The effects of tissue fixation on sequencing and transcript abundance of nucleic acids from microdissected liver samples of smallmouth bass (Micropterus dolomieu)

Iron, hepcidin, and microcytosis in canine hepatocellular carcinoma

BACKGROUND

Erythrocyte microcytosis in some dogs with hepatocellular carcinoma (HCC) suggests a derangement in systemic iron. Hepcidin, the master regulator of iron, is secreted by the liver in response to interleukin 6 (IL-6) and/or bone morphogenetic protein 6 (BMP6) and can cause microcytosis.

OBJECTIVES

Pilot study to compare the quantities of hepcidin, IL-6, and BMP6 RNA molecules in archival tumoral (HCC) and adjacent peritumoral (non-HCC) hepatic tissue to determine if they are different between tissue types or associated with microcytosis.

METHODS

RNA was isolated from formalin-fixed, paraffin-embedded HCC and non-HCC tissue from seven microcytic dogs and four normocytic dogs. Digital RNA counts of hepcidin, IL-6, or BMP6, and six other iron-regulatory genes were determined using the Nanostring nCounter system. The area of blue on each section was digitally evaluated to measure the extent of Prussian blue staining objectively. Parameters were compared between HCC and non-HCC tissue and between microcytic and normocytic groups.

RESULTS

Hepcidin was decreased, and transferrin receptor 1 (TfR1) was increased in HCC tissue compared with non-HCC tissue. Non-HCC hepcidin RNA counts correlated negatively with MCV and positively with the extent of iron staining. Hepcidin expression was higher in non-HCC tissue of microcytic cases than in normocytic cases.

CONCLUSIONS

Canine HCC cases showed relatively increased iron staining in non-HCC tissue and decreased hepcidin RNA in HCC tissue. Microcytic cases had higher hepcidin RNA in non-HCC tissue than normocytic cases. Future studies may extend these findings to protein quantification, cellular localization of RNA changes, and determining if iron loading in canine liver is a predisposing factor for HCC.

Do Tissues Fixed in a Non-crosslinking Fixative Require a Dedicated Formalin-free Processor?

We evaluate the consequences of processing alcohol-fixed tissue in a processor previously used for formalin-fixed tissue. Biospecimens fixed in PAXgene Tissue Fixative were cut into three pieces then processed in a flushed tissue processor previously used for formalin-fixed, paraffin-embedded (FFPE) blocks (neutral buffered formalin [NBF]^+ve), a formalin-free system (NBF^-ve), or left unprocessed. Histomorphology and immunohistochemistry were compared using hematoxylin/eosin staining and antibodies for MLH-1, Ki-67, and CK-7. Nucleic acid was extracted using the PAXgene Tissue RNA/DNA kits and an FFPE RNA extraction kit. RNA integrity was assessed using RNA integrity number (RIN), reverse transcription polymerase chain reaction (RT-PCR) (four amplicons), and quantitative RT-PCR (three genes). For DNA, multiplex PCR, quantitative PCR, DNA integrity number, and gel electrophoresis were used. Compared with NBF^-ve, RNA from NBF^+ve blocks had 88% lower yield and poorer purity; average RIN reduced from 5.0 to 3.8, amplicon length was 408 base pairs shorter, and Cq numbers were 1.9-2.4 higher. Using the FFPE extraction kit rescued yield and purity, but RIN further declined by 1.1 units. Differences between NBF^+ve and NBF^-ve in respect of DNA, histomorphology, and immunohistochemistry were either non-existent or small in magnitude. Formalin contamination of a tissue processor and its reagents therefore critically reduce RNA yield and integrity. We discuss the available options users can adopt to ameliorate this problem.