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. 2024 May-Jun;21(3):260-271.
doi: 10.21873/cgp.20445.

Genetic Analyses of Primary Liver Cancer Cell Lines: Correspondence With Morphological Features of Original Tumors

Jun Akiba  1 , Sachiko Ogasawara  2 , Hirohisa Yano  2
Affiliations

Genetic Analyses of Primary Liver Cancer Cell Lines: Correspondence With Morphological Features of Original Tumors

Jun Akiba et al. Cancer Genomics Proteomics. 2024 May-Jun.

Abstract

Background/aim: Advancements in genetic analysis technologies have led to establishment of molecular classifications systems for primary liver cancers. The correlation between pathological morphology and genetic mutations in hepatocellular carcinoma (HCC) is becoming increasingly evident. To construct appropriate experimental models, it is crucial to select cell lines based on their morphology and genetic mutations. In this study, we conducted comprehensive genetic analyses of primary liver cancer cell lines and examined their correlations with morphology.

Materials and methods: Thirteen primary liver cancer cell lines established in our Department were investigated. Eleven cell lines were HCC cell lines, whereas 2 were combined hepatocellular-cholangiocarcinoma (CHC) cell line characteristics. Whole exome sequencing and fusion gene analyses were conducted using a next generation sequencing platform. We also examined correlations between cell mutations and morphological findings and conducted experiments to clarify the association between morphological findings and genetic alterations.

Results: Mutations in TP53, HMCN1, PCLO, HYDIN, APOB, and EYS were found in 11, 5, 4, 4, 3, and 3 cell lines, respectively. CTNNB1 mutation was not identified in any cell line. The original tumor of four cell lines (KYN-1, KYN-2, KYN-3, and HAK-6) showed morphologically macrotrabecular massive patterns and these cell lines harbor TP53 mutations. Two cell lines (KYN-2 and KMCH-2) showed an extremely high tumor mutation burden. These two cell lines possess ultra-mutations associated with DNA repair and/or DNA polymerase.

Conclusion: The study identified correlations between morphological findings and genetic mutations in several HCC cell lines. Cell lines with unique genetic mutations were found. This information will be a valuable tool for the selection of suitable experimental models in HCC research.

Keywords: Combined hepatocellular cholangiocarcinoma; comprehensive genetic analysis; hepatocellular carcinoma; mutation.

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Conflict of interest statement

The Authors declare that no conflicts of interest exist.

Figures

Figure 1
Figure 1. Mutational landscape of representative gene variants in 13 liver cancer cell lines compared with HCC primary tumors. Top panel shows the total mutation rate for each cell line. The heatmap represents mutations and copy number alteration in 13 liver cancer cell lines. On the left, histograms show a comparison of gene alteration frequency between 13 liver cancer cell lines and HCC (Fisher’s exact test, *p<0.05, **p<0.01, ***p<0.0001). HCC: Hepatocellular carcinoma; CHC: combined hepatocellular-cholangiocarcinoma.
Figure 2
Figure 2. Summary of genetic alterations of 13 liver cancer cell lines. Although various types of mutations were observed, most mutations were of the missense variant type, followed by the frameshift variant and stop gain variant.
Figure 3
Figure 3. Morphological findings of a selection of original tumors. Original tumors of KYN-1 (A), KYN-2 (B), KYN-3 (C), and HAK6 (D) cell lines showing a macrotrabecular massive pattern.
Figure 4
Figure 4. Morphological features of the original tumors of HAK-1A and HAK-1B cells. (A) Panoramic view of the original tumor (hematoxylin and eosin staining). The nodule is composed of a three-layered structure with a different histological grade in each layer. The areas surrounded by the red dotted line, with the light green dotted line and with the blue dotted line consist of well differentiated HCC, well differentiated HCC with fatty change, and poorly differentiated HCC, respectively. (B) Higher magnification of original part of HAK-1A. (C) Higher magnification of original part of HAK-1B. (D) Comparison of mutation number in HAK-1A and HAK-1B. Approximately 75% of genes were identical in HAK-1A and HAK-1B. HCC: Hepatocellular carcinoma.
Figure 5
Figure 5. Immunohistochemical staining for DNA mismatch repair protein using tissues obtained from the KMCH-2 mouse xenograft. MLH1 (A) and PMS2 (B) protein expression was undetected in tumor cells. Both MLH1 (A) and PMS2 (B) protein expression was detected in stromal cells. MSH2 (C) and MSH6 (D) protein expression was retained in tumor cells.
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