Epidemiology and the genetic basis of disease.
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Genetic Predisposition to Disease↗
Biomedical subjects
E Spanakis
Publications and source records attributed to E Spanakis.
Microplate array diagonal gel electrophoresis for mutation research in DNA banks.
Molecular genetic epidemiology, association and linkage studies in populations, human or other species, is now yielding powerful new insights into disease and susceptibility genes. Inter alia, the subject requires laboratory analytical methodologies focused on achieving high throughput. Here we review one suite of methodology suitable for such laboratories. Microplate array diagonal gel electrophoresis (MADGE) was invented for molecular genetic epidemiological studies. It combines direct compatibility with microplates, convenient polyacrylamide gel electrophoresis and economy of time and reagents, at minimal capital cost, and enables one user to run up to several thousand gel lanes per day for direct assay of single-base variations. Melt-MADGE combines temporal thermal ramp apparatus to achieve similar throughput for de novo mutation scanning.
Animals↗
Microplate array diagonal gel electrophoresis (MADGE), CpG-PCR and temporal thermal ramp-MADGE (Melt-MADGE) for single nucleotide analyses in populations.
Important requirements for molecular genetic epidemiological studies are economy, sample parallelism, convenience of setup and accessibility, goals inadequately met by existent approaches. We invented microplate array diagonal gel electrophoresis (MADGE) to gain simultaneously the advantages of simple setup, 96-well microplate compatibility, horizontal electrophoresis, and the resolution of polyacrylamide. At essentially no equipment cost (one simple plastic gel former), 10-100-fold savings on time for sample coding, liquid transfers, and data documentation, in addition to volume reductions and gel re-use, can be achieved. MADGE is compatible with ARMS, restriction analysis and other pattern analyses. CpG-PCR is a general PCR approach to CpG sites (10-20% of all human single base variation): both primers have 3' T, and are abutted to the CpG, forcing a TaqI restriction site if the CpG is intact. Typically, a 52 bp PCR product is then cut in half. CpG-PCR also illustrates that PAGE-MADGE readily permits analysis of 'ultrashort' PCRs. Melt-MADGE employs real-time-variable-temperature electrophoresis to examine duplex mobility during melting, achieving DGGE-like de novo, mutation scanning, but with the conveniences of arbitrary programmability, MADGE compatibility and short run time. This suite of methods enhances our capability to type or scan thousands of samples simultaneously, by 10-100-fold.
CpG Islands↗
Microplate-array diagonal-gel electrophoresis (MADGE) and melt-MADGE: tools for molecular-genetic epidemiology.
Microplate-array diagonal-gel electrophoresis (MADGE) was invented for molecular-genetic epidemiological studies. It combines direct compatibility with microplates, convenient polyacrylamide-gel electrophoresis and economy of time and reagents at minimal capital cost, and enables one user to run up to several-thousand gel lanes per day for the direct assay of single-base variations. Melt-MADGE adds temporal-thermal-ramp apparatus to achieve similar throughput for de novo mutation scanning.
Electrophoresis↗
Discrimination of fibroblast subtypes by multivariate analysis of gene expression.
Fibroblasts and myofibroblasts from normal, fibrotic or tumoral breast tissues present multiple quantitative differences in gene expression even when grown in isolation. We were therefore prompted to investigate whether one could recognize various subtypes by their constitutive-gene expression profile. Quantitative autoradiographic data for 34 constitutively expressed transcripts were submitted to multivariate analysis of variance, followed by discriminant analysis and single linkage cluster analysis. Models assuming up to 8 putative fibroblast subtypes (among fibroblasts or myofibroblasts from breast skin, normal mammary stroma, tumor-adjacent "normal" stroma, post-radiation fibrosis lesions and benign or malignant tumors) and an epithelial-cell group used as an internal control resulted in 100% correct classification. Myofibroblasts from various origins clustered close to, although distinctly apart from, their corresponding alpha-smooth-muscle-actin-negative counterparts. Malignant tumor fibroblasts were phenotypically more distant from normal cells compared with other pathological types. Our results support the hypothesis of co-adaptive transformation of stromal and epithelial tissues during breast tumoral development and suggest that different types of fibroblasts give rise to different types of myofibroblasts. Discriminant analysis of quantitative molecular variation may be considered for the development of a powerful artificial-intelligence method for cell typing and should be particularly useful when no reliable discrete molecular markers are available.
Breast↗
Indeterminate human immunodeficiency virus type 1 western blot may indicate an abortive infection in some low-risk blood donors.
BACKGROUND: The infectious status of persons with an indeterminate human immunodeficiency virus type 1 (HIV-1) Western blot must be established. STUDY DESIGN AND METHODS: Evaluation of the CD4 and CD8 T-cell subsets and the expression of HIV-1-integrated sequences by Southern blot and polymerase chain reaction were studied in a group of low-risk subjects with an indeterminate Western blot. RESULTS: From a total of 45,000 blood donors and 50 patients with chronic renal failure on hemodialysis who were tested during the period of 1985 through 1990, 50 sera (0.1%) had an indeterminate Western blot. A low CD4:CD8 ratio (0.7-1.2) was detected in 14 of 24 tested subjects, whereas the unfractionated and adherence-enriched cells of 7 (32%) and 5 (23%) of 22 patients, respectively, could be stained with a p24 monoclonal antibody. A transient positive culture was detected in 3 of 20 subjects, but these viral isolates could not be transmitted to CEM-A310 cells. Ultracentrifuged culture supernatants hybridized under high-stringency conditions with genomic gag-pol (4 cases), env (3 cases), and tat (1 case) cDNA fragments of the HXB2 HIV-1 clone. In one case, DNA obtained from adherent but not unfractionated mononuclear cells contained 3.3- and 3.9-kb env- and gag-pol-related HIV-1 sequences, respectively; these sequences were heavier than expected. Polymerase chain reaction analysis for gag and pol but not env sequences was positive in 1 and 2 of 7 cases, respectively. A female patient with a positive viral culture and who was positive for pol in polymerase chain reaction demonstrated a full seroconversion 19 months later. CONCLUSION: The results strongly suggest that, rarely, some low-risk subjects with indeterminate Western blot results might be infected with low-level replicative strains or HIV-related viruses; thus, an exhaustive immunologic and virologic workup is needed for the investigation of these subjects.
Adolescent↗
On the distribution of insulin-like growth factors in breast tissues.
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Breast↗
Determining the specificity of quantitative variation in gene expression.
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Animals↗
Quantitative variation of proto-oncogene and cytokine gene expression in isolated breast fibroblasts.
Transcripts coding for transcription factors (RB, P53, FOS, MYC, MYB, ERBA, REL), growth factors (FGF1, FGF2, INT2, TGFA, TGFB, PDGF, IGF1, IGF2), interleukins, (IL1, IL2, IL3, IL4, IL6, TNF), growth-factor receptors or cytosolic protein kinases (RAF, PIM, FES, MET, SRC, ROS, TRK, KIT, CSFR, IGFR, PDGFR, EGFR, NEU) were quantified in cultured human mammary fibroblasts from normal tissues, benign tumours, carcinomas and post-radiation fibrosis lesions by slot-blot autoradiography and image analysis. The effects of a differentiating agent (cholera toxin) and of a tumour promoter (12-O-tetradecanoyl-phorbol-13-acetate) were also examined. The drugs modulated the levels of the anti-oncogene transcripts (RB, P53) and of ERBA, REL, RAF, MET, ROS, TRK, CSFR, EGFR, NEU, FGF1, INT2, IGF1, IL1, IL2, IL4 and IL6. Apart from this variation, there were multiple differences in gene expression among normal and pathological cells (concerning all but P53, TGFB and interleukin transcripts) and between sub-types defined by the presence of alpha-sm-actin (myofibroblasts) or EDB-fibronectin (RAF, ROS, FES, KIT, IGFR, NEU, INT2, TGFB, PDGF, IGFs, ILs). It appears, therefore, that mammary stroma progress irreversibly along with the epithelium during tumoral development, and that breast cancer is not only a multi-gene but also a multi-tissue phenotype.
Breast↗
Selective interactions between mammary epithelial cells and fibroblasts in co-culture.
Paracrine interactions between breast-cancer cells (MCF7) and stromal fibroblasts were studied in relation to the presence of steroid hormones, using co-cultures in which the 2 populations were separated by a microporous membrane. Densities and DNA-synthesis rates of the co-existing populations were interrelated. Proliferation was, therefore, viewed as the cumulative result of several factors, some of which are non-specific, e.g., are density-dependent, and some are specifically related to the feeders' origin and/or to culture conditions. Specific effects were measured and evaluated by stepwise analysis of covariance. MCF7 stimulated proliferation of fibroblasts differentially. Malignant-tumour fibroblasts were stimulated more than non-pathological ones. The magnitude of these effects was dependent on the presence of steroids. A similar analytical method was used for evaluating differential stromal influences on 4 epithelial phenotypic characters commonly used as prognostic markers. The estrogen-receptor, progesterone-receptor, pS2 and cathepsine-D phenotypes of MCF7, as well as their interrelations, were dependent on the origin of the fibroblasts, i.e., embryonic or adult, normal or tumoral.
Adenocarcinoma↗
Evaluation of quantitative variation in gene expression.
We investigate the behaviour of the gene-expression rate as a statistical variable using autoradiographic data for 39 transcripts from a heterogeneous set of 80 breast-tissue cultures. Despite standardization, the data distributions of all transcripts showed intervals of normality and intervals of systematic departure from normality which most frequently resulted in a significant skewness and/or kurtosis. Non-normal shapes are attributed to modulation of gene expression. This statistical particularity creates difficulties in the evaluation of differences among specimens. Using classical parametric and non-parametric procedures for normal and non-normal variation, respectively, we demonstrate that large differences in optical density are neither necessary nor sufficient for associating expression rates with biological factors. The transcripts coding for the metalloprotease stromelysin-3 (ST3) and for the receptor to insulin-like growth factors (IGFR) are used as examples and their variation is presented in detail. ST3 expression appeared to be specifically associated with mammary stroma fibroblasts derived from post-radiation fibrosis lesions. IGFR was expressed at higher rates in mammary gland and skin fibroblasts than in mammary epithelial cells and was subject to frequent and strong modulation.
Animals↗
Proliferative responses of epithelial cells to 8-bromo-cyclic AMP and to a phorbol ester change during breast pathogenesis.
We have explored the relationship of changes in proliferative responses of human mammary epithelial cells to a phorbol ester (TPA) and to 8-Br-cAMP, which modulate the activities of protein kinases A and C (PKA and PKC), with breast tumour progression. Treatment with TPA had no effect on nontumorigenic cell lines established from human fibrocystic biopsies and apparently normal tissue around a tumour. In contrast, TPA strongly inhibited the proliferation of numerous human tumorigenic breast cell lines. Treatment with 8-Br-cAMP decreased the proliferation of all studied nontumorigenic and tumorigenic cell lines. We have also studied the effect of TPA and 8-Br-cAMP on growth of epithelial cells in short-term culture obtained from surgical human mammary biopsies with different states of breast disease. Both drugs enhanced growth of normal breast cells but had no significant effects on cells from biopsies with benign breast disease. In contrast, all examined cultures from breast cancer biopsies were strongly inhibited by 8-Br-cAMP. Otherwise, TPA had an inhibitory effect only in the case of invasive ductal carcinoma of grade III. Malignant Ha-ras-transformation of nontumorigenic TPA-insensitive breast HBL-100 cells induced an inhibitory effect of TPA. In addition, a TPA-insensitive MCF7 clone was much less tumorigenic in athymic mice than the parental strain shown to be inhibited by TPA. These data suggest that the two intracellular transduction pathways change at different stages of breast pathogenesis. Alterations in the PKA pathway are early events and are probably important to cell immortalization but do not necessarily lead to malignant development. In contrast, changes in PKC pathway are rather later events associated with advanced malignant transformation.
8-Bromo Cyclic Adenosine Monophosphate↗
Problems related to the interpretation of autoradiographic data on gene expression using common constitutive transcripts as controls.
The 28S rRNA, a ribosomal RNA, and the ACTB and GAPD mRNAs, coding respectively for beta-actin and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), are frequently presented as controls of modulated gene expression. These transcripts were quantified by replicate slot-blot autoradiography and image analysis in mammary epithelial cells and fibroblasts from breast tissues. Each cell-type group comprised strains with different pathological backgrounds, growth rates, antigenic phenotypes and culture histories. The effects of a differentiating agent (cholera toxin) and/or a tumor promoter (12-O-tetradecanoyl-phorbol-13-acetate) were also examined. Despite the impression that visual examination of autoradiographs might create, image analysis suggests that 28S rRNA, ACTB and GAPD are substantially and independently influenced by the above biological factors and by the drugs. Therefore, these transcripts represent specifically regulated cellular activities and may not be taken as alternative indicators of the overall transcription rate or of the amount of material being examined. Instead, such nonspecific variation may be accurately measured and removed from quantitative data using a principal component function. A methodology that allows comparison of expression (or amplification) patterns between genes, between experiments or, even, between laboratories is presented with an example of quantification of transcripts related to cell-growth, differentiation, signaling and cancer.
Actins↗
Abnormal expression of IL-2R beta (p70)-binding polypeptide on HIV-infected patients' cells.
The constitutively expressed IL-2R beta (p70) chain participates in the formation of high-affinity (h.a.) IL-2R and transduces IL-2-mediated signals to normal cells. Its expression on HIV-infected patients' PBMC was evaluated and was found to be decreased in both nonstimulated CD4+ and CD8+ cells. Mitogenic cell stimulation induced IL-2R beta chain expression on both CD4+ and CD8+ cells from asymptomatic and persistent generalized lymphadenopathy patients but not on those from AIDS patients. Comparison of mean fluorescence intensity of IL-2R beta positively stained cells from normals and patients did not reveal significant differences. Cross-linking of 125I-rIL-2 on patients' PHA-blasts revealed decreased signals corresponding to both IL-2-binding chains and, in some cases, neither IL-2R alpha nor IL-2R beta chains could be detected. Decreased expression of IL-2R beta polypeptide was associated with impaired accumulation of the corresponding mRNA transcripts. Binding experiments with 125I-rIL-2 under h.a. conditions showed a decreased number of IL-2-binding sites/cell which was more pronounced in patients with AIDS than in patients with less advanced clinical stages. In vitro HIV infection of normal PHA-blasts also resulted in a decreased number of h.a. IL-2R/cell. High concentrations of rIL-2 in the absence of other mitogenic stimuli induced a decreased cell proliferation and expression of the IL-2R alpha chain and did not enhance the constitutive NK and the generation of LAK activity in several patients, suggesting an impaired IL-2R beta chain-mediated cell activation.
Antibodies, Monoclonal↗
Effects of the developmental colour mutations silver and recessive spotting on proliferation of diploid and immortal mouse melanocytes in culture.
The developmental mouse coat-colour mutations silver (si, chromosome 10) and recessive spotting (rs, chromosome 5, mapping very close to the dominant white spotting or W/c-kit locus), appear to reduce the numbers of functional melanocytes in the skin. They were studied at the cellular level by melanocyte culture. Cellular morphology, differentiation and survival appeared normal. However, both mutations were found to reduce the melanocyte proliferation rate in primary cultures, as measured by [3H]thymidine labelling indices. Two immortal si/si melanocyte lines (designated melan-si1 and melan-si2) and one rs/rs line (melan-rs) were established. Melan-si1 and melan-rs were cloned. All three immortal lines at low passage levels had doubling times significantly greater than those of our other melanocyte lines melan-a, melan-b and melan-c. Thus they retained the phenotype of slow proliferation.
Animals↗
Interleukin 2 production and interleukin 2 receptor expression by human immature leukemic T cells.
In order to determine the role of interleukin 2 (IL2) on the proliferation of leukemic cells from patients with T-cell acute lymphoblastic leukemia (T-ALL) we studied the production of IL2, the function of IL2 receptors (IL2R) expressed on T-ALL cells and their IL-2-dependent in vitro proliferation. Leukemic cells from six out of 17 T-ALL/T-cell non-Hodgkin's lymphoma patients with a prothymocyte (stage I) or a mature thymocyte (stage III), but not with a common thymocyte (stage II) phenotype, could proliferate, in a dose-dependent manner, in response to recombinant IL2 (rIL2) and anti-Tac and TU27 moAbs as well as polyclonal anti-IL2 purified immunoglobulin G could inhibit this IL2-induced cell proliferation. Both crude or/and Amicon-concentrated media conditioned by T-ALL cells from 10 out of 13 tested patients contained IL2 activity as assessed by colorimetric biological and immunoenzymatic assays; this biologic activity was due to a 14.5 kDa molecule adsorbed by anti-IL2 antibodies in an immunoaffinity assay. Although less than 10% of fresh leukemic cells expressed IL2R alpha (Tac) chain, a 24 h cell incubation in the absence of any mitogenic stimulation induced IL2R alpha chain expression in five out of 13 patients (11-83% Tac+ cells). Morever, Tac mRNA transcripts could be detected in fresh cells from all 10 patients tested. Staining of fresh leukemic cells with an IL-2R beta-chain-specific monoclonal antibody and flow cytometry analysis revealed that 4-13% of leukemic cells were positive. Binding experiments with 125I-rIL2 showed a small number of high affinity IL2R on fresh cells from three T-ALL patients (114-200 sites/cell, dissociation constant = 101-181 pm). Finally, antibodies against IL2R alpha, IL2R beta and IL2 could inhibit both IL2 driven and spontaneous cell proliferation of most patients' T-ALL cells, although in some cases an heterogenous pattern of inhibition was observed. Taken together, these findings strongly suggest that an IL2/IL2R-dependent mechanism could be involved in the proliferation of some T-ALL cells.
Antigens, CD↗
[Histological study of the remains of periodontal membrane at the alveolar wall after tooth extraction].
Histological study of 40 alveolar wounds of altogether 5 dogs have given evidence to the fact that remains of the periodontal membrane could remain in the apical area of the alveoli in their whole width. In the middle part of the alveoli, remains of it are found in a thin layer. In the marginal area, bone can be found lying open with torn remnants, which are lying free in the coagulum. In these adhering rests of the periodontal membrane plenty of dynamic cells as well as dilated vessels can be observed. All these facts lead to the idea of considering the part that the remains of the periodontal membrane may possibly play in the beginning process of alveolar wound healing.
Alveolar Process↗
[Orbital floor reconstruction using implants of compact hydroxyapatite ceramic in midfacial injuries].
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Bone Plates↗