Dysregulation of Anti-Sense Transcription Revealed in Eye Tissues with Macular Degeneration

Eun Ji Kim, MSc

While previous studies have looked at the biological pathways in different stages of age-related macular degeneration (AMD), including observations of particular genetic mutations or variations, none have looked for variances in the transcriptome expression between normal retinal tissues and those in patients with AMD, until now.

A recent study led by Eun Ji Kim, MSc, aimed to examine anti-sense and non-coding RNA regulation in patients with AMD, and how RNA may be targeted for specific treatment therapies.

AMD has the most notable effect on the retina and retinal pigment epithelium in the posterior eyes. It has been known to cause vision loss, especially when it progresses to its more advanced forms, exudative/neovascular or dry/atrophic.

Kim and colleagues at the University of Pennsylvania examined tissues obtained from 16 eyes of volunteer donors to an eye bank, all of whom were Caucasian and did not have diabetes. The first group of eye donors had a mean age of 73.9 years ± 12.5 years and the second group’s mean age was 84.6 ± 7.2 years. According to the authors, this grouping was arranged “to maximize the number of eyes with AMD pathology.”

The research team said their goal for the study was “an investigation of the non-coding RNA and anti-sense transcription in AMD as compared to normal.”

According to the authors, “Peripheral human retina (PR) and peripheral RPE-Choroid-Scleral (PRCS) tissues (from normal and AMD donors) were high throughout RNA sequenced to identify unknown transcripts and quantify transcripts of coding and noncoding RNA that is not possible with microarrays or SAGE.” Although, they acknowledged that dissimilarly to the PR samples, the transcriptome investigation of the PRCS tissues were cross-examined together, mainly due to an inability to avoid contamination when separating individual layers in cadaver donor eye tissues.

“Access to high-quality tissues and greater sequencing depth allowed for a robust transcriptome profiling which includes many non-coding species. Many unannotated non-coding genes exist in introns as anti-sense to the parent gene. Strand-specific sequencing was employed to more easily identify such unannotated genes,” they wrote.

The authors also used strand-specific sequencing to uncover “considerable differential anti-sense transcription of protein-coding genes with significant enrichment of several pathways,” adding that, “This high level of differential anti-sense expression suggests its potential functional and clinical relevance in AMD.”

“As far as we are aware,” they continued, “this is the first demonstration of a consistent and dramatic global effect on antisense transcription that is associated with a disease state in humans and therefore is important information to provide the macular degeneration research community.”

With technology for sequencing advancing and the cost of this technology falling, the authors predict there will be more analysis in this area, with more opportunities to discover pathways and physiologies of various eye diseases.

Kim and colleagues noted that their study “increased our knowledge of the coding and non-coding regions of the genome expressed in these tissues. However, the exact spatial expression patterns of most of these genes and ncRNA are still unclear, as are the in vivo functions of these ncRNAs in retinal/ocular development and AMD pathogenesis. Functional studies of ncRNAs in the retina and other ocular tissues have the potential to greatly enrich our understanding of normal and disease processes of the eye and inspire novel therapeutic strategies.”

The study, “Complete Transcriptome Profiling of Normal and Age-Related Macular Degeneration Eye Tissues Reveals Dysregulation of Anti-Sense Transcription,” was published in Nature's Scientific Reports.