p27/Kip1 mutation found in breast cancer.

The p27/Kip1 protein belongs to the recently identified family of proteins called cyclin-dependent kinase inhibitors. These proteins play an important role as negative regulators of cell cycle-dependent kinase activity during progression of the cell cycle. Since cyclin-dependent kinase inhibitors can inhibit cell proliferation, they may have a role as tumor suppressor genes. To determine whether p27 alterations may be involved in tumorigenesis, we examined its mutational status in 36 primary breast carcinomas and 9 breast cancer cell lines using PCR-single-strand conformational polymorphism, direct DNA sequencing, and Southern blot analysis. Southern blot analysis showed no homozygous deletions of the p27 gene in either the clinical samples or cell lines. Two point mutations were found in primary tumors. One represents a previously undescribed polymorphism at codon 142; another is a nonsense mutation at codon 104. The latter mutation was absent in the normal matched control sample, and, in addition, it was accompanied with the loss of heterozygosity (LOH) of a microsatellite marker in the vicinity of the p27 gene on chromosome 12p13. These data indicate that p27 mutations are a rare event in breast cancer, but may play an important role in the development of a minority of these cancers. Furthermore, LOH analysis of the 12p13 locus revealed that an additional four of six matched DNA samples had LOH at 12p13 but did not have an alteration of the p27 gene, suggesting that another tumor suppressor gene is located on the short arm of human chromosome 12 which may be frequently involved in the pathogenesis of breast cancers.

Molecular analysis of the cyclin-dependent kinase inhibitor gene p27/Kip1 in human malignancies.

Cyclin and cyclin-dependent kinase (CDK) complexes play important roles in controlling the cell cycle. The CDK inhibitors (CDKIs) inhibit the kinase activities of the complexes and block transitions of the cell cycle. Recently several CDKI genes have been cloned, and evidence suggests that at least a couple of these may be tumor suppressor genes. In this study, the partial structure of a CDKI gene, p27/Kip1, was determined. In addition, a large number of human cancers (432 cases) and cancer cell lines (20 lines) were analyzed for alterations of the p27/Kip1 gene by Southern blot analysis and PCR/single-strand conformation polymorphism. The coding region of the p27/Kip1 gene consists of at least two exons and an intron of about 600 bp. In 140 tumors of various tissues and 18 transformed cell lines, no deletions or rearrangements of the gene were detected by Southern blot analysis using a part of the coding sequence as a probe. One polymorphism and one silent mutation were detected by PCR/single-strand conformation polymoprhism. The polymorphism was a nucleotide substitution of guanine for thymine (GTC-->GGC) at codon 109, resulting in an amino acid substitution of glycine for valine (Val-->Gly). In summary, no abnormalities of the p27/Kip1 gene were detected in human malignancies. Now, two groups of CDKIs are classified based on the structure of the proteins. One group includes the p15, p16, and p18 CDKIs, which have ankyrin repeat motifs. The p15 and p16 CDKI genes are very frequently mutated in a variety of cancers. The p27/Kip1 and p21 CDKIs belong to the other group. We reported previously that abnormalities of the p21 gene were very rare. The latter group of the CDKIs, including p27/Kip1 and p21, are rarely mutated in human malignancies.

Expression of tenascin-C splice variants in normal and bullous keratopathy human corneas.

PURPOSE: To characterize the expression patterns of tenascin-C (TN-C) splice variants in normal corneas and in those affected by pseudophakic-aphakic bullous keratopathy (PBK-ABK). METHODS: Alternatively spliced variants of TN-C mRNA from normal and age-matched human corneas with PBK-ABK were analyzed by semiquantitative reverse transcription-polymerase chain reaction (RT-PCR) and Southern blot hybridization, using beta2-microglobulin as a housekeeping gene to normalize the samples. Normal and PBK-ABK corneas were studied by immunofluorescence and western blot analysis with antibodies to specific fibronectin type III-like (FN-III) repeats of TN-C. RESULTS: Tenascin-C mRNA expression was detected in epithelial, stromal, and endothelial cells of normal and PBK-ABK central corneas, although the protein was seen only in diseased corneas. Assessed by RT-PCR, PBK-ABK corneas expressed approximately three times more total TN-C mRNA than did normal corneas. Four major TN-C mRNA variants (with no FN-III insertional repeats or with retained insertional repeats D, A1, or A1+D) and three minor variants (with retained repeats A1+A2, A1+A2+D, or A1+A2+B+D) were much more abundant in PBK-ABK than in normal corneas. Repeat A1 was more abundant in PBK-ABK TN-C protein than repeats A2, A3, B, or D. Major TN-C variants in PBK-ABK corneas were in the range of 190 kDa to 240 kDa. CONCLUSIONS: Expression of TN-C mRNA and protein is higher in PBK-ABK corneas than in normal corneas. This increase mainly concerns relatively small TN-C splice variants that may affect corneal cell adhesion and migration and contribute to the exacerbation of PBK-ABK.

Analysis of gene expression in human bullous keratopathy corneas containing limiting amounts of RNA.

PURPOSE: To validate the use of polymerase chain reaction (PCR)-amplified full-length cDNA as a substitute for mRNA in nucleic acid array and gene expression analysis. METHODS: Total RNA was isolated from age-matched normal autopsy corneas and pseudophakic bullous keratopathy (PBK) corneas. Full-length cDNA was generated and PCR amplified using the Smart cDNA synthesis technology. Southern blot analysis of this cDNA was compared with Northern blot analysis of the RNA. Amplified cDNA was used to probe a commercial gene array. By immunohistochemistry, the expression pattern of several adhesion molecules represented on the array was assessed. RESULTS: The cDNA produced by the Smart cDNA system gave results very similar to those of northern blot analysis when examined for beta2-microglobulin, Rab geranylgeranyl transferase, and tenascin-C. This cDNA obtained from normal or PBK corneas was labeled and used to probe a 588 gene array (Clontech). Among other differences, beta6 integrin was detected only with the PBK probe, beta-catenin was markedly elevated in PBK, and beta4 integrin appeared to be reduced in PBK. Immunohistochemical patterns of these proteins were consistent with the hybridization signals on the gene array. CONCLUSIONS: Smart cDNA synthesis and nucleic acid arrays were combined and validated for the first time to identify differential gene expression in normal and diseased corneas. These techniques require very little RNA such as that equivalent to a half of a single cornea, which is useful when the amount of tissue is limiting. Altered expression of adhesive proteins beta6 integrin and beta-catenin may be related to the formation of epithelial bullae and microcystic changes in PBK patients.

Increased expression of fibrillin-1 in human corneas with bullous keratopathy.

PURPOSE: To characterize the expression of fibrillins, microfibril components, in human corneas with pseudophakic/aphakic (PBK/ABK) bullous keratopathy. METHODS: Normal and PBK/ABK corneas were stained by immunofluorescence for fibrillin-1 and -2. The expression of fibrillin-1 messenger RNA (mRNA) was studied by semiquantitative reverse transcription-polymerase chain reaction (RT-PCR) and Southern analysis. RESULTS: Only fibrillin-1 was detected in normal and diseased corneas. As described previously, in normal corneas, it was found in the limbal stroma and basement membrane (BM) and in the peripheral corneal epithelial BM for a short distance near the limbus. Central corneal BM, stroma, and Descemet's membrane were negative. All PBK/ABK corneas were positive for fibrillin-1, which was detected in fibrillar deposits at the endothelial face of Descemet's membrane, in the epithelial BM, subepithelial fibrosis areas, and posterior collagenous layer. By RT-PCR, low levels of fibrillin-1 mRNA were detected in normal corneas, and they increased significantly in PBK/ABK corneas. CONCLUSION: The deposition of fibrillin-1, together with tenascin-C, in PBK/ABK corneas may be part of an abnormal fibrotic/wound-healing process that occurs during the development of postsurgical corneal edema with the formation of bullae and posterior collagenous layer.

Basement membrane and growth factor gene expression in normal and diabetic human retinas.

PURPOSE: Recently, we found abnormal accumulation of several extracellular matrix components in retinal basement membranes in human diabetic retinopathy (DR). Others have described increased levels of various growth factors within the vitreous of DR patients. This study examined mRNA levels of these extracellular matrix components and growth factors within human retinal tissues. METHODS: Total retinal RNA was analyzed by semiquantitative reverse transcription-polymerase chain reaction (RT-PCR). RT-PCR products were identified by Southern blotting. Samples were normalized with respect to beta2-microglobulin cDNA. Twenty-one retinas were analyzed: 6 normal, 7 diabetic without DR and 8 diabetic with DR. RESULTS: In diabetic retinas without DR, the expression levels of most genes were similar to normal. In DR retinas, tenascin-C mRNA expression increased compared to both normal and diabetics without DR. By RT-PCR and Northern blotting, mainly small tenascin-C mRNA isoforms were expressed, and some of them were elevated in DR retinas. Fibronectin mRNA was elevated in DR compared to normal retinas, possibly due to the overexpression of extradomain A-containing isoform (ED-A+, or cellular fibronectin). In DR retinas, gene expression of vascular endothelial growth factor and placenta growth factor was elevated compared to normal, although mRNA for these growth factors receptors (VEGFR-1/Flt-1 and VEGFR-2/KDR) did not change significantly. Transforming growth factor-beta1 mRNA also increased in DR retinas. CONCLUSIONS: The data suggest that proliferative DR development may be associated with increased retinal expression of vascular endothelial growth factor, placenta growth factor and transforming growth factor-beta1 that possibly triggers the deposition of small tenascin-C isoforms in the blood vessel walls. Angiogenesis-stimulating tenascin-C may further promote diabetic retinal neovascularization.

[Mechanism of formation of associated oligonucleosomes during electrophoresis]. / Mekhanizm obrazovaniia assotsiatov oligonukleosom pri élektroforeze.

Here we used DNP electrophoresis to study the mechanism of formation of associated oligonucleosomes (A-particles) which have been previously shown by Weintraub to contain the DNA of silent but not of transcriptionally-active genes from chicken erythrocyte nuclei. We found out that A-particles are generated in the course of electrophoresis and that their assembly is inhibited as the result of redistribution of the most mobile fraction of histones H1 and H5. The mechanism and the conditions for the assembly of A-particles at the start line of DNP electrophoresis are discussed in the paper. The DNA molecules constituting A-particles appeared to be about 60 base pairs longer than the DNA of free oligonucleosomes. Thus in course of nuclease treatment of erythrocyte nuclei two chromatin fractions can be observed, one of them containing the DNA of transcriptionally active genes loses its terminal DNA regions owing to rapid degradation of cleaved nucleosome linkers, while the other containing the DNA of repressed genes maintains its terminal linker DNA and gives rise to the associated oligonucleosomes.

[son Pseudogenes do not contain five repeating elements of the region of complete tandem repeats present in the homologous sequence of the son gene]. / Psevdogen son ne soderzhit piati povtoriaiushchikhsia élementov oblasti sovershennykh tandemnykh povtorov, prisutstvuiushchikh v gomologichnoi posledovatel;nosti gena son.

Recently we have published a sequence of the coding region of the son gene, containing at least six areas of the tandem repeats [V.V. Bliskovsky, F.B. Berdichevsky, A.V. Tkachenko, M.E. Belova, I.M. Chumakov--Molecularnaya biologiya, 1992, V. 26. P. 793-806; V.V. Bliskovsky, A.V. Kirillov, V.M. Zacharyev, I.M. Chumakov--Molecularnaya biologiya, 1992, V. 26. P. 807-812]. The presence of several areas of tandem repeats with different nucleotide sequences of the repeated elements within one and the same gene supports the proposition that genomic localization of the sequence influences its duplication. Here we present a nucleotide sequence of the son pseudogene isolated as the result of hybridization screening of a human genomic library using the sequence of the son gene as a probe. The comparison of the gene and the pseudogene nucleotide sequences shows that the sequence of pseudogene does not contain five repeated units of an area of the tandem repeats, which are presented in the homology sequence of the son gene. Because the pseudogene was probably generated by the reverse son-gene transcript insertion to the genome, and so the nucleotide sequences of the coding region of the gene and the sequence of the pseudogene were identical at this moment, the differences between the gene and the pseudogene are the results of their evolution after the generation of the pseudogene. Possible factors, influenced the son gene and the son pseudogene evolution are discussed.

Loosened nucleosome linker folding in transcriptionally active chromatin of chicken embryo erythrocyte nuclei.

We have investigated the mechanism of the electrophoresis-driven chromatin aggregation which had been described by Weintraub (1984, Cell 38, 17-27) as a putative mean for propagation of genetic repression in eukaryotes. We show that the oligonucleosome aggregates are assembled de novo at the starting zone of DNP electrophoresis. A new system of native two-dimensional DNP electrophoresis has been worked out to separate the oligonucleosome aggregates ('A' particles) and the freely-migrating oligonucleosomes ('B' particles). The 'B' particle fraction which is derived from transcriptionally-active chromatin regions undergoes an extensive nuclease degradation of its DNA termini during the nuclease digestion. This fraction is partially depleted of histones H1 and H5 and is enriched in HMG nonhistone proteins. 'A' particles comprise the repressed chromatin DNA fragments which are about 60 b.p. longer than the corresponding DNA oligomers of 'B' particles. An oligonucleosome preparation containing the elongated DNA oligomers has been also isolated by means of sucrose gradient ultracentrifugation. Exonuclease III mapping reveals that the two chromatin fractions differ by an extent of terminal linker DNA trimming during the Micrococcal nuclease digestion rather than by the nucleosome repeat length. The complex character of nuclease digestion is not observed when the chromatin is digested in solution after the nuclear lysis. We argue that the protection of terminal oligonucleosome linkers is due to selective condensation of inactive chromatin in chicken erythrocyte nuclei and that the terminal DNA tails together with linker histones bound to them mediate the aggregation of repressed chromatin fragments.

A novel nonhistone protein (MENT) promotes nuclear collapse at the terminal stage of avian erythropoiesis.

The terminal stage of differentiation of nucleated chicken erythrocytes is associated with an overall gene repression and a condensation of the repressed chromatin portion. Two-dimensional DNP electrophoresis has been used to separate transcriptionally active and repressed chromatin of mature chicken erythrocytes. The repressed chromatin fraction is shown to be enriched with histone H5 as well as with a 42-kDa nonhistone chromosomal protein. The 42-kDa protein designated here as MENT (mature erythrocyte nuclear termination stage-specific protein) is hyperexpressed at the terminal stage of chicken erythropoiesis and is accumulated in adult chicken erythrocyte nuclei. This protein was purified by ion-exchange chromatography from 0.4 M NaCl extracts of the erythrocyte nuclei. It appeared to be a basic polypeptide (pI 9.2) which, however, precipitated at low pH. When reconstituted in vitro with immature erythrocyte nuclei, MENT promoted condensation of intact nuclear chromatin and enhanced the solubilization of nuclease-digested polynucleosomes, thus mimicking the processes occurring in vivo at the final stage of erythrocyte maturation. The extent of dissociation of specific gene sequences from the nuclear matrix in MENT-treated nuclei is in striking correlation with their transcriptional activity. No other basic proteins (H5, cytochrome c, RNase A) added to the nuclear preparation at the same level as MENT (protein/DNA = 0.005) caused any effect on nuclear organization. No alterations were observed when MENT was mixed with erythroblasts and nonerythroid nuclei having little or no histone H5. We propose that MENT cooperates with histone H5 to complete the nuclear collapse in mature nucleated erythrocytes.

Id2 expression increases with differentiation of human myeloid cells.

Id proteins are helix-loop-helix (HLH) transcriptional factors that lack the basic DNA binding domain. The Id proteins have been reported generally to function as inhibitors of cell differentiation, and their gene expression is often downregulated during cell differentiation. We examined the expression of human Id mRNAs by Northern hybridization in 11 human myeloid cell lines, several myeloid cell lines induced to differentiate, fresh myeloid leukemia samples, and normal human myeloid cells. Id2 mRNA was expressed in myelomonoblastic and monoblastic leukemic cells (PLB-985, THP-1, and U-937) but was weakly expressed in myeloblastic leukemic cells (KG-1 and HL-60). Id2 mRNA levels markedly increased with induction of differentiation of myeloid blasts (HL-60, PLB-985, THP-1, and U-937) toward either granulocytes or macrophages. Examination of fresh acute myeloid leukemic samples from 22 individuals also showed prominent Id2 mRNA expression in those samples having more differentiated blasts. Using the French-American-British classification, only 2 of 8 M0/M1 samples expressed Id2 mRNA; however, 10 of 13 M2/M3/M4 samples expressed it. In normal human myeloid cells, Id2 mRNA was expressed in cultured macrophages from bone marrow and in mature granulocytes and monocytes from peripheral blood. The half-life of Id2 mRNA was short (1 hour), and its expression was inducible by cessation of protein synthesis. Id3 mRNA was moderately expressed in monoblastic cell lines (THP-1 and U-937), and levels decreased with their differentiation. Almost no Id3 expression was detectable in either other myeloid leukemia lines, fresh leukemic samples, or normal human myeloid cells by Northern analyses. Id1 mRNA was not detected by polymerase chain reaction in either leukemic or normal myeloid cells except in K562 myeloid/erythroid cells. These results showed that Id2 mRNA was constitutively expressed in more mature myeloid blast cells and level markedly increased with terminal myeloid differentiation, suggesting that Id2 protein may inhibit an HLH transcriptional complex that normally represses myeloid differentiation.

Overexpression of matrix metalloproteinase-10 and matrix metalloproteinase-3 in human diabetic corneas: a possible mechanism of basement membrane and integrin alterations.

We have previously described decreased immunostaining of nidogen-1/entactin; laminin chains alpha1, alpha5, beta1,gamma1; and epithelial integrin alpha3beta1 in human diabetic retinopathy (DR) corneas. Here, using 142 human corneas, we tested whether these alterations might be caused by decreased gene expression levels or increased degradation. By semiquantitative reverse transcription-polymerase chain reaction, gene expression levels of the alpha1, alpha5, and beta1 laminin chains; nidogen-1/entactin; integrin alpha3 and beta1 chains in diabetic and DR corneal epithelium were similar to normal. Thus, the observed basement membrane and integrin changes were unlikely to occur because of a decreased synthesis. mRNA levels of matrix metalloproteinase-10 (MMP-10/stromelysin-2) were significantly elevated in DR corneal epithelium and stroma, and of MMP-3/stromelysin-1, in DR corneal stroma. No such elevation was seen in keratoconus corneas. These data were confirmed by immunostaining, zymography, and Western blotting. mRNA levels of five other proteinases and of three tissue inhibitors of MMPs were similar to normal in diabetic and DR corneal epithelium and stroma. The data suggest that alterations of laminins, nidogen-1/entactin, and epithelial integrin in DR corneas may occur because of an increased proteolytic degradation. MMP-10 overexpressed in the diabetic corneal epithelium seems to be the major contributor to the observed changes in DR corneas. Such alterations may bring about epithelial adhesive abnormalities clinically seen in diabetic corneas.