Office of Technology Transfer – University of Michigan

Analysis of Pseudogene Expression in the Transcriptomic Landscape of Cancer

Technology #5067

Discovery of Breast and Prostate cancer-specific pseudogenes

Cancer-specific pseudogenes were found by high throughput transcriptome analysis. Current evidence suggests that pseudogenes may provide another layer of gene regulation. Recent work to identify pseudogenes has been difficult given the high sequence similarity with coding genes. However, using RNA-Seq and high throughput sequencing, investigators were able to find and group pseudogenes based on expression profile. Interestingly, some of the pseudogenes were found to have differential expression in cancerous and healthy tissues or in different kinds of cancer, making pseudogene typing a viable option for cancer diagnosis and staging.

High throughput transcriptome analysis reveals diagnostic pseudogenes

Diagnostic pseudogenes were found through genome-wide RNA-Seq and high throughput transcriptome analysis. The pseudogenes that were found were classified as ubiquitous, tissue-specific, or cancer-specific. Analysis of prostate and breast cancer revealed differential expression of a pseudogene in cancerous versus healthy tissue and luminal versus basal, respectively. Sequencing of pseudogenes versus coding genes provides a diagnostic advantage in that the number of pseudogenes in the genome is comparatively small, and pseudogenes can be epistatic regulators to many coding genes. Pseudogenes may modulate their cognate gene’s function through generation of endogenous siRNAs, antisense transcripts, or miRNA binding sites. With gene sequencing-based diagnosing becoming more prevalent, finding methods to further specify and type conditions/disorders is becoming increasingly imperative. Pseudogene typing may provide another layer of specificity to current genetic diagnostics since pseudogenes may regulate the genes and others that are currently being typed in cancer.

Applications and Advantages

Applications

  • Genetic-based diagnosing of conditions/diseases
  • Study of gene regulation through identification of pseudogene regulatory networks
  • Study of cancer/disorder pathogenesis through identification of differentially regulated pseudogenes

Advantages

  • Increased identification of another layer of gene regulation, pseudogenes
  • Further specification of cancer/disorders based on typing of pseudogenes