Genomic landscape of hepatocellular carcinoma in Egyptian patients by whole exome sequencing

Abstract

Background: Hepatocellular carcinoma (HCC) is the most common primary liver cancer. Chronic hepatitis and liver cirrhosis lead to accumulation of genetic alterations driving HCC pathogenesis. This study is designed to explore genomic landscape of HCC in Egyptian patients by whole exome sequencing.

Methods: Whole exome sequencing using Ion Torrent was done on 13 HCC patients, who underwent surgical intervention (7 patients underwent living donor liver transplantation (LDLT) and 6 patients had surgical resection}.

Results: Mutational signature was mostly S1, S5, S6, and S12 in HCC. Analysis of highly mutated genes in both HCC and Non-HCC revealed the presence of highly mutated genes in HCC (AHNAK2, MUC6, MUC16, TTN, ZNF17, FLG, MUC12, OBSCN, PDE4DIP, MUC5b, and HYDIN). Among the 26 significantly mutated HCC genes-identified across 10 genome sequencing studies-in addition to TCGA, APOB and RP1L1 showed the highest number of mutations in both HCC and Non-HCC tissues. Tier 1, Tier 2 variants in TCGA SMGs in HCC and Non-HCC (TP53, PIK3CA, CDKN2A, and BAP1). Cancer Genome Landscape analysis revealed Tier 1 and Tier 2 variants in HCC (MSH2) and in Non-HCC (KMT2D and ATM). For KEGG analysis, the significantly annotated clusters in HCC were Notch signaling, Wnt signaling, PI3K-AKT pathway, Hippo signaling, Apelin signaling, Hedgehog (Hh) signaling, and MAPK signaling, in addition to ECM-receptor interaction, focal adhesion, and calcium signaling. Tier 1 and Tier 2 variants KIT, KMT2D, NOTCH1, KMT2C, PIK3CA, KIT, SMARCA4, ATM, PTEN, MSH2, and PTCH1 were low frequency variants in both HCC and Non-HCC.

Conclusion: Our results are in accordance with previous studies in HCC regarding highly mutated genes, TCGA and specifically enriched pathways in HCC. Analysis for clinical interpretation of variants revealed the presence of Tier 1 and Tier 2 variants that represent potential clinically actionable targets. The use of sequencing techniques to detect structural variants and novel techniques as single cell sequencing together with multiomics transcriptomics, metagenomics will integrate the molecular pathogenesis of HCC in Egyptian patients.

Keywords: Hepatocelleular carcinoma (HCC); Living Donor Liver Transplantation (LDLT); Mutational signature; Whole exome sequencing.

Fig. 1

Percentage of different variant sequence ontologies in HCC samples

Fig. 2

Mutational signatures in HCC samples showing predominance of S1, S5 and S23 in FFPE samples (LT2, LT6, LT7, LT8) and S1, S5, S6, and S12) in fresh tissue samples (LT10, LT11, LT13, LT14, LT16, LT17, LT18, LT19, LT20) [21]

Fig. 3

Variants in highly mutated genes HCC from our study (Above the bar), and the variants from TCGA HCC (Below the bar) are shown as a lollipop diagram, Protein domains are shown as brown bars. Variants in multiple samples are taller. Color Sequence ontology of variant

Fig. 4

Unique pathogenic variants involving TCGA SMGs in both (a) HCC and (b) Non-HCC

Fig. 5

Unique pathogenic variants in Oncogenes, tumor suppressor genes (TSGs) HCC with Phred score > 20, Fs = frameshift-truncation, Sc = Splice site, T1 = Tier1, T2 = Tier 2, T3 = Tier 3, T4 = Tier4. A higher CHASM + LIHC score (liver hepatocellular carcinoma) in colored areas indicates a higher possibility of being a driver mutation in HCC

Fig. 6

Unique pathogenic variants in Oncogenes, tumor suppressor genes (TSGs) Non- HCC with Phred score > 20, Fs = frameshift-truncation, Ss = Splice site, T1 = Tier1, T2 = Tier 2, T3 = Tier 3, T4 = Tier4. A higher CHASM + LIHC score (liver hepatocellular carcinoma) in colored areas (CHASMplus LIHC score) indicates a higher possibility of being a driver mutation in Non-HCC