Search

By contrast with the extensive palaeolimnological studies carried out in North America and Europe, relatively few studies have described the anthropogenic and/or climate impacts in Patagonian lakes. We addressed these issues by analysing geochemistry, lithology, pigments and chironomid remains from sediment cores collected from Lake Hess (41° 22´ 20” S, 71° 44´ 0” W) located in the Nahuel Huapi National Park, in northern Patagonia. The aim of this study is to provide a palaeoenvironmental and climate reconstruction of the past ca. three centuries for this cold oligotrophic, quasi-pristine lake which receives melt waters from the Tronador ice cap. Chronology was based on 137Cs and 210Pb measurements of the upper sediments and the inferred sedimentation rate of 23.2 mg cm-2 y-1 (0.15 cm y-1) was consistent with both sets of measurements. The sediment from Lake Hess was rich in tephra deposits particularly evident in the lower part of the cores. Tephras are valuable to use for core correlation and can be traced through peaks in the magnetic susceptibility profiles. Results from the multiproxy analyses in the longest core (83 cm) identify three main phases of change. From the bottom up to 42 cm (ca. A.D.1800), the sediment is composed of light-grey organically rich clays. Both pigments and chironomids suggest variable trends in productivity and precipitation regime. At the end of the Little Ice Age chronozone (A.D. 1770-1850), pigment concentrations were very low. From 42 cm to ca. 25 cm (A.D. 1800-1940), the sedimentary record is composed of alternating black and dark organic-matter rich mud with variable amounts of macrophyte remains. Pigment concentrations and chironomid head capsule counts were also very low. These facies are composed of very fine plastic sediments with some faintly laminated intervals and an organic matter composition gradually decreasing towards the top of the zone. A sharp change occurs at 25 cm (ca. A.D. 1940) showing a strong increase in organic matter content, algal nutrients, and plant pigments together with a change in the chironomid assemblages. This might document a change in the trophic condition of the lake associated with changes in erosion/deposition rates. Although there are records of human impact in the area studied, involving the use of fires, most of the observed chemical and biological changes in Lake Hess sediment sequence were interpreted in terms of climate changes, especially to changes in moisture balance brought about by variations in the strength of the westerlies.

A pilot study using Affymetrix Gene Chip(R) Porcine Genome Arrays was set up to evaluate the impact of time lags from death on gene expression profiling of porcine skeletal muscle at four post mortem times (up to 24 h) during the routine processing of fresh thighs. All post chip parameters and data analyses (Average background, Scale Factors, Percent Presence, 3'/5' ratios of beta-actin and glyceraldehyde-3-phosphase dehydrogenase control genes, RNA degradation diagnostics, principal component analysis, hierarchical clustering, mixed regression models with time effects) did not show any effect of post mortem time. Therefore, microarray data obtained from muscle specimens collected in a processing plan over a quite long period have the potential to identify treatments or pre mortem conditions without any potential bias derived from subtle RNA degradation. These results open new perspectives to develop and analyse gene expression biomarkers for pig production and product authentication.

Approximately 10%-15% of gastrointestinal stromal tumors (GISTs) in adults do not harbor any mutation in the KIT or PDGFRA genes (ie, KIT/PDGFRA wild-type GISTs). Recently, mutations in SDHB and SDHC (which encode succinate dehydrogenase subunits B and C, respectively) but not in SDHA and SDHD (which encode subunits A and D, respectively) were identified in KIT/PDGFRA wild-type GISTs. To search for novel pathogenic mutations, we sequenced the tumor transcriptome of two young adult patients who developed sporadic KIT/PDGFRA wild-type GISTs by using a massively parallel sequencing approach. The only variants identified as disease related by computational analysis were in SDHA. One patient carried the homozygous nonsense mutation p.Ser384X, the other patient was a compound heterozygote harboring a p.Arg31X nonsense mutation and a p.Arg589Trp missense mutation. The heterozygous nonsense mutations in both patients were present in germline DNA isolated from peripheral blood. Protein structure analysis indicates that all three mutations lead to functional inactivation of the protein. This is the first report, to our knowle dge, that identifies SDHA inactivation as a common oncogenic event in GISTs that lack a mutation in KIT and PDGFRA.

In addition to KIT and PDGFRA mutations, sequential accumulation of other genetic events is involved in the development and progression of gastrointestinal stromal tumors (GISTs). Until recently, the significance of these other alterations has not been thoroughly investigated. We report the first study that integrates gene expression profiling and high-resolution genomic copy number analyses in GIST. Fresh tissue specimens from 25 patients with GIST were collected, and gene expression profiling and high-resolution genomic copy number analyses were performed, using Affymetrix U133Plus and SNP array 6.0. We found that all 21 mutant GIST patients showed both macroscopic cytogenetic alterations and cryptic microdeletions or amplifications, whereas 75% (three of four) of wild-type patients with GIST did not show genomic imbalances. The most frequently observed chromosomal alterations in patients with mutant GIST included 14q complete or partial deletion (17 of 25), 1p deletion (14 of 25) and 22q deletion (10 of 25). Genetic targets of the chromosomal aberrations were selected by integrated analysis of copy number and gene expression data. We detected the involvement of known oncogenes and tumor suppressors including KRAS in chr 12p amplification and KIF1B, PPM1A, NF2 in chr 1p, 14q and 22p deletions, respectively. The genomic segment most frequently altered in mutated samples was the 14q23.1 region, which contains potentially novel tumor suppressors, including DAAM1, RTN1 and DACT1. siRNA-mediated RTN1 downregulation showed evidence for the potential role in GIST pathogenesis. The combination of gene expression profiling and high-resolution genomic copy number analysis offers a detailed molecular portrait of GISTs, providing an essential comprehensive knowledge necessary to guide the discovery of novel target genes involved in tumor development and progression.

Comment on: "Pediatric-type" gastrointestinal stromal tumors in adults: distinctive histology predicts genotype and clinical behavior. Rege TA, Wagner AJ, Corless CL, Heinrich MC, Hornick JL. Am J Surg Pathol. 2011 Apr; 35(4):495-504.

Nowadays molecular biology represents one of the most interesting topics in medical oncology, because it provides a global and detailed view on the molecular changes involved in tumour progression, leading to a better understanding of the carcinogenesis process, to discovering new prognostic markers and novel therapeutic targets. The gene expression profiling analysis with microarray technology has shown a great potential in cancer research and in medical oncology, mapping simultaneously the expression of thousands of genes in a single tumour sample and giving a measurement of articulated genes expression patterns. Colorectal cancer represents a wide and exciting area of research for molecular biology, due to the growing need of a molecular classification as well as prognostic and predictive molecular factors that may guide oncologists in patient's clinical management. The aim of this review is to analyze the state of art of gene expression profile in colorectal cancer using microarrays technologies and to explore some perspectives in this research field.