Optimization of liver biopsy RNA sampling and use of reference RNA for cDNA microarray analysis

Miniaturization applied to analysis of nucleic acids in heterogeneous tissues

Despite huge efforts in sample analysis, the measurement of marker nucleic acids within tissues remains largely nonquantitative. Gene analyses have benefited from sensitivity gains through in vitro gene amplification, including PCR. However, whilst these processes are intrinsically suited to highly reproducible, accurate and precise gene measurement, the term semiquantitative analysis is still commonly used, suggesting that other fundamental limitations preclude a generic quantitative basis to gene analysis. The most poorly defined aspect of gene analysis relates to the sample itself. The amount of cells and, particularly, cell subtype composition are rarely annotated before analysis; indeed, they are often extrapolated after analysis. To advance our understanding of pathogenesis, assay formats will benefit from resembling the dimensions of the cell, to assist in the analysis of cellular components of tissue complexes. This review is partly a perspective on how current miniaturization technologies, in association with molecular biology, microfluidics and surface chemistries, may evolve from the parts of a paradigm to enable the unambiguous quantitative analysis of complex biologic matter.

Comparison of different methods to obtain and store liver biopsies for molecular and histological research

Background

To minimize the necessary number of biopsies for molecular and histological research we evaluated different sampling techniques, fixation methods, and storage procedures for canine liver tissue. For addressing the aim, three biopsy techniques (wedge biopsy, Menghini, True-cut), four storage methods for retrieval of RNA (snap freezing, RNAlater, Boonfix, RLT-buffer), two RNA isolation procedures (Trizol and RNAeasy), and three different fixation protocols for histological studies (10% buffered formalin, RNAlater, Boonfix) were compared. Histological evaluation was based on hematoxylin-eosin (HE) and reticulin (fibrogenesis) staining, and rubeanic acid and rhodanine stains for copper. Immunohistochemical evaluation was performed for cytokeratin-7 (K-7), multidrug resistance binding protein-2 (MRP-2) and Hepar-1.

Results

RNA quality was best guaranteed by the combination of a Menghini biopsy with NaCl, followed by RNAlater preservation and RNAeasy mini kit extraction. These results were confirmed by quantitative RT-PCR testing. Reliable histological assessment for copper proved only possible in formalin fixed liver tissue. Short formalin fixation (1–4 hrs) improved immunohistochemical reactivity and preservation of good morphology in small liver biopsies.

Conclusion

At least two biopsies (RNAlater and formalin) are needed. Since human and canine liver diseases are highly comparable, it is conceivable that the protocols described here can be easily translated into the human biomedical field.

Identification of osteopontin as the most consistently over-expressed gene in intrahepatic cholangiocarcinoma: Detection by oligonucleotide microarray and real-time PCR analysis

AIM: To investigate the molecular pathways involved in human cholangiocarcinogenesis by gene expression profiling.

METHODS: Oligonucleotide arrays (Affymetrix U133A) were used to establish a specific gene expression profile of intrahepatic CCC in comparison to corresponding non-malignant liver tissue. To validate the expression values of the most overexpressed genes, RT-PCR experiments were performed.

RESULTS: Five hundred and fifty-two statistically differentially expressed genes/ESTs (221 probes significantly up-regulated, 331 probes down-regulated; P < 0.05; fold change > 2; ≥ 70%) were identified. Using these data and two-dimensional cluster analysis, a specific gene expression profile was obtained allowing fast and reproducible differentiation of CCC, which was confirmed by supervised neuronal network modelling. The most consistently overexpressed gene (median fold change 33.5, significantly overexpressed in 100%) encoded osteopontin. Furthermore, an association of various genes with the histopathological grading could be demonstrated.

CONCLUSION: A highly specific gene expression profile for intrahepatic CCC was identified, allowing for its fast and reproducible discrimination against non-malignant liver tissue and other liver masses. The most overexpressed gene in intrahepatic CCC was the gene encoding osteopontin. These data may lead to a better understanding of human cholangiocarcinogenesis.