Chromosomal localization of genes by scanning electron microscopy using in situ hybridization with biotinylated probes: Y chromosome repetitive sequences

Metallographic in situ hybridization

Metallographic methods, in which a target is visualized using a probe or antibody that deposits metal selectively at its binding site, offers many advantages for bright-field in situ hybridization (ISH) detection as well as for other labeling and detection methods. Autometallographically enhanced gold labeling procedures have demonstrated higher sensitivity than conventional enzyme chromogens. Enzyme metallography, a novel procedure in which an enzymatic probe is used to deposit metal directly from solution, has been used to develop bright-field ISH methods for HER2 gene determination in breast cancer and other biopsy specimens. It provides the highest level of sensitivity and resolution, both for visualizing endogenous gene copies in nonamplified tissues and for resolving multiple gene copies to allow copy enumeration in amplified tissues without the need for oil immersion or fluorescence optics. An automated enzyme metallography procedure, silver ISH, has been developed for use in slide-staining instruments. Metallographic staining also provides excellent results for immunohistochemistry and may be combined with other staining procedures for the simultaneous detection of more than one gene or combinations of genes and proteins.

rRNA sequence-based scanning electron microscopic detection of bacteria

A new scanning electron microscopic method was developed for gaining both phylogenetic and morphological information about target microbes using in situ hybridization with rRNA-targeted oligonucleotide probes (SEM-ISH). Target cells were hybridized with oligonucleotide probes after gold labeling. Gold enhancement was used for amplification of probe signals from hybridized cells. The hybridized cells released a strong backscatter electron signal due to accumulation of gold atoms inside cells. SEM-ISH was applied to analyze bacterial community composition in freshwater samples, and bacterial cell counts determined by SEM-ISH with rRNA-targeted probes for major phyla within the domain Bacteria were highly correlated to those by fluorescent in situ hybridization (FISH). The bacterial composition on surface of river sediment particles before and after cell dispersion treatment by sonication was successfully revealed by SEM-ISH. Direct enumeration of bacterial cells on the surface of sonicated sediment particles by SEM-ISH demonstrated that members of Cytophaga-Flavobacterium existed tightly on the surface of particles. SEM-ISH allows defining the number and distribution of phylogenetically defined cells adherent to material surfaces, which is difficult in FISH, and it gives new insight into electron microscopic studies of microorganisms in their natural environment.

In situ hybridization by scanning electron microscopy for painting, centromeric, and YAC localization

The hybridization site of a DNA probe was detected using a scanning electron microscope (SEM), modifying the standard in situ hybridization (ISH) method. The experiments were performed on human metaphases obtained from lymphocyte cultures of human peripheral blood. The libraries and probes used were: 1-chromosome library for the painting of chromosome 1 (wcp 1), an alphoid centromere-specific probe of chromosome 8 (pZ8.4), and the yeast artificial chromosome (YAC) 964-C10 mapped at band p13 on chromosome 12. These probes were labeled by nick translation with biotin and displayed with a gold-conjugated anti biotin goat antibody. The gold signal was amplified by silver enhancement. The chromatides appeared as packages of thin filaments 120 nm high; some of them collapsed, probably due to ISH procedures. All the probes were clearly detected as small gold particles grouped on the surface of the target chromosomes and chromosome sites. Thus, this procedure is useful to clarify the positional relationship between the chromatin filaments and the probe.

Ultrastructure of in situ hybridization

Techniques for the ultrastructural localization of structures identified by in situ hybridization are being developed for both preembedding labeling and labeling on thin sections (postembedding). Successful labeling of both RNA and DNA sequences has been reported in recent years. Biotinylated nucleic acid probes are becoming increasing available. Colloidal gold is the only successful ultrastructural label with meaningful spatial localization, and the best results have been obtained with small (20-5 nm) gold particles. The link between biotinylated nucleic acid probes and gold has been protein A, antibiotin, or avidin binding. The size of the target nucleotide sequence, the size of the probe, and the number of gold particles attached to the labeling protein must be understood before there can be meaningful interpretation of micrographs. In addition, the spatial considerations depend on whether preembedding or postembedding is used.

The course of giardiavirus infection in the Giardia lamblia trophozoites

The subcellular distribution of Giardia lamblia virus RNA in infected G. lamblia trophozoites was examined by in situ hybridization using biotinylated DNA probe and riboprobe. In G. lamblia Portland I strain, which is chronically infected by G. lamblia viruses, the viral RNA was detected in the cytoplasm as well as in the twin nuclei. When riboprobe was used to examine the course of virus infection in WB strain, accumulation of viral RNA was detected only in the cytoplasm prior to the first 72 hr of infection. Using DNA probe, further accumulation of viral RNA in increasing number of cells occurred after the 72nd hr of infection, with the RNA found in both the cytoplasm and nuclei. Eventually, the cell nuclei showed damaged morphology that deteriorated rapidly toward the final stage of infection. These observations indicate that early phase of viral RNA replication may take place in the cytoplasm of infected G. lamblia, but the nuclei are also involved during the late phase of viral replication.

Detection of HPV DNA in neoplastic and non-neoplastic cervical specimens from Pakistan and Japan by non-isotopic in situ hybridization

In order to determine the prevalence and type-specific distribution of human papillomavirus (HPV) in women from Pakistan, a country with a low cervical cancer rate (hospital-based data), and to compare these results with their counter-parts in Japan, we studied 56 non-neoplastic cervical tissues and 162 cervical carcinoma cases from both countries. HPV infection was defined by in situ hybridization in paraffin-embedded tissues using biotinylated HPV 6/11, 16 and 18 probes. The overall positivity rates in non-neoplastic and neoplastic cervical tissues from Pakistan were 33% and 88%, while in those from Japan the rates were 46% and 80%, respectively. High-risk HPVs (16 & 18) were found in 17% of the non-neoplastic specimens and in 69% of cervical carcinoma cases from Pakistan, while Japanese figures in this respect were 19% and 68%, respectively. No correlation was found between the type-specific distribution or prevalence of HPV and the geographic location of the cases examined in the 2 countries. However, in comparison to Japanese women, the incidence of HPV-16-positive cervical carcinoma in Pakistani women decreased significantly (p less than 0.05) in the oldest age group as compared to the youngest age group.

Origin of marrow stromal cells and haemopoietic chimaerism following bone marrow transplantation determined by in situ hybridisation

The origin and cell lineage of stromal cells in the bone marrow is uncertain. Whether a common stem cell exists for both haemopoietic and stromal cells or whether these cell lines arise from distinct stem cells is unknown. Using in situ hybridisation for detection of the Y chromosome, we have examined histological sections of bone marrow from seven patients who received marrow transplants from HLA-matched donors of the opposite sex. Stromal cells (adipocytes, fibroblasts, endothelial cells, osteoblasts and osteocytes) were identified in these recipients as being of host origin. This result is consistent with the concept of a distinct origin and separate cell lineage for cells of the haemopoietic and stromal systems. It also shows that engraftment of marrow stromal cell precursors does not occur and that host stromal cells survive conditioning regimens for marrow transplantation. With the exception of one case, with a markedly hypocellular marrow, mixed chimaerism was seen in haemopoietic cells, indicating that this is not a rare event after marrow transplantation.

Non-isotopic detection of in situ nucleic acid in cervix: an updated protocol

Recently, sensitive non-isotopic in situ hybridisation (NISH) methodology for the detection of human DNA and human papilloma virus (HPV) DNA in archival paraffin blocks of cervix was described. An amended protocol, now used in this laboratory for detection of these genes by NISH is presented. The amendments include the following: protease digestion at 37 degrees C; tissue dehydration in air rather than ethanol; stringency washing in formamide solution; blocking non-specific binding of avidin alkaline phosphatase with a modified buffer; and increasing the concentration of avidin alkaline phosphatase for detecting low abundance DNA. These changes simplify and increase the sensitivity of the protocol such that "Y" chromosome repeats are visualised in almost all female cells.

Direct visualization of single copy genes on banded metaphase chromosomes by nonisotopic in situ hybridization

A rapid method is described for non isotopic in situ mapping of single copy genes directly on G-banded chromosomes by "one-step" regular light microscopy. It is based on hybridizing biotinylated probes to metaphase chromosomes. Biotin residues are detected by rabbit antibiotin antibody and anti-rabbit Ig labelled with peroxidase or colloidal gold. The peroxidase reaction product or colloidal gold signals are amplified by silver precipitation. The final product is a black silver dot at the gene locus on a purple G-banded chromosome. N-ras and alpha-1-antitrypsin genes have been mapped using plasmids with inserts of 1.5 and 1.3kb to 1p13.1 and the junction of 14q31/32 respectively. The signal to noise ratio in these experiments ranged from 32:1-46:1. This technology is at least as sensitive as radioisotopic in situ hybridization and gives results within 1 day of hybridization and has much better resolution. Additionally, genes are visualized by regular light microscopy without specialized techniques such as reflection contrast, fluorescence or phase microscopy. This methodology should facilitate more precise chromosomal gene localization.

Cytochemical applications of X-ray microanalysis

X-ray microanalysis (XRMA) has been applied to a wide variety of cytochemical problems, but the most valuable applications have been to the validation of cytochemical methods (by the qualitative or quantitative analysis of reaction products), and to the simultaneous localization of more than one substance, which cannot easily be achieved by using alternative methods. The latter applications involve stoichiometric studies (the quantitative relationships between reaction products and substrates), and distribution studies. Ultrastructural cytochemistry with XRMA is limited by the need to use high-brightness electron sources. Apart from the limited availability of such sources, they may cause unacceptable damage to the specimen. Preparation methods for cytochemistry using XRMA are reviewed; in principle these do not differ from those used for other cytochemical applications, but it is important not to introduce extraneous elements (from fixative, buffer, or embedding medium) into the specimen, where the additional X-ray peaks may interfere with the analysis. Quantification in XRMA of cytochemical preparations poses special problems, because the addition of the reaction product to the specimen alters the yield of continuum X rays, used for assessing the mass of the specimen, and also dilutes endogenous elements. However, measurement of ratios between characteristic elemental peaks is a useful method in X-ray microanalytical cytochemistry, and it is concluded that one of the most important attributes of XRMA for cytochemical purposes is the ease with which the substances of interest can be measured.

Simultaneous extraction from clinical biopsies of high-molecular-weight DNA and RNA: comparative characterization by biotinylated and 32P-labeled probes on Southern and Northern blots

A method for efficient simultaneous extraction of high-molecular-weight DNA and RNA from solid mammalian tissues including clinical biopsies is described. It is based on the disruption and subsequent melting of deep frozen tissue in the presence of frozen phenol and nucleic acid extraction buffer; this allows for simultaneous disruption of tissue and inactivation of nucleases. The yield is about 0.7-5.8 mg of DNA and 0.5-8.1 mg of total RNA/g of tissue depending upon the tissue type; this is higher than the yield of other methods tested. Analysis of total RNA by denaturing gel electrophoresis, and of DNA and poly(A)+ RNA by Southern and Northern blot hybridization using 32P and biotinylated probes, indicated that c-Ha-ras gene and its transcripts were undegraded. Biotinylated and 32P probes had approximately the same sensitivity in detecting nucleic acids on Southern and Northern blots. This extraction procedure is simple and, when used with biotinylated probes, is rapid, inexpensive, and nonhazardous. The methodology can be modified for use with other clinical samples and cells grown in culture.

Non-radioactive in situ hybridization. A comparison of several immunocytochemical detection systems using reflection-contrast and electron microscopy

A number of immunocytochemical detection systems for determining the chromosomal localization of specific nucleic acid sequences by non-radioactive in situ hybridization have been compared. The procedures were: 1. the peroxidase/diaminobenzidine (PO/DAB) combination, either or not gold/silver intensificated; 2. alkaline phosphatase marking using the nitro-blue tetrazolium plus bromochloro-indolyl phosphate substrate combination (AP/NBT + BCIP); and 3. immunogold with or without silver enhancement. The procedures were first tested and optimized in dot blot experiments and then applied to in situ hybridization. As hybridization probes, both a middle-repetitive and a unique sequence (modified with 2-acetylaminofluorene (AAF] were used. The advantages and disadvantages of the various methods for reflection contrast (RC) or transmission electron microscopic (TEM) visualization of hybrids are discussed.

Detection of low copy human papilloma virus DNA and mRNA in routine paraffin sections of cervix by non-isotopic in situ hybridisation

In analysing human papilloma virus (HPV) infection of the cervix in formalin fixed paraffin sections by non-isotopic in situ hybridisation two main problems were found: detachment of sections from the glass during hybridisation and probe detection; inadequate sensitivity and inability to assess sensitivity of the in situ procedure. The first problem was investigated by assessing the efficiency of various tissue adhesives individually and in combination. The second problem was addressed by optimising conditions for DNA unmasking, hybridisation, and biotinylated probe detection. Sensitivity of the final in situ procedure developed was assessed by using the detection of pHY2.1 repeats as a built-in control. Extrapolation of data showed that less than 10 copies of HPV DNA can be visualised by these procedures. HPV nucleic acid, mainly in the form of DNA, was detected not only in koilocytic nuclei but also in suprabasal cells in condylomas and CIN lesions. HPV mRNA was also visualised in the cytoplasm (and probably also nuclei) of the same cell types. These non-isotopic in situ procedures give results comparable to those obtained with radiolabelled probes, but they are less time consuming and provide better morphological resolution.

High resolution gene mapping of the human alpha globin locus

A combination of polymorphic DNA markers, cytogenetic analysis, and in situ hybridisation has been used for the high resolution assignment of the human alpha globin gene cluster on chromosome 16. Multiallelic DNA probes from within the alpha globin cluster were used to determine the number of copies of this locus in three cell lines containing trisomies of the short arm of chromosome 16 and one with a familial inversion, inv(16). The breakpoints in these rearrangements flank the alpha globin locus and locate a shortest region of overlap to 16p13.1. A meiotic crossover was also localised to this band. In situ hybridisation of biotinylated DNA probes to normal and inverted chromosomes 16 [inv(16)(p13.1;q22)] showed hybridisation sites at opposite ends of the chromosomes, consistent with this regional localisation.

Human and viral gene detection in routine paraffin embedded tissue by in situ hybridisation with biotinylated probes: viral localisation in herpes encephalitis

A simple reproducible protocol for detecting multiple copy human genes and viral DNA in routine formalin fixed paraffin embedded tonsil and brain, by in situ hybridisation with biotinylated probes, is described. The protocol consists of digestion of formalin fixed paraffin sections, with 0.4% pepsin in 0.01 M hydrochloric acid for one hour at 37 degrees C, followed by hybridisation with biotinylated probes. The biotinylated probes used for establishing the conditions for in situ localisation of DNA were total placental DNA (TG1), pHY 2.1 (a Y chromosome probe), and herpes simplex virus I and II. In human male tonsil TG1 labelled all nuclei and pHY 2.1 reacted only with nuclear Y bodies. In herpes encephalitis the virus was detected in some glial cells and neurones.