OMICS Based Biomarker Discovery And Its Importance - Khushman Taunk

Fundamental Research, Clinical, Analytical Omics, Biomarker Discovery and Artificial Intelligence.

Diseases are complex abnormalities at the molecular level in a living organism. Living organisms are made up of cells. Dysregulation of normal functioning of molecular machinery of the cells leads to disease progression. At the core of such diseases, the major responsible elements are alterations in genes and proteins. The genetic information in our body is encoded in deoxyribonucleic acid (DNA), which gets transcribed into ribonucleic acid (RNA) and further translated into proteins. This complete sequence of events is termed as ‘the Central Dogma of Biology’. Presently, it is known that the Human Genome encodes for around 20,000 predicted protein-coding genes. Moreover, there are a number of complex regulatory mechanisms due to which a single gene could code for more than one protein. Transcriptional and post- transcriptional regulations lead to the formation of many protein-coding mRNAs.
Similarly, translational and post-translational mechanisms convert mRNA to nearly 6.13 million protein species. Post-translational mechanisms majorly include proteolytic cleavage of the parent protein, addition of chemical groups to specific amino acids, formation of multisubunit complexes, etc. These modifications result in proteins with different functions. Many diseases have high mortality rates and the best way to tackle any disease, is to diagnose it early. In this regard, finding the Biomarkers of diseases will serve the purpose well. Biomarkers are the biomolecules such as proteins, lipids, metabolites, mRNA and genes that are capable of differentiating the healthy and pathophysiologically altered state of a complex biological system. The identification and characterization of biomarkers with analytical research tools such as genomics, proteomics, transcriptomics, lipidomics, and metabolomics collectively constitutes the
OMICS pipeline of research.
The total protein content of a cell is termed as proteome. Similarly, in a cell, the total lipid content is called lipidome, the total metabolite content is called metabolome and the total gene content is called genome. The analytical study of these biomolecules of a living system is suffixed by term ‘omics’ after the name of the biomolecule species. For instance, study of genome is called genomics, proteome is called proteomics, transcriptome is called transcriptomics, lipidome is called lipidomics, and metabolome is called metabolomics. All such biomolecules within the cell determines the functions of each cell and intercellular interactions in turn regulate the physiology of the living system. Alterations in the status of any of these biomolecules from those in the normal functioning state of the cell lead to different clinical conditions. There are immense challenges in investigating the magnitude and complexity of these alterations. These challenges have to be overcome so that we can identify the changes that have occurred and relate them to clinical presentations for disease management. Towards this the OMICS technologies have helped the scientific community to reliably address these  challenges.
The advent of OMICS technologies has provided various tools that can be used for understanding complex diseases. Since the late 1900 s, there has been a fast-paced, consistent evolution of genomics technologies that have identified several genes that are responsible for various diseases. The research focus has thereafter shifted toward proteins as these are the workhorses within the cell. Proteins are the molecules that are components of the cellular architecture. They catalyze reactions, mediate inter and intracellular communications via signal transduction through a series of proteins and their dynamic changes, and have many other roles as well. Similarly, the research focus has also gained momentum in understanding the role of mRNA, lipids and metabolites in various diseases. The OMICS based study of these biomolecular content of a living system, is therefore undoubtedly important for mining key molecules for risk assessment, diagnosis, prognosis, prediction of the disease process, response to therapy, and drug development. The outcome of such an investigation could provide a
potential bio-signature of that would eventually help in better disease management.

Our lab at National Centre for Cell Science, Pune, India, led by Dr Srikanth Rapole aims towards finding novel potential biosignatures for various diseases. Primarily, our lab is currently focused on multi-omics based biomarker discovery for breast cancer and blood cancers. We use modern state of the art high resolution mass spectrometry platforms to identify and  haracterize proteins, metabolites and lipids in biological systems. Analysis of proteomic, metabolomic and lipidomic data reveals significant insights that facilitate the molecular  haracterization of human diseases. It also provides the ability to decipher the diverse molecular mechanisms for the initiation and progression of diseases. Eventually, this leads to the  dentification of novel potential targets, which could be further evaluated for disease management.


 Khushman Taunk is from Kharagpur, West Bengal, India. After
completing her M.Tech in Biotechnology in 2012, she  got trained in mass spectrometry
based omics technologies at National Centre for Cell Science, Pune, India. She started  her
doctoral studies in 2018 in the area of biomarker discovery and cancer biology. Her
research aims towards elucidation of markers for breast cancer and deciphering the
molecular mechanisms that are specific to subtypes of breast cancer. She enjoys working in
the laboratory and in free time she explore new places, music and read scientific journal


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