Publications and Presentations

Comparative multiomic analyses of pancreatic ductal adenocarcinoma tumors with normal adjacent and pancreatic ductal tissues provide insight into genomic, proteomic, and immune dysregulation in driving disease.

Layering proteomic and genomic data from ovarian tumors provides insights into how signaling pathways correspond to specific genome rearrangements and points to the benefit of using protein signatures for assessing prognosis and treatment stratification.

We performed lipidomics analysis and characterized the lipidome changes during CD8+ effector T (Teff) cell differentiation. We applied 13C-glucose stable isotope labeling and identified unique PIPn (phosphoinositides) marked by saturated fatty acyl chains (0–2 double bonds).

Comprehensive proteogenomic characterization in 103 treatment-naive clear cell renal cell carcinoma patient samples highlights tumor-specific alterations at the proteomic level that are unrevealed by transcriptomic profiling and proposes a revised subtyping scheme based on integrated omics analysis.

Neurofibromatosis 1 is a hereditary syndrome. We found sixteen (out of 50) MPNSTs but none of the neurofibromas to have somatic mutations in SUZ12, implicating it as having a central role in malignant transformation.

Through metabolomics assays, we have shown that glutamate oxaloacetate transaminase 1 (GOT1) plays an important role in TH17 cell differentiation. Furthermore, we have identified the potential off-target effects of AOA, a non-selective pharmacological inhibitor of all aminotransferase.

Describes a process to detect and quantify minute amounts of predefined antigens. First time identify and quantify a neoantigen from a single cell perspective. Foundational to developing digitalized biopsy-based applications for companion diagnostics.

A method for the selective isolation, identification and quantification of peptides that contain N-linked carbohydrates. Groundbreaking methodology paper for glycosylated proteomics analysis.

Describes a process for selectively detect and quantify a neoantigen derived from a common cancer driver gene, TP53. Identify and quantify the neoantigen from a variety of cell lines and tumor tissues, assisting the development of a therapeutic bi-specific antibody.

Identify and quantify a group of shared neoantigens by TN breast cancer derived from Human endogenous retroviruses (HERV). HERVs represent 8% of the human genome.

Identifying and quantifying a neoantigen derived from K-Ras mutations, assisting the therapeutic method development. The target is later confirmed by numerous labs and companies. Quantification is strongly correlated with immunogenicity.

Using multi-omics analysis, we show that H9T, an engineered interleukin-2 partial agonist, promotes the expansion of CD8+ T cells without driving terminal differentiation. We demonstrated that engineered cytokine variants can be potential promising novel drugs.

By using the amide-labeled 15N-glutamine stable isotope tracing approach, we succefully identified the critical role of the CAD enzyme (carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase) in promoting the rapid recall response characteristic of memory T cells.

More than a decade after publication of the draft human genome sequence, there is no direct equivalent for the human proteome. In this issue of Nature Raghothama's group presented mass spectrometry-based analysis of human tissues, body fluids and cells mapping the large majority of the human proteome.

A comprehensive characterization of glycoproteins and providing information about the total N-linked glycan, glycosite-containing peptide and glycoprotein content of complex samples.

With different metabolomics approaches, we characterized the metabolic characteristics of tumors and immune cells after treatment of a glutamine antagonist. We demonstrated a novel difference in metabolic plasticity between cancer cells and effector T cells, potentially a “metabolic checkpoint” for cancer immunotherapy.