Antisense and Allele-specific Transcription in Human Cancer

In recent years, our view of gene expression has changed profoundly, revealing pervasive transcription of the genome and we now appreciate the complexity of its regulation. Although we now know that regulation can take place at any level of the gene expression process, only certain layers of control such as transcriptional regulation and chromatin modifications have been extensively studied. However, researchers have not paid much attention to others such as antisense and allele-specific expression despite their widespread occurrence. This was largely due to underestimation of their importance and technical limitations. Antisense transcripts are at least partially complementary to a corresponding (mainly protein-coding) sense transcript and can have diverse functional roles in gene regulation (e.g., modifying epigenetic marks). This genomic arrangement also clearly suggests that antisensetranscripts are mainly involved in allele-specific gene regulation/silencing. We propose for the first time an extended approach reaching beyond conducting individual studies on antisense and allele-specific expression. We aim to construct a comprehensive picture of these processes in a large panel of cancer samples and healthy controls by making use of the current wealth of transcriptomics and (epi)genomics data provided in the constantly growing public repositories. In order to investigate the two processes, we plan to analyse these datasets in a high-throughput and highly optimised manner to obtain transcriptional resolution on all four DNA strands (both alleles) - this is not routinely performed in expression studies and will resolve confounding results for numerous transcripts, which otherwise would remain undetected. Identification of new biomarkers is fundamental for the development of novel diagnostic/prognostic stratification tools and innovative cancer therapies. The construction of comprehensive expression profiles and the correlation with patient survival are central to this. Antisense transcripts have barely been studied in this regard but are likely to exhibit high potential for such applications, which highlights the importance of the planned investigation. We further aim to investigate antisense transcripts of germline genes as a model to determine whether antisense expression might link to oncogenesis, as a number of these genes are aberrantly expressed in cancer as well as linked to oncogenesis and/or prognosis. In addition, we will investigate the association of antisense transcription with allele-specific expression as well as with allele-specific epigenetic regulation, using multi-omics datasets. In summary, we will investigate two widespread transcriptional phenomena, antisense and allele-specific transcription, in a large-scale study. This will not only lead to new insights into gene regulation and provide new diagnostic/prognostic marker and drug target candidates for clinical applications, but could also change the paradigm on how we conduct gene expression analyses in the future.

This project investigated cis non-coding natural antisense transcripts (ncNATs). What makes these transcripts so interesting is that they are transcribed from the same locus as other transcripts, deriving however from the opposite strand. This genomic arrangement suggests that many ncNATs act in cis on their sense partners and could be involved in allele-specific gene regulation. The progress in research on ncNATs is far behind the one of their protein-coding counterparts, but recent findings have unraveled manifold regulatory roles for some of these transcripts. This highlights their importance in gene expression regulation, which in turn is often disrupted in cancer. In this project, we aimed to reach beyond conducting individual studies and constructed a comprehensive picture of antisense transcription in a large collection of healthy and cancerous tissues. We exploited the current wealth of publicly available data in repositories and processed thousands of curated samples with a high-throughput analysis pipeline. We further generated a meta-collection of ncNATs by merging available annotations with newly assembled ncNATs. This provided the basis for detailed profiling of the antisense transcriptome. We deciphered global expression patterns of ncNATs, including the extent of antisense expression occurring in the evaluated tissue panel, tissue/cancer-associated expression patterns, chromosomal distribution and dysregulation in cancer. Furthermore, we compared many evaluated characteristics to the ones of protein-coding gene expression. Interestingly, testis presents with an elevated antisense expression, and we identified a large set of testis-specific ncNATs, some of which are activated in cancer - similarly to a group of protein-coding germline-specific genes that are aberrantly expressed in cancer. Altogether, this project led to new insights into the antisense transcriptome, and the generated data will serve as a basis to investigate many interesting aspects of ncNAT expression in the future. Further translational studies based on this work could yield novel biomarker and drug target candidates for clinical applications.