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DNA and RNA sequencing identified a novel oncogene VPS35 in liver hepatocellular carcinoma


Liver hepatocellular carcinoma (LIHC) is the second leading cause of cancer mortality worldwide. Although cancer driver genes identified so far have been considered to be saturated or nearly saturated, challenges remain in discovering novel genes underlying carcinogenesis due to significant tumor heterogeneity. Here, in a small cohort of hepatitis B virus (HBV)-associated LIHC, we investigated the transcriptional patterns of tumor-mutated alleles using both whole-exome and RNA sequencing data. A graph clustering of the transcribed tumor-mutated alleles characterized overlapped functional clusters, and thus prioritized potentially novel oncogenes. We validated the function of the potentially novel oncogenes in vitro and in vivo. We showed that a component of the retromer complex—the vacuolar protein sorting-associated protein 35 (VPS35)—promoted the proliferation of hepatoma cell through the PI3K/AKT signaling pathway. In VPS35-knockout hepatoma cells, a significantly reduced distribution of membrane fibroblast growth factor receptor 3 (FGFR3) demonstrated the effects of VPS35 on sorting and trafficking of transmembrane receptor. This study provides insight into the roles of the retromer complex on carcinogenesis and has important implications for the development of personalized therapeutic strategies for LIHC.

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Fig. 1: Somatic mutations identified by whole-exome sequencing and their transcriptional patterns.
Fig. 2: Identification of a potentially novel oncogene of VPS35.
Fig. 3: VPS35 promoted the proliferation of hepatoma cells by facilitating the G1/S transition.
Fig. 4: VPS35 exerts its oncogenic roles via the PI3K/AKT signaling.
Fig. 5: A xenograft tumor model of VPS35.
Fig. 6: A significantly reduced FGFR3 in VPS35-KO SK-Hep1 cell line.
Fig. 7: A proposed model depicts how VPS35 participates in the trafficking of FGFR3 and its effects in the downstream PI3K/AKT signaling.

Data availability

Supplementary materials including tables and figures. Whole exome sequencing data for LIHC tumor and its paired cirrhotic tissues, and peripheral blood lymphocytes, as well as RNA sequencing data for LIHC tumor and its paired cirrhotic tissues have been submitted to the Sequence Read Archive (SRA) ( under the number SUB6779164. RNA sequencing data for parental and VPS35-KO SK-Hep1 cell lines have been submitted to the SRA under the number SUB6834808. The source code is available upon request. Supplementary information is available at Oncogene’s website.


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We thank Dr. T-C He (University of Chicago, Chicago, IL) for providing the plasmids pAdEasy system, Dr. Ding Xue (School of Life Sciences, Tsinghua University) for supplying the CRISPR/Cas9 system, and Ms Yihong Sun and Ms Fang Huang for preparing the Supplementary materials.


This work was funded by the China National Natural Science Foundation (no. 81672780, KD, nos. 81872270 and 81572683, NT, and 81602417, KW), the Major National S&T program (2017ZX10202203-004 to NT), the Recruitment Program of Global Youth Experts in China (KD), the program of Artificial Intelligence in Medicine of CQ CSTC (ZHYX2019004, KD), Natural Science Foundation Project of CQ CSTC (cstc2018jcyjAX0254 to NT), the Program for Innovation Team of Higher Education in Chongqing (grant no. CXTDX201601015), the Leading Talent Program of CQ CSTC (grant no. CSTCCXLJRC201719 to NT) and Talent Development Program of CQMU for Postgraduate (grant no. BJRC201728).

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GZ and LL performed in vitro and in vivo experiments; XT and KD performed data analysis; WZ participated in bioinformatics analysis; YC conducted FACS analysis; YZ generated recombinant adenoviruses; DL and XL collected clinical samples; DZ performed pathological review; BH and KW participated in the discussion and design; GZ, XT, and KD wrote the manuscript with input from BH and NT; and KD and NT conceived and designed the study. All authors read and approved the final manuscript.

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Correspondence to Kai Wang, Ni Tang or Keyue Ding.

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The authors declare no conflict of interest.

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All authors approved the final manuscript.


The collection of human tumor samples and the protocols for the investigations were approved by the Institutional Review Board (IRB) in each site where the patients were recruited.

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Written informed consent was obtained from the patients. All animal studies were conducted according to the animal protocol approved by Chongqing Medical University (2017012).

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Zhang, G., Tang, X., Liang, L. et al. DNA and RNA sequencing identified a novel oncogene VPS35 in liver hepatocellular carcinoma. Oncogene 39, 3229–3244 (2020).

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