Development of molecular diagnostics platforms for cancer diagnosis and prognosis.
Molecular diagnostics is a rapidly growing area for diagnosis, prognosis and treatment of diseases on the basis of molecular alterations. The profiling of molecular alterations not only helps in stratifying diseases but also helps in providing and choosing a targeted therapy on the basis of disease driving molecular alterations. Our lab is actively involved developing biomarkers for diagnosis, prognosis and treatment of various cancers by identifying molecular markers on the basis of multi-dimensional diagnosis of omics data using systems biology approaches. We have developed a platform for comprehensive precision medicine by isolating the cancer driving mutations by performing integrated analysis of genetics, epigenomics and transcriptome data .
Identification of biomarkers for early detection of pancreatic cancer, glioblastoma and colon cancer.
Our lab is invoved in development of novel biomarkers early detection, outcome prediction, risk assessment, companion diagnostic, patient stratification and treatment of different cancers by developing novel methods for meta-analysis of omics data and predictor development. We have a novel therapeutic targets and biomarkers for early detection, and treatment of Pancreatic Adenocarcinoma on the basis of expression profile of genes and miRNA by using innovative approach for data integration. The overview of Pancreatic cancer biomarker is shown below and spinned out as startup “Biomarx therapeutics” for further validation. Similar Biomarkers are also developed for Renal , Colon and Glioblastoma which are undergoing validation to determine their performance.
Identification of genomic determinance of alternative therapies like relaxation response, yoga in treatment of diff diseases including hypertension, inflammatory bowel disease.
Mind–body interventions (MBI) encompasses a wide range of practices and therapies designed to facilitate the mind’s capacity to affect health and well-being. There is a wide spectrum of mind body approaches available, however the most commonly used ones are yoga, breathing exercises, mindfulness and meditation. These practices elicit the relaxation response (RR); which is defined as a mind body intervention that offsets the physiological effects caused by stress, leading to reducing symptoms of multiple diseases including hypertension, inflammatory bowel disease, pain and cancers . Despite widespread interest in mind–body therapies and their potential as useful medical treatments, it is important to understand their biological mechanism using modern omics and systems biology approaches. In 2008, we first time identified genomics determinants of mind body therapies. Furthermore , using systems biology approach we demonstrated Relaxation Response induces temporal transcriptome changes in energy metabolism, insulin secretion and inflammatory pathways. RR intervention result upregulation of energy production and insulin secretion and reduction in NFKB cascade mediated inflammation (Fig below)[2, 3]. Now we have also shown in inflammatory Bowel disease  and Hypertension that RR may deliver its beneficial effects by reducing inflammation by downregulating NFKB Downstream and upstream genes. We have developed novel assays for monitoring the relaxation response in a subject by measuring the expression level of one or more genes that are modulated in a relaxation response.
To know more about this sphere, you can also go through the following publications:
- 1. Niles, H., et al., Functional genomics in the study of mind-body therapies. Ochsner J, 2014. 14(4): p. 681-95.
- Bhasin, M.K., et al., Relaxation response induces temporal transcriptome changes in energy metabolism, insulin secretion and inflammatory pathways. PLoS One, 2013. 8(5): p. e62817.
- Dusek, J.A., et al., Genomic counter-stress changes induced by the relaxation response. PLoS One, 2008. 3(7): p. e2576.
- Kuo, B., et al., Genomic and clinical effects associated with a relaxation response mind-body intervention in patients with irritable bowel syndrome and inflammatory bowel disease. PLoS One, 2015. 10(4): p. e0123861.
Development of novel algorithms for analysis of omics data including RNA sequencing, chip sequencing, DNA sequencing and proteomics.
MolintDB:Database of interactome information contains Protein-Protein, Protein-DNA, Protein-RNA, Co-expression and TFs-Target interaction information obtained from various public databases and literature.
SeqXbox: Collection of scripts for analysis of next-generation sequencing data. The collection has tools and scripts for basic processing, alignments, unsupervised and supervised analysis of next-generation sequencing data. It has standardized workflows for automated analysis of RNAseq (Figure 1), genotyping (Figure 2), methylation and proteomics data. It contains novel scripts for ultrafast alignment better alignment of sequencing data.The collection contain >100 scripts for supervised, functional and systems biology analysis of data.
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