Scanning Microscopy of Colonic Mucin during Carcinogenesis: Is It Clinically Applicable?

The integrity of the colonic mucin layer has been reported to be altered during carcinogenesis in both humans and rodents. Prior to attempting scanning microscopic techniques on colonic mucosa of patients at high risk to develop colorectal cancer, these procedures were performed on colonic mucosa from rats with chemically induced colon cancers. Substantial technical difficulties in preparation and serious subjectivity in interpretation of the scanning micrographs were encountered. The major technical problem was the unpredictable retention of the mucin layer upon both normal and cancerous mucosae. Visual interpretation of the integrity or disruption of the mucin layer with the scanning electron microscope revealed variable fenestration and fraying of the mucin in both normal and cancerous colons. Our findings suggest that scanning electron microscopy of colonic mucin may not be a reliable screening procedure for (pre)cancerous changes in human colonic mucosae.     

Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics

Current genomic studies are limited by the poor availability of fresh-frozen tissue samples. Although formalin-fixed diagnostic samples are in abundance, they are seldom used in current genomic studies because of the concern of formalin-fixation artifacts. Better characterization of these artifacts will allow the use of archived clinical specimens in translational and clinical research studies. To provide a systematic analysis of formalin-fixation artifacts on Illumina sequencing, we generated 26 DNA sequencing data sets from 13 pairs of matched formalin-fixed paraffin-embedded (FFPE) and fresh-frozen (FF) tissue samples. The results indicate high rate of concordant calls between matched FF/FFPE pairs at reference and variant positions in three commonly used sequencing approaches (whole genome, whole exome, and targeted exon sequencing). Global mismatch rates and C·G > T·A substitutions were comparable between matched FF/FFPE samples, and discordant rates were low (<0.26%) in all samples. Finally, low-pass whole genome sequencing produces similar pattern of copy number alterations between FF/FFPE pairs. The results from our studies suggest the potential use of diagnostic FFPE samples for cancer genomic studies to characterize and catalog variations in cancer genomes.     

Central Nervous System Alterations in Liver Cirrhosis: The Role of Portal-Systemic Shunt and Portal Hypoperfusion

The role of portal-systemic shunting and portal liver hypoperfusion in the pathophysiology of central nervous system dysfunction of cirrhosis is not yet well defined. It is well known that one of the most important collateral vessels (CV) is a patent paraumbilical vein (PUV) but there is controversy regarding its clinical significance. We have evaluated the relationships between neuropsychological and EEG alterations, ammonia plasma level (NH₄), hepatic function, and portal hemodynamics (Doppler Ultrasound) in 95 cirrhotic patients. Patency, diameter, or flow of PUV or the presence of other CV were not related to an increased prevalence of neuropsychological or EEG abnormalities. Patients with effective portal flow (EPF = portal flow – PUV flow) lower than 692 mL/min (median) had a significantly higher risk of failing the neuropsychological test, or of having an altered EEG. Low EPF and prothrombin time (<50%), and high NH₄ (51 mol/L) were independent predictors of an abnormal EEG. Considering both low EPF and the numerosity of CV, only low EPF was found to explain EEG alterations. In conclusion, portal liver hypoperfusion and decreased liver function were associated with an increased risk of central nervous system dysfunction in cirrhotic patients, whereas PUV patency per se was not.