Splice Variants of mRNA of Cytochrome P450 Genes: Analysis by the Nanopore Sequencing Method in Human Liver Tissue and HepG2 Cell Line

Deynichenko, K. A.; Ptitsyn, K. G.; Radko, Sergey P.; Курбатов, Л. К.; Вахрушев, И. В.; Buromski, I.V.; Markin, S. S.; Archakov, Alexander I.; Lisitsa, Andrey; Ponomarenko, Elena A.

doi:10.1134/s1990750822040047

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“…HepG2 and Huh7 are cell lines derived from hepatoblastoma and hepatocellular carcinoma tumor tissues, respectively [24,25], which are widely used as models in biotransformation studies (e.g., [26][27][28]) or for studying the processes associated with the malignant transformation of hepatocytes ( [29][30][31][32], to mention a few). Among these cell lines, long-read nanopore sequencing was only applied to AS profiling in HepG2 cells, which focused either on a particular group of genes such as cytochrome P450 genes [33] or on nonpolyadenylated transcripts [34].…”

Section: Introductionmentioning

confidence: 99%

Comparison of Alternative Splicing Landscapes Revealed by Long-Read Sequencing in Hepatocyte-Derived HepG2 and Huh7 Cultured Cells and Human Liver Tissue

Kozlova,

Sarygina,

Deinichenko

et al. 2023

Biology

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The long-read RNA sequencing developed by Oxford Nanopore Technologies provides a direct quantification of transcript isoforms, thereby making it possible to present alternative splicing (AS) profiles as arrays of single splice variants with different abundances. Additionally, AS profiles can be presented as arrays of genes characterized by the degree of alternative splicing (the DAS—the number of detected splice variants per gene). Here, we successfully utilized the DAS to reveal biological pathways influenced by the alterations in AS in human liver tissue and the hepatocyte-derived malignant cell lines HepG2 and Huh7, thus employing the mathematical algorithm of gene set enrichment analysis. Furthermore, analysis of the AS profiles as abundances of single splice variants by using the graded tissue specificity index τ provided the selection of the groups of genes expressing particular splice variants specifically in liver tissue, HepG2 cells, and Huh7 cells. The majority of these splice variants were translated into proteins products and appeal to be in focus regarding further insights into the mechanisms underlying cell malignization. The used metrics are intrinsically suitable for transcriptome-wide AS profiling using long-read sequencing.

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