ping protein expression of endothelial cells (EC) in vivo is fundamental to understanding cellular function and may yield new tissueselective targets. We have developed a monoclonal antibody, MAb J120, to a protein expressed primarily in rat lung and heart endothelium. The antigen was identified as CD34, a marker of hematopoietic stem cells and global marker of endothelial cells in human and mouse tissues. PCR-based cloning identified two CD34 variant proteins, full length and truncated, both of which are expressed on luminal endothelial cell plasma membranes (P) isolated from lung. Truncated CD34 predominated in heart P, and neither variant was detected in P from kidney or liver. CD34 in lung was readily accessible to 125 I-J120 inoculated intravenously, and immunohistochemistry showed strong CD34 expression in lung EC. Few microvessels stained in heart and kidney, and no CD34 was detected in vessels of other organs or in lymphatics. We present herein the first complete sequence of a rat CD34 variant and show for the first time that the encoded truncated variant is endogenously expressed on EC in vivo. We also demonstrate that CD34 expression in rat EC, unlike mouse and human, is restricted in its distribution enabling quite specific lung targeting in vivo.immunohistochemistry; immunofluorescence; PCR; SPECT imaging; biodistribution THE COHORT OF PROTEINS EXPRESSED in each particular cell type helps define the cell's function. The molecular fingerprint exhibited by different cells and tissues can provide insights into protein function within a given phenotypic setting. In vitro protein expression, even in cells freshly isolated from tissues and/or grown in culture, can vary considerably from in vivo expression under native conditions found in tissues. Creation of a well-defined molecular atlas is crucial to efforts to identify cell type-specific markers, including disease biomarkers, to use as diagnostic tools and as specific targets for treatment.The proteomic signature of blood vessels, and especially endothelial cells (EC), has gained a great deal of attention in the search for specific vascular targets as a means of delivering drugs, nanomedicines, and imaging agents to blood vessels (11,25,42). Specific delivery of these agents, however, relies on identification of unique targets whose expression is restricted to the desired tissue. While the majority of studies have focused on tumor vessels (for a review see Ref. 6), there is also a need to identify and characterize molecules expressed on normal endothelia, to find reliable endothelial cell markers and to develop good, specific antibodies with which to detect these proteins. While most studies rely on antibodies to proteins such as CD31 and CD34 to detect endothelial cells in vivo and in vitro, not all have been fully characterized in rodent tissues.Accurately defining the endogenous expression of a given protein is critical to understanding the function of a given protein in vivo. We have used a silica nanoparticle-coating method to isolate the luminal p...