Fluorescence in situ hybridization analysis of formalin fixed paraffin embedded tissues, including tissue microarrays

Optimization of Fluorescence In Situ Hybridization Protocols in the Era of Precision Medicine

Fluorescence in situ hybridization (FISH) is a cytogenetic assay that is widely used in both clinical and research settings to validate genetic aberrations. Simple in principle, it is based on denaturation and hybridization of a DNA probe and its complementary sequence; however, it is subject to continuous optimization. Here we share how in-house FISH can be optimized using different control tissues to visualize and ultimately validate common and novel genetic abnormalities unearthed by next-generation sequencing (NGS). Seven specific FISH probes were designed and labeled, and conditions for eight tissue types and one patient-derived tumor organoid were optimized. Formalin-fixed paraffin-embedded (FFPE) tissue slides were used for each experiment. Slides were first deparaffinized, then placed in a pretreatment solution followed by a digestion step. In-house FISH probes were then added to the tissue to be denatured and hybridized, and then washed twice. To obtain optimal results, probe concentration, pepsin incubation time, denaturation, and the two post-hybridization washes were optimized for each sample. By modifying the above conditions, all FISH experiments were optimized in separate tissue types to investigate specific genomic alterations in tumors arising in those tissues. Signals were clear and distinct, allowing for visualization of the selected probes. Following this protocol, our lab has quickly optimized 11 directly labeled in-house FISH probes to support genetic aberrations nominated by NGS, including most recent discoveries through whole-genome sequencing analyses. We describe a robust approach of how to advance in-house labeled FISH probes. By following these guidelines, reliable and reproducible FISH results can be obtained to interrogate FFPE slides from benign, tumor tissues, and patient-derived tumor organoid specimens. This is of most relevance in the era of NGS and precision oncology. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Metaphase FISH optimization Support Protocol 1: In-house probe labeling and preparation Support Protocol 2: Metaphase spread preparation Basic Protocol 2: Optimization of FISH on formalin-fixed paraffin-embedded tissue.

Molecular Approaches to Diagnosis in Ewing Sarcoma: Fluorescence In Situ Hybridization (FISH)

The differential diagnosis of small round cell tumors (SRCT) crucially relies on the synoptic evaluation of morphology, immunohistochemical patterns, and molecular features. Though the implementation of broad RNA sequencing in diagnostic molecular pathology routines has substantially changed the standards of molecular affirmation of diagnoses, fluorescence in situ hybridization (FISH) on formalin-fixed, paraffin-embedded (FFPE) tissue sections is still an elementary tool to provide a rapid molecular corroboration of diagnoses, essentially required for therapeutic decisions. We discuss here the major FISH approaches currently employed in diagnostic molecular pathology, addressing classic Ewing sarcoma and differential diagnoses among SRCT which cannot sufficiently be ruled out by immunohistochemistry. This chapter will approach technical issues but particularly strategies and pitfalls in the interpretation of FISH patterns.

Molecular intrinsic versus clinical subtyping in breast cancer: A comprehensive review

Breast cancer is a heterogeneous disease manifesting diversity at the molecular, histological and clinical level. The development of breast cancer classification was centered on informing clinical decisions. The current approach to the classification of breast cancer, which categorizes this disease into clinical subtypes based on the detection of estrogen receptor, progesterone receptor, human epidermal growth factor receptor 2, and proliferation marker Ki67, is not ideal. This is manifested as a heterogeneity of therapeutic responses and outcomes within the clinical subtypes. The newer classification model, based on gene expression profiling (intrinsic subtyping) informs about transcriptional responses downstream from IHC single markers, revealing deeper appreciation for the disease heterogeneity and capturing tumor biology in a more comprehensive way than an expression of a single protein or gene alone. While accumulating evidences suggest that intrinsic subtypes provide clinically relevant information beyond clinical surrogates, it is imperative to establish whether the current conventional immunohistochemistry-based clinical subtyping approach could be improved by gene expression profiling and if this approach has a potential to translate into clinical practice.

Optimization of trypsin treatment condition utilizing immunohistochemistry for chromogenic in situ hybridization

Chromogenic in situ hybridization (CISH) is a molecular technique used to visualize specific genes. Both heat treatment and protease treatment play important roles for the success of CISH on formalin-fixed paraffin-embedded (FFPE) tissue sections. In contrast to heat treatment, the optimal condition of protease treatment may vary depending on each sample. Because trypsin has a substrate specificity to cleave lysine and arginine, we hypothesized that trypsin could effectively degrade histones rich in lysine and arginine and that the removal of histones from DNA following heat treatment could improve CISH results. We selected 21 patients with lung adenocarcinoma previously known to be positive or negative for anaplastic lymphoma kinase (ALK) gene rearrangement and used FFPE tissue sections collected from these patients. Then, we assessed histone degradation among the following protease treatments; trypsin, pepsin, and proteinase K, and compared the ALK CISH results with results obtained using commercially available kits and these protease treatments. The results showed that trypsin effectively degraded histones. Additionally, compared with the other treatments, ALK CISH with trypsin treatment showed the most evaluable cells and the smallest standard deviation. Our study suggests that the degradation of histones by trypsin subsequent to heat treatment might improve CISH results.

One-fits-all pretreatment protocol facilitating Fluorescence In Situ Hybridization on formalin-fixed paraffin-embedded, fresh frozen and cytological slides

Background

The Fluorescence In Situ Hybridization (FISH) technique is a very useful tool for diagnostic and prognostic purposes in molecular pathology. However, clinical testing on patient tissue is challenging due to variables of tissue processing that can influence the quality of the results. This emphasizes the necessity of a standardized FISH protocol with a high hybridization efficiency. We present a pretreatment protocol that is easy, reproducible, cost-effective, and facilitates FISH on all types of patient material simultaneously with good quality results.

During validation, FISH analysis was performed simultaneously on formalin-fixed paraffin-embedded, fresh frozen and cytological patient material in combination with commercial probes using our optimized one-fits-all pretreatment protocol. An optimally processed sample is characterized by strong specific signals, intact nuclear membranes, non-disturbing autofluorescence and a homogeneous DAPI staining.

Results

In our retrospective cohort of 3881 patient samples, overall 93% of the FISH samples displayed good quality results leading to a patient diagnosis. All FISH were assessed on quality aspects such as adequacy and consistency of signal strength (brightness), lack of background and / or cross-hybridization signals, and additionally the presence of appropriate control signals were evaluated to assure probe accuracy. In our analysis 38 different FISH probes from 3 commercial manufacturers were used (Cytocell, Vysis and ZytoLight). The majority of the patients in this cohort displayed good signal quality and barely non-specific background fluorescence on all tissue types independent of which commercial probe was used.

Conclusion

The optimized one-fits-all FISH method is robust, reliable and reproducible to deliver an accurate result for patient diagnostics in a lean workflow and cost-effective manner. This protocol can be used for widespread application in cancer and non-cancer diagnostics and research.

Cell Type-Specific Quantification of Telomere Length and DNA Double-strand Breaks in Individual Lung Cells by Fluorescence In Situ Hybridization and Fluorescent Immunohistochemistry

Telomeres are small repetitive DNA sequences at the ends of chromosomes which act as a buffer in age-dependent DNA shortening. Insufficient telomere repeats will be recognized as double-strand breaks. Presently, it is becoming more evident that telomere attrition, whether or not caused by mutations in telomere maintenance genes, plays an important role in many inflammatory and age-associated diseases. In this report, a method to (semi)quantitatively assess telomere length and DNA double-strand breaks in formalin-fixed paraffin-embedded (FFPE) tissue is described. Therefore, a novel combination of quantitative fluorescence in situ hybridization, tissue elution, and immunofluorescence staining techniques was developed. Caveolin-1 (type 1 pneumocytes), pro-surfactant protein C (type 2 pneumocytes), club cell-10 (club cells), and alpha smooth muscle actin (smooth muscle cells) markers were used to identify cell types. To visualize all the different probes, restaining the tissue by heat-mediated slide elution is essential. Fluorescent signals of telomeres and DNA double-strand breaks were quantified using the Telometer plugin of ImageJ. As example, we analyzed lung tissue from a familial pulmonary fibrosis patient with a mutation in the telomere-associated gene poly(A)-specific ribonuclease ( PARN). The protocol displays a novel opportunity to directly quantitatively link DNA double-strand breaks to telomere length in specific FFPE cells.

Rare Incidence of ROS1 Rearrangement in Cholangiocarcinoma

Purpose

The recent discovery and characterization of an oncogenic ROS1 gene rearrangement has raised significant interest because small molecule inhibitors are effective in these tumors. The aim of this study was to determine frequency and clinicopathological features associated with ROS1 rearrangement in patients with cholangiocarcinoma (CCA).

Materials and Methods

A total of 261 patients who underwent surgery for CCA between October 1997 and August 2013 were identified from an international, multi-institutional database. ROS1 rearrangement was evaluated by break-apart fluorescence in situ hybridization using tissue microarrays of these patients.

Results

Of 261 CCA evaluated, three cases (1.1%) showed ROS1 rearrangement by fluorescence in situ hybridization (FISH), all of which were derived from intrahepatic origin. ROS1 protein expression was observed in 38 samples (19.1%). Significantly larger tumor size was observed in ROS1 immunohistochemistry (IHC)–negative patients compared with ROS1 IHC–positive patients. ROS1 FISH–positive patients had a single tumor with a median size of 4 cm and well-to-moderate differentiation. Overall, there was no difference in terms of baseline characteristics, overall survival, and recurrence-free survival between ROS1-positive and -negative patients.

Conclusion

ROS1 rearrangement was detected in 1.1% of CCA patients. Although rare, conduct of clinical trials using ROS1 inhibitors in these genetically unique patients is warranted.

TALEN-mediated targeting of HPV oncogenes ameliorates HPV-related cervical malignancy

Persistent HPV infection is recognized as the main etiologic factor for cervical cancer. HPV expresses the oncoproteins E6 and E7, both of which play key roles in maintaining viral infection and promoting carcinogenesis. While siRNA-mediated targeting of E6 and E7 transcripts temporarily induces apoptosis in HPV-positive cells, it does not eliminate viral DNA within the host genome, which can harbor escape mutants. Here, we demonstrated that specifically targeting E6 and E7 within host DNA with transcription activator-like effector nucleases (TALENs) induces apoptosis, inhibits growth, and reduces tumorigenicity in HPV-positive cell lines. TALEN treatment efficiently disrupted E6 and E7 oncogenes, leading to the restoration of host tumor suppressors p53 and retinoblastoma 1 (RB1), which are targeted by E6 and E7, respectively. In the K14-HPV16 transgenic mouse model of HPV-driven neoplasms, direct cervical application of HPV16-E7-targeted TALENs effectively mutated the E7 oncogene, reduced viral DNA load, and restored RB1 function and downstream targets transcription factor E2F1 and cycling-dependent kinase 2 (CDK2), thereby reversing the malignant phenotype. Together, the results from our study suggest that TALENs have potential as a therapeutic strategy for HPV infection and related cervical malignancy.

Thyroid transcription factor-1 amplification and expressions in lung adenocarcinoma tissues and pleural effusions predict patient survival and prognosis

INTRODUCTION

Thyroid transcription factor-1 (TTF1) plays a role in lung adenocarcinoma development. We investigated the significance of TTF1 in primary lung adenocarcinomas, lymph node metastases, and malignant pleural effusions (MPEs).

METHODS

We studied TTF1 in 175 primary lung adenocarcinomas, 52 lymph node metastases, and 46 MPE using microarray-based fluorescence in situ hybridization, immunohistochemistry, and messenger RNA (mRNA) in situ hybridization. Real-time reverse transcription polymerase chain reaction was used to investigate correlations between TTF1 amplification and mRNA expression. Correlations between clinicopathologic characteristics, TTF1 amplification, TTF1 expressions, overall survival, and prognosis were analyzed.

RESULTS

TTF1 was amplified in 7% of primary lung adenocarcinomas, 4% of lymph node metastases, and 4% of MPE. TTF1 amplification in lung adenocarcinomas was associated with pathologic subtypes (p = 0.029). Patients with positive TTF1 protein and mRNA expressions had improved overall survival if TTF1 was unamplified compared with those with TTF1 amplification (p = 0.068). A multivariate model did not show patients with positive TTF1 expressions tended to have better prognoses if TTF1 was unamplified compared with those with TTF1 amplification (p = 0.068). Survival time was longer for patients with TTF1 expressions in both primary lung tissues (p < 0.001) and MPE (p = 0.045). A multivariate model confirmed the prognostic value of TTF1 expressions in lung adenocarcinoma (p < 0.001). A multivariate model confirmed the prognostic value of TTF1 expressions in lung adenocarcinoma tissues (p < 0.001) while not in MPE (p = 0.058). TTF1 mRNA level was higher in cases with TTF1 amplification compared with those without TTF1 amplification.

CONCLUSIONS

Patients with lung adenocarcinoma without TTF1 amplification tend to have better prognoses than those with TTF1 amplification in cases with positive TTF1 expressions. Positive TTF1 expressions in lung adenocarcinoma tissues are favorable prognostic parameters in patients with lung adenocarcinoma.

Ferritin as a reporter gene for in vivo tracking of stem cells by 1.5-T cardiac MRI in a rat model of myocardial infarction

The methods currently utilized to track stem cells by cardiac MRI are affected by important limitations, and new solutions are needed. We tested human ferritin heavy chain (hFTH) as a reporter gene for in vivo tracking of stem cells by cardiac MRI. Swine cardiac stem/progenitor cells were transduced with a lentiviral vector to overexpress hFTH and cultured to obtain cardiospheres (Cs). Myocardial infarction was induced in rats, and, after 45 min, the animals were subjected to intramyocardial injection of ∼200 hFTH-Cs or nontransduced Cs or saline solution in the border zone. By employing clinical standard 1.5-Tesla MRI scanner and a multiecho T2* gradient echo sequence, we localized iron-accumulating tissue only in hearts treated with hFTH-Cs. This signal was detectable at 1 wk after infarction, and its size did not change significantly after 4 wk (6.33 ± 3.05 vs. 4.41 ± 4.38 mm2). Cs transduction did not affect their cardioreparative potential, as indicated by the significantly better preserved left ventricular global and regional function and the 36% reduction in infarct size in both groups that received Cs compared with control infarcts. Prussian blue staining confirmed the presence of differentiated, iron-accumulating cells containing mitochondria of porcine origin. Cs-derived cells displayed CD31, α-smooth muscle, and α-sarcomeric actin antigens, indicating that the differentiation into endothelial, smooth muscle and cardiac muscle lineage was not affected by ferritin overexpression. In conclusion, hFTH can be used as a MRI reporter gene to track dividing/differentiating stem cells in the beating heart, while simultaneously monitoring cardiac morpho-functional changes.