Biomarker Detection Using Omics

Tuesday, 14 November • 15:45 – 17:15

This session will provide information on how next-gen sequencing platforms like proteomics and RNA-Seq help establish gene signatures and PD markers in a disease-relevant context. 

Session Chair:

Kalyani Gampa, M.S. (Novartis)

Speakers:

Spatial Proteomics Enables Identification of Prognostic Biomarkers in Kidney Cancer
Anupama Reddy, M.S., Ph.D. (Vindhya Data Science)

Unraveling the Complex Transcriptional Heterogeneity of the Pancreatic Tumor Microenvironment for Novel Biomarker and Target Discovery 
David Ruddy (Novartis Institutes for BioMedical Research)
Novartis BioMedical Research (BR) and the Massachusetts General Hospital (MGH) Pancreatic Research Group within the Department of Surgery collaborated closely on an ambitious project profiling surgical resections of the pancreatic cancer tumor microenvironment (TME) using single cell technologies. This project, referred to simply as the OHANA project, represents the largest single cell collection conducted at BR with approximately 0.5 mil cells from 45 patients in normal, non-cancerous inflamed (pancreatitis), treated and treatment-naïve pancreatic ductal adenocarcinoma (PDAC). We will present learnings from OHANA, including technical challenges presented in the handling and processing of human-derived single cell data, novel assays developed to characterize KRAS mutations on single cells as potential biomarkers and discuss plans to translate clinical observations from large single cell datasets into novel target identification in both the cancer and TME cell compartments.

Platelet Releasate Proteomics – A Robust Biomarker Discovery Platform
Luisa Weiss, M.Sc., Ph.D. (University College Dublin)
Large-scale proteomic biomarker studies are often hampered by the low abundance of disease-specific targets in biological fluids. To overcome these limitations, we developed a novel platelet-based diagnostics platform (PALADINTM). Upon activation, platelets release a multitude of soluble, cleaved, and vesicular (exosomes and microparticles) signals into the ex-ternal milieu, collectively termed the "platelet releasate" (PR). This releasate contains both megakaryocyte-derived as well as endocytosed plasma components and plays an important role in haemostasis, wound healing, inflammation, and pathologic sequelae. There is accumulating evidence that platelets actively “sense” their environment and that released signals are altered in inflammation and disease, frequently correlating with disease stage and treatment efficacy. Therefore, this PR may serve as a diagnostic fingerprint in platelet-related disease, containing important concurrent information from both the bone marrow and plasma environments.