Many Different LINE-1 Retroelements Are Activated in Bladder Cancer.

Patcharawalai Whongsiri,Tobias Lautwein,Christiane Hader,Günter Niegisch,Wolfgang A Schulz,Karl Köhrer,Wolfgang Goering,Michèle J Hoffmann

doi:10.3390/ijms21249433

Patcharawalai Whongsiri, Tobias Lautwein + Show 6 more

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https://doi.org/10.3390/ijms21249433

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Abstract

Human genomes contain about 100,000 LINE-1 (L1) retroelements, of which more than 100 are intact. L1s are normally tightly controlled by epigenetic mechanisms, which often fail in cancer. In bladder urothelial carcinoma (UC), particularly, L1s become DNA-hypomethylated, expressed and contribute to genomic instability and tumor growth. It is, however, unknown which individual L1s are activated. Following RNA-immunoprecipitation with a L1-specific antibody, third generation nanopore sequencing detected transcripts of 90 individual elements in the VM-Cub-1 UC line with high overall L1 expression. In total, 10 L1s accounted for >60% of the reads. Analysis of five specific L1s by RT-qPCR revealed generally increased expression in UC tissues and cell lines over normal controls, but variable expression among tumor cell lines from bladder, prostate and testicular cancer. Chromatin immunoprecipitation demonstrated active histone marks at L1 sequences with increased expression in VM-Cub-1, but not in a different UC cell line with low L1 expression. We conclude that many L1 elements are epigenetically activated in bladder cancer in a varied pattern. Our findings indicate that expression of individual L1s is highly heterogeneous between and among cancer types.

Highlights

One-sixth of the human genomes are derived from long interspersed element 1 (LINE-1, L1) retroelements
We had observed that L1 mRNA and ORF1p expression vary strongly among urothelial carcinoma (UC) cell lines [16,18]
Other UC cell lines, like 5637 or UM-UC-3, express very little ORF1p, and the protein is undetectable in non-transformed urothelial cells like HBLAK

Summary

Introduction

One-sixth of the human genomes are derived from long interspersed element 1 (LINE-1, L1) retroelements. Intact elements contain an internal promoter at their 5 -end and two open reading frames encoding the RNA-binding protein ORF1p and the reverse transcriptase/endonuclease ORF2p [1,2] Their transcription is restrained by epigenetic mechanisms including DNA methylation and heterochromatic histone modifications like H3K9me3 [2,3,4,5]. Together with additional mechanisms acting at the posttranscriptional level and at the genomic insertion step, L1 expression and retrotransposition events are limited to short periods during germ cell development and embryogenesis. These controls often fail during cancer development, evidenced by L1 DNA hypomethylation, increased expression of transcripts and encoded proteins and actual retrotransposition events [1,6,7,8]. Reactivation of L1 in cancer may contribute to tumor development and progression in various ways, e.g., by increasing genomic instability, disrupting tumor suppressor genes, altering transcription of adjacent genes and stabilizing telomeres to counter senescence [1,9]

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