In situ hybridization

Challenges and future of biomarker tests in the era of precision oncology: Can we rely on immunohistochemistry (IHC) or fluorescence in situ hybridization (FISH) to select the optimal patients for matched therapy?

Molecular techniques have improved our understanding of the pathogenesis of cancer development. These techniques have also fueled the rational development of targeted drugs for patient populations stratified by their genetic characteristics. These novel methods have changed the classic paradigm of diagnostic pathology; among them are IHC, FISH, polymerase chain reaction (PCR) and microarray technology. IHC and FISH detection methods for human epidermal growth factor receptor-2 (HER2), epidermal growth factor receptor (EGFR) and programmed death ligand-1 (PD-L1) were recently approved by the Food and Drug Administration (FDA) as routine clinical practice for cancer patients. Here, we discuss general challenges related to the predictive power of these molecular biomarkers for targeted therapy in cancer medicine. We will also discuss the prospects of utilizing new biomarkers for fibroblast growth factor receptor (FGFR) and hepatocyte growth factor receptor (cMET/MET) targeted therapies for developing new and robust predictive biomarkers in oncology.

Inhibition of DNAse activity in PFGE analysis of DNA from Campylobacter jejuni

DNAse-positive strains of Campylobacter jejuni degrade their chromosomal DNA during standard preparative procedures before pulsed-field gel electrophoresis (PFGE). A simple method for inactivation of this DNAse activity is described. Formaldehyde fixation of the bacterial cells resulted in the preservation of the DNA in a state suitable for restriction digestion and subsequent electrophoretic analysis.

Non-radioactive analysis of biomolecules

An overview on non-radioactive bioanalytical indicator systems is presented. The nature of labels being important for direct as well as indirect systems is discussed. This is followed by the description of enzymatic, photochemical and chemical methods for labeling nucleic acids, proteins and glycans. These methods can be applied either for direct labeling of these biomolecules or for labeling of respective probes (DNA, RNA, oligonucleotides, antibodies, lectins). In the second part, various optical, luminescent and fluorescent detection approaches are described. The possibility to enhance the sensitivity by coupled amplification reactions (signal amplification, target-specific signal amplification, target amplification) is shown in a separate section. Finally, the wide variety of qualitative and quantitative reaction formats related to different applications is collected.

In situ hybridizations of Eperythrozoon suis visualized by electron microscopy

Eperythrozoon suis is an extracellular red blood cell parasite that causes icteroanemia and poor growth performance in feeder pigs and has been associated with anemias in baby pigs and reproductive failures in sows. At present, few efficient tests are available for the diagnosis and study of E. suis infection in swine. This report discusses how a recently developed recombinant DNA probe (KSU-2) specific to E. suis DNA was utilized in in situ DNA hybridizations that couple biotinylated TaqI digested products of KSU-2 DNA with an immunogold detection system allowing the visualization by transmission electron microscopy of the gold particles within eperythrozoon organisms. Specific labelling by the probe of eperythrozoon organisms demonstrated a pattern that changed with the various stages of the eperythrozoon life cycle.

From immunohistochemistry to in situ hybridization

The revolutionary evolution in science and technology has made it possible to face adequately three main challenges in modern medicine: old diseases changing, new diseases appearing, diseases remaining unknown. In this paper we review the road travelled by the pathologist in search of a method which is based upon the application to routine work of instruments and techniques which once were available for research only. Application to tissue studies of immunological and molecular biology techniques allows a dynamic interpretation of biological phenomena with special regard to gene regulation and expression. The method implies stepwise investigations, including immunohistochemistry, EM and in situ hybridization, in order to progress from the suggestive features detectable in routinely stained preparations to more characteristic, specific and, finally, pathognomonic features. HE-stained preparations and appropriate immunohistochemical stains enable recognition of phenotypic changes which may reflect genotypic alterations. Thus there is a logical and methodological link between the simple HE and the most powerful techniques so far introduced in pathology: immunohistochemistry and in situ hybridization.

Alkyl- and aryl-substituted salicyl phosphates as detection reagents in enzyme-amplified fluorescence DNA hybridization assays on solid support

Nine salicyl phosphate esters with hydrophobic substituents (5-phenyl, 5-(2,4-difluorophenyl), 5-tert-octyl, 5-cumyl, 5-(4-tert-butylphenyl, 5-(1-adamantyl), 5-(n-dodecyl), 5-(1,1-diphenylethyl, and 5-trityl) were synthesized and found to be good substrates for calf intestinal alkaline phosphatase. The enzymatic hydrolysis produced the corresponding salicylates, which were strongly fluorescent when excited by ultraviolet light around 300 nm with maximum emission at 420-435 nm. The salicylates were less soluble and/or more adhesive than the nonfluorescent salicyl phosphate substrates, resulting in localization of fluorescence signal, which is a requirement for membrane-based assays. The salicyl phosphates bearing 8-14 carbon substitutents were found to be suitable detection reagents for dot-blot DNA hybridization assays on nylon membrane using a biotinylated probe, allowing the detection of 125 pg of target pBR322 plasmid DNA using a simple apparatus consisting of a transilluminator, a camera. and a 455-nm cutoff optical filter.

Molecular hybridization techniques in current diagnosis of chronic hepatitis B in childhood

Following the cloning and sequencing of the hepatitis B virus genome, molecular hybridization techniques have been established to detect hepatitis B virus (HBV) DNA in serum and liver tissue. Analyses can be performed by dot blot, Southern blot and in situ hybridization. HBV DNA is regarded to be the most sensitive marker of viral replication and infectivity which was previously related to the presence of hepatitis B e antigen in serum and hepatitis B core antigen in liver cells. In liver tissue different molecular patterns can be recognized as free viral DNA and integrated sequences. Furthermore, introduction of the polymerase chain reaction allows the detection of very small amounts of viral DNA and has markedly improved diagnostic sensitivity. Thus the study of HBV DNA has become a valuable part of the routine diagnosis in chronic hepatitis B, providing a more reliable evaluation of virus replication and infectivity, and facilitating more precise statements about course and prognosis of the disease.

Detection of rabies virus mRNA in mouse brain by using in situ hybridization with digoxigenin-labelled RNA probes

A non-isotopic method of in situ hybridization (ISH) was developed for the detection of rabies virus RNA in paraffin-embedded tissues. Digoxigenin-labelled RNA probes for rabies virus glycoprotein mRNA were used. The method had good sensitivity and low backgrounds, and there was excellent cellular localization of signals. ISH wih digoxigenin-labelled probes was compared with ISH with 3H-labelled probes. This non-isotopic method of ISH is more convenient than the radiolabelled method, and it is quicker because a long autoradiographic exposure is not required.

Localization of elastase and tumor necrosis factor alpha mRNA by non-radioactive in situ hybridization in cultures of alveolar macrophages

Digoxigenin is a new tool for labeling probes which can be detected with the help of specific antibodies in the cell by indirect or direct immunostaining. In contrast to the biotin-reaction, the advantage of digoxigenin is that it does not appear in animal or human cells in nature. In comparison to radioactive labeling methods it is favorable in terms of short exposure time and precise localization of signals in the cell. In this paper we describe the localization of elastase and tumor necrosis factor alpha (TNF alpha) mRNA by non-radioactive in situ hybridization of rat alveolar macrophages in cell culture after stimulation with welder steam dusts. Using digoxigenin labeled probes the determination of specific mRNA's expression and their precise localization in the cytoplasm of the cell could be achieved within one day.

The digoxigenin:anti-digoxigenin (DIG) technology--a survey on the concept and realization of a novel bioanalytical indicator system

A review is given on the novel non-radioactive digoxigenin:anti-digoxigenin (DIG) bioanalytical indicator system. After a general introduction on direct and indirect indicator systems based on previous non-radioactive indicator reactions as well as in vitro and in vivo amplification procedures the principle of the new digoxigenin:anti-digoxigenin technology is demonstrated. The novel system is based on the specific high-affinity interaction between the cardenolide digoxigenin from Digitalis plants and a digoxigenin-specific antibody coupled with a reporter group. A variety of methods for digoxigenin modification of nucleic acids, proteins and glycans are presented. In addition, various applications of the novel non-radioactive indicator system in a variety of direct or indirect detection approaches with either insoluble or soluble substrates are described. It is also shown that with these applications alternative reaction formats are used which are partly characterized by additional amplification steps.

Expression of chromogranin A mRNA in small cell carcinoma of the lung

Chromogranin A (CgA) is the most specific neuroendocrine marker but in small cell carcinoma of the lung (SCCL) CgA immunoreactivity cannot always be detected, possibly owing to poor granularity. The localization of CgA mRNA could be a more useful indicator of CgA synthesis in SCCL. We have therefore studied the expression of CgA mRNA in SCCL, using in situ hybridization and Northern blot analysis, comparing it with CgA immunoreactivity. The expression of CgA mRNA and immunoreactivity in other types of lung tumours was also investigated. Freshly fixed, surgically resected SCCL (n = 5), adenocarcinoma (n = 10), squamous cell carcinoma (n = 10), large cell carcinoma (n = 5), and primary lymphoma (n = 2) were examined. Weak immunoreactivity to CgA was seen in one SCCL but all five strongly expressed CgA mRNA. The specificity of the in situ hybridization signal and the probe was confirmed by the use of a sense probe and Northern blot analysis. Non-SCCLs were negative for both CgA mRNA and immunoreactivity. This study provides evidence for CgA synthesis in SCCL and confirms the specificity of CgA for neuroendocrine differentiation. In situ hybridization appears to be a very useful tool for investigating the nature of tumour cells, especially in the absence of the end product of the gene transcript.

Non-radioactive labeling and detection of nucleic acids. I. A novel DNA labeling and detection system based on digoxigenin: anti-digoxigenin ELISA principle (digoxigenin system)

A novel highly sensitive non-radioactive DNA labeling and detection system based on the ELISA principle has been developed. DNA is modified with the cardenolide-hapten digoxigenin by enzymatic incorporation of digoxigenin-labeled deoxyuridine-triphosphate with Klenow enzyme. Digoxigenin is linked to dUTP via an 11-atom linear spacer (Dig-[11]-dUTP). Following hybridization of membrane-bound target-DNA with a digoxigenin-labeled probe, the hybrids are detected by an ELISA reaction using digoxigenin-specific antibodies covalently coupled to the marker enzyme alkaline phosphatase [(Dig):CIAP]. This binding of antibody: marker enzyme-conjugate is followed by an enzyme-catalysed coupled redox reaction with the colour substrates 5-bromo-4-chloro-3-indolyl phosphate (BCIP) and nitroblue tetrazolium salt (NBT) giving rise to a deep-blue coloured, water-insoluble precipitate directly adhering to the membrane. The digoxigenin system allows the detection of 0.1 pg homologous DNA within 16 h in dot- and Southern-blots on nitrocellulose or nylon membranes avoiding any significant background even after a prolonged period of color development. Due to its high sensitivity and specificity, the new system is appropriate for detection of single-copy genes in genomic blots as well as for Northern, slot, colony, plaque and in situ hybridizations.

Cellular gene expression for calbindin-D28k in mouse kidney

Gene expression for calbindin-D28k, the 28,000 relative molecular mass vitamin D-dependent calcium-binding protein, was measured in cells of the murine nephron by in situ hybridization on tissue sections (hybridization cytochemistry). Radiolabeled (35S-UTP), single-stranded RNA complementary to calbindin-D28k-mRNA (probe RNA) was prepared from linearized cDNA template and used for the hybridizations. Autoradiography was carried out and cellular levels of hybridization signal (silver grains) were quantified. After correction for background the concentration of silver grains was more than 350% greater in the distal tubule than in either the proximal tubule or the glomerulus. The relative cellular level of mRNA in the cytoplasm, as reflected in silver grains/cell, of the distal tubules with probe RNA was 3.4 times greater than that with control RNA. Cells of the distal tubule were the only apparent sites of specific hybridization with probe RNA. The presence of calbindin-D28k-mRNA in the distal tubule corresponded to the localization of calbindin-D28k by immunocytochemistry.

Detection of rabies virus RNA in the central nervous system of experimentally infected mice using in situ hybridization with RNA probes

Rabies virus is usually demonstrated in human or animal tissues using antigen-detection or viral isolation techniques. Rabies virus RNA can be demonstrated in paraffin-embedded tissues using in situ hybridization. Negative (-) sense 35S- and 3H-labeled RNA probes, specific for rabies virus nucleocapsid protein mRNA, were used for the detection of rabies virus RNA in the nervous system of mice experimentally infected with fixed and street strains of rabies virus. In situ hybridization signals were compared with rabies virus antigen demonstrated with immunoperoxidase staining. Rabies virus RNA and antigen were also demonstrated in the same neurons using a double-labeling technique. In situ hybridization has potential applications as a diagnostic test for rabies and in studies of rabies pathogenesis.

Detection of parvovirus B19 DNA in fetal tissues by in situ hybridisation and polymerase chain reaction

Attempts were made to detect human parvovirus B19-DNA by in situ hybridisation and the polymerase chain reaction in placental and fetal tissues from a case of intrauterine fetal death. In the in situ hybridisation experiments radioactive and non-radioactive (labelled with 2-acetyl-aminofluorene, AAF) DNA probes were used. B19-DNA was detectable in paraffin wax embedded fetal tissue from the liver, heart, lung, brain and thymus. The resolution with the AAF-labelled probes was higher than with the radiolabelled DNA. Parvovirus B19 DNA sequences were also detected in these tissues by an enzymatic in vitro amplification technique--the polymerase chain reaction. Amplification of a B19-DNA sequence before detection increases the rapidity and sensitivity of detection. The rapid, specific, and sensitive analysis of parvovirus B19 in normal and diseased tissues using these techniques may contribute considerably to determining the role of this virus as a risk factor in the outcome of pregnancy.

Detection of yellow fever virus nucleic acid in infected mosquitoes by RNA:RNA in situ hybridization

An in situ hybridization technique was developed for the strand-specific detection of yellow fever virus (YFV) RNA. An 35S-labeled, transcribed RNA probe was used to detect positive-sense polarity YFV genomic RNA in infected C6/36 (Aedes albopictus) cells, dissected mosquito tissues, and sections of plastic-embedded, YFV-infected Aedes aegypti mosquitoes. Mosquito tissues fixed in buffered Formalin retained morphological integrity. The low concentrations of probe used yielded high specific signal on infected specimens and low background signal on uninfected specimens.