Differential expression of selected genes in human leukemia leukocytes

Age-associated changes in histology and gene-expression profile in the rat ventral prostate

The incidence of prostate diseases rises dramatically with age in men, yet little is understood of the mechanisms underlying prostatic senescence and its contribution to disease development in the gland. In Noble rats, aging of the ventral prostate (VP) is characterized morphologically by widespread atrophy of acini, increased accumulation of concretions in glandular lumen, infiltration of inflammatory cells, and focal epithelial atypia. We used a cDNA microarray containing 2388 known transcripts, together with the Tyramide Amplification System and t statistics, to identify differentially expressed genes in the VPs of young (3 months old) and old (16 months old) rats. A total of 78 VP genes were found to be differentially expressed by the two groups; in old rats, 65 VP genes (83%) showed reduced expression and 13 genes (17%) showed increased expression compared with young animals. The age-dependent underexpressed genes fell into several functional clusters: those involved in amino-acid metabolism, protein synthesis, protein secretion and degradation, vesicle/membrane trafficking, energy metabolism, signal transduction, spermidine and spermine syntheses, and cellular defense against stress. The overexpressed genes included iduronate 2-sulfatase, HLA class I locus C heavy chain, membrane cofactor protein of the complement system, TRPM-2, cadherin-associated protein-related, and X-CGD. Post hoc analyses confirmed a progressive decline in the expression of ribophorin II and BiP and a gradual increase in the expression of TRPM-2 in rat VPs as animals aged from 3 to 19 months old. In conclusion, the observed widespread declines in expression of genes involved in protein synthesis, protein fidelity maintenance, anabolism, growth inhibition, and energy metabolism, together with increased expression of genes implicated in cell survival in the VPs of senescent rats, may help explain the susceptibility of the prostates of elderly men to development of disease.

Molecular Cloning of Forebrain mRNAs which are Modulated by Sleep Deprivation

Sleep deprivation (SD) experiments have suggested that specific endogenous substances mediate the control of sleep and waking. However, such 'sleep substances' have not yet been unambiguously identified. The isolation of specific molecular markers would make it possible to obtain new insights into the regulatory mechanism underlying sleep and waking. For this purpose, we have used a molecular genetical approach based on subtractive cDNA cloning. Using these techniques, we were able to detect and isolate in rat forebrain four cDNA clones whose corresponding transcripts are expressed at a lower level after 24 h of SD, and six cDNA clones whose corresponding transcripts are expressed at a higher level. For two of the former transcripts, the level showed a significant reduction of approximately 50% after 24 h of SD and a non-significant reduction after 12 h of SD. A significant reduction was also observed after 12 h of cold exposure. A regional analysis of their level under baseline conditions revealed variation during the 24-h cycle. The highest levels tended to occur at the onset of darkness, the beginning of the rat's activity period. Our results are compatible with the hypothesis that the cloned transcripts are associated with the regulation of the sleep-waking cycle. Analysis of their primary structure indicated that these mRNAs have not yet been characterized. The in vivo distribution of these transcripts in the forebrain shows some correspondence to that of receptors of excitatory amino acids, suggesting an association between the functional role of the cloned sequences and this neurotransmission system.

Hybridization fingerprinting of high-density cDNA-library arrays with cDNA pools derived from whole tissues

As part of an integrated mapping and sequencing analysis of genomes, we have developed an approach allowing the characterization of large numbers of cDNA library clones with a minimal number of experiments. Three basic elements used in the analysis of cDNA libraries are responsible for the high efficiency of this new approach: (1) high-density library arrays allowing thousands of clones to be screened simultaneously; (2) hybridization fingerprinting techniques to identify clones abundantly expressed in specific tissues (by hybridizations with labeled tissue cDNA pools) and to avoid the repeated selection of identical clones and of clones containing noncoding inserts; and (3) a computerized system for the evaluation of hybridization data. To demonstrate the feasibility of this approach, we hybridized high-density cDNA library arrays of human fetal brain and embryonal Drosophila with radiolabeled cDNA pools derived from whole mouse tissues. Fingerprints of the library arrays were generated, localizing clones containing cDNA sequences from mRNAs expressed at middle to high abundance (> 0.1-0.15%) in the respective tissue. Partial sequencing data from a number of clones abundantly expressed in several tissues were generated to demonstrate the value of the approach, especially for the selection of cDNA clones for the analyses of genomes based on expressed sequence tagged sites. Data obtained by the technique described will ultimately be correlated with additional transcriptional and sequence information for the same library clones and with genomic mapping information in a relational database.

Chromosome 17- and p53 changes in lymphoma

The clinical course of lymphoma patients in whom rearrangements or deletions of the short arm of chromosome 17 (17p) were evident by cytogenetics was rapidly progressive with a short survival. The gene for the protein designated p53 resides in 17p. We studied four lymphoma cell lines derived from human tumours, and 25 tumour samples of patients with lymphomas, for any evidence of p53 genomic changes by Southern blot technique. The four cell lines and four of the 25 tumour samples showed numerical changes of chromosome 17 or structural abnormalities of 17p (translocations or deletions). Allelic loss of the p53 gene was found in two of the four cell lines, and one of these in addition showed a rearrangement of the 3' end of the gene. Of the four tumours known to have chromosome 17 abnormality, one specimen showed allelic loss of the p53 gene. None of the remaining tumour samples showed any significant change. These studies suggest that acquisition of changes in the short arm of chromosome 17, which may be interrelated with the p53 gene, may carry a poor prognosis in patients with non-Hodgkin's lymphoma.

A sequence previously identified as metastasis-related encodes an acidic ribosomal phosphoprotein, P2

We have used a metastasis-related human cDNA isolated from a liver metastasis from a colonic adenocarcinoma to screen a human breast carcinoma cDNA library for homologous sequences. Nucleotide sequence analysis of positive clones revealed that the cDNA represents a ribosomal phosphoprotein. P2. The expression of P2 mRNA was significantly higher (Student's t test, one tail; P less than or equal to 0.01) in seven fibroadenomas than in seven carcinomas, with an average five-fold difference. This enhanced expression level P2 mRNA in benign fibroadenomas compared with malignant carcinomas is contrary to that expected, based on earlier work with normal colonic mucosa, colorectal carcinoma and hepatic metastasis. The identification of gene transcripts which differ in abundance and correlate with the metastatic phenotype may be of considerable importance both as diagnostic aids and in defining the changes associated with tumour progression and metastasis at the molecular level. The possible role that ribosomal proteins may play in the progression of carcinoma of the breast is discussed.

Characterisation of a messenger RNA selectively expressed in human breast cancer

A complementary DNA library from MCF-7 cells was screened using 32P-cDNA derived from a breast carcinoma and from normal breast tissue. From 10(5) plaques (20% of library) we obtained a clone (Md2) which was differentially expressed in the carcinoma. The distribution of its corresponding transcript of 6-700 nucleotides was examined in normal and neoplastic cells, by filter and in situ hybridisation. We observed localisation of 35S-Md2 to the tumour cells of breast cancers with no significant reaction over stromal or vascular elements or on normal ductal epithelia. M13 sequencing showed Md2 to be 250 nucleotides in length, of which 197 were homologous to the 3'-untranslated region and a short open reading frame of the pS2 gene (Masiakowski et al., 1982). Md2 mRNA was found principally in breast carcinoma cell lines and tumours, with low levels in benign breast disease and no expression in non-breast squamous cell lines. Approximately 43% (23/54) of carcinomas contained this mRNA (varying from + to + + + + level); it was present in 20/38 (53%) of ER positive carcinomas compared to 3/16 (19%) of ER negative carcinomas. In 21 patients who had undergone primary endocrine therapy for recurrent disease expression of Md2 in the primary tumour correlated with the subsequent response to treatment (P = 0.041) and was of similar predictive value as ER status. Both tests correctly predicted outcome in about 76% of cases.

Oncogenes in human leukemias

Eukaryotic cells contain a family of genes termed cellular oncogenes or proto-oncogenes thought to regulate normal cell growth and development. In some abnormal circumstances, such as following transduction by retroviruses, activation of these genes causes leukemias in animals. Possible mechanisms of activation of cellular oncogenes include: point mutation, deletion, or insertion; amplification; activation by internal rearrangement, chromosomal translocation, or promoter insertion; recombinatorial events resulting in the formation of novel chimeric genes; among others. In this review, we consider data implicating activation of cellular oncogenes in the pathogenesis of leukemia in humans. We discuss possible mechanisms whereby oncogene activation may induce leukemias, as well as potential diagnostic and therapeutic implications.

Oncogenes and human leukemias

Eukaryotic cells contain a family of genes termed "cellular oncogenes" or "proto-oncogenes," thought to regulate normal cell growth and development. In some circumstances, such as following transduction by retroviruses, activation of these genes causes tumors and leukemias in animals. Possible mechanisms of cellular oncogene activation include: 1) DNA point mutation, deletion or insertion, 2) gene amplification, 3) gene activation by internal rearrangement, chromosomal translocation or promoter insertion, 4) recombinative events resulting in the formation of novel chimeric genes, and others. In this review, we consider data which implicates cellular oncogene activation in the pathogenesis of leukemia in humans. We discuss possible mechanisms by which oncogene activation may induce leukemias, as well as potential diagnostic and therapeutic implications.

HLA class II antigen associated invariant chain gene expression in malignant lymphoma

Expression of the gene encoding HLA class II antigen-associated invariant chain was studied in several types of fresh human malignant lymphoma by Northern blot analysis or slot-blot analysis. The invariant chain mRNA levels decreased with the stage of B-lymphocyte differentiation to plasma cells such as in immunoblastic lymphoma (IBL) or multiple myeloma (MM). The invariant chain gene (In-gene) was expressed in diffuse large cell lymphoma (DLCL), while its expression was hardly detected in IBL. It is suggested that the difference in In-gene expression between DLCL and IBL could be useful in distinguishing these two morphologically similar diseases.

Preferentially expressed genes in stomach adenocarcinoma cells

cDNA clones complementary to mRNA of neoplastic cells of human stomach tissue were used to examine quantitative changes in the mRNA levels of specific genes in neoplastic cells. Poly(A)+ RNA from poorly differentiated adenocarcinoma cells of a female patient with stomach cancer was used for construction of a complementary DNA (cDNA) library. Screening of the 18,000 colonies utilizing 32P-cDNAs derived from normal human tissue and stomach carcinoma tissue samples was used to select clones likely to represent sequences preferentially expressed in stomach carcinoma cells. Twenty-six recombinants were initially selected and further analysis of these clones indicated that eight (4-3D, 9-2D, 9-4G, 29-1G, 29-6F, 37-1B, 115-5A and 52-5F) contain sequences preferentially expressed in stomach carcinoma cells. We have identified the 9-4G, 29-1A, and 29-6F genes which are differentially expressed in human neoplasia.

Molecular hybridization studies with scrapie brain nucleic acids. II. Differential expression in scrapie hamster brain

RNA and DNA fractions prepared from nucleic acids obtained from normal and scrapie-infected hamster brains following exhaustive treatment with nuclease were used as probes in a search for a specific scrapie nucleic acid. Employing RNA blot hybridization a 2.3 Kb RNA was detected in higher concentration in scrapie-infected hamster brains than in normal controls. Our data suggests that scrapie disease may be associated with the differential expression of a series of host genes.

Structure of the human gene encoding the invariant gamma-chain of class II histocompatibility antigens

The primary structures of a cDNA and the genomic DNA of a gene selectively expressed in chronic lymphocytic leukemia were determined. A computer search of the nucleotide sequence data bank identified this gene as the invariant gamma-chain associated with class II histocompatibility antigens. The invariant gamma-chain genomic sequence spans about 11 kilobases, with eight exons and seven introns. Three of the introns contain members of the Alu repeat family. A putative cap site and promoter sequence were identified at the 5' end of the gene. One or two copies of the gene is present in each haploid genome, and no evidence for amplification or polymorphism was obtained.

Lineage-specific and differentiation-stage-specific gene expression in normal and leukaemic human myeloid cells

One example of each of two approaches to the isolation of molecular hybridization probes and their use for the comparative investigation of gene expression and its control during differentiation of normal and leukaemic leukocytes is described. RNA preparations from the peripheral blood leukocytes of human leukaemias of various types were assayed for the relative abundance of the mRNA homologous with a cellular oncogene, c-myc. All types of leukaemia except chronic lymphatic leukaemia (CLL) showed varying levels of myc-related RNA; the highest concentrations occurred in cell populations in which blast cells predominated. In contrast, a recombinant plasmid (pCG14), isolated from a cDNA recombinant plasmid library that represented polyadenylated RNAs from the peripheral blood leukocytes of a chronic granulocytic leukaemia (CGL), hybridized with an mRNA whose occurrence is diagnostic of CGL leukocytes. This mRNA was also found in normal bone marrow cells; in both bone marrow and in CGL leukocytes, pCG14-homologous RNA occurs only in cells around the myelocyte stage in differentiation. It is suggested that these probes, and others for mRNAs whose occurrence is specific to a particular cell lineage and/or stage in differentiation, detect a new series of potential diagnostic markers. These might usefully supplement existing ones to provide a more detailed, objective subclassification of the leukaemias which could have important implications for diagnosis and therapy.

Cloning of sequences expressed specifically in tumors of rat

The sequences specifically transcribed in tumor cells are believed to be closely related to transformed phenotypes. For the isolation of such sequences, a cDNA clone library was constructed by using poly(A)+ RNAs from azo-dye-induced rat ascites hepatomas. Thirty-one tumor RNA-responsive clones were isolated by screening 4,000 clones of this library with conventional techniques, differential colony hybridization, and RNA blot hybridization. These clones were categorized into two groups with respect to their size distribution of mRNAs from which clones were derived. The first group was complementary to a single distinct species, either about 1.5 or 0.6 kilobases in length, of poly(A)+ RNA, and the second showed no distinct bands but a smear on a RNA blot. Semiquantitative RNA dot blot assays revealed that the sequences of these clones were expressed very little, if at all, in normal and regenerating livers, while generally high in ascites hepatomas. This specificity was also true for other solid lines of tumors, such as Morris hepatoma 5123D of Buffalo rat and Walker 256 carcinosarcoma of Wistar rat. The smear class sequences were transcribed from middle-repetitive sequences of DNA, indicating that a class of middle-repetitive sequences is specifically transcribed in tumor cells.

Recombinant DNA strategies in genetic neurological diseases

The application of recombinant DNA techniques applied to the study of genetic neurological diseases will play a major role in the practice of neurology in upcoming years. Strategies are now available to develop useful and relatively simple biochemical diagnostic tests for heterozygous individuals with diseases inherited as autosomal dominant traits. In addition, molecular genetic methods will lead to the delineation of the genomic mutations responsible for these diseases. This review will update the current status of research in several neurological genetic diseases including myotonic muscular dystrophy, Huntington's disease, Charcot-Marie-Tooth disease and Duchenne muscular dystrophy (X-linked). An introduction and overview of the methodology is provided. Specific research strategies including random screening of libraries, chromosome walking, messenger RNA selection, and messenger RNA translation are described. These strategies are designed to provide heterozygote identification, prenatal diagnosis and gestational management, the development of rational therapies, and the understanding of the molecular basis of disease expression.