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PubMed1998

Further study of hepatitis C virus RNA detection in formalin-fixed, paraffin-embedded liver tissues by ligation-dependent polymerase chain reaction.

Ligation-dependent polymerase chain reaction (LD-PCR) is a novel, simple and sensitive PCR assay that could be useful for the molecular diagnosis of various viral infections. This assay uses two capture probes for RNA isolation and two hemiprobes for the subsequent PCR. To investigate its usefulness in the field of pathological diagnosis, further study of this new PCR technology to detect hepatitis C virus (HCV) RNA was carried out in formalin-fixed, paraffin-embedded (FFPE) liver tissues and the results compared with those obtained by the reverse transcription (RT)-PCR method. We analyzed routinely processed FFPE liver specimens of surgical origin from 13 anti-HCV-seropositive Japanese patients with hepatocellular carcinoma (HCC). As a result, HCV-RNA was detected in FFPE liver specimens in 12 of the tested patients (92.3%) by the LD-PCR method without the use of reverse transcription. In contrast, HCV-RNA was detectable in eight out of 13 cases (61.5%) by the RT-PCR method. These results indicated that LD-PCR was useful for HCV-RNA detection in routinely processed FFPE liver specimens.

Adult↗

PubMed1992

HIV-1 in postmortem brain tissue from patients with AIDS: a comparison of different detection techniques.

OBJECTIVE: The presence of HIV-1 in postmortem brain tissue from 31 patients with AIDS and 12 HIV-1-negative controls was investigated. DESIGN: Most laboratories have access to the methods used. We readily applied in situ hybridization and immunohistochemistry to archival formalin-fixed paraffin-embedded (FFPE) brain specimens. METHODS: The techniques used to detect HIV-1 were explant culture, in situ hybridization with 35S-labeled polymerase (pol) gene riboprobes and immunohistochemistry with monoclonal antibody to gp41. RESULTS: HIV-1 was isolated from explant cultures in 13 out of 20 (65%) patients, whereas HIV-1-infected cells were detected in FFPE brain tissue from nine out of 26 (35%) patients examined by in situ hybridization and in seven out of 26 (27%) patients examined by immunohistochemistry. CONCLUSIONS: Although the isolation technique was the most sensitive of the three techniques tested, infected cells may be identified with in situ hybridization in conjunction with immunohistochemistry.

AIDS-Related Opportunistic Infections↗

PubMed2006

Expression of human telomerase reverse transcriptase, Survivin, DD3 and PCGEM1 messenger RNA in archival prostate carcinoma tissue.

INTRODUCTION: The wide spectrum of biological behavior displayed by prostate cancer (PCa) warrants investigation of potential PCa-specific biomarkers that could identify more aggressive tumor types and therefore provide prognostic value. Upregulation of expression of human telomerase reverse transcriptase (hTERT), Survivin, DD3 and PCGEM1 mRNAs in PCa lesions has recently been described. The purpose of this study was to evaluate the clinical value of detection of over-expression of these biomarkers in the diagnosis and prognosis of PCa. MATERIAL AND METHODS: Archival formalin-fixed, paraffin-embedded (FFPE) prostatectomy tissue from 26 patients with PCa (Gleason score 3-9, mean 7) and 14 patients with benign prostatic hyperplasia (BPH) were analyzed by reverse transcription polymerase chain reaction (RT-PCR) for semiquantitative transcript levels of hTERT, Survivin, DD3 and PCGEM1. In addition, 25 matched normal (MN) tissue samples were examined. The expression of biomarker mRNA relative to b2-microglobulin mRNA was determined using AlphaImager 2200 data analysis software. RESULTS: The biomarkers had sensitivities ranging from 91% to 100%. Clinical specificities evaluated with the BPH tissue were the following: hTERT mRNA (93%), DD3 mRNA (57%), Survivin (29%) and PCGEM1 (14%). Biomarker expressions were up to 13.5-fold higher in PCa tissue as compared to MN tissue. None of the tumor biomarkers showed a positive correlation with pathological stage and Gleason score. CONCLUSIONS: The results of this study indicate potential utility of the hTERT mRNA and DD3 mRNA as diagnostic but not prognostic biomarkers for PCa.

Antigens, Neoplasm↗

PubMed2025

Spatial transcriptomic analysis of mouse parathyroid gland cells expressing an activating variant of Gcm2.

Glial cells missing 2 (GCM2) is an essential transcription factor for the development of parathyroid glands. Germline GCM2 variants that repress or enhance transcriptional activity predispose a subset of patients to hypoparathyroidism or hyperparathyroidism, respectively. A recurrent germline heterozygous activating missense variant of GCM2, p.Y394S has been identified in some patients with primary hyperparathyroidism. A genetically engineered knock-in mouse model of this variant corresponding to p.Y392S in the mouse Gcm2 gene (Gcm2 +/Y392S) did not show obvious parathyroid tumors. However, in GCM2-binding site mediated luciferase reporter assays in HEK293 cells, the mouse and the human variant both exhibited enhanced transcriptional activity. Therefore, we assessed the effect of this variant on gene expression in vivo in parathyroid glands from Gcm2 +/Y392S and WT mice. Using the 10x Genomics Visium platform, spatially resolved transcriptomic analysis was performed on formalin-fixed and paraffin-embedded (FFPE) tracheal tissue sections of Gcm2 +/Y392S and WT mice to capture RNA from parathyroid glands together with other cell types in the tissue sections. Transcriptome sequence data analysis detected 8 different clusters in the tissue sections based on similarity of gene expression profiles. Cluster-1, which contained parathyroid gland cells expressing Pth and Gcm2, was further evaluated for transcripts that were differentially expressed more than 2-fold in Gcm2 +/Y392S compared to WT. Increased transcript level of Lgals3 (galectin-3) was seen in Gcm2 +/Y392S parathyroid gland cells which is among markers of parathyroid carcinoma. Galectin-3 protein was detected in available FFPE human parathyroid samples of patients with germline heterozygous activating GCM2 variants, p.Y394S (n = 4/10) or p.L379Q (n = 2/2). These results indicate a potential for growth and malignancy of parathyroid glands expressing GCM2 variants. The transcriptomic data of mouse parathyroid gland cells generated in this study can serve as a valuable resource for investigating genes and pathways in normal or abnormal parathyroid gland growth and physiology.

GCM2, gene↗

PubMed2026

LCM-Enriched Proteomic Characterization of Antibody-Mediated Glomerular Damage and Complement Activation in Pre-Clinical Models.

Biologics, lipid nanoparticles, and other therapeutic modalities can result in adverse events, often detected as lesions during preclinical pathology assessments. Characterization of these lesions provides valuable information during drug development to contextualize mechanisms of injury and assess species translatability. Here, we investigated the utility of a laser capture microdissection (LCM)-enriched mass spectrometry proteomics approach to analyze two well-characterized preclinical models of regional (glomerular) injury: Passive Heyman Nephritis in rats and bovine gamma globulin-induced glomerular injury in nonhuman primates (NHPs). Using LCM-enriched proteomics, glomeruli were isolated from formalin-fixed paraffin-embedded kidney tissue in the rat model, enabling identification of 4,661 proteins and quantification of 3,410. Proteinuria measurements were compared with digital pathology metrics of glomerular morphology and proteomics results, with all modalities yielding concordant evidence of glomerular injury and proteomics confirming the role of complement activation. The same LCM- enriched proteomics workflow was applied to an NHP model of induced glomerular damage, identifying 4,623 proteins, quantifying 3,000, and confirming qualitative concordance with established features of complement-mediated glomerular injury. Together, these findings illustrate the applicability of LCM-enriched proteomics for region-specific characterization of antibody-mediated tissue injury and support its use as a hypothesis-generating platform in translational toxicologic pathology.

Animals↗

PubMed2026

Transcriptomic profiling across stages of non-muscle-invasive bladder cancer identifies fibroblast activation protein-alpha as a stromal biomarker associated with progression.

BACKGROUND: T1 non-muscle-invasive bladder cancer (NMIBC) represents a biologically aggressive subgroup with substantial heterogeneity in recurrence and progression risk. Current clinicopathological risk stratification tools lack sufficient precision to identify patients at the highest risk of progression to muscle-invasive bladder cancer (MIBC). OBJECTIVE: To characterize transcriptomic differences between T1 and < T1 (Ta/Tis) NMIBC and to explore the association of fibroblast activation protein-α (FAP) gene expression with disease progression. METHODS: Transcriptomic profiling was performed on formalin-fixed paraffin-embedded (FFPE) tumor tissue from 66 patients with primary, treatment-naïve NMIBC and 5 patients with T2 disease (included for exploratory comparisons). Analyses included differential gene expression, gene set enrichment analysis (GSEA), molecular subtyping, immune cell deconvolution, and evaluation of FAP expression in relation to recurrence and progression. External validation of FAP was conducted in three independent NMIBC cohorts. RESULTS: T1 tumors demonstrated a distinct transcriptomic profile compared with < T1 tumors, characterized by enrichment of cell cycle-related and metabolic pathways and a higher prevalence of aggressive molecular subtypes. Despite these molecular differences, no statistically significant differences in recurrence-free, progression-free, cancer-specific, and overall survival were observed, likely reflecting limited event numbers. Among recurrent tumors, early recurrences (≤ 24 months) were associated with epithelial-mesenchymal transition signatures. FAP expression increased with tumor stage (p = 0.0005) and was associated with progression (p = 0.002) and mortality (p = 0.01). Patients with tumors in the highest quartile of FAP expression had worse progression-free survival. This association was consistently observed in three external NMIBC cohorts. CONCLUSIONS: T1 NMIBC exhibits distinct transcriptomic features suggestive of increased biological aggressiveness. Elevated FAP expression is reproducibly associated with progression risk across multiple cohorts, supporting its potential role as a biomarker of aggressive disease. Given the limited number of progression events, these findings should be considered hypothesis-generating and warrant prospective validation before clinical implementation.

Humans↗

PubMed2026

Association of HPV16 infection with p53 and survivin expression in oral squamous cell carcinoma.

Oral squamous cell carcinoma (OSCC) is the most common malignancy of the oral cavity and a major public health concern worldwide. This study aimed to investigate the relationship between p53 and survivin expression, clinicopathologic parameters and HPV16 infection in OSCC in order to elucidate the potential role of HPV16 in its pathogenesis.The study enrolled 45 patients who underwent surgical treatment for histologically confirmed OSCC. Tumor specimens were formalin-fixed and paraffin-embedded (FFPE) and histologically analyzed using hematoxylin/eosin staining. Immunohistochemistry for p53 and survivin was performed using the DAKO system. DNA extracted from FFPE tumor tissues was analyzed for HPV16 genome presence using polymerase chain reaction (PCR). All patients were followed for three years after primary treatment.No statistically significant associations were observed between p53 or survivin expression and clinicopathologic parameters including age, gender, tumor site, grade, stage, recurrence, metastasis or HPV16 status (P > 0.05). Among HPV16-positive patients (11/45, 24.4%), low survivin expression (<5%) was found in 8/11 (73%) patients, while high p53 expression (>10%) was observed in 7/11 (64%) patients. Disease-free interval did not differ significantly between patients with low vs. high p53 (P = 0.220) or survivin expression (P = 0.580). A significant correlation was detected between p53 and survivin expression (P = 0.04). HPV16 positivity was significantly associated with the absence of p53 immunoreactivity.These findings suggest that HPV16-independent oncogenic pathways are likely predominant in OSCC, while HPV16 infection may be associated with a distinct molecular subset characterized by absent p53 expression (p53-; survivin+/-; HPV16+). These results underscore the biological heterogeneity of OSCC and may have implications for future biomarker-based stratification of patients.

HPV16↗

PubMed2005

A study of glutathione S-transferase pi expression in central nervous system of subjects with amyotrophic lateral sclerosis using RNA extraction from formalin-fixed, paraffin-embedded material.

The expression of glutathione S-transferase pi (GST pi), an enzyme responsible for inactivation of a large variety of toxic compounds was studied in spinal cord, motor and sensory brain cortex obtained from patients who died in the course of amyotrophic lateral sclerosis (ALS). The studies were performed on formalin-fixed, paraffin-embedded (FFPE) and freshly frozen tissues. The method of RNA isolation from FFPE was modified. A significant decrease of GST pi-mRNA expression was found in cervical spinal cord and motor brain cortex of ALS subjects comparing to analogue control tissues (P<0.01), as well as in motor cortex of ALS subjects comparing to their sensory cortex (P<0.05). In spinal cords the decrease in GST pi-mRNA expression was accompanied by a decrease of GST pi protein level. Results indicated lowered GST pi expression on both mRNA and protein levels in the regions of nervous system affected by ALS. The non-properly inactivated by GST toxic electrophiles and organic peroxides may thus contribute to motor neurons damage.

Adult↗

PubMed1994

Detection of keratinocyte growth factor (KGF) transcripts from normal human and archival canine benign prostatic hyperplastic tissues.

This study examined the expression of keratinocyte growth factor (KGF) gene in human and canine prostatic tissues. KGF transcript was detected in normal human prostatic tissues by reverse transcription and polymerase chain reactions (RT-PCR). PCR-generated human KGF complementary DNA (cDNA) clone was confirmed by restriction enzyme digestion analysis and partial DNA sequencing. Expression of KGF in archival canine benign prostatic hyperplastic tissues was also examined. In a pilot experiment, RNAs isolated from formalin-fixed (FF) and formalin-fixed and paraffin-embedded (FFPE) canine prostatic tissues were shown to be of sufficient quality to permit amplification of KGF mRNA by RT-PCR. The transcript of a housekeeping gene, glucose-6-phosphate dehydrogenase (G6PD), was detected by RT-PCR indicating the quality of RNAs to be more than adequate for RNA expression analysis. Later, total RNA from two archival canine FF prostate tissue types, benign prostatic hyperplasis and mild glandular hyperplasia, were used to amplify canine KGF transcripts. Southern hybridization analysis using rat and human KGF cDNAs as probes confirmed the fidelity of the amplified PCR product and it was indeed canine KGF.

Animals↗

PubMed2006

SARS-CoV virus-host interactions and comparative etiologies of acute respiratory distress syndrome as determined by transcriptional and cytokine profiling of formalin-fixed paraffin-embedded tissues.

These studies attempt to understand more fully the host response and pathogenesis associated with severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) by monitoring gene expression using formalin-fixed paraffin-embedded (FFPE) pulmonary autopsy tissues. These tissues were from patients in different hospitals in Singapore who were diagnosed with various microbial infections, including SARS-CoV, that caused acute respiratory distress syndrome (ARDS). Global expression patterns showed limited correlation between end-stage ARDS and the initiating pathogen, but when focusing on a subset of genes implicated in pulmonary pathogenesis, molecular signatures of pulmonary disease were obtained and appeared to be influenced by preexisting pulmonary complications and also bacterial components of infection. Many factors detected during pulmonary damage and repair, such as extracellular matrix (ECM) components, transforming growth factor (TGF) enhancers, acute-phase proteins, and antioxidants, were included in the molecular profiles of these ARDS lung tissues. In addition, differential expression of cytokines within these pulmonary tissues were observed, including notable genes involved in the interferon (IFN) pathway, such as Stat1, IFN regulatory factor-1 (IRF-1), interleukin-6 (IL-6), IL-8, and IL-18, that are often characterized as elevated in ARDS patients.

Aged↗

PubMed2026

Antibody-Based Proximity Labeling Reveals Bait-Proximal Proteomes in Paraffin-Embedded and Snap-Frozen Tissue Samples.

Proximity-based labeling approaches have proven highly valuable for uncovering protein-protein interactions, yet their application to primary patient material remains challenging. Here, we present a workflow enabling the use of the antibody-based ProtA-Turbo proximity labeling system in both formalin-fixed paraffin-embedded (FFPE) and snap-frozen tissue specimens. Our method efficiently directs biotinylation to diverse antibody baits across tissues of different origins. Downstream mass spectrometry-based proteomics analyses demonstrate the specificity of the method by profiling the proximal proteome of H3K27ac-marked chromatin, the nuclear lamina-associated protein EMD, and the Ser2-phosphorylated POLR2A subunit of RNA polymerase II. Using this method, we identified cell-type-specific factors and transcriptional regulators in salivary gland carcinoma, healthy testis, and testicular cancer tissue sections. The ability to detect disease-associated complexes directly within their native, spatially resolved cellular context using ProtA-Turbo can provide new insights into the molecular basis of human disease and may reveal novel, potentially actionable factors with translational relevance.

Humans↗

PubMed2026

Diagnostic performance of panfungal PCR on tissue specimens for the diagnosis of invasive fungal diseases: a systematic review and meta-analysis of the Fungal PCR Initiative (FPCRI).

UNLABELLED: Invasive fungal diseases are difficult to diagnose because of the limited sensitivity of culture. Panfungal PCR amplicon sequencing assays (targeting ribosomal RNA, such as 18S, 28S, ITS) are recommended for fungal identification in histopathology samples showing fungal elements. However, data describing its overall performance and consistency are lacking. This systematic literature review and meta-analysis assessed the performance of panfungal PCR on formalin-fixed paraffin-embedded (FFPE) and non-fixed (fresh or frozen) tissue samples. A systematic literature search was performed to include studies reporting the use of panfungal PCR for fungal identification in FFPE or non-fixed tissue samples. PCR sensitivity and specificity were assessed using the reference standard of histopathology showing fungal elements. Quality assessment was performed using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. Pooled estimates were obtained using random-effects meta-analysis. Twenty-eight studies were included. In FFPE samples (18 studies, 852 samples), sensitivity and specificity were 75.4% (95% confidence interval [CI], 59.2-86.6) and 93.5% (70.2-98.9), respectively. Sensitivity in non-fixed samples (13 studies, 207 samples) was 86.5% (74.7-93.3), while specificity could not be assessed (insufficient data). Comparative analyses showed a significantly higher sensitivity of panfungal PCR over culture (88.2%; 76-94.7 vs 52.2%; 39-65, P = 0.001). Sub-analyses could not demonstrate the superiority of one PCR target over another due to limited data. Panfungal PCR exhibited adequate sensitivity and good specificity in FFPE samples. Sensitivity was even higher in non-fixed samples and largely superior to culture. Nevertheless, large interstudy variability was observed, warranting interlaboratory studies to define the optimal PCR target and standardized protocols. IMPORTANCE: Invasive fungal diseases are difficult to diagnose because of the low sensitivity of culture. Panfungal PCRs are widely used for fungal identification in tissue specimens but suffer from heterogeneous procedures and performance. This meta-analysis shows an acceptable sensitivity (75.4% and 86.5% in fixed and non-fixed samples, respectively) and good specificity (93.5%) of panfungal PCR, supporting its use, not only on histopathology-positive fixed samples but also in non-fixed samples concomitantly with other diagnostic tools (cultures and fungal-specific PCRs if available). These results provide a strong basis for further standardization of panfungal PCR techniques via interlaboratory assays to assess reproducibility and optimize analytical protocols. CLINICAL TRIALS: This study is registered with PROSPERO as CRD42023461148.

Humans↗

PubMed2003

Towards quantitative mRNA analysis in paraffin-embedded tissues using real-time reverse transcriptase-polymerase chain reaction: a methodological study on lymph nodes from melanoma patients.

Improved extraction techniques combined with sensitive real-time reverse transcriptase-polymerase chain reaction may allow detection of mRNA in formalin-fixed, paraffin-embedded (FFPE) materials, but the factors affecting mRNA quantification in clinical material using these methods have not been systematically analyzed. We designed analyses using real-time reverse transcriptase-polymerase chain reaction for quantification of MART-1, beta-actin, and beta(2)-microglobulin mRNAs. The analytical intra- and interassay imprecision (coefficient of variation) was in the range 10 to 20% for all three genes studied. Using these protocols, we studied the influence of tissue autolysis and length of formalin-fixation on mRNA detection in metastatic melanoma. Delay in freezing reduced detectable mRNA, although this was less than predicted and mostly occurred early in autolysis. MART-1, beta-actin, and beta(2)-microglobulin mRNAs were consistently detected in FFPE metastatic melanoma even after fixation for up to 3 weeks, although the total mRNA detected was markedly reduced in fixed compared with fresh tissues (up to 99%). Quantification of MART-1 was, however, possible if this was expressed relative to a housekeeping gene. The polymerase chain reaction product from FFPE tissues could be increased up to 100-fold amplifying short (<136 bp) compared with long amplicons. Variations in time before tissue processing and in fixation length seem to be less important sources of imprecision than previously assumed. Our findings suggest that quantitative analysis of mRNA in archive and routine diagnostic tissues may be possible.

Actins↗

PubMed1997

Human parvovirus B19 in bone marrows from adults with acquired immunodeficiency syndrome: a comparative study using in situ hybridization and immunohistochemistry.

Human parvovirus B19, which infects and lyses erythroid precursors, can cause severe anemia in patients with immunodeficiency. The incidence of parvovirus infection in adult acquired immunodeficiency syndrome (AIDS) patients is unknown. Eighty-one archival formalin-fixed, paraffin-embedded (FFPE) bone marrow biopsies from 73 AIDS adults were immunostained with monoclonal R92F6 against B19 VP1 and VP2 capsid proteins using streptavidin peroxidase and streptavidin alkaline phosphatase techniques. In addition, the same tissues were hybridized in situ with a digoxigenin-labeled parvovirus B19 DNA probe. Five FFPE bone marrows, from 3 HIV-negative patients with positive immunoglobulin M (IgM) serology for parvovirus B19, and 1 parvovirus B19-infected fetal liver were positive controls. By immunoperoxidase, all tissues were negative with R92F6 except the fetal liver, which exhibited strong positivity predominantly in viral inclusions. With immunoalkaline phosphatase, all positive controls were immunoreactive with R92F6; however, the AIDS marrows were negative. With in situ hybridization (ISH), all positive controls and 7 of 81 (8.6%) of AIDS marrows were positive for B19 parvovirus DNA. We conclude that ISH is more sensitive than R92F6 immunohistochemistry in parvovirus B19 detection. A small but significant number of bone marrows from AIDS adults shows evidence of human parvovirus B19 infection.

Acquired Immunodeficiency Syndrome↗

PubMed2006

Heat-induced antigen retrieval: mechanisms and application to histochemistry.

Since the introduction of the fluorescence-labeled antibody method by Coons et al. [Immunological properties of antibody containing a fluorescent group. Proc Soc Exp Biol Med 47, 200-2002], many immunohistochemical methods have been refined to obtain high sensitivity with low background staining at both light and electron microscopic levels. Heat-induced antigen retrieval (HIAR) reported by Shi et al. in the early 1990s has greatly contributed to immunohistochemical analysis for formalin-fixed and paraffin-embedded (FFPE) materials, particularly in the field of pathology. Although antigen retrieval techniques including enzyme digestion, treatment with protein denaturants and heating have been considered tricky and mysterious techniques, the mechanisms of HIAR have been rapidly elucidated. Heating cleaves crosslinks (methylene bridges) and add methylol groups in formaldehyde-fixed proteins and nucleic acids and extends polypeptides to unmask epitopes hidden in the inner portion of antigens or covered by adjacent macromolecules. In buffers having an appropriate pH and ion concentration, epitopes are exposed without entangling the extended polypeptides during cooling process, since polypeptides may strike a balance between hydrophobic attraction force and electrostatic repulsion force. Recent studies have demonstrated that HIAR is applicable for immunohistochemistry with various kinds of specimens, i.e., FFPE materials, frozen sections, plastic-embedded specimens, and physically fixed tissues at both the light- and electron-microscopic levels, and have suggested that the mechanism of HIAR is common to aldehyde-fixed and aldehyde-unfixed materials. Furthermore, heating has been shown to be effective for flow cytometry, nucleic acid histochemistry (fluorescein in situ hybridization (FISH), in situ hybridization (ISH), and terminal deoxynucleotidyl transferase-mediated nick labeling (TUNEL)), and extraction and analysis of macromolecules in both FFPE archive materials and specimens processed by other procedures. In this article, we review mechanism of HIAR and application of heating in both immunohistochemistry and other histochemical reactions.

Animals↗

PubMed2002

In situ polymerase chain reaction detection of transfusion-transmitted virus in liver biopsy.

The potential role of transfusion-transmitted virus (TTV) infection in determining liver damage is poorly understood and no information exists about TTV replication within hepatocytes. In this study, we assess TTV in situ PCR in liver tissue. Twenty-one patients with different degrees of liver damage were studied by both serum TTV-DNA detection and in situ TTV PCR analysis and extractive PCR in liver biopsy paraffin sections (FFPE). Extractive PCR and in situ PCR detected TTV-DNA both in serum and liver tissue of five patients. The presence of TTV in serum matched with that found in the liver and TTV sequences were never found independently in liver or serum. Four out of five TTV-DNA-positive patients have not other known cause of liver damage while in one a coinfection from HCV was observed. Our data indicate that in situ PCR appears to be a reliable tool for the detection of TTV-DNA in FFPE, and may help detecting unknown origin of liver damage.

DNA Virus Infections↗

PubMed2004

[Thymidylate synthase and dihydropyrimidine dehydrogenase gene expressions in colorectal cancer using the Danenberg tumor profile method].

Thymidylate synthase (TS) and dihydropyrimidine dehydrogenase (DPD) have been identified as a predictor of response to 5-fluorouracil (5-FU). Danenberg et al. developed a technology to evaluate gene expressions in formalin-fixed paraffin-embedded (FFPE) specimens (DTP; Danenberg tumor profile). In this study, TS and DPD gene expressions were measured in 47 primary colorectal cancer tumors and 12 metastatic tumors using FFPE specimens. In primary tumors, expression of TS genes in cancerous tissues was statistically higher than in stromal tissues, while DPD gene expressions in stromal tissues were higher than those in cancerous tissues. The median TS mRNA level was 0.86 in hepatic metastasis and 1.95 in lymph node metastasis. The median DPD mRNA level was 0.86 in hepatic metastasis and 1.96 in lymph node metastasis. Both gene expressions differed among primary tumors and metastatic tumors, especially in metastatic sites. DTP might be useful to evaluate the 2 gene expressions in colorectal cancer. Further studies would be needed to clarify the mechanisms of difference of gene expressions in cancerous and stromal tissues, or in primary tumors and metastatic tumors.

Colorectal Neoplasms↗

PubMed2003

Detection of hepatitis C virus RNA in formalin-fixed, paraffin-embedded thin-needle liver biopsy specimens.

We examined the feasibility of detecting hepatitis C virus (HCV) RNA in formalin-fixed, paraffin-embedded (FFPE) specimens obtained by thin-needle biopsy (TNB). Specimens obtained by large-needle biopsy (LNB) and unfixed frozen tissue served as controls. A total of 23 biopsy specimens, 13 obtained by TNB and 10 by LNB, from 20 patients with chronic hepatitis C were included in the study. HCV RNA was detected by nested reverse transcription-polymerase chain reaction (RT-PCR). HCV RNA was found in FFPE archival specimens obtained by TNB (11 [85%]) or LNB (7 [70%]). The sensitivity was similar in unfixed tissue in which HCV RNA was found in 7 (88%) of 8 TNB specimens and 6 (86%) of 7 LNB specimens. The detection of HCV RNA did not seem to be affected by storage of the paraffin blocks, the presence of advanced fibrosis and cirrhosis, or fragmentation of the core cylinder. TNB yields enough qualitative suitable material to detect HCV RNA by RT-PCR.

Adult↗