Dr. Pandey’s lab uses system biology approaches to decipher cancer signaling networks and discover novel biomarkers and therapeutic targets. Dr. Pandey’s lab studies multiple cancer types including breast, pancreatic, lung, colorectal, esophagus and gastric cancer. SILAC and other labeling approaches including tandem mass tag (TMT) have been widely employed to study cancer biomarkers and therapeutic targets. Proteomics analysis of circulating tumor cells (CTCs) is another variant of cancer biomarker detection for early detection and prognosis of cancer.
Protein posttranslational modifications are key mechanisms in regulating protein activity and stability. Dr. Pandey’s lab has successfully used these quantitative proteomic strategies to study global protein phosphorylation, ubiquitination, acetylation and methylation. With these technologies, Dr. Pandey’s group has made seminal discoveries in multiple signaling pathways including EGFR/HER2, PI3K-AKT, RAS-RAF-MAPK and TSLP signaling. Cancer signaling research implying genetic engineering tools by either overexpressing or silencing of genes with the latest technologies like clustered regularly interspaced short palindromic repeat guide RNA associated with a Cas nuclease (CRISPR/Cas9).
Recently, Dr. Pandey’s group has developed a novel approach known as BioSITe for direct detection and quantification of site-specific biotinylation. This technology dramatically improves the confidence and sensitivity of the biotin proximity labeling-based protein interactome studies. Dr. Pandey’s lab employs this new technology to quantitatively and systematically explore the dynamic interactomes of key signaling molecules and proteins involved in cancer initiation and progression.
Highly sensitive targeted mass spectrometry-based assays for protein and small molecules will be at the forefront of diagnostics. One of our goals is to develop tests for early diagnosis, disease monitoring, risk assessment and personalized therapy. We are working in collaboration with clinicians to develop diagnostics tests for various diseases including many cancers and neurological disorders like Alzheimer’s disease and Parkinson’s disease. We are working in close association with Advanced Diagnostics Lab to develop and test lab developed assays that can be routinely used in clinic. These tests along with clinical and pharmacogenomics will serve as a platform for individualized medicine.
Clinical Assay Development
Clinical assays based on biomarkers have emerged as a highly-practical and sensitive means in medical research as opposed to the conventional diagnostics. Dr. Pandey’s lab employs advanced multi-omics methods coupled with rigorous computational analysis to discover molecular features that are significantly altered in disease. Biomarkers are validated in a large set of patients’ samples by evaluating their reproducibility, sensitivity and specificity. Validated biomarkers are then translated into rigorous assays optimized for sample preparations and LC-MS parameters for each assay to predict or diagnose disease.
Cellular Models of Disease
Cellular models provide a comprehensive, efficient and cost-effective way of studying human diseases. We culture primary cells derived from patients, iPSCs and established cell lines to understand molecular mechanisms of disease, study drug interactions and discover biomarkers. Using technologies like SILAC, CRISPR-Cas9, metabolic labeling and drug treatment, we investigate living cells and use them in several ways for downstream analysis including proteomic, lipidomic and metabolomic studies. We are studying many diseases using cellular models, including cancers, chromosomal anomalies and several rare single-gene disorders.
Pandey lab is involved in the investigation of sequence variation in inherited disorders like primary/secondary immune disorders, intellectual disability, hearing loss and developmental delay. Identification of genetic mutations in case of cancers can help understand the disease pathology and also guide selection of appropriate drugs that can specifically target the oncogenes or aberrantly activated signaling pathways. Research at Pandey lab involves identification of somatic mutations in cancers by DNA and RNA sequencing and studies their molecular phenomenon using mono-genic model systems of cell lines and mouse models.
The increasing global epidemic of infectious diseases can be effectively identified and managed by DNA sequencing of infectious microbes isolated from patient samples. Sequencing of clinical strains from non-responding patients leads to understand the mechanisms of drug resistance and development of active drugs against them. Pandey lab is involved in development of methods of accurate diagnosis of infectious diseases such as Lyme disease, tuberculosis, drug-resistant and hospital acquired infections.
Multi-omics analysis is a part of the systems biology approach employed by our laboratory.
Glycomics and glycoproteomics are a part of the systems biology approach employed by our laboratory.
Extracellular vesicle are a part of the systems biology approach employed by our laboratory.