Comparison of Alternative Splicing Landscapes Revealed by Long-Read Sequencing in Hepatocyte-Derived HepG2 and Huh7 Cultured Cells and Human Liver Tissue
Anna Kozlova,
Elizaveta Sarygina,
Kseniia Deinichenko,
Sergey Radko,
Konstantin Ptitsyn,
Svetlana Khmeleva,
Leonid Kurbatov,
Pavel Spirin,
Vladimir Prassolov,
Ekaterina Ilgisonis,
Andrey Lisitsa,
Elena Ponomarenko
Affiliations
Anna Kozlova
Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia
Elizaveta Sarygina
Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia
Kseniia Deinichenko
Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia
Sergey Radko
Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia
Konstantin Ptitsyn
Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia
Svetlana Khmeleva
Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia
Leonid Kurbatov
Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia
Pavel Spirin
Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991 Moscow, Russia
Vladimir Prassolov
Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991 Moscow, Russia
Ekaterina Ilgisonis
Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia
Andrey Lisitsa
Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia
Elena Ponomarenko
Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia
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.
