At the dawn of the transcriptomic medicine

Abstract

Impact statement This review describes the impact of transcriptomics on experimental biology and its integration into medical practice. Transcriptomics is an essential part of modern biomedical research based on highly sophisticated and reliable technology. Transcriptomics can aid clinical practice and improve the precision of clinical diagnoses and decision-making by complementing existing clinical best practice. The power of which will be increased when combined with genomic variation from genome wide association studies and next generation sequencing. We are witnessing the implementation of RNA-based technologies in clinical practice that will eventually lead to the establishment of transcriptional medicine as a routine tool in diagnosis. Progress in genomic analytical technologies has improved our possibilities to obtain information regarding DNA, RNA, and their dynamic changes that occur over time or in response to specific challenges. This information describes the blueprint for cells, tissues, and organisms and has fundamental importance for all living organisms. This review focuses on the technological challenges to analyze the transcriptome and what is the impact of transcriptomics on precision medicine. The transcriptome is a term that covers all RNA present in cells and a substantial part of it will never be translated into protein but is nevertheless functional in determining cell phenotype. Recent developments in transcriptomics have challenged the fundamentals of the central dogma of biology by providing evidence of pervasive transcription of the genome. Such massive transcriptional activity is challenging the definition of a gene and especially the term “pseudogene” that has now been demonstrated in many examples to be both transcribed and translated. We also review the common sources of biomaterials for transcriptomics and justify the suitability of whole blood RNA as the current optimal analyte for clinical transcriptomics. At the end of the review, a brief overview of the clinical implications of transcriptomics in clinical trial design and clinical diagnosis is given. Finally, we introduce the transcriptome as a target for modern drug development as a tool for extending our capacity for precision medicine in multiple diseases.

Expression Quantitative Trait Loci (eQTLs) Associated with Retrotransposons Demonstrate their Modulatory Effect on the Transcriptome

“…Genome-wide transcriptome analysis supplies a useful tool for understanding the basis of multifactorial diseases as it offers a great opportunity to identify both biomarkers and a better understanding of disease mechanisms [23,25,29]. Profiling of the transcriptome is easy to perform and often supplies insight into pathological processes [30,31]. Our data indicates that it is important to consider, not only the SNP based genotype profile of the patients, but also the potential impact of the variation due to RIPs when analysing transcriptomes.…”

Mulberry and Hippophae‐based solid beverage attenuate hyperlipidemia and hepatic steatosis via adipose tissue–liver axis

“…As shown above, better efficacy was observed in the high‐dose treatment of MHP, and thus MHP‐H was chosen for further investigations. As a growing number of studies indicate that transcriptomics has practical applications in phytomedicine development (Koks et al., 2021 ), we performed transcriptomic analysis to investigate the mechanism of MHP. To investigate the impact of MHP on the global gene expression of rats, hepatic transcriptomics analysis was performed.…”