Mass Spectrometry

We are using state-of-the-art mass spectrometric methods for identification of proteins and for characterizing post-translational modifications in signal transduction pathways and in the analysis of several different cancers. We are using different techniques that help us quantitate levels of protein as well as post-translational modifications. We are also developing computational methods that allow us to extract annotated information from existing databases including genomic databases while performing searches using mass spectrometry-derived data.

Cancer Biomarkers

Our lab is involved in identification of biomarkers and therapeutic targets of a number of cancers including pancreatic cancer, hepatocellular carcinoma, breast cancer and cholangiocarcinoma. We use SILAC and iTRAQ based strategies to identify differentially regulated proteins between non-neoplastic and neoplastic conditions of these cancers. Candidate molecules are further validated using tissue microarrays to determine the prevalence.

  • Pancreatic Cancer

    Pancreatic cancer is one of the leading causes of cancer deaths in the United States. High mortality rates in pancreatic cancer have been attributed to late clinical presentation and lack of effective therapies. We are using high resolution mass spectrometry to carry out proteomic profiling studies to identify biomarkers and therapeutic targets of pancreatic cancer. Our efforts include proteomic profiling of pancreatic juice (Gronborg et al.), secretome analysis (Gronborg et al.) to identify biomarkers, phosphoproteomic profiling to identify activated signaling pathways (Harsha et al.) and compilation of candidate biomarkers (Harsha et al.) and molecular alterations reported in the context of pancreatic cancers (Ranganathan et al.).

  • Hepatocellular Carcinoma

    Hepatocellular carcinoma (HCC) is the fifth most common cancer worldwide. Early diagnosis of HCC in known to improve the outcome with appropriate clinical intervention. Our lab has previously published iTRAQ based quantitative proteomic efforts to identify candidate biomarkers of hepatocellular carcinoma (Chaerkady et al.). Further, we have also identified differentially regulated glycoproteins in hepatocellular carcinoma using 18O based quantitative proteomic strategy (Chaerkady et al.).

  • Cholangiocarcinoma

    Cholangiocarcinoma is the second most common form of hepatic tumor and accounts for 3% of all gastrointestinal cancers in the world. Early detection of cholangiocarcinoma offers best hope for cure. However, the existing markers to diagnose cholangiocarcinoma suffer from lack of specificity and sensitivity. Towards this end, we carried out proteomic profiling of bile from cholangiocarcinoma patients to identify secreted biomarkers (Kristiansen et al.). We have also carried out 18O based quantitative proteomic study to identify membrane markers differentially expressed in cholangiocarcinoma as compared to non-neoplastic biliary tract tissue (Kristiansen et al.).

Stem Cell Proteomics

Embryonic stem cell differentiation to neuronal cells or astrocytes involves multiple stages. Quantitative proteomics was carried out to map the temporal events during embryonic stem cell differentiation to neuronal cells, the results of which were published in Journal of proteome research (Chaerkady et al.).  In this study we took advantage of multiplex quantitative proteomic analysis, capable of analyzing eight different samples simultaneously to monitor the temporal dynamics of protein abundance as human embryonic stem cells differentiate into motor neurons or astrocytes .This study was funded by Maryland stem cell research foundation.

In collaboration with Institute of Stem cell engineering lab at Hopkins, a study was done to identify the differences between embryonic stem cells and embryonal carcinoma cells .Though the two cell types are pluripotent, being derived from teratocarcinomas, embryonic carcinoma cells differ from embryonic stem cells in their oncogenic potential. We were able to identify differences that contribute to oncogenicity versus pluripotency. A summary of identified results were published in the Journal Proteomics (Chaerkady et al.)

miRNA Targets

We have used a quantitative proteomic approach to identify targets of miR-21 at the protein level. miR-21 is a miRNA that has been reported to be associated with multiple cancer-related processes including proliferation, apoptosis, invasion, and metastasis. This study was published in the journal Proteomics (Yi et al) .Although only 4 targets of this miRNA were known when we initiated our studies, we identified 58 putative targets from a single proteomics experiment, several of which we were able to validate using luciferase assays. Given the success of this approach, we are embarking on carrying out systematic proteomic analyses to identify targets of miRNAs that are involved in cancers.