We read with great interest the article by Allain et al.1 and were intrigued by the UGT2B17-mediated direct drug inactivation or indirect anti-leukaemic response modification of various therapeutic agents in chronic lymphocytic leukaemia (CLL). In human, UGT2B17 gene expression is detected in hepatic tissues as well as in steroid target tissues.2 Nonetheless, shown elegantly in the study by Allain et al.1 is that in lymphoid cell models and in CLL patients occurs a lineage-inappropriate UGT2B17 overexpression, predominantly mediated from the alternative UGT2B17_n2 transcript that comprises the additional exon 1c, extending the 5′-untranslated region. Lower UGT2B17 expression from the alternative UGT2B17_n3 and n4 transcripts, comprising the alternative 1b exon, was also reported. Of note, all novel transcripts identified encode a functional UGT2B17 protein.1 Since UGT2B17 represents a main conjugating enzyme for fludarabine glucuronidation and consequently UGT2B17 misexpression could affect primary response to first-line treatment with fludarabine in CLL patients, we fully agree with Allain et al.1 that the molecular machinery underlying high UGT2B17 expression in lymphoid cells warrants further clarification. Herein, we present evidence that both UGT2B17 exons 1b and 1c were evolutionarily derived from endogenous-retrovirus (ERV) sequences and that UGT2B17 overexpression in B cells of CLL patients is driven by the in cis aberrant activation of long terminal repeats (LTRs) of the ERV1 family.
ERVs represent heritable provirus insertions into the host genome DNA, remnants of exogenous infectious retroviruses.3 The typical genomic structure of a retrovirus consists of a gag, pro, pol, and env genes flanked by two LTRs that naturally comprise core transcription regulatory elements and transcription factor (TF) binding sites.3 The majority of ERVs in human genome has undergone recombination events between the 5′- and 3′-LTRs, resulting in solitary LTRs.4 Interestingly, many solitary LTRs have preserved their ancestral promoter function and, when positioned in the sense orientation of an adjacent host gene, could drive ectopic transcription initiation.4 Accordingly, because epigenetic silencing represents the predominant path to ERV transcription inactivation, alterations of the epigenetic landscape occurring during cellular transformation events could likely lead to ERV derepression with a significant impact on host gene transcriptional networks, a process designated as onco-exaptation.5
Interestingly, molecular evolutionary analysis6 of the genomic segment comprising UGT2B17 exon 1c and its non-canonical proximal promoter sequence reveals that these genetic elements are comprised within a Harlequin-int LTR/ERV1 sequence, of sense orientation to UGT2B17 gene (Fig. 1). Accordingly, UGT2B17 exon 1b and the corresponding proximal promoter were also evolutionary derived from an HERVH48-int LTR/ERV1 sequence. However, because the HERVH48-int LTR is of anti-sense orientation (Fig. 1), a less potent promoter activity compared to Harlequin-int LTR would be expected,4 as is the case in the study by Allain et al.1
TF chromatin immunoprecipitation and sequencing (ChIP-seq) data in 91 cell types from the ENCODE Project7 reveal that the Harlequin-int LTR sequence comprises a binding site for RNA polymerase II subunit A (POLR2A), which, among 74 cell types examined, is functional specifically in the lymphoid cell lines (Fig. 1). Likewise, the HERVH48-int LTR comprises a POLR2A site that is also specific for B cells. Interestingly, short upstream of the HERVH48-int POLR2A site located is a B-lineage functional binding site for RELA proto-oncogene (Fig. 1). In this sense, the identification in this retroelement-derived genomic segment of DNA binding sites for the CCCTC-binding factor (CTCF) is also of importance (Fig. 1). CTCF has the potential to act as transcriptional insulator disabling the interaction between enhancers and non-canonical promoters;8 therefore, in a tantalising scenario, a B-lineage-specific aberration of CTCF function could allow the RELA binding site to serve as an unrestricted enhancer of UGT2B17 inordinate transcription in B-cancerous cells.9 These findings are likely in accordance with the results from the study by Allain et al.,1 where a co-expression signature of UGT2B17 with several nuclear factor-κB (NF-κB)-regulated genes was documented, subsequently pointing to NF-κB as a key regulatory “hub point” that targets the non-canonical promoter and drives UGT2B17 misexpression in CLL cells.
It has been shown that the positive selection of novel hypomethylation motifs, which could subsequently allow the epigenetic derepression of ERV transcription, entails co-evolution of genetic sub-clonal complexity in CLL.10 Subsequently, it would be tempting to deduce that the efficacy of UGT2B17 expression as a prognostic marker of high-risk CLL2 is mechanistically linked to the retroviral origin of its ectopic promoters. Most importantly, since the LTR-driven misexpression of UGT2B17 may impact the effectiveness of fludarabine-based interventions, quantitative PCR-based assays of LTR-driven UGT2B17 ectopic transcription in cancerous B cells would help tailor fludarabine dosage to better stratified CLL patients.
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Acknowledgements
S.I.P. gratefully acknowledges Professor George Kassiotis at the Francis Crick Institute for the enlightening discussion on endogenous retroviruses during the EMBO|EMBL Symposium “The Mobile Genome” and the fruitful mentoring provided ever since.
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Conception and design of the work: S.I.P. Data collection: S.I.P. Data analysis and interpretation: S.I.P. Drafting of the paper: S.I.P., C.J. Supervision of the work: C.J. Critical revision of the article: S.I.P., C.J.
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The ChIP-seq data reported in this study represent publicly available material, generated from the Encyclopaedia of DNA Elements (ENCODE) Consortium, and are archived at the UCSC Genome Browser Database (https://genome.ucsc.edu/).
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Papamichos, S.I., Jungbauer, C. Comment on: “UGT2B17 modifies drug response in chronic lymphocytic leukaemia”. Br J Cancer 123, 1345–1346 (2020). https://doi.org/10.1038/s41416-020-1005-5
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DOI: https://doi.org/10.1038/s41416-020-1005-5