Sensitivity Of In Situ Hybridization Research Articles

Fluorescence quenching by high-power LEDs for highly sensitive fluorescence in situ hybridization.

Recent technical advances have made fluorescent in situ hybridization (ISH) a pivotal method to analyze neural tissue. In a highly sensitive ISH, it is important to reduce tissue autofluorescence. We developed a photobleaching device using a light-emitting diode (LED) illuminator to quench autofluorescence in neural tissue. This device was equipped with 12 high-power LEDs (30 W per single LED) and an evaporative cooling system, and these features achieved highly efficient bleaching of autofluorescence and minimized tissue damage. Even after 60 min of photobleaching with evaporative cooling, the temperature gain of the tissue slide was suppressed almost completely. The autofluorescence of lipofuscin-like granules completely disappeared after 60 min of photobleaching, as did other background autofluorescence observed in the mouse cortex and hippocampus. In combination with the recently developed fluorescent ISH method using the hybridization chain reaction (HCR), high signal/noise ratio imaging was achieved without reduction of ISH sensitivity to visualize rare mRNA at single copy resolution by quenching autofluorescence. Photobleaching by the LED illuminator was also effective in quenching the fluorescent staining of ISH-HCR. We performed multiround ISH by repeating the cycle of HCR staining, confocal imaging, and photobleaching. In addition to the two-round ISH, fluorescent immunohistochemistry or fluorescent Nissl staining was conducted on the same tissue. This LED illuminator provides a quick and simple way to reduce autofluorescence and quench fluorescent dyes for multiround ISH with minimum tissue degradation.

Comparative aspects of laboratory testing for the detection of Toxoplasma gondii and its differentiation from Neospora caninum as the etiologic agent of ovine abortion

Histologic examination of aborted material is an essential component in the diagnosis of ovine toxoplasmosis. However, the detection of Toxoplasma gondii in histologic sections, and its differentiation from the closely related protozoan Neospora caninum, is challenging. We developed a chromogenic in situ hybridization (ISH) assay for the identification of T. gondii in paraffin-embedded tissue samples. We examined retrospectively the archived placental tissue of 200 sheep abortion submissions for the presence of T. gondii by immunohistochemistry (IHC), ISH, and real-time PCR (rtPCR). All placental samples that tested positive for T. gondii by rtPCR (9 of 200) were also positive by IHC, with inconclusive IHC staining in an additional 7 rtPCR-negative cases. Further testing for N. caninum of all 200 placentas by rtPCR revealed 7 Neospora-positive cases. T. gondii ISH was positive in 4 of 9 IHC-positive samples and 1 of the 7 N. caninum rtPCR-positive samples. Real-time PCR was used as the reference standard for specificity and sensitivity calculations regarding placenta samples. Specificity of ISH and IHC was 99% and 96-100%, respectively. The sensitivity of ISH (44%) was quite low compared to IHC (100%). The exclusive use of ISH for the detection of T. gondii, and thus for the diagnosis of ovine toxoplasmosis, was not acceptable. However, combined with rtPCR, both ISH and IHC can be useful detection methods to improve histologic evaluation by visualizing the parasite within tissue sections.

Multiplex in situhybridization within a single transcript: RNAscope reveals dystrophin mRNA dynamics.

Dystrophin plays a vital role in maintaining muscle health, yet low mRNA expression, lengthy transcription time and the limitations of traditional in-situ hybridization (ISH) methodologies mean that the dynamics of dystrophin transcription remain poorly understood. RNAscope is highly sensitive ISH method that can be multiplexed, allowing detection of individual transcript molecules at sub-cellular resolution, with different target mRNAs assigned to distinct fluorophores. We instead multiplex within a single transcript, using probes targeted to the 5' and 3' regions of muscle dystrophin mRNA. Our approach shows this method can reveal transcriptional dynamics in health and disease, resolving both nascent myonuclear transcripts and exported mature mRNAs in quantitative fashion (with the latter absent in dystrophic muscle, yet restored following therapeutic intervention). We show that even in healthy muscle, immature dystrophin mRNA predominates (60-80% of total), with the surprising implication that the half-life of a mature transcript is markedly shorter than the time invested in transcription: at the transcript level, supply may exceed demand. Our findings provide unique spatiotemporal insight into the behaviour of this long transcript (with implications for therapeutic approaches), and further suggest this modified multiplex ISH approach is well-suited to long genes, offering a highly tractable means to reveal complex transcriptional dynamics.

Expression profiles of RA synthases and catabolic enzymes in newly hatched and metamorphosing larvae of Japanese flounder, Paralichthys olivaceus

Retinoic acid (RA) plays various embryogenesis and post-embryogenesis roles in vertebrates. As exposure of metamorphosing flounder larvae to RA has teratogenic effects on skin color and vertebral column development, harmonized RA synthesis and catabolism are likely essential in metamorphic development. To approach understanding of the roles of RA in flounder metamorphic development, we here examined the tissue mRNA expression of RA synthases (aldh1a1, aldh1a2, aldh1a3) and catabolic enzymes (cyp26a1, cyp26b1, cyp26c1) in newly hatched and metamorphosing larvae, and three-month-old juveniles by in situ hybridization (ISH). No ISH signal was detected for any genes from the skin and vertebral column susceptible to the teratogenic effects by RA. Since the intestine expressed aldh1a2 at high level in larvae but not in juvenile, it is a possibility that the larval intestine serves as a source of RA, and RA catabolic enzymes function at the level below sensitivity of ISH at vertebral column and skin development. We found that aldh1a2 and aldh1a3 were expressed along the margin of the tectum and the neurohypophysis of pituitary, respectively, both in contact with the cerebrospinal fluid (CSF), and cyp26b1 at the posterior tectum and cerebellum. We hypothesize that RA is supplied from the tectum and pituitary via the CSF for brain growth and maintenance, and cyp26b1 locally regulates RA contents in the brain.

Abstract 537: Evaluation of immune function in the tumor microenvironment by RNA in situ hybridization to reveal spatial information on immune cell infiltration and the expression of functional mRNA biomarkers

Abstract Growing evidence for the antitumor activity of the immune system has supported recent success in cancer immunotherapy. Therapeutic approaches such as anti-cancer vaccines and suppression of immune checkpoints have been successfully applied in various cancers to raise specific immune responses and to enhance antitumor immune responses. In particular, blocking immune checkpoint pathways such as CTLA-4 and PD-1/PD-L1 is transforming cancer therapeutics. Based on these successes, clinical trials of combinatorial strategies are in progress to target multiple pathways. While many biomarker analysis technologies are employed to guide specific therapeutic approaches, spatially mapped biomarker expression data at the single-cell level is crucial to understanding the composition and activities of various immune cells in the tumor microenvironment. In this study, in order to visualize gene expression of key immune biomarkers in the tumor microenvironment, we have applied the RNAscope® technology, an RNA in situ hybridization (ISH) method that provides single molecule RNA detection with spatial and morphological context. This highly sensitive ISH presents a unique advantage to the visualization of mRNA biomarkers for secreted proteins such as cytokines and chemokines in individual cells. Specific probes for key cytokines (e.g., IL6, IL12A, TGF-β, IFN-γ, TNF-α), chemokines (e.g., CCL5, CXCL9, CXCL10, CXCL13), and immune subset markers (e.g., CD3, CD4, CD8A, FOXP3) were designed in addition to key receptor/ligand pairs in immune check points (e.g., PD1/PD-L1, OX40/OX40L). Expression of each target and combinations of multiple targets were assessed on formalin-fixed paraffin embedded (FFPE) tissue sections derived from multiple tumor types. Using this approach, the various functional mRNA biomarker profiles of the immune cell types infiltrated in the tumor are directly visualized as punctate dots. The visible mRNA dots are readily quantifiable, so that enumeration of immune cells is feasible. RNAscope® based ISH is well-suited to study immune function in the tumor microenvironment by visualizing gene expression. By applying this method, it is feasible to evaluate the relationship of specific biomarkers in different cell types. With the emerging effort towards combinatorial approaches to target multiple pathways, the method presented here can be applied as a universal platform to study both cancer specific molecular pathways as well as immune function. Citation Format: Ming-Xiao He, Courtney Anderson, Na Li, Xiao-Jun Ma, Emily Park. Evaluation of immune function in the tumor microenvironment by RNA in situ hybridization to reveal spatial information on immune cell infiltration and the expression of functional mRNA biomarkers. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 537.

Localization of Bovine Papillomavirus Nucleic Acid in Equine Sarcoids.

Bovine papillomaviruses (BPV1/BPV2) have long been associated with equine sarcoids; deciphering their contribution has been difficult due to their ubiquitous presence on skin and in the environment, as well as the lack of decent techniques to interrogate their role in pathogenesis. We have developed and characterized an in situ hybridization (ISH) assay that uses a pool of probes complementary to portions of the E5, E6, and E7 genes. This assay is highly sensitive for direct visualization of viral transcript and nucleic acid in routinely processed histopathologic samples. We demonstrate here the visualization of BPV nucleic acid in 18 of 18 equine sarcoids, whereas no detectable viral DNA was present in 15 of 15 nonsarcoid controls by this technique. In nearly 90% (16/18) of the sarcoids, 50% or more of the fibroblastic cell nuclei distributed throughout the neoplasm had detectable hybridization. In the remaining 2 cases, fewer than half of the fibroblastic cells contained detectable hybridization, but viral nucleic acid was also detected in epithelial cells of the sebaceous glands, hair follicles and epidermis. A sensitive ISH assay is an indispensable addition to the molecular methods used to detect viral nucleic acid in tissue. We have used this technique to determine the specific cellular localization and distribution of BPV in a subset of equine sarcoids.

Sensitive and specific in situ hybridization for early drug discovery.

High-throughput analyses of gene expression such as microarrays and RNA-sequencing are widely used in early drug discovery to identify disease-associated genes. To further characterize the expression of selected genes, in situ hybridization (ISH) using RNA probes (riboprobes) is a powerful tool to localize mRNA expression at the cellular level in normal and diseased tissues, especially for novel drug targets, where research tools like specific antibodies are often lacking.We describe a sensitive ISH protocol using radiolabelled riboprobes suitable for both paraffin-embedded and cryo-preserved tissue. The riboprobes are generated by in vitro transcription using PCR products as templates, which is less time consuming compared to traditional transcription from linearized plasmids, and offers a relatively simple way to generate several probes per gene, e.g., for splice variant analyses. To ensure reliable ISH results, we have incorporated a number of specificity controls in our standard experimental setup. We design antisense probes to cover two non-overlapping parts of the gene of interest, and use the corresponding sense probes as controls for unspecific binding. Probes are furthermore tested on sections of paraffin-embedded or cryo-preserved positive and negative control cells with known gene expression. Our protocol thus provides a method for sensitive and specific ISH, which is suitable for target validation and characterization in early drug discovery.

HPV Testing in Liquid Cytology Specimens

To compare the analytic sensitivity and specificity of Hybrid Capture 2 (HC2) (Digene Corporation, Gaithersburg, Maryland, U.S.A.) with in situ hybridization (ISH) in detecting high-risk types of HPV (HR-HPV).Performance characteristics of ISH and HC2 were compared in 99 consecutive cervical cytology samples diagnosed as low grade squamous intraepithelial lesion and processed by either the ThinPrep (Cytyc Corporation, Boxborough, Massachusetts, U.S.A.) or SurePath (TriPath Imaging Systems, Research Triangle Park, North Carolina, U.S.A.) method at 2 geographically different centers. Polymerase chain reaction (PCR) was used as the gold standard.Of the samples, 67% were positive for HR-HPV viral types by PCR. ISH had a sensitivity of 0.87 as compared to 0.95 (p = 0.11) for HC2. The specificity of ISH was significantly different from that of HC2 (0.57 vs. 0.13, respectively; p = 0.0004). The performance characteristics of ISH were not affected by the processing method or population tested.The sensitivity of ISH is comparable to that of HC2, with significantly superior specificity, and is therefore an efficacious alternative to HC2 for triaging patients with abnormal cervical cytology results.

Gene Expression Profiling, Frozen and Paraffin Section Immunohistochemistry, and In Situ Hybridization for Determination of Monoclonality in Diffuse Large B-Cell Lymphoma.

Background: Determining monotypia of surface immunoglobulin (SIg) is often an important step in the diagnosis of B-cell lymphomas. Many competing methods have been developed and are commonly used in clinical practice. The role of gene expression profiling (GEP) in determining light chain restriction is yet to be clarified. The goal of this study was to compare 4 methods by which light chain restriction can be determined: frozen section immunohistochemistry (FS-IHC), paraffin section IHC (PS-IHC), in-situ hybridization (ISH), and GEP.Design: 40 cases of DLBCL, part of a previous GEP study of DLBCL (Rosenwald et al, NEJM 2002), were made into a tissue microarray (TMA). FS-IHC slides, previously stained using by-hand streptavidin and diaminobenzidine, were re-examined for κ:λ restriction. PS-IHC was done on the TMA using the Benchmark system according to manufacturer's protocols for κ/λ staining (Ventana Medical Systems VMSI, Tucson, AZ). ISH was performed on the TMA with a newly developed sensitive ISH procedure from VMSI which uses a purified streptavidin reagent to reduce background and increase sensitivity. The FS-IHC, PS-IHC, and ISH arrays were reviewed and scored as κ/λ monotypic, SIg-negative or indeterminate by 3 pathologists. The averaged gene expression ratios for microarray elements probing for κ and λ on each case were plotted on a log2 scale. Monoclonality was determined using 2 different GEP criteria: (1) κ-monoclonal if κ:λ expression was >2log2 or λ-monoclonal if expression was λ>κ or (2) κ and λ light chain relative expression on either side of the median. These data from all 4 techniques were used to determine a consensus clonality in which the majority of the results agreed. The results for each technique were then compared to the consensus for that case.Results: 7 Cases had a 4/4 consensus, 9 cases a 3/4, 11 cases a 3/3, 7 cases a 2/3, and 1 case a 2/2. 5 cases were excluded from the study because there was no majority consensus. 19 cases (47.5%) were κ monoclonal, 10 (25%) λ monoclonal, 6 (15%) SIg-negative, and 5 cases (12.5%) indeterminate. Compared to the consensus clonality FS-IHC was accurate in 21/26 (81%), PS-IHC in 28/32 (87%), sensitive ISH in 29/29 (100%) cases. GEP was accurate in 31/35 (89%) cases using either criteria (1) or (2); in 27/35 (77%) using criterion (1) alone, in 28/35 (80%) using criterion (2) alone, and 24/35 (69%) of cases when both criteria (1) and (2) were met. 6 SIg-negative cases failed all GEP criterion, but were considered correctly classified as neitherκ nor λ monoclonal.Discussion: The technique with the highest accuracy compared to consensus was the sensitive ISH assay, in part because samples were eliminated if the mRNA control (polyT probe) staining was suboptimal. GEP was also accurate using either of our criteria. The SIg-negative cases were not classified as either κ or λ monoclonal using any of our criteria. Given the increasing role GEP is likely to play in hematopathology, the application of GEP to B cell clonality may have diganostic utility.

Detection of peroxisomal proteins and their mRNAs in serial sections of fetal and newborn mouse organs.

We present a protocol for detection of peroxisomal proteins and their corresponding mRNAs on consecutive serial sections of fetal and newborn mouse tissues by immunohistochemistry (IHC) and nonradioactive in situ hybridization (ISH). The use of perfusion-fixation with depolymerized paraformaldehyde combined with paraffin embedding and digoxigenin-labeled cRNA probes provided a highly sensitive ISH protocol, which also permitted immunodetection with high optical resolution by light and/or fluorescence microscopy. Signal enhancement was achieved by the addition of polyvinyl alcohol (PVA) for ISH color development. For IHC, signal amplification was obtained by antigen retrieval combined with biotin-avidin-HRP and Nova Red as substrate or by the catalyzed reporter deposition of fluorescent tyramide. Using this protocol, we studied the developmental changes in localization of the peroxisomal marker enzymes catalase (CAT) and acyl-CoA oxidase 1 (AOX), the key regulatory enzyme of peroxisomal beta-oxidation, at the protein and mRNA levels in mice from embryonic Day 14.5 to birth (P0.5). The mRNA signals for CAT and AOX were detected in sections of complete fetuses, revealing organ- and cell-specific variations. Here we focus on the localization patterns in liver, intestine, and skin, which showed increasing mRNA amounts during development, with the strongest signals in newborns (P0.5). Immunolocalization of the corresponding proteins revealed, in close correlation with the mRNAs, a distinct punctate staining pattern corresponding to the distribution of peroxisomes. (J Histochem Cytochem 49:155-164, 2001)

Analysis of immunoglobulin light-chain mRNA in gastric malignant lymphoma using new highly sensitive in situ hybridization method.

BACKGROUND: To analyze B-cell monoclonality, we need fresh materials for the Southern blotting method. In situ hybridization (ISH) for the detection of immunoglobulin light-chain mRNA can be used in formalin-fixed and paraffin-embedded tissues. However, it is difficult to detect low levels of mRNA copies. So we must develop new highly sensitive in situ hybridization methods to diagnose gastric malignant lymphoma.METHODS: We analyzed materials from 15 patients with gastric malignant lymphoma, using a new highly sensitive ISH method, and compared the results with those of a conventional method.RESULTS: With this new method, 13 of 15 cases were shown to have monotypic cytoplasmic signals, and monoclonality was detected in 3 of 4 cases of mucosa-associated lymphoid tissue (MALT) lymphoma.CONCLUSIONS: The accuracy of endoscopic biopsies is not satisfactory. However, the detection of immunoglobulin light chain mRNA, using the new highly sensitive ISH method with a non-radioactive isotope oligonucleotide probe, can be used to diagnose gastric malignant lymphoma even when conventional immunoglobulin light-chain mRNA or proteins alone cannot demonstrate the clonality.

Detection of human papillomavirus in cervical intra-epithelial neoplasia, using in situ hybridization and various polymerase chain reaction techniques.

One hundred and forty-eight randomly chosen neutral-buffered formaldehyde-fixed cervical biopsies in which cervical intra-epithelial neoplasia (CIN) I-III had been diagnosed were tested for HPV (human papilloma virus) DNA by in situ hybridization (ISH) and polymerase chain reaction (PCR). For ISH, we utilized a biotinylated panprobe and type-specific, genomic probe sets. For PCR, we used the general primers GP5/GP6 and their recently described, elongated version GP5+/GP6+, and included the modification of hot-start PCR. Amplified DNA was detected by gel electrophoresis and slot blot hybridization. The positivity rate of ISH was 59% for all biopsies and 69%, 62% and 46% for CIN I, II and III, respectively. The sensitivity of GP5/GP6 was 74% with cold-start PCR and 78% with hot-start PCR. When GP5+/GP6+ was used, the sensitivity increased to 89% with cold-start PCR and to 95% with hot-start PCR. Based on the most sensitive PCR technique, HPV detection was 93%, 95% and 96% in CIN I, II and III, respectively. The number of HPV types decreased with the severity of the lesion, and HPV 16 was the predominant type. Multiple HPVs were rare and almost all HPV-positive cases could be typed. ISH and slot blot hybridization correlated well regarding HPV typing specificity. Our results confirm that distinct HPV types are present in a high proportion of cases of CIN. The sensitivity of ISH is lower than that of PCR. Furthermore, the modified general primers GP5+/GP6+ give a higher yield than GP5/GP6, while hot-start PCR increases sensitivity even further.

Polymerase chain reaction and in situ hybridization: applications in toxicological pathology.

Polymerase chain reaction (PCR) and in situ hybridization (ISH) have revolutionized the study of genes and gene expression, and many of these molecular biology advances will greatly impact research in toxicological pathology. PCR is one of the most powerful tools in molecular biology and involves primer-mediated enzymatic in vitro amplification of specific target DNA sequences. Recent innovative methods utilizing PCR technology have been developed to detect mutations in neoplastic and small subpopulations of cells, to study biomarkers of genetic susceptibility and genes involved with carcinogen metabolism, to estimate mutation frequencies, to find novel genes induced by chemical exposure, and to characterize gene expression. ISH provides data on individual cells rather than an average of total cellular populations and allows analysis for heterogeneity. When combined with PCR, the sensitivity of ISH is elevated, and single-copy DNA sequences, single-base mutations, or low copies of messenger RNA (mRNA) can potentially be detected within individual cells. Herein are reviewed ISH- and PCR-based techniques such as single-strand conformation polymorphism analysis to detect point mutations, allelotypic analysis for loss of heterozygosity, differential display of mRNA to characterize gene expression, quantitative reverse transcriptase polymerase chain reaction, and in situ polymerase chain reaction with emphasis on current or potential applications in toxicological pathology. These new and evolving techniques offer tremendous potential in providing new insights into the molecular basis of toxicity and carcinogenesis.

Detection of tumor necrosis factor-α protein and messenger RNA in human glial brain tumors: comparison of immunohistochemistry with in situ hybridization using molecular probes

Tumor necrosis factor-alpha (TNF alpha) protein and messenger (m)RNA distribution was studied in biopsy samples of glial brain tumors, using immunohistochemistry and in situ hybridization with molecular probes, to investigate the role of this cytokine in tumor proliferation and immunological host defense. Focal expression of TNF alpha was detected in four of four glioblastomas, one of two anaplastic astrocytomas, and four of five low-grade astrocytomas, regardless of their subtype or grade of malignancy, but in none of the normal peritumoral brain tissues used as controls. The TNF alpha protein and mRNA were present in reactive astrocytes and protoplasmic tumor cells, confined to areas of leukocyte or T-lymphocyte infiltrating, and less pronounced in tumor cells at the edge of necrosis. Additionally, TNF alpha reactivity was found in infiltrating macrophages and perivascular microglia. Immunohistochemistry and in situ hybridization for TNF alpha showed comparable reaction patterns and numbers of TNF alpha-positive cells, even though the sensitivity of in situ hybridization was significantly higher. Quantitative evaluation of TNF alpha protein, TNF alpha mRNA, and leukocyte infiltration revealed a significant positive correlation between the TNF alpha-positive reactive astrocytes and the number of lymphocytes present in corresponding areas. Together, these data lead to the conclusion that TNF alpha in reactive astrocytes and monocytic cells within tumor areas of high leukocyte infiltration and in tumor cells at the border of necrosis may represent one defense pathway of the immune system against tumor proliferation.

PCR Production of a Digoxigenin-labeled Probe for the Detection of Human Cytomegalovirus in Tissue Sections

In situ hybridization (ISH) provides a means for identifying viral genomes in the context of tissue pathology. We have developed a specific and sensitive ISH probe for the detection of cytomegalovirus (CMV) DNA in formalin-fixed, paraffin-embedded tissue sections. Digoxigenin-11-dUTP was incorporated into a 435-base pair fragment of the CMV Major Immediate Early (MIE) gene with use of the polymerase chain reaction (PCR). Hybridized probe was detected by reaction with antidigoxigenin antibody coupled to alkaline phosphatase and chromogenic substrates. This method has detected CMV infection in routine clinical specimens from a variety of tissue types, including colon, kidney, liver, and stomach. Infection in cells with and without characteristic inclusions is revealed with this probe. The background is so low that single infected cells are detected unambiguously. No cross-hybridization was observed with cells infected with other viruses of Herpesviridae. This approach may be useful for producing probes for the detection of other viral genomes in tissue sections.

ビオチン化水痘・帯状疱疹ウイルス (VZV) DNAを用いた<I>In Situ</I> Hybridization法による帯状疱疹皮疹部塗抹標本のVZV DNAの検出

We performed the in situ hybridization (ISH) study of the smear cells taken from the patients of herpes zoster. We used the biotinylated EcoRI-B, H fragment of varicella-zoster-virus (VZV) DNA as the probe. In the control study of ISH VZV-infected cells showed strong staining, but no staining was observed in the infected cells by other herpes virus. We examined the smear cells of 19 patients of herpes zoster and 2 patients of herpes simplex by ISH. 30 of the 35 specimens of herpes zoster was positive by ISH. We detected VZV DNA in the smear cells of all cases of the bullous stage, but the sensitivity was about 75% in the later stage. Smear cells of herpes simplex was not stained by ISH. We also performed virus isolation of 13 cases of herpes zoster. But the sensitivity of ISH was higher than that of virus isolation in the other stages of herpes zoster. This method is very simple and can be completed in about 1 hour. It also has high specificity and sensitivity. So this method is very useful for the rapid diagnosis of VZV infection.