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Human epidermal stem cells express higher levels of beta1 integrins than their more differentiated daughters, transit amplifying cells. In a search for additional stem and transit cell markers we used proteomics and differential cDNA hybridisation to compare keratinocytes fractionated on the basis of beta1 integrin expression. There were remarkably few differences between the two populations and none of the RNAs differed in abundance by more than 2-fold. Nevertheless, proteomics revealed upregulated expression of epidermal fatty acid binding protein (PA-FABP, also known as E-FABP), Annexin II and two keratin related proteins in the transit population. An unknown high molecular mass protein was upregulated in the stem cell population. The upregulation of PA-FABP was confirmed by Northern blotting and conventional and whole mount labelling of human epidermis. We conclude that PA-FABP is a novel marker of epidermal transit amplifying cells.

Proteomics is an emerging area of research of the post-genomic era that deals with the global analysis of gene expression using a plethora of techniques to resolve (high resolution two-dimensional polyacrylamide gel electrophoresis, 2D PAGE), identify (peptide sequencing by Edman degradation, mass spectrometry, Western immunoblotting, etc.), quantitate and characterize proteins, as well as to store (comprehensive 2D PAGE databases), communicate and interlink protein and DNA sequence and mapping information from genome projects. Here we review the current status as well as applications of human and mouse proteomic 2D PAGE databases that are being systematically constructed for the global analysis of gene expression in both health and disease (http://biobase.dk/cgi-bin/celis). Furthermore, we discuss the problems one faces when using powerful proteomic technology to study heterogeneous tissue and tumor biopsies, and emphasize the importance of building comprehensive databases that contain a critical mass of information for both known and novel proteins in normal and disease conditions.

We report a novel approach for identifying monomeric GTP-binding proteins that is based on probing cDNA expression libraries with [alpha-32P]GTP. In short, a nitrocellulose replica from a plated cDNA expression library is treated with 2% SDS to block the GTP-binding activity of various G proteins expressed by E. coli, thus allowing the direct identification of positive clones. Using this procedure we have cloned several small GTP-binding proteins from human keratinocytes including the human homolog of rheb, a novel member of the ras-related GTP-binding proteins. Human rheb cDNA shares 90% identity with the rat counterpart and it is highly upregulated in transformed human cells of various origin. Northern analysis showed that human rheb is ubiquitously expressed, with the highest levels observed in skeletal and cardiac muscle, and not in brain, as it is the case for rat rheb. The human RHEB gene was mapped to chromosome 10q11.

Two-dimensional gel analysis of basic proteins in developing human smooth muscle identifies calponin as a prominent marker of the differentiated phenotype. Adult tissue (human and mouse) typically expresses up to four calponin isoforms, three of which appear sequentially during fetal development: adult myometrial cells express the same three isoforms in primary culture in vitro and these are down-regulated, in reverse order, during the subsequent modulation of phenotype. Monospecific, polyclonal antibodies against calponin identify a lower molecular weight variant of calponin (L-calponin) that is strongly and specifically expressed in adult smooth muscles of the human urogenital tract. L-calponin is down-regulated in benign smooth muscle derived tumors (leiomyoma) and is not expressed in primary cultures of normal uterine tissue.

Nuclear Factor IV (NFIV) is a heterodimeric DNA-binding protein from HeLa cells, recognizing molecular ends and is identical to the autoantigenic target Ku. We have identified the two NFIV/Ku subunits, by comigration, in the 2D-gel database of transformed human amnion cell (AMA) proteins. We observed that the large subunit of NFIV/Ku consists of at least 3 charge variants that correspond to SSP IEFs 5705 (81.2 kDa, pI 5.74), 6707 (81.2 kDa, pI 5.67) and 6706 (81.9 kDa, pI 5.60) in the AMA catalogue. The relative amounts of the 2 major variants (IEFs 5705 and 6707) was dependent on the state of cell proliferation. Inhibition of DNA-synthesis by hydroxyurea also changed the relative levels of the variants, whereas aphidicolin or a thymidine block had no effect. These results suggest a possible role for NFIV/Ku in DNA replication.

Neuronal protein gene product 9.5 (PGP 9.5) most likely identical to ubiquitin carboxyl-terminal hydrolase isozyme L1 (UCH-L1) has been reported to be expressed almost exclusively in neuronal and neuroendocrine tissues. By two-dimensional (2D) immunoblotting, comigration and microsequencing of proteins recovered from 2D gels we have identified PGP 9.5 UCH-L1 as polypeptide IEF SSP 6104 (Mr = 27,000, pI = 5.49) in the comprehensive 2D gel cellular protein database of human embryonal lung MRC-5 fibroblasts [(1989) Electrophoresis 10, 76 115; (1990) Electrophoresis 11, 1072 1113]. This protein is expressed at high levels in quiescent and proliferating cultured normal fibroblasts and is strongly down-regulated (about 10 times) in their transformed counterparts.

Analysis using two-dimensional (2D) gel electrophoresis of the [35S]-methionine-labelled proteins synthesized by non-cultured total epidermal keratinocytes obtained from normal and psoriatic skin revealed 6 proteins that are strongly up-regulated (5 times or more) in psoriatic skin. These proteins are synthesized at albeit lower levels by keratinocytes from normal and normal-appearing (uninvolved) skin of psoriatic patients, and correspond to isoelectric focusing sample spot numbers 4311 (40.3 kDa), 4003 (12.4 kDa), 5008 (11.9 kDa), 3012 (11.6 kDa), 6016 (11.6 kDa) and 1015 (10.1 kDa) in the normal keratinocyte 2D gel protein database [Celis et al, (1990) Electrophoresis, in press]. These proteins are also detected in the labelling medium indicating that they are at least in part secreted. Given their striking regulatory behavior, these proteins may play a role in the pathogenesis of psoriasis.

Two-dimensional gel electrophoresis (IEF) analysis of short-term [32P]orthophosphate-labelled intermediate-sized filament proteins (keratins and vimentin) from transformed mitotic amnion cells (AMA), have shown that these proteins are modified coordinately and that the half life of the phosphate is about 13 min for the keratins and 11 min for vimentin. These results support the notion that the preferential modification of intermediate-sized filament proteins during mitosis may play a role in modulating filament associations with organelles and other cellular structures.

The core proteins of HeLa 40 S hnRNP monoparticles have been identified in the HeLa protein catalogue. Human proteins previously identified as proliferation-sensitive [NEPHGE 21 and 17; Bravo, R. and Celis, J.E. (1982) Clin. Chem. 28, 766], as well as two proteins characterized in this study (NEPHGE 16 W and 16 W1), are shown to be components of these particles. These basic nuclear polypeptides correspond to core proteins A1, B1a, B2 and C4, respectively. The significance of these results in terms of composition and function of hnRNP particles is discussed.

Indirect immunofluorescence studies of HeLa cells using PCNA autoantibodies specific for cyclin have revealed striking changes in the nuclear localization of this protein during S-phase. Two-dimensional gel electrophoretic analysis of the [32P]orthophosphate and [35S]methionine labelled proteins from synchronized cells showed that phosphorylation, or other post-translational modifications that are expected to moderately affect the charge of cyclin (acetylation, glycosylation, sialylation, etc.) are not likely part of the mechanism(s) triggering the migration of this protein.

The sequence of cyclin (proliferating cell nuclear antigen, PCNA), antigen staining throughout the cell cycle of African green monkey kidney cells (BS-C-1) has been determined by indirect immunofluorescence using PCNA autoantibodies specific for this protein. Patterns of cyclin staining observed between the beginning of S-phase and maximum DNA synthesis are similar to those reported in human AMA cells [(1985) Proc. Natl. Acad. Sci. USA 82, 3262-3266], while those detected thereafter are significantly different; the most striking feature being the continuous staining of the nucleoli up to or very near the S/G2 border of the cell cycle. Using [3H]thymidine autoradiography and indirect immunofluorescence of the same cells we show a remarkable correlation between cyclin antigen distribution and topographical patterns of DNA synthesis. In addition, we present evidence showing that DNase I treatment of Triton-extracted monolayers abolishes cyclin antigen staining but does not result in a substantial release of this protein. Taken together the above observations argue for a role of cyclin in some aspect of DNA replication.

A novel proliferation-sensitive and cell cycle-specific basic protein, termed progressin (Mr = 33,000), has been identified in proliferating human cells of epithelial, fibroblast and lymphoid origin. Progressin is synthesized almost exclusively during the S-phase of transformed human amnion cells (AMA). Increased synthesis of this protein is first detected late in G1, at or near the G1/S transition border, reaches a maximum in mid to late S-phase, and declines thereafter. Contrary to histones, progressin synthesis is not coupled to DNA replication. As expected for an S-phase-specific protein, no detectable synthesis of progressin was observed in non-proliferating human MRC-5 fibroblasts and epidermal basal keratinocytes. Elevated, but variable levels of this protein were observed in proliferating normal fibroblasts and transformed cells of fibroblast, epithelial and lymphoid origin. Taken together the above observations suggest that progressin may be a component of the common pathway leading to DNA replication and cell division.

A mouse monoclonal antibody (mAB 22-II-D8B) raised against lysed transformed human amnion cells (AMA) has been characterized. The mAB decorated the Golgi apparatus in growing and quiescent cultured monolayer cells (fibroblasts and epithelial cells) of various species as determined by double immunofluorescence labeling and colocalization with galactosyltransferase antibodies. It reacted with the acidic human proteins IEF 58 (Mr = 29,000) and 57a, respectively (Mr = 30,000) (HeLa protein catalogue number; [(1982) Clin. Chem. 28, 766]), Golgi staining was also observed in BS-C-1 cells microinjected with mAB 22-II-D8B suggesting that the epitopes recognized by the antibody are most likely located on the cytoplasmic face of the membranes. The precise localization of the antigens to the various cisternae of the Golgi apparatus could not be demonstrated by immunogold cytochemistry on ultrathin cryosections due to either weak reactivity of the antibody or low concentration of the antigens. Immunofluorescence staining with mAB 22-II-D8B of lymphoid human Molt-4 cells and some human tissues failed to reveal any significant staining even though these expressed high levels of both IEF 58 and 57a. These results are taken to imply that the epitopes recognized by mAB 22-II-D8B may be masked in some cell types.

Quantitative two-dimensional gel electrophoretic analysis (IEF) of the nuclear polypeptide cyclin in normal human skin biopsies, growing and senescent fibroblasts and morphologically transformed skin fibroblasts (limited life span) has revealed a direct correlation between the levels of this protein and proliferative state of the cells. These results strengthen the notion that cyclin may be a key component of the pathway(s) that control cell proliferation.

PCNA autoantibodies specific for cyclin/PCNA were used to determine the nuclear distribution of this protein in transformed human amnion cells (AMA) irradiated with ultraviolet light (254 nm) under conditions that induced nucleotide excision DNA repair synthesis. The results showed a striking increase in nuclear cyclin/PCNA antigen staining of non S-phase cells that was not abolished by cycloheximide (20 micrograms/ml, added 2 h before irradiation), and that is most likely due to a redistribution of pre-existing cyclin. These observations raise the possibility that cyclin/PCNA may play a role in nucleotide excision DNA repair synthesis in addition to its putative role in replicative DNA synthesis.

Cyclin, also known as PCNA or the auxiliary protein of mammalian DNA polymerase delta, is a stable cell cycle regulated (synthesized mainly in S-phase) nuclear protein of apparent Mr 36,000 whose rate of synthesis correlates directly with the proliferative state of normal cultured cells and tissues. Cyclin (PCNA) is absent or present in very low amounts in normal non-dividing cells and tissues, but it is synthesized in variable amounts by proliferating cells of both normal and transformed origin. All available information indicates that this ubiquitous and tightly regulated DNA replication protein is a central component of the pathway(s) leading to DNA replication and cell division.

Comprehensive, computerized databases of cellular protein information derived from the analysis of two-dimensional gels, together with recently developed techniques to microsequence proteins offer a new dimension to the study of genome organization and function. In particular, human protein databases provide an ideal framework in which to focus the human genome sequencing effort.