IOB has a well-equipped bioinformatics and experimental facilities to carry out research in molecular biology, cell culture, bioinformatics, genomics, proteomics, metabolomics and lipidomics. The focus is on combining experimentation with computational biology to understand biological systems and human diseases.
We study gene expression profiles, genome copy number variations, microRNAs, and alternative splicing of genes using cutting edge technologies. We carry out molecular biology experiments including cell culture, DNA and RNA isolation, cloning and quantitative real time PCR to study signaling pathways in various cancers. To translate discoveries from bench to bedside, tissue microarrays are used for validation of candidate molecules.
We use quantitative proteomics approaches for the identification of candidate biomarkers in human diseases and infectious microorganisms. We also routinely employ high-resolution proteomics for proteogenomic characterization of various organisms. State-of-the-art mass spectrometry facility at IOB include an LTQ Orbitrap Velos mass spectrometer which is a hybrid Fourier Transform mass spectrometer that combines features of linear ion trap and orbitrap mass analyzer. We also have Agilent 1260 Infinity series HPLC system and Thermo Scientific Easy nLC II liquid chromatography systems. Apart from mass spectrometry, facilities to carry out other proteomic experiments like yeast-two hybrid, GST-pull down and western blotting are also available at IOB. These platforms help us to study cell signaling molecules and their interactions in cancer and other diseases.
Metabolomics and Lipidomics
Metabolomics is the “systematic study of the unique chemical fingerprints that specific cellular processes leave behind”. A metabolomics analysis provides a deeper understanding of metabolite expression within complex biological systems, and the proper analysis and interpretation of such results may potentially indicate the metabolite function.
We use both targeted and untargeted metabolomics/lipidomics approaches for developing markers for human diseases with the major emphasis towards rare diseases. We routinely develop targeted methods for absolute quantification of metabolites/lipids from different biological fluids. We use Altis TSQ for targeted and Q-exactive HFX for the untargeted analysis with Dionex and Vanquish UHPLCs in the front end. Currently, we are performing metabolomics/ lipidomics on different biological fluids like serum, dried blood spots (DBS), urine, tissue and cell extracts. Our methods can identify variety of lipids like ceramides, dihydroceramides, glucosyl ceramides, phosphatidyl cholines, phosphatidyl ethanolamine, phosphatidyl serines and free fatty acids and metabolites like amino acids, organic acids and carnitines on our LC-MS platform. We are continuously working to enhance the coverage. For absolute quantification of these metabolites/lipids, we apply specific stable isotopically labelled internal standards.
With a vision of providing a platform for future Systems Biology approaches, we developed several highly curated databases on various aspects of Omics data, which can act as essential ingredients for discovery themes which use Systems Biology. We have successfully developed highly curated protein databases such as Human Protein Reference Database (HPRD) and Plasma Proteome Database. We have developed several resources for gene expression data pertaining to cancers including breast cancer and primary immunodeficiency diseases. We also curated information about signaling pathways in humans and developed the resource ‘NetPath’. We also developed a mass spectrometry data analysis pipeline for proteogenomic investigations. We are currently working on the development of machine-learning based models for the integration of multi-omics data.