Gene expression in normal and neoplastic mammary tissue

Effective Alu repeat based RT-Qpcr normalization in cancer cell perturbation experiments

Background

Measuring messenger RNA (mRNA) levels using the reverse transcription quantitative polymerase chain reaction (RT-qPCR) is common practice in many laboratories. A specific set of mRNAs as internal control reference genes is considered as the preferred strategy to normalize RT-qPCR data. Proper selection of reference genes is a critical issue, especially in cancer cells that are subjected to different in vitro manipulations. These manipulations may result in dramatic alterations in gene expression levels, even of assumed reference genes. In this study, we evaluated the expression levels of 11 commonly used reference genes as internal controls for normalization of 19 experiments that include neuroblastoma, T-ALL, melanoma, breast cancer, non small cell lung cancer (NSCL), acute myeloid leukemia (AML), prostate cancer, colorectal cancer, and cervical cancer cell lines subjected to various perturbations.

Results

The geNorm algorithm in the software package qbase+ was used to rank the candidate reference genes according to their expression stability. We observed that the stability of most of the candidate reference genes varies greatly in perturbation experiments. Expressed Alu repeats show relatively stable expression regardless of experimental condition. These Alu repeats are ranked among the best reference assays in all perturbation experiments and display acceptable average expression stability values (M<0.5).

Conclusions

We propose the use of Alu repeats as a reference assay when performing cancer cell perturbation experiments.

Prolactin and mammary gland development

Prolactin (PRL) regulates the development of the mammary gland at three stages in the reproductive life history of females. The first stage is mammary gland organogenesis, during which PRL contributes to the maturation of the mammary glands from a primary ductal system, which grows from terminal end buds, to the fully mature nonpregnant gland. The mature mammary gland is characterized by an absence of terminal end buds, and the development of a highly branched architecture, which is decorated by lobular buds. During pregnancy PRL, placental lactogens, and progesterone stimulate the expansion and physiological differentiation of the lobuloalveolar system from the lobular buds. After delivery PRL, in the context of falling progesterone, stimulates the final induction of milk protein gene expression and lactation. PRL acts directly on the mammary epithelium, and indirectly by stimulating luteal progesterone secretion in rodents. Disruption of the genes for PRL and the PRL receptor, as well as those for transcription factors important in mammary gland regulation (Stat proteins), have provided a new set of animal models with which to study normal mammary gland development and the relationships of PRL to breast carcinogenesis. Two major deficiencies in our current knowledge of PRL actions are our understanding of the role of epithelial-stromal interactions in PRL-induced mammary morphogenesis, and the identity of developmentally important genes that are regulated by PRL during normal mammary gland organogenesis.

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.

Subdivision of the acute non-lymphoblastic leukaemias by measurement of the relative abundance of a specific RNA sequence

A recombinant plasmid library representing the more abundant polyadenylated RNA of a relapsed acute myelomonocytic leukaemic (FAB class M4) has been constructed. One recombinant, designated pAM6, contains a DNA sequence complementary to an RNA of about 1100 nucleotides in length. The relative concentrations of pAM6 RNA in the RNAs from cloned human haematopoietic cell lines and from fractionated leukaemic leukocytes and normal bone marrow cells, measured by an RNA dot hybridization method, indicated that pAM6 RNA occurs in myeloid cells, probably those of the monocyte lineage at the earlier stages in differentiation. Similar assays showed that pAM6 RNA could not be detected in the peripheral blood leukocytes of normal individuals, or of ALL and CLL patients, but that the relative abundance of pAM6 RNA varied widely in leukocytes from CGL chronic phase, CGL acute phase, and ANLL. No correlation between pAM6 RNA occurrence and FAB classification of ANLL could be made; thus it would appear that the relative abundance of pAM6 RNA in ANLL leukocytes can be used to subdivide the ANLLs in a novel manner. It is suggested that this criterion, in conjunction with existing diagnostic markers, may provide a subclassification of the ANLLs that could be of some prognostic and therapeutic value.

Sequence complexity and diversity of polyadenylated RNA molecules transcribed in human myeloid cells. Leukemic myeloblasts and HL60 promyelocytes uninduced and induced to terminal differentiation with retinoic acid

The kinetic composition of the polyadenylated RNAs of leukemic myeloblasts and HL60 promyelocytes was examined by the cDNA-poly (A) +RNA reassociation technique before and after the induction of differentiation with retinoic acid. The data obtained in the homologous hybridizations show the following main features: the sequence complexity of the total poly(A) +RNA molecules is 72,000 different sequences in leukemic myeloblasts, 64,000 in HL60 promyelocytes before induction and 26,000 after treatment of HL60 with retinoic acid; the number of sequences reacting as abundant is clearly higher in HL60 promyelocytes (5,000) than in leukemic myeloblasts (1,000), and the number decreases sharply after induction (300); the repetition frequency of the abundant and rare components is almost unchanged between leukemic myeloblasts and HL60 promyelocytes, while it is markedly increased after induction with retinoic acid. The heterologous reactions show that the observed differences in complexity are mainly related to the missing of rare sequences. Moreover, an important portion of sequences already present in leukemic myeloblasts has a definitely higher repetition frequency in HL60 promyelocytes. Finally, the most abundant sequences in HL60 cells after induction are already present before treatment. The data presented here suggest that, during human myeloid differentiation, important, possibly transcriptional, regulatory mechanisms of gene expression are active long after the first commitment event of the hemopoietic undifferentiated stem cell.

Milk-protein mRNAs and poly(A) in the involuting rat mammary gland return to the levels found during late pregnancy

Analyses of the rat mammary gland show that the increase in the milk-protein mRNAs during the development of lactation and the rapid disappearance of these sequences during involution are not accompanied by similar changes in the poly(A) content. During the development of lactation the casein mRNA is initially in great excess to the whey-protein mRNA and this differential expression of the genes for the two types of milk proteins is again observed during early involution. Since the amounts of poly(A) and of both milk-protein mRNAs are also similar to the amounts found in the gland during late pregnancy, these results indicate that during early involution the mammary gland has reverted to the pattern of mRNA metabolism that occurs during late pregnancy.

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.

A new approach to the classification of human leukaemias: measurement of the relative abundance of a specific RNA sequence by means of molecular hybridisation

A recombinant plasmid library representing polyadenylated RNAs in the leucocytes of a Ph1-positive chronic granulocytic leukaemia (CGL) has been constructed. One recombinant (designated pCG14) isolated from this library contains a DNA sequence complementary to a small polyadenylated RNA that is abundant in RNA from CGL leucocytes. The relative concentrations of pCG14 RNA in the RNAs from a variety of normal and leukaemic leucocytes and human haemopoietic cell lines have been measured with a molecular hybridisation assay. This has shown that pCG14 RNA is 10 to 50 times more abundant in RNA from CGL leucocytes than in the RNAs from these other cells. The data indicate that the occurrence of pCG14 RNA in high abundance is sufficiently characteristic of a CGL leucocyte population to distinguish it from other populations of leucocytes. They suggest that the measurement of the concentrations of specific RNA species in leucocyte RNA by means of molecular hybridisation with cloned complementary DNAs may provide additional markers for the objective classification of human leukaemias which could be particularly useful since the method exploits a criterion different from any currently in use.

Abundant messenger RNA sequences common to transplanted mouse tumours of different tissue origins

Radioactive cDNA, cell-free-synthesised on poly(A)-rich mRNAs from mouse FLS-ascites tumour cells, were separated into two fractions corresponding to abundant mRNA species and to rare mRNA species respectively, the former being nearly 100-times more abundant per cell than the latter. Aliquots of each fraction were hybridized to a large excess of RNA of different origins; three ascites tumours (the FLS, Krebs 2 and Ehrlich tumours) all transplanted in animals; one established line of Friend erythroleukemia cells serially passaged in culture; adult organs and whole mouse embryos. It was shown that all or nearly all the mRNA species, in particular the abundant ones, were present and similarly distributed in the three transplanted tumour strains studied, despite their different tissue origins. The great majority of abundant mRNA species were also present in Friend erythroleukemia cells but about two-times less frequent relative to transplanted tumours. Much greater differences were found as compared with non-malignant cells. In particular, although the majority of the abundant mRNA species were also found in all normal tissues studied, they were on the average 7-8-times less abundant in adult liver or in 10-days-old embryos, and 10-times less abundant in adult brain, than in tumour cells. Finally about 10% of the abundant RNA species common to all transplanted tumours appeared to be absent in normal cells, whatever their growth rates or stage of differentiation. The possible implications of these findings are discussed.

Characterization of Giemsa dark- and light-band DNA

Using synchronized cultures of V79-8 Chinese hamster lung fibroblasts, we either alternately labeled early- and late-replicating DNA, or substituted one of these with bromodeoxyuridine to separate them in CsCl density gradients or to identify the bromodeoxyuridine-containing chromosome bands by fluorescence microscopy. The Giemsa light R bands were shown to replicate in the first half of S phase, and the dark G bands were shown to replicate in the last half of S phase. S phase was bimodal, with a distinct pause in the rate of DNA synthesis that separated the period of R-band DNA synthesis from that of G-band DNA synthesis. G-band DNA was found to be 3.2% richer in AT than R-band DNA. Surprisingly, G- and R-band DNA appeared equally transcriptionally active in that alternate labels in chromatin were digested with the same kinetics by DNAase I, and in reassociation experiments, total poly(A)+ RNA drove nick-translated G- and R-band DNA probes similarly. G- and R-band DNA also reassociated with identical kinetics, demonstrating that they contain equal proportions of all kinetic-complexity classes of sequences.

Differential expression of selected genes in human leukemia leukocytes

cDNA clones complementary to mRNA of cells from patients having chronic lymphocytic leukemia (CLL) were used to examine quantitative changes in the mRNA levels of specific genes in human leukemia leukocytes. Fourteen (of 400) CLL-positive clones that did not hybridize with placental mRNA were studied. Three of the 14 clones were highly represented in mRNA from CEM, a T-cell line. One clone was highly represented in mRNA from CLL and two were highly represented in mRNA from patients with chronic myelocytic leukemia. Ten clones were not significantly represented in normal leukocytes and spleen mRNA. We have identified several genes that are differentially expressed in human leukemia leukocytes.

A microcomputer program for analysis of nucleic acid hybridization data

The study of nucleic acid hybridization is facilitated by computer mediated fitting of theoretical models to experimental data. This paper describes a non-linear curve fitting program, using the 'Patternsearch' algorithm, written in BASIC for the Apple II microcomputer. The advantages and disadvantages of using a microcomputer for local data processing are discussed.