP11‐476K15.1‐CTD‐2015H3.2, by RT‐PCR and Sanger sequencing of 14 pairs of HBV‐related HCC samples. In summary, our study provides new insights into gene fusions in HCC and may contribute to the development of anti‐HCC therapy. |
format | Online Article Text |
id | pubmed-6487730 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-64877302019-05-07 The fusion landscape of hepatocellular carcinoma Zhu, Chengpei Wu, Liangcai Lv, Yanling Guan, Jinxia Bai, Xue Lin, Jianzhen Liu, Tingting Yang, Xiaobo Robson, Simon C. Sang, Xinting Xue, Chenghai Zhao, Haitao Mol Oncol Research Articles Most cases of hepatocellular carcinoma (HCC) are already advanced at the time of diagnosis, which limits treatment options. Challenges in early‐stage diagnosis may be due to the genetic complexity of HCC. Gene fusion plays a critical function in tumorigenesis and cancer progression in multiple cancers, yet the identities of fusion genes as potential diagnostic markers in HCC have not been investigated. Here, we employed STAR‐Fusion and identified 43 recurrent fusion events in our own and four public RNA‐seq datasets. We identified 2354 different gene fusions in two hepatitis B virus (HBV)‐HCC patients. Validation analysis against the four RNA‐seq datasets revealed that only 1.8% (43/2354) were recurrent fusions. Comparison with the four fusion databases demonstrated that 19 recurrent fusions were not previously annotated to diseases and three were annotated as disease‐related fusion events. Finally, we validated six of the novel fusion events, including RP11‐476K15.1‐CTD‐2015H3.2, by RT‐PCR and Sanger sequencing of 14 pairs of HBV‐related HCC samples. In summary, our study provides new insights into gene fusions in HCC and may contribute to the development of anti‐HCC therapy. John Wiley and Sons Inc. 2019-04-11 2019-05 /pmc/articles/PMC6487730/ /pubmed/30903738 http://dx.doi.org/10.1002/1878-0261.12479 Text en © 2019 The Authors. Published by FEBS Press and John Wiley & Sons Ltd. This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Articles Zhu, Chengpei Wu, Liangcai Lv, Yanling Guan, Jinxia Bai, Xue Lin, Jianzhen Liu, Tingting Yang, Xiaobo Robson, Simon C. Sang, Xinting Xue, Chenghai Zhao, Haitao The fusion landscape of hepatocellular carcinoma |
title | The fusion landscape of hepatocellular carcinoma |
title_full | The fusion landscape of hepatocellular carcinoma |
title_fullStr | The fusion landscape of hepatocellular carcinoma |
title_full_unstemmed | The fusion landscape of hepatocellular carcinoma |
title_short | The fusion landscape of hepatocellular carcinoma |
title_sort | fusion landscape of hepatocellular carcinoma |
topic | Research Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6487730/ https://www.ncbi.nlm.nih.gov/pubmed/30903738 http://dx.doi.org/10.1002/1878-0261.12479 |
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