Interdisciplinary Initiatives Program Round 7 - 2014

Pehr Harbury, Biochemistry
Tushar Desai, Internal Medicine, Pulmonary & Critical Care

Human diseases occur in the context of the living body, a dynamic environment in which individual cells of a multitude of types collaborate at every stage of a disease, from initiation to progression through response to therapy. Because of this complexity, some diseases cannot be studied outside of the body. Yet, studying diseases in vivo is currently fraught with technical difficulties. A central challenge is to measure gene expression at the single-cell level in primary tissues. The two experimental options, in situ hybridization and single-cell mRNA sequencing, each paint a partial picture that lacks key information. On the one hand, in situ hybridization gives exquisite spatial localization of mRNA's, but only reports on a handful of transcripts. Conversely, single-cell mRNA sequencing provides deep inventories of mRNA's in single cells, but says nothing about the location and distribution of the individual cells within the disease microenvironment. We propose to develop a novel technology that merges comprehensive (high content) single cell molecular characterization with the capacity to spatially localize each cell in the tissue. The approach relies on hybrid parallel/ serial multiplexing of lanthanide labeled nucleic acid probes, enabling the co localization of 100's of mRNAs in formalin-fixed paraffin-embedded tissue sections (the routine mode used for preservation of clinical specimens). We propose to apply this technique to illuminate the molecular nature of alveolar myofibroblast foci, the stereotyped multi-cellular lesions seen in the lungs of patients with Idiopathic Pulmonary Fibrosis, a fatal disease for which no animal model exists and that lacks any known medical treatment. The potential applications of this technology are tremendous, including the delineation of specific signals that cells use to communicate and cooperate in virtually any tissue, healthy or diseased, in human or mice. The resulting gene-expression maps may suggest novel pathways that can be therapeutically targeted, and will provide a window into the molecular mechanisms of disease relapse or resistance to therapy.