Qiang Gao1, Zhi-Chao Wang1, Meng Duan1, Yi-Hui Lin2, Xue-Ya Zhou3, Daniel L Worthley4, Xiao-Ying Wang1, Gang Niu2, Yuchao Xia5, Minghua Deng5, Long-Zi Liu1, Jie-Yi Shi1, Liu-Xiao Yang1, Shu Zhang1, Zhen-Bin Ding1, Jian Zhou6, Chun-Min Liang7, Ya Cao8, Lei Xiong2, Ruibin Xi5, Yong-Yong Shi9, Jia Fan10. 1. Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China. 2. Institute of Precision Medicine, 3D Medicines Inc., Shanghai, China. 3. Department of Psychiatry, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong SAR, China. 4. Cancer Theme, South Australian Health and Medical Research Institute and Department of Medicine, University of Adelaide, Adelaide, Australia. 5. School of Mathematical Sciences and Center for Statistical Science, Peking University, Beijing, China. 6. Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China; Cancer Center, Institute of Biomedical Sciences, Fudan University, Shanghai, China. 7. Department of Anatomy and Histology and Embryology, Shanghai Medical College, Fudan University, Shanghai, China. 8. Cancer Research Institute, Xiangya School of Medicine, Central South University, Hunan, China. 9. Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China. Electronic address: shiyongyong@gmail.com. 10. Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China; Cancer Center, Institute of Biomedical Sciences, Fudan University, Shanghai, China. Electronic address: fan.jia@zs-hospital.sh.cn.
Abstract
BACKGROUND & AIMS: No targeted therapies have been found to be effective against hepatocellular carcinoma (HCC), possibly due to the large degree of intratumor heterogeneity. We performed genetic analyses of different regions of HCCs to evaluate levels of intratumor heterogeneity and associate alterations with responses to different pharmacologic agents. METHODS: We obtained samples of HCCs (associated with hepatitis B virus infection) from 10 patients undergoing curative resection, before adjuvant therapy, at hospitals in China. We collected 4-9 spatially distinct samples from each tumor (55 regions total), performed histologic analyses, isolated cancer cells, and carried them low-passage culture. We performed whole-exome sequencing, copy-number analysis, and high-throughput screening of the cultured primary cancer cells. We tested responses of an additional 105 liver cancer cell lines to a fibroblast growth factor receptor (FGFR) 4 inhibitor. RESULTS: We identified a total of 3670 non-silent mutations (3192 missense, 94 splice-site variants, and 222 insertions or deletions) in the tumor samples. We observed considerable intratumor heterogeneity and branched evolution in all 10 tumors; the mean percentage of heterogeneous mutations in each tumor was 39.7% (range, 12.9%-68.5%). We found significant mutation shifts toward C>T and C>G substitutions in branches of phylogenetic trees among samples from each tumor (P < .0001). Of note, 14 of the 26 oncogenic alterations (53.8%) varied among subclones that mapped to different branches. Genetic alterations that can be targeted by existing pharmacologic agents (such as those in FGF19, DDR2, PDGFRA, and TOP1) were identified in intratumor subregions from 4 HCCs and were associated with sensitivity to these agents. However, cells from the remaining subregions, which did not have these alterations, were not sensitive to these drugs. High-throughput screening identified pharmacologic agents to which these cells were sensitive, however. Overexpression of FGF19 correlated with sensitivity of cells to an inhibitor of FGFR 4; this observation was validated in 105 liver cancer cell lines (P = .0024). CONCLUSIONS: By analyzing genetic alterations in different tumor regions of 10 HCCs, we observed extensive intratumor heterogeneity. Our patient-derived cell line-based model, integrating genetic and pharmacologic data from multiregional cancer samples, provides a platform to elucidate how intratumor heterogeneity affects sensitivity to different therapeutic agents.
BACKGROUND & AIMS: No targeted therapies have been found to be effective against hepatocellular carcinoma (HCC), possibly due to the large degree of intratumor heterogeneity. We performed genetic analyses of different regions of HCCs to evaluate levels of intratumor heterogeneity and associate alterations with responses to different pharmacologic agents. METHODS: We obtained samples of HCCs (associated with hepatitis B virus infection) from 10 patients undergoing curative resection, before adjuvant therapy, at hospitals in China. We collected 4-9 spatially distinct samples from each tumor (55 regions total), performed histologic analyses, isolated cancer cells, and carried them low-passage culture. We performed whole-exome sequencing, copy-number analysis, and high-throughput screening of the cultured primary cancer cells. We tested responses of an additional 105 liver cancer cell lines to a fibroblast growth factor receptor (FGFR) 4 inhibitor. RESULTS: We identified a total of 3670 non-silent mutations (3192 missense, 94 splice-site variants, and 222 insertions or deletions) in the tumor samples. We observed considerable intratumor heterogeneity and branched evolution in all 10 tumors; the mean percentage of heterogeneous mutations in each tumor was 39.7% (range, 12.9%-68.5%). We found significant mutation shifts toward C>T and C>G substitutions in branches of phylogenetic trees among samples from each tumor (P < .0001). Of note, 14 of the 26 oncogenic alterations (53.8%) varied among subclones that mapped to different branches. Genetic alterations that can be targeted by existing pharmacologic agents (such as those in FGF19, DDR2, PDGFRA, and TOP1) were identified in intratumor subregions from 4 HCCs and were associated with sensitivity to these agents. However, cells from the remaining subregions, which did not have these alterations, were not sensitive to these drugs. High-throughput screening identified pharmacologic agents to which these cells were sensitive, however. Overexpression of FGF19 correlated with sensitivity of cells to an inhibitor of FGFR 4; this observation was validated in 105 liver cancer cell lines (P = .0024). CONCLUSIONS: By analyzing genetic alterations in different tumor regions of 10 HCCs, we observed extensive intratumor heterogeneity. Our patient-derived cell line-based model, integrating genetic and pharmacologic data from multiregional cancer samples, provides a platform to elucidate how intratumor heterogeneity affects sensitivity to different therapeutic agents.
Authors: L X Xu; M H He; Z H Dai; J Yu; J G Wang; X C Li; B B Jiang; Z F Ke; T H Su; Z W Peng; Y Guo; Z B Chen; S L Chen; S Peng; M Kuang Journal: Ann Oncol Date: 2019-06-01 Impact factor: 32.976
Authors: Ioannis D Kyrochristos; Georgios K Glantzounis; Demosthenes E Ziogas; Ioannis Gizas; Dimitrios Schizas; Efstathios G Lykoudis; Evangelos Felekouras; Anastasios Machairas; Christos Katsios; Theodoros Liakakos; William C Cho; Dimitrios H Roukos Journal: Int J Mol Sci Date: 2017-01-18 Impact factor: 5.923
Authors: Ling Li; Hildur Knutsdottir; Ken Hui; Matthew J Weiss; Jin He; Benjamin Philosophe; Andrew M Cameron; Christopher L Wolfgang; Timothy M Pawlik; Gabriel Ghiaur; Andrew J Ewald; Esteban Mezey; Joel S Bader; Florin M Selaru Journal: JCI Insight Date: 2019-01-24