Advances and Trends in Omics Technology Development

Abstract

The human history has witnessed the rapid development of technologies such as high-throughput sequencing and mass spectrometry that led to the concept of "omics" and methodological advancement in systematically interrogating a cellular system. Yet, the ever-growing types of molecules and regulatory mechanisms being discovered have been persistently transforming our understandings on the cellular machinery. This renders cell omics seemingly, like the universe, expand with no limit and our goal toward the complete harness of the cellular system merely impossible. Therefore, it is imperative to review what has been done and is being done to predict what can be done toward the translation of omics information to disease control with minimal cell perturbation. With a focus on the "four big omics," i.e., genomics, transcriptomics, proteomics, metabolomics, we delineate hierarchies of these omics together with their epiomics and interactomics, and review technologies developed for interrogation. We predict, among others, redoxomics as an emerging omics layer that views cell decision toward the physiological or pathological state as a fine-tuned redox balance.

Keywords: mass spectrometry; next generation sequencing; omics; redoxomics; third generation sequencing.

Figure 1

Conceptual illustration on the hierarchy of different omics covered in this paper. We classify omics technologies into two categories, i.e., technology- and knowledge- based. Technology-based omics are based on technologies developed for understanding the “central dogma,” which can be further divided into three groups, i.e., the “four big omics” (genomics, transcriptomics, proteomics, and metabolomics), epiomics (epigenomics, epitranscriptomics, and epiproteomics), and their interactomics (DNA-RNA interactomics, RNA-RNA interactomics, DNA-protein interactomics, RNA-protein interactomics, protein-protein interactomics, and protein-metabolite interactomics). Omics indicated by the horizontal (above) and vertical (right-hand side) pink boxes of each interactomic term constitute to its two interacting omics. Knowledge-based omics are developed to understand a particular knowledge domain in a systematic way through integrating multiple omics information. Examples of this category include immunomics, microbiomics, and beyond.

Figure 2

Conceptual illustration on the future trend in omics technology development. There are three trends regarding the developmental paths of omics technologies. The first category of tasks is to resolve the technical problems existing in current omics techniques. The second trend is the identification of novel types of omics especially novel epiomics derived from modifications by various intermediate metabolites. With increased understanding on the importance of cell homeostasis at various levels regarding human disease management, there is a trend of cutting into a particular knowledge domain from a systematic angle via omics data integration as demonstrated by immunomics and microbiomics. In this trend, we propose “redoxomics” as an emerging type of knowledge-based omics given the critical roles of redox homeostasis in maintaining cells at the healthy state and the pathogenesis of various diseases including cancers.