ations in the relative synthesis rates of many specific polypeptides. Similar results have been reported in associa tion with altered growth rates in clo nal rat cell lines. Alterations in the synthesis rates of specific proteins have been seen in hepatoma lines treated with glucocorticoids, a mouse lymphoma line treated with cyclic AMP, fibroblasts in the presence of interferon, and a variety of other sys tems. Alterations in protein synthetic pat terns during differentiation have been defined with 2-D gels during myogenesis in rabbits, in nerve cell lines treat ed with nerve growth factor, and in a mouse myeloid leukemia that differ entiates in response to DMSO. Since protein synthetic patterns seem to re flect both the tissue of origin and the state of differentiation of the cell pop ulation studied, we and others have begun to examine the potential clini cal applications of the technique. As an oncologist, I (E.P.L.) would find it particularly useful to be able to deter mine the precise cell type and state of differentiation of the malignancies I treat, and 2-D gels may make this pos sible in a single analysis of the tumor tissue. The very large data base im plicit in a single 2-D gel pattern of tumor cell proteins may further con
tain a wealth of prognostic informa tion, clues to expected biological be havior, and indications of likely re sponses to therapy, once we learn to interpret the data. Yet another area in which 2-D gels are finding important applications is in genetics and the analysis of genetic diseases. Two-dimensional gels can readily detect shifts in the location of a single polypeptide spot in mutant E. coli strains known to differ from a control strain in a single genetic locus (protein). Studies are currently under way in our laboratory to identify mu tant or deleted gene products in human genetic diseases such as cystic fibrosis. At a more basic level, 2-D gel tech nology has shed light on one of the central concerns of genetics—the ex tent of genetic polymorphism in pro tein gene products. Whereas classical charge-dependent electrophoretic studies of cellular enzymes have shown a high frequency of polymor phism, 2-D gels, which visualize pri marily structural proteins when ap plied in the usual fashion to whole cell extracts, show a very low frequency of polymorphism. This implies a high de gree of evolutionary conservation of structural, as opposed to enzymatic, gene products.
Computerized 2-D Gel Image Analysis Simple inspection of a 2-D gel image may often be adequate to pro vide an important experimental result, such as detection of an alteration in the synthesis rate of a specific poly peptide of interest. Such a result, of course, largely ignores the often im mense amount of data about other polypeptides visualized concurrently. Furthermore, simple inspection leads to essentially qualitative rather than quantitative conclusions. We, and others, have been primarily concerned with the computerized analysis of 2-D gels of biosynthetically pulse-labeled polypeptides, since these provide information about the relative synthetic rates of a large num ber of polypeptides, potentially very useful data for a wide variety of bio logical problems. Here we shall con fine our discussion to this problem, al though analysis of other types of 2-D gel data (e.g., stained patterns) is quite analogous. We have called our system GELLAB—a software labora tory for gel analysis. To realize the true potential of 2-D gels we must have an analysis of these images that is at once comprehensive, covering all polypeptides visualized,
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