Abstract
In eukaryotic cells the genome is highly spatially organized. Functional relevance of higher order genome organization is implied by the fact that specific genes, and even whole chromosomes, alter spatial position in concert with functional changes within the nucleus, for example with modifications to chromatin or transcription. The exact molecular pathways that regulate spatial genome organization and the full implication to the cell of such an organization remain to be determined. However, there is a growing realization that the spatial organization of the genome can be used as a marker of disease. While global genome organization patterns remain largely conserved in disease, some genes and chromosomes occupy distinct nuclear positions in diseased cells compared to their normal counterparts, with the patterns of reorganization differing between diseases. Importantly, mapping the spatial positioning patterns of specific genomic loci can distinguish cancerous tissue from benign with high accuracy. Genome positioning is an attractive novel biomarker since additional quantitative biomarkers are urgently required in many cancer types. Current diagnostic techniques are often subjective and generally lack the ability to identify aggressive cancer from indolent, which can lead to over- or under-treatment of patients. Proof-of-principle for the use of genome positioning as a diagnostic tool has been provided based on small scale retrospective studies. Future large-scale studies are required to assess the feasibility of bringing spatial genome organization-based diagnostics to the clinical setting and to determine if the positioning patterns of specific loci can be useful biomarkers for cancer prognosis. Since spatial reorganization of the genome has been identified in multiple human diseases, it is likely that spatial genome positioning patterns as a diagnostic biomarker may be applied to many diseases.
Highlights
Relocation to blocks of heterochromatin is associated with gene repression for some genes (Brown et al, 1997, 1999; Francastel et al, 1999; Wijchers et al, 2015); this is not a general rule as other silenced gene loci do not associate with blocks of heterochromatin (Moen et al, 2004; Takizawa et al, 2008a)
There is no way to predict which genes will reposition in cancer
As we gain a better understanding of how spatial positioning is regulated in a normal cell, it may become easier to predict regions that will be diagnostically interesting
Summary
A SHORTAGE OF QUANTITATIVE CANCER BIOMARKERS indolent and aggressive cancers, to aid the determination of the best possible treatment plan for the patient. Due to a lack of additional markers to identify aggressive cancer, many overdiagnosed patients are being overtreated since they are receiving unnecessary therapies Are these patients receiving no therapeutic benefit, as their cancer would never have significantly progressed, they are being harmed by the cancer treatment itself, because treatments can have both short-term and long-term effects that cause illness, reduce quality of life, create large financial burdens (for example by loss of income), and can even lead to death (Cooperberg et al, 2010; Welch and Black, 2010; Bleyer and Welch, 2012; Sandhu and Andriole, 2012). It has become a major focus of research to find markers that can distinguish between
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