GLOSSARY

E

• E-selectin (CD62E) #

  Alternative names: ELAM-1, LECAM-2

  In humans and in mice, E-selectin can be found on the surface of: endothelial cells

  Ligands and associated molecules: CD162, Sialyl Lewis x/a carbohydrates

  Function: cell adhesion

  Additional information: E-selectin is also known as CD62E. CD62E expression on the surface of endothelial cells is activated by cytokines and the expression of CD62P. CD62E plays an important role in the body’s inflammatory response, recruiting leukocytes to inflamed areas. In inflamed tissue, macrophages release IL-1 and TNF-α, which cause endothelial cells to upregulate CD62E surface expression. Surface CD62E binds to CD162 on leukocytes that flow past the infected area at high velocity, capturing the leukocytes and mediating their tethering and rapid rolling on activated endothelium in the initial stages of inflammation.

• ENCODE (ENCyclopedia Of DNA Elements) #

  A program that aims to catalog all the functional elements in the human genome and genomes of model organisms (mouse, fly, worm, etc.) that determine cell function in normal and disease states, to develop and validate assays for that purpose, to develop computational tools to process the data, integrate, and analyze the data, and to make all of this available to the world’s research community. Techniques used to define the elements include, but are not limited to: profiling chromosomal transcripts to identify sequences encoding RNA for protein coding and non-coding functions and to define transcription start sites, identifying sites of chromatin accessibility, DNA methylation, protein–DNA binding, and protein–RNA binding. The program also includes identifying protein modifications that affect interactions with proteins, DNA, and RNA. An example of the type of data within ENCODE is GENCODE, an annotated database of transcribed elements in the human genome that includes transcripts of protein-coding, long non-coding RNA loci, and alternatively transcribed/spliced variants. ENCODE is an international consortium of research groups and is managed by the National Human Genome Research Institute.

• Endocytic Recycling Compartment (ERC) #

  Membrane-bound vesicles formed by invagination of the plasma membrane, a complex process involving the capture of extracellular and membrane-bound molecules. These endosomes typically fuse with early/sorting endosomes, and are sorted to lysosomes for degradation or trafficked through the recycling pathway to return components to the plasma membrane. Endocytic recycling is key for a variety of cellular processes, including plasma membrane homeostasis, cell shape, receptor reuse, cleavage of daughter cells in cell division, cell migration, and cell polarity.

• Endoplasmic Reticulum (ER) #

  A large intracellular structure defined by a membrane-enclosed space that is continuous with the perinuclear space, but separate from the cytosol. It functions as the processing domain for synthesis and export of proteins and membrane lipids, maintains calcium homeostasis, affects cell survival if subjected to stress, and is fundamental to immune functions in its role in assembly of MHC-I–antigen/peptide complexes.

• ER-Golgi Intermediate Compartment (ERGIC) #

  A cell compartment through which proteins destined for secretion or for the plasma membrane traffic from the endoplasmic reticulum (ER) to the Golgi complex. ERGIC clusters are thought to function as mobile transport complexes that deliver secretory cargo from ER exit sites to the Golgi.

• ERGIC-53 #

  A mannose-specific cargo receptor that transports glycoproteins from the endoplasmic reticulum (ER) to the ER-Golgi Intermediate Compartment (ERGIC).

• Exitrons #

  Internal regions of an exon that contain both protein-coding and potential splicing sequences. If RNA expressed from these exitrons is spliced, it could encode protein isoforms, including in-frame deletions or out-of-frame open reading frames, either of which could result in neoantigens. Exitrons expressed uniquely in tumor cells and not in normal tissue are referred to as tumor-specific exitrons (TSE).