MOLECULAR TARGETING OF THE HUMAN DARK GENOME FOR TREATING DISEASES INCLUDING CANCER, CVDs, etc.

MOLECULAR TARGETING OF THE HUMAN DARK GENOME FOR TREATING DISEASES INCLUDING CANCER, CVDs, etc.

Prof Dr John Giannios, Director of Postgraduate Studies in Genomic Medicine and Healthcare, USW, UK.

The human dark genome is containing repetitive-sequences that are generated by the action of mobile genetic-elements, termed as transposable-elements or transposons which are moving among different genomic-locations. There are the DNA-transposons characterized by a mechanism of cut and paste, and retrotransposons which comprise more than 40 % of the human-genome with a mechanism of copy and paste involving a RNA-intermediate. Retrotransposons consist of LTRs divided in Class-I human ERV or HERV, Class-II ERV and Class-III ERV which are generated by exogenous retrovirus, and non-LTR elements that are consisting of short noncoding-RNAs termed as SINEs composed of more than one million copies of Alu in humans and MIR which are hijacking the LINE protein-machinery required for retrotransposition. LINE is composed by L2 and L1 which is encoded by the RNA chaperone-protein ORF1p and endonuclease, reverse-transcriptase protein ORF2p. Thus, retrotransposons may use a reverse transcriptase- enzyme or RT for copying an RNA-transcript into the host-genome. Both LINE-1 and HERV are coding for endogenous reverse-transcriptase. Non-nucleoside reverse-transcriptase inhibitors may induce cancer cell-differentiation and tumor growth-arrest. Also, similar effects can be induced with RNA-interfering treatment by targeting specific-siRNAs against upregulated LINE-1 retrotransposition and dysregulated HERVs, such as HERV-K or HML-2 which is an endogenous reverse-transcriptase protein-structure implicated in diseases including cancer, type-1 diabetes, neurodegenerative-diseases and autoimmune-diseases.   The retrotransposons with advancing-age get activated and become deleterious by accumulating deletions, insertions, inversions, translocations, duplications, somatic-mosaicism, chromosome-breakage and rearrangements, alterations of regulatory gene-structure and expression by creating new polyadenylation-sites, new exons or exon-skipping and modifying with alternative-splicing, deleterious-mutations or other genomic-rearrangements which may affect the activity of encoded-proteins leading to activation of DNA- damage mechanisms, immunity and piRNA-PIWI pathways, and genomic or epigenomic-effects including DNA-methylation, histone-modifications and/or dysregulation of noncoding-RNAs  which are linked to retrotransposition that may lead to pathogenesis of diseases. Heritable epigenetic-modifications, such as DNA-methylation of CpG-dinucleotides may be used for the therapeutic suppression of L1-mobilization and deleterious or pathogenic LINE-1 or L1 retrotransposon-insertions into human proto-oncogenes which may contribute to oncogenesis and its progression. Furthermore, overexpressed LINE-1 or L1 encoded-protein ORF1p has been linked to post ischemic myocardial-damage which may be inhibited with nanodelivery of antisense-oligonucleotides in cardiomyocyte-nuclei leading to reduction of infarct-size and improvement of post ischemic-recovery by upregulating Akt and phosphorylation of PKB. Thus, a potential anti ischemic therapeutic-approach consisting of the modification of the L1’s transcriptional-activity may be implemented in the healthcare system as a Genomic-Medicine approach. The L1-copies which compose more than one quarter of the human-genome are overexpressed after reperfusion of cardiac ischemic-tissues leading to microvascular-injury, activation of inflammatory-response due to the localization of WBCs, and subsequent release of interleukins and ROS which may cause redox-signaling and apoptosis or type-I PCD in the endothelium of small-capillaries, reduction of nitric-oxide, oxidative-damage, and acceleration of necrosis. Furthermore, the restoration of the blood flow may reintroduce oxygen in cells destroying their proteins, DNA and plasma-membranes which may induce the release of additional free-radicals that may cause more ischemic-obstruction. Thus, ischemic-preconditioning is required for myocardial-protection which may be achieved by the inhibition of a large component of the dark genome, such as L1 that can be achieved by antisense-therapy. Another therapeutic approach for inhibiting the pathogenic-effects of retrotransposons may be achieved by targeting epigenomic-mechanisms. For instance, DNA hypomethylation may activate mobility of retrotransposons, and insertion of LINE-1 in genomic-regions may lead to chromatin-methylation in CG-dinucleotides or CpG-islands causing genomic-instability. WGS, RNA-seq and DNA-methylation seq using blood-samples may detect upregulation of LINE-1, HERV-K, SVA-retrotransposons or LINE-1 methylation, etc. Thus, genomic and epigenomic evidence may lead to personalized medicine approaches against hemoglobinopathies, metabolic diseases, psychiatric and neurological-diseases, cancer, CVDs, autoimmune-disorders, diabetes and other serious diseases improving  their screening, prevention, prognosis, monitoring, diagnosis and mainly treatment by tailoring the administration of targeted agents based on pharmacogenomics and even pharmacoepigenomics which may circumvent drug resistant pathways. Delivery of targeted therapeutic molecules may be facilitated with nanodelivery systems enhancing therapeutic index and reducing systemic toxicity. Analyzing and targeting the disease causative components of the dark genome may offer revolutionary solutions against many currently incurable diseases.