Formalin-fixed paraffin-embedded (FFPE) samples are the only remaining biological archive for many toxicological and clinical studies, yet their use in genomics has been limited due to nucleic acid damage from formalin fixation. Older FFPE samples with highly degraded RNA pose a particularly difficult technical challenge. Probe-based targeted sequencing technologies show promise in addressing this issue but have not been directly compared to standard whole-genome RNA-Sequencing (RNA-Seq) methods. In this study, we evaluated dose-dependent transcriptional changes from paired frozen (FROZ) and FFPE liver samples stored for over 20 years using targeted resequencing (TempO-Seq) and whole-genome RNA-Seq methods. Samples were originally collected from male mice exposed to a reference chemical (dichloroacetic acid, DCA) at 0, 198, 313, and 427 mg/kg-day (n = 6/dose) by drinking water for 6 days. TempO-Seq showed high overlap in differentially expressed genes (DEGs) between matched FFPE and FROZ samples and high concordance in fold-change values across the two highest dose levels of DCA vs. control (R2 ≥ 0.94). Similarly, high concordance in fold-change values was observed between TempO-Seq FFPE and RNA-Seq FROZ results (R2 ≥ 0.92). In contrast, RNA-Seq FFPE samples showed few overlapping DEGs compared to FROZ RNA-Seq (≤5 for all dose groups). Modeling of DCA-dependent changes in gene sets identified benchmark doses from TempO-Seq FROZ and FFPE samples within 1.4-fold of RNA-Seq FROZ samples (93.9 mg/kg-d), whereas RNA-Seq FFPE samples were 3.3-fold higher (310.3 mg/kg-d). This work demonstrates that targeted sequencing may provide a more robust method for quantifying gene expression profiles from aged archival FFPE samples.

BACKGROUND: Meningiomas that are progesterone receptor positive have a low recurrence rate and good prognosis compared to those that are progesterone receptor negative. This study aimed to determine the prevalence of expression of progesterone in meningiomas and its association with clinicopathological characteristics.
METHODS: This was a cross-sectional laboratory-based study that was conducted at Muhimbili National Hospital. The study included 112 formalin-fixed paraffin-embedded tissue blocks of patients who were confirmed to have meningiomas on histological basis from January 2010 to December 2014. Immunohistochemical expression of progesterone receptor was tested using a primary monoclonal progesterone receptor antibody ready to use (IR 068 Dako). The χ2 test was used to determine the association between clinicopathological characteristics and progesterone receptor expression. A 2-tailed P < 0.05 was considered significant.
RESULTS: The mean age of the patients was 45.5 ± 3.601 years, and majority (66.1%, n = 74) were in the age group between 31 and 60 years. Also, majority of the patients (60%, n = 67) in this study were females. Over one-third of the cases (34.8%, n = 39) comprised of meningotheliomatous subtype, and majority of the cases (89.3%, n = 100) were of grade I. The prevalence of progesterone expression was 54.5% (n = 61), and only age was associated with progesterone receptor expression (P = 0.043).
CONCLUSIONS: The finding of high expression of the progesterone receptor for grade I cases in this study indicates that progesterone receptor expression in meningiomas is of prognostic value and may be considered when evaluating patients for management. Lack of expression of progesterone receptor in all the malignant cases is intriguing and needs further studies that can investigate its prognostic role.

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Functional loss of expression of breast cancer susceptibility gene 1(BRCA1) has been implicated in genomic instability and cancer progression. There is emerging evidence that BRCA1 gene product (BRCA1) also plays a role in cancer cell migration. We performed a quantitative proteomics study of EOC patient tumor tissues and identified changes in expression of several key regulators of actin cytoskeleton/cell adhesion and cell migration (CAPN1, 14-3-3, CAPG, PFN1, SPTBN1, CFN1) associated with loss of BRCA1 function. Gene expression analyses demonstrate that several of these proteomic hits are differentially expressed between early and advanced stage EOC thus suggesting clinical relevance of these proteins to disease progression. By immunohistochemistry of ovarian tumors with BRCA1(+/+) and BRCA1(null) status, we further verified our proteomic-based finding of elevated PFN1 expression associated with BRCA1 deficiency. Finally, we established a causal link between PFN1 and BRCA1-induced changes in cell migration thus uncovering a novel mechanistic basis for BRCA1-dependent regulation of ovarian cancer cell migration. Overall, findings of this study open up multiple avenues by which BRCA1 can potentially regulate migration and metastatic phenotype of EOC cells.