Premature transcript termination, trans-splicing and DNA repair: a vicious path to cancer

American Journal of Blood Research 01/2011; 1(1):1-12.
Source: PubMed


So far, about 800 different chromosomal translocations have been characterized in hemato-malignant and solid tumors. Chromosomal translocations mostly result in the expression of chimeric fusion proteins associated with enhanced proliferation and/or malignant transformation. Here, we demonstrate that genes frequently involved in such genetic rearrangements exhibit a unique feature: premature transcriptional termination. These early-terminated RNA molecules have an abundance of 10-20% when compared to their cognate full-length transcripts. They exhibit an unsaturated splice donor site that gives rise to trans-splicing events, leading to RNAs displaying exon repetitions or chimeric fusion RNAs. These arbitrary fusion RNAs mimic the presence of a chromosomal translocation in genetically unaffected cells. Based on our and published data, we propose the hypothesis that these artificial "chimeric fusion transcripts" may influence DNA repair processes, resulting in the generation of de novo chromosomal translocations. This idea provides a rational explanation why different individuals suffer from nearly identical genetic rearrangements.

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Available from: Rolf Marschalek, Oct 09, 2015
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    • "Interestingly, several fusion transcripts tested as positive in leukocytes contained ‘wrong’ junction between BCR and ABL exons, resulting into a non-functional fusion protein representing false positivity. As it was demonstrated later, a premature termination of transcripts participating in intergenic trans-splicing events in the absence of corresponding chromosomal translocation may represent another source of positivity [34]. More recently, Song et al [19] demonstrated 42% (21/50) incidence of BCR-ABL p190 in UCBs using both nested and RT qPCR with identical sensitivity of 10−4, and this fusion transcript was detected in 74% (59/80) of healthy individuals. "
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    ABSTRACT: The first event in origination of many childhood leukemias is likely the presence of preleukemic clone (transformed hematopoietic stem/progenitor cells with preleukemic gene fusions (PGF)) in newborn. Thus, the screening of umbilical cord blood (UCB) for PGF may be of high importance for developing strategies for childhood leukemia prevention and treatment. However, the data on incidence of PGF in UCB are contradictive. We have compared multiplex polymerase chain reaction (PCR) and real-time quantitative PCR (RT qPCR) in neonates from Slovak National Birth Cohort. According to multiplex PCR, all 135 screened samples were negative for the most frequent PGF of B-lineage acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML). To explore the prevalence of prognostically important TEL-AML1, MLL-AF4 and BCR-ABL (p190), 200 UCB were screened using RT qPCR. The initial screening showed an unexpectedly high incidence of studied PGF. The validation of selected samples in two laboratories confirmed approximately ¼ of UCB positive, resulting in ∼4% incidence of TEL-AML1, ∼6.25% incidence of BCR-ABL1 p190, and ∼0.75% frequency of MLL-AF4. In most cases, the PGF presented at very low level, about 1-5 copies per 105 cells. We hypothesize that low PGF numbers reflect their relatively late origin and are likely to be eliminated in further development while higher number of PGF reflects earlier origination and may represent higher risk for leukemia.
    PLoS ONE 03/2014; 9(3):e91116. DOI:10.1371/journal.pone.0091116 · 3.23 Impact Factor
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    • "However, this was not the case, because we demonstrated more than a decade later that normal cells are indeed capable of producing such transcripts. In fact, these fusion transcripts were not produced by genomic alterations rather they are derived from trans-splicing events [11]. cDNA-synthesized from nucleic acids isolated from peripheral mononuclear cells (PBMCs) of healthy individuals demonstrated in nested PCR experiments that e.g., MLL-AF4 and NPM-ALK fusion transcripts can be readily identified in each of the investigated samples. "
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    ABSTRACT: We among others have recently demonstrated that normal cells produce "fusion mRNAs". These fusion mRNAs do not derive from rearranged genomic loci, but rather they are derived from "early-terminated transcripts" (ETTs). Premature transcriptional termination takes place in intronic sequences that belong to "breakpoint cluster regions". One important property of ETTs is that they exhibit an unsaturated splice donor site. This results in: (1) splicing to "cryptic exons" present in the final intron; (2) Splicing to another transcript of the same gene (intragenic trans-splicing), resulting in "exon repetitions"; (3) splicing to a transcript of another gene (intergenic trans-splicing), leading to "non-genomically encoded fusion transcripts" (NGEFTs). These NGEFTs bear the potential risk to influence DNA repair processes, since they share identical nucleotides with their DNA of origin, and thus, could be used as "guidance RNA" for DNA repair processes. Here, we present experimental data about four other genes. Three of them are associated with hemato-malignancies (ETV6, NUP98 and RUNX1), while one is associated with solid tumors (EWSR1). Our results demonstrate that all genes investigated so far (MLL, AF4, AF9, ENL, ELL, ETV6, NUP98, RUNX1 and EWSR1) display ETTs and produce transpliced mRNA species, indicating that this is a genuine property of translocating genes.
    Cancers 12/2012; 4(4):1036-49. DOI:10.3390/cancers4041036
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    ABSTRACT: The biological process of differentiation - from a fertilized egg to a human being - is a consecutive mechanism that leads to the establishment of tissue-specific gene expression, but also to a coordinated shut-down of all those genes that are not necessary for a given cell type. This process is accompanied by posttranslational modifications of the chromatin (DNA methylation and covalent histone modifications), also termed the "epigenetic layer". All epigenetic processes are mediated by protein complexes that either mediate specific DNA methylation patterns, or modify nucleosomal proteins in a covalent fashion (acetylation, methylation, phosphorylation and ubiquitinylation). One important player involved in epigenetics is the MLL protein which represents a histone H3 methyltransferase. The MLL gene gained much attention because of its frequent genetic rearrangements, thereby creating oncogenic MLL fusion genes that cause acute leukemia in pediatric and adult patients. This article is summarizing certain functional aspects about MLL, but is mainly emphasizing on an alternative splice event within the PHD domain. This changes the biological properties of the MLL protein, thereby influencing its ability of being either a transcriptional activator or repressor.
    Pharmazie 07/2013; 68(7):601-7. DOI:10.1691/ph.2013.6514 · 1.05 Impact Factor
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