Research Papers:

Inferring the progression of multifocal liver cancer from spatial and temporal genomic heterogeneity

Jie-Yi Shi, Qingfeng Xing, Meng Duan, Zhi-Chao Wang, Liu-Xiao Yang, Ying-Jun Zhao, Xiao-Ying Wang, Yun Liu, Minghua Deng, Zhen-Bin Ding, Ai-Wu Ke, Jian Zhou, Jia Fan, Ya Cao, Jiping Wang, Ruibin Xi and Qiang Gao _

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Oncotarget. 2016; 7:2867-2877. https://doi.org/10.18632/oncotarget.6558

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Jie-Yi Shi1,, Qingfeng Xing2,, Meng Duan1,, Zhi-Chao Wang1,, Liu-Xiao Yang1, Ying-Jun Zhao3, Xiao-Ying Wang1, Yun Liu2, Minghua Deng2, Zhen-Bin Ding1, Ai-Wu Ke1, Jian Zhou1,4, Jia Fan1,4, Ya Cao5, Jiping Wang6, Ruibin Xi2, Qiang Gao1

1Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, P. R. China

2School of Mathematical Sciences and Center for Statistical Science, Peking University, Beijing, P. R. China

3Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shangai, P. R. China

4Institute of Biomedical Sciences, Fudan University, Shanghai, P. R. China

5Cancer Research Institute, Xiangya School of Medicine, Central South University, Hunan, P. R. China

6Division of Surgical Oncology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA

Co-first authors

Correspondence to:

Qiang Gao, e-mail: [email protected]

Ruibin Xi, e-mail: [email protected]

Jiping Wang, e-mail: [email protected]

Keywords: hepatocellular carcinoma, multifocal tumors, whole-exome sequencing, intratumor heterogeneity, FAT4

Received: July 20, 2015     Accepted: November 21, 2015     Published: December 11, 2015


Multifocal tumors developed either as independent tumors or as intrahepatic metastases, are very common in primary liver cancer. However, their molecular pathogenesis remains elusive. Herein, a patient with synchronous two hepatocellular carcinoma (HCC, designated as HCC-A and HCC-B) and one intrahepatic cholangiocarcinoma (ICC), as well as two postoperative recurrent tumors, was enrolled. Multiregional whole-exome sequencing was applied to these tumors to delineate the clonality and heterogeneity. The three primary tumors showed almost no overlaps in mutations and copy number variations. Within each tumor, multiregional sequencing data showed varied intratumoral heterogeneity (21.6% in HCC-A, 20.4% in HCC-B, 53.2% in ICC). The mutational profile of two recurrent tumors showed obvious similarity with HCC-A (86.7% and 86.6% respectively), rather than others, indicating that they originated from HCC-A. The evolutionary history of the two recurrent tumors indicated that intrahepatic micro-metastasis could be an early event during HCC progression. Notably, FAT4 was the only gene mutated in two primary HCCs and the recurrences. Mutation prevalence screen and functional experiments showed that FAT4, harboring somatic coding mutations in 26.7% of HCC, could potently inhibit growth and invasion of HCC cells. In HCC patients, both FAT4 expression and FAT4 mutational status significantly correlated with patient prognosis. Together, our findings suggest that spatial and temporal dissection of genomic alterations during the progression of multifocal liver cancer may help to elucidate the basis for its dismal prognosis. FAT4 acts as a putative tumor suppressor that is frequently inactivated in human HCC.

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