Practical tips to using formalin-fixed paraffin-embedded tissue archives for molecular diagnostics in a South African setting

Background: Formalin-fixed paraffin-embedded (FFPE) tissue archives in hospitals, biobanks, and others offer a vast collection of extensive, readily available specimens for molecular testing. Unfortunately, the use of tissue samples for molecular diagnostic applications is challenging; thus, the forensic pathology FFPE tissue archives in Africa have been a largely unexploited genetic resource, with the usability of DNA obtainable from these samples being unknown.Intervention: The study, conducted from January 2015 to August 2016, determined the usefulness of FFPE tissue as a reliable source of genetic material for successful post-mortem molecular applications and diagnostics. Formalin-fixed paraffin-embedded tissue samples were collected and archived from autopsies conducted over 13 years in the forensic medicine department of the University of Pretoria (Pretoria, South Africa). Deoxyribonucleic acid from FFPE tissue samples and control blood samples was amplified by high-resolution melt real-time polymerase chain reaction before sequencing. The procurement parameters and fixation times were compared with the quantity and quality of the extracted DNA and the efficiency of its subsequent molecular applications.Lessons learnt: This study has shown that FFPE samples are still usable in molecular forensics, despite inadequate sample preparation, and offer immense value to forensic molecular diagnostics.Recommendations: FFPE samples fixed in formalin for more than 24 h should still be used in molecular diagnostics or research, as long as the primer design targets amplicons not exceeding 300 base pairs.

Evaluación de la metilación del DNA en tejidos de cáncer colorrectal fijados en formalina y embebidos en parafina (FFPE) / Evaluation of DNA methylation in formalin-fixed, paraffin embedded colorectal cancer tissues (FFPE)

Resumen Las alteraciones en la metilación de dinucleótidos CpG en regiones promotoras es uno de los mecanismos epigenéticos implicados en cáncer que tiene uso potencial como biomarcador. Su evaluación, a partir de tejidos fijados en formalina y embebidos en parafina (FFPE), representa un gran desafío dadas la degradación parcial, el entrecruzamiento y las bajas cantidades del DNA obtenido. En esta nota técnica, describimos un protocolo para el estudio del estado de metilación del promotor distal del proto-oncogén K-RAS, a partir de varias muestras obtenidas de dos tejidos FFPE de cáncer colorrectal con antigüedad de 11 años. Se empleó un protocolo de conversión con bisulfito alternativo al usual; se usó una DNA polimerasa modificada y una PCR anidada y se optimizó la secuenciación directa del DNA convertido con bisulfito. Este protocolo podría ser aplicado para determinar estados de metilación en otros genes y tipos de cáncer en tejidos FFPE.

Abstract Alterations in the methylation of CpG dinucleotides in promoter regions is one of the epigenetic mechanisms involved in cancer that has potential use as a biomarker. Its evaluation from formalin-fixed and paraffin-embedded (FFPE) tissues represents a great challenge given the partial degradation, crosslinking, and low amounts of the obtained DNA. In this technical note we describe a protocol for the study of the methylation status of the distal promoter of the K-RAS proto-oncogene from several samples obtained from two 11-years old FFPE tissues of colorectal cancer. An alternative bisulfite conversion protocol to the usual one was used; a modified DNA polymerase and a nested PCR were used and the direct sequencing of the converted DNA with bisulfite was optimized. This protocol could be applied to determine methylation states in other genes and types of cancer.

Multistaining Optimization for Epstein-Barr Virus–Encoded RNA In Situ Hybridization and Immunohistochemistry of Formalin-Fixed Paraffin-Embedded Tissues Using an Automated Immunostainer

BACKGROUND: Single staining is commonly performed for practical pathologic diagnoses. However, this method is limited in its ability to specify cellular morphology and immunophenotype and often requires consumption of limited tissue. This study aimed to describe an optimized protocol for multiple in situ hybridization (ISH) and immunohistochemistry (IHC). METHODS: The quality of multistaining was evaluated by carefully changing each step of ISH and IHC in an angioimmunoblastic T-cell lymphoma (AITL) case on a Ventana BenchMark XT automated immunostainer. The optimized protocols were also performed using another immunostainer and in 15 cases of five Epstein-Barr virus (EBV)–associated malignancies using formalin-fixed paraffin-embedded tissue. RESULTS: The quality of various ISH-IHC staining protocols was semi-quantitatively evaluated. The best EBV-encoded RNA (EBER)-ISH/double IHC staining quality, equivalent to single staining, was obtained using the following considerations: initial EBER-ISH application, use of protease and antigen retrieval reagent (cell conditioning 1 [CC1] treatment time was minimized due to impact on tissue quality), additional baking/deparaffinization not needed, and reduced dilution ratio and increased reaction time for primary antibody compared with single immunostaining. Furthermore, shorter second CC1 treatment time yielded better results. Multiple staining was the best quality in another immunostainer and for different types of EBV-associated malignancies when it was performed in the same manner as for the Ventana BenchMark XT as determined for AITL. CONCLUSIONS: EBER-ISH and double IHC could be easily used in clinical practice with currently available automated immunostainers and adjustment of reagent treatment time, dilution ratio, and antibody reaction time.

Comorbid Gastric Adenocarcinoma and Gastric and Duodenal Strongyloides stercoralis Infection: A Case Report

Strongyloides stercoralis can cause systemic infection, termed strongyloidiasis, and gastrointestinal ulcer disease in immunocompromised patients. However, to our knowledge, there are no reported cases of comorbid gastric adenocarcinoma and S. stercoralis infection. Here, we report a case of an 81-year-old Korean man who presented with S. stercoralis infection coexisting with early gastric adenocarcinoma (T1aN0M0). S. stercoralis eggs, rhabditiform larvae, and adult females were observed in normal gastric and duodenal crypts. They were also observed in atypical glands representative of adenocarcinoma and adenoma. Preliminary laboratory tests revealed mild neutrophilic and eosinophilic leukocytosis. A routine stool test failed to detect rhabditiform larvae in the patient's fecal sample; however, S. stercoralis was identified by PCR amplification and 18S rRNA sequencing using genomic DNA extracted from formalin-fixed paraffin-embedded tissues. Postoperatively, the patient had a persistent fever and was treated with albendazole for 7 days, which alleviated the fever. The patient was followed-up by monitoring and laboratory testing for 4 months postoperatively, and no abnormalities were observed thus far. The fact that S. stercoralis infection may be fatal in immunocompromised patients should be kept in mind when assessing high-risk patients.

Comorbid Gastric Adenocarcinoma and Gastric and Duodenal Strongyloides stercoralis Infection: A Case Report

Strongyloides stercoralis can cause systemic infection, termed strongyloidiasis, and gastrointestinal ulcer disease in immunocompromised patients. However, to our knowledge, there are no reported cases of comorbid gastric adenocarcinoma and S. stercoralis infection. Here, we report a case of an 81-year-old Korean man who presented with S. stercoralis infection coexisting with early gastric adenocarcinoma (T1aN0M0). S. stercoralis eggs, rhabditiform larvae, and adult females were observed in normal gastric and duodenal crypts. They were also observed in atypical glands representative of adenocarcinoma and adenoma. Preliminary laboratory tests revealed mild neutrophilic and eosinophilic leukocytosis. A routine stool test failed to detect rhabditiform larvae in the patient's fecal sample; however, S. stercoralis was identified by PCR amplification and 18S rRNA sequencing using genomic DNA extracted from formalin-fixed paraffin-embedded tissues. Postoperatively, the patient had a persistent fever and was treated with albendazole for 7 days, which alleviated the fever. The patient was followed-up by monitoring and laboratory testing for 4 months postoperatively, and no abnormalities were observed thus far. The fact that S. stercoralis infection may be fatal in immunocompromised patients should be kept in mind when assessing high-risk patients.

Epidermal growth factor receptor gene expression evaluation in colorectal cancer patients.

Background: Colorectal cancer is one of the most common causes of death in the world and third and fourth most common cancer among men and women in Iran respectively. Epidermal growth factor receptor (EGFR) is a tyrosine kinase receptor that shows over expression in epithelial tumors and regulates important processes in tumorigenesis. Incidence and characteristics of colorectal cancer are based on the geographic region and race. Aim: In this research work, the over expression of EGFR in formalin fixed paraffin-embedded (FFPE) colorectal cancer tumor tissue of patients was studied. Materials and Methods: Fifteen FFPE colorectal cancer tumor tissues (10 women and 5 men; 25-65 years old and stage IV) and 15 non-patients (nine women and six men; 25-65 years old) that were collected during 2006-2012. EGFR gene expression level was analyzed by real-time quantitative reverse transcriptase polymerase chain reaction (PCR). All PCR reactions were performed in triplicate for both target gene and internal control (18s ribosomal ribonucleic acid) with the 2−ΔΔCT method. Gene expression differences in patients and controls were evaluated with t-test. Results: The results were showed EGFR gene over expression in 12 (80%) of 15 patients. There was a statistically significant difference in the prevalence of EGFR expression between patients and control (P < 0.05). Conclusion: Our results demonstrated EGFR gene over expression in colorectal cancer tumor tissue compared with controls.

Direct and Rapid Diagnosis of Extra-Pulmonary Tuberculosis in Archival Tissue by Nested and Touchdown PCR.

Aims: To identify and differentiate mycobacterium spp. in archival formalin-fixed, paraffinembedded tissue by PCR to supply additional differential diagnostic method for Mycobacterium infections, where tuberculosis had been tested for by histopathological methods but without culturing. Place and Duration of Study: Department of Medical Laboratory Sciences, Department of Pathology and Microbiology (Faculty of Medicine) and King Abdulla University Hospital, between January 2004 and July 2010. Methodology: Fifty-six extra-pulmonary specimens of formalin-fixed, paraffin-embedded tissue obtained from patients showing granulomatus inflammation and/or other histopathologic features. Specimens were analyzed by a hemi-nested PCR assay targeting the gene encoding for 16S ribosomal RNA, which is common to all mycobacteria spp. The PCR positive specimens were amplified by a touch-down PCR targeting a fragment in the insertion sequence IS6110 specific to Mycobacterium tuberculosis complex. Results were compared to acid fast bacilli stain and with histopathology of each specimen. Results: M. tuberculosis complex DNA was detected in 27 (48.2%) specimens, and non-tuberculous mycobacteria in four specimens, compared to 10 (18%) specimens that were positive by acid fast staining. The positive cases were observed more in the lymph nodes, and pleural specimens. Conclusions: This study is among few studies to use the touch-down PCR assay as a promising auxiliary tool for the diagnosis of extra-pulmonary tuberculosis in archival tissue specimens. It could be used in conjunction with routine laboratory tests (e.g., cultures, acid fast staining) and clinical criteria of the patient to increase the accurate diagnosis of such cases. It is also recommended that culture be routinely done for all tuberculosis suspected cases.

Expression and significance of Hsa-miR-181a in endometrial carcinoma / 实用医学杂志

Objective To explore the expression and significance of hsa-miR-181a (miR-181a) in can-ceration progression of endometrial carcinoma. Methods A total of 75 formalin-fixed paraffin-embedded tissue specimens were studied in this study , of which , 13 were normal endometrium , 18 were endometrial hyperplasia , 44 were endometrial carcinoma. After total RNA had been extracted , real-time PCR was applied to detect the ex-pression level of miR-181a in endometrial tissue in each group. Results miR-181a expression in formalin-fixed paraffin-embedded tissue specimens can be detected. Expression of miR-181a in endometrial carcinoma was high-er than that in endometrial hyperplasia , its expression in endometrial hyperplasia was also higher than that in normal endometrium, and the difference was statistically significant (P < 0.05). The expression of miR-181a in endometrial carcinoma was associated with FIGO stages (P < 0.05). Conclusion The up-regulation of miR-181a expression in women with endometrial carcinoma may play the role of oncogenes. Abnormal expression of miR-181a is probably associated with the occurrence and development of endometrial carcinoma.

An improved method to recover high quality genomic DNA from paraffin-embedded tissues / 中南大学学报(医学版)

Objective To establish a high quality genomic DNA preparation method from formalin fixed and paraffin embedded tissues (FFPET) by integrating previous DNA extraction methods. Methods We combined classical genomic DNA extraction methods and commercially available DNA affinity column, replaced the de-waxing by dimethylbenzene with water-bath, designed a fast and improved genomic DNA preparation method. We also extracted genomic DNA from paraffin embedded cervical cancer tissues, and checked the quality of DNA by agarose gel electrophoresis and polymerase chain reaction detection. Results The improved genomic DNA extraction method combined the advantages of the water-bath de-waxing and DNA affinity column, making it possible to get high quality genomic DNA from paraffin embedded cervical cancer tissues, and especially efficient to recover genomic DNA fragments larger than 20 kb. Conclusion The improved DNA extraction method is fast and convenient to recover high quality genomic DNA from paraffin embedded tissues.

Effects of tissue handling and processing steps on PCR for detection of Mycobacterium tuberculosis in formalin-fixed paraffin-embedded samples / Efeitos das etapas de tratamento e processamento do tecido na PCR para detecção de Mycobacterium tuberculosis em amostras fixadas em formalina e incluídas em parafina

Development and standardization of reliable methods for detection of Mycobacterium tuberculosis in clinical samples is an important goal in laboratories throughout the world. In this work, lung and spleen fragments from a patient who died with the diagnosis of miliary tuberculosis were used to evaluate the influence of the type of fixative as well as the fixation and paraffin inclusion protocols on PCR performance in paraffin embedded specimens. Tissue fragments were fixed for four h to 48 h, using either 10 percent non-buffered or 10 percent buffered formalin, and embedded in pure paraffin or paraffin mixed with bee wax. Specimens were submitted to PCR for amplification of the human beta-actin gene and separately for amplification of the insertion sequence IS6110, specific from the M. tuberculosis complex. Amplification of the beta-actin gene was positive in all samples. No amplicons were generated by PCR-IS6110 when lung tissue fragments were fixed using 10 percent non-buffered formalin and were embedded in paraffin containing bee wax. In conclusion, combined inhibitory factors interfere in the detection of M. tuberculosis in stored material. It is important to control these inhibitory factors in order to implement molecular diagnosis in pathology laboratories.

O desenvolvimento e a padronização de métodos confiáveis para a detecção de Mycobacterium tuberculosis em amostras clínicas é um objetivo importante nos laboratórios de todo o mundo. Neste trabalho, fragmentos de pulmão e baço de paciente que morreu com o diagnóstico de tuberculose miliar foram usados para avaliar a influência do tipo de fixador e dos protocolos de fixação e inclusão em parafina na performance da PCR. Fragmentos de tecido foram fixados por quatro h a 48 h, usando formalina não tamponada a 10 por cento ou formalina tamponada a 10 por cento e incluídos em parafina pura ou misturada a cera de abelha. As amostras foram submetidas a PCR para amplificação do gene da beta-actina humana e, separadamente, para amplificação da sequência de inserção IS6110, específica do complexo M. tuberculosis. O resultado da amplificação do gene da beta-actina foi positivo em todas as amostras. Não foram gerados amplicons na PCR-IS6110 em amostras de tecido pulmonar fixadas usando formalina não tamponada a 10 por cento e incluídas em parafina com cera de abelha. Em conclusão, fatores inibitórios combinados interferiram na detecção de M. tuberculosis em material de arquivo. É importante controlar estes fatores inibitórios para poder implementar o diagnóstico molecular em laboratórios de patologia.

TNFalpha Expression in the Paraffin-embedded Tissues of Leprosy / 대한피부과학회지

BACKGROUND: Tumor necrosis factor alpha (TNFalpha ) plays various roles in the pathogenesis of leprosy. Expression of TNFalpha according to the clinical type of leprosy has been studied in the patient serum, stimulated PBMC, and the skin lesions, but these results were controversial. Also, all studies of the skin lesions have been limited because of a small number of frozen tissues. OBJECTIVE: The purposes of this study were to estimate the availability of paraffin-embedded skin tissue of leprosy for the detection of TNFalpha mRNA and protein, to analysis the TNFalpha expression according to the clinical types of leprosy and lepra reaction, and to demonstrate various TNFalpha -positive cells in the skin lesions. METHODS:In the paraffin-embedded tissues of 17 new cases of leprosy, TNFalpha mRNA expression was detected by in situ hybridization with digoxigenin labelled oligonucleotide probe cocktail and TNFalpha protein expression by immunohistochemical stain. In addition, serum TNFalpha level was estimated by ELISA for the evaluation of the relationship between before and after lepra reaction. RESULTS: 1. The density of TNFalpha mRNA-positive cells ranged from 8 to 26 percent (mean 17 percent) and that of TNFalpha protein-positive cells ranged from 3 to 8 percent (mean 7 percent). They were the highest in borderline lepromatous leprosy lesions. The density of TNFalpha -positive cells was significantly higher by in situ hybridization than by immunohistochemical stain. 2. The TNFalpha -positive cells in paraffin-embedded skin lesion were CD8 positive lymphocytes, CD68 positive macrophages, endothelial cells, histiocytes, Schwann cells, and keratinocytes. The number of these cells before leprosy treatment was not significantly different from that after leprosy treatment. 3. The density of CD8-positive cells was significantly higher in lesions without lepra reaction than in lesions with lepra reaction, and that of CD68-positive cells was significantly higher in lepromatous leprosy lesions than in borderline lepromatous leprosy lesions. 4. Serum TNFalpha level was higher during lepra reaction than before lepra reaction and the high level continued even after resolution of lepra reaction. CONCLUSION: It suggested that the paraffin-embedded tissue in leprosy is an effective and available material for detecting expression of TNFalpha mRNA and protein. Also, in situ hybridization was more sensitive than immunohistochemical stain. The number of TNFalpha -positive cells was the highest in borderline lepromatous leprosy lesions. With further refinement, this may be an easier application of study for TNFalpha expression in leprosy.