Field effect in cancer, also called “field cancerization”, attempts to explain the development of multiple primary tumors and locally recurrent cancer. The concept of field effect in cancer has been reinforced, since molecular alterations were found in tumor-adjacent tissues with normal histopatho-logical appearances. With the aim of investigating field effects in gastric cancer (GC), we conducted a high-throughput sequencing of the miRnome of four GC samples and their respective tumor-adjacent tissues and compared them with the miRnome of a gastric antrum sample from patients without GC, assuming that tumor-adjacent tissues could not be considered as normal tissues. The global number of miRNAs and read counts was highest in tumor samples, followed by tumor-adjacent and normal samples. Analyzing the miRNA expression profile of tumor-adjacent miRNA, hsa-miR-3131, hsa-miR-664, hsa-miR-483, and hsa-miR-150 were significantly downregulated compared with the antrum without tumor tissue (P-value < 0.01; fold-change <5). Additionally, hsa-miR-3131, hsa-miR-664, and hsa-miR-150 were downregulated (P-value < 0.001) in all paired samples of tumor and tumor-adjacent tissues, compared with antrum without tumor mucosa. The field effect was clearly demonstrated in gastric carcinogenesis by an epigenetics-based approach, and potential biomarkers of the GC field effect were identified. The elevated expression of miRNAs in adjacent tissues and tumors tissues may indicate that a cascade of events takes place during gastric carcinogenesis, reinforcing the notion of field effects. This phenomenon seems to be linked to DNA methylation patterns in cancer and suggests the involvement of an epigenetic network mechanism.

The Pirarucu (Arapaima gigas) is one of the world’s largest freshwater fishes and member of the superorder Osteoglossomorpha (bonytongues), one of the oldest lineages of ray-finned fishes. This species is an obligate air-breather found in the basin of the Amazon River with an attractive potential for aquaculture. Its phylogenetic position among bony fishes makes the Pirarucu a relevant subject for evolutionary studies of early teleost diversification. Here, we present, for the first time, a draft genome version of the A. gigas genome, providing useful information for further functional and evolutionary studies. The A. gigas genome was assembled with 103-Gb raw reads sequenced in an Illumina platform. The final draft genome assembly was ∼661 Mb, with a contig N50 equal to 51.23 kb and scaffold N50 of 668 kb. Repeat sequences accounted for 21.69% of the whole genome, and a total of 24,655 protein-coding genes were predicted from the genome assembly, with an average of nine exons per gene. Phylogenomic analysis based on 24 fish species supported the postulation that Osteoglossomorpha and Elopomorpha (eels, tarpons, and bonefishes) are sister groups, both forming a sister lineage with respect to Clupeocephala (remaining teleosts). Divergence time estimations suggested that Osteoglossomorpha and Elopomorpha lineages emerged independently in a period of ∼30 Myr in the Jurassic. The draft genome of A. gigas provides a valuable genetic resource for further investigations of evolutionary studies and may also offer a valuable data for economic applications.

The loss of variability in farmed populations and the risks of interactions with wild populations support the need for the genetic monitoring of species farmed throughout the world. In Brazil, the tambaqui is the most widely farmed native fish species. Despite this, there are no data on the pedigree of the farmed stocks, and the potential for interactions with wild populations in the Amazon basin has raised concerns with regard to the genetic variability of these stocks. The present study analysed sequences of the mitochondrial Control Region and 12 microsatellites to characterize the genetic variability of seven historically important commercial tambaqui breeding centres located in four different regions of Brazil, and compared these sequences with those obtained from individuals collected from a wild population. High levels of genetic diversity were found in the wild population, whereas genetic diversity was reduced in both markers in most captive populations, except for the broodstock located near the Amazon River. High FST and DEST indices were recorded between the wild population and most of the captive stocks analysed. The drastic reduction in genetic diversity found in most captive stocks and the difference between these stocks and the wild population may have been the result of the small size of the founding populations and the absence of breeding management. The renewal of the broodstocks and the application of breeding management techniques are recommended. In the Amazon region, in addition, the use of broodstocks that are genetically very different from local wild populations should be avoided.

BackgroundMicroRNAs are small non-coding nucleotide sequences that regulate gene expression. These structures are fundamental to several biological processes, including cell proliferation, development, differentiation and apoptosis. Identifying the expression profile of microRNAs in healthy human gastric antrum mucosa may help elucidate the miRNA regulatory mechanisms of the human stomach.Methodology/Principal FindingsA small RNA library of stomach antrum tissue was sequenced using high-throughput SOLiD sequencing technology. The total read count for the gastric mucosa antrum region was greater than 618,000. After filtering and aligning using with MirBase, 148 mature miRNAs were identified in the gastric antrum tissue, totaling 3,181 quality reads; 63.5% (2,021) of the reads were concentrated in the eight most highly expressed miRNAs (hsa-mir-145, hsa-mir-29a, hsa-mir-29c, hsa-mir-21, hsa-mir-451a, hsa-mir-192, hsa-mir-191 and hsa-mir-148a). RT-PCR validated the expression profiles of seven of these highly expressed miRNAs and confirmed the sequencing results obtained using the SOLiD platform.Conclusions/SignificanceIn comparison with other tissues, the antrum’s expression profile was unique with respect to the most highly expressed miRNAs, suggesting that this expression profile is specific to stomach antrum tissue. The current study provides a starting point for a more comprehensive understanding of the role of miRNAs in the regulation of the molecular processes of the human stomach.

Gastric cancer has a high incidence and mortality rate worldwide; however, the use of biomarkers for its clinical diagnosis remains limited. The microRNAs (miRNAs) are biomarkers with the potential to identify the risk and prognosis as well as therapeutic targets. We performed the ultradeep miRnomes sequencing of gastric adenocarcinoma and gastric antrum without tumor samples. We observed that a small set of those samples were responsible for approximately 80% of the total miRNAs expression, which might represent a miRNA tissue signature. Additionally, we identified seven miRNAs exhibiting significant differences, and, of these, hsa-miR-135b and hsa-miR-29c were able to discriminate antrum without tumor from gastric cancer regardless of the histological type. These findings were validated by quantitative real-time polymerase chain reaction. The results revealed that hsa-miR-135b and hsa-miR-29c are potential gastric adenocarcinoma occurrence biomarkers with the ability to identify individuals at a higher risk of developing this cancer, and could even be used as therapeutic targets to allow individualized clinical management.

We isolated 13 tri and tetranucleotide microsatellite markers for the species Colossoma macropomum that can be used in management programmes for this species of Amazon fish. This panel of microsatellite markers was used in the genotyping of 20 individual specimens collected in the lakes of Ó bidos city, in the Brazilian Amazon. The number of alleles per locus varied from four to ten. The observed heterozygosity varied from 0.31 to 0.95. We observed no significant deviation from the expected Hardy-Weinberg equilibrium assumption. In the sample investigated, it was not possible to identify any significant linkage disequilibrium among the 78 possible loci pairs. In our analysis, we found no indication of genotyping error attributed to stutter bands, large allele dropout or null alleles.

ABSTRACT. The tambaqui, Colossoma macropomum, native to Brazil, is widely used in aquaculture systems. We developed a multiplex PCR panel for this species, comprising 12 microsatellite loci. This panel was used to genotype 73 specimens collected from Juruti, a city in the Brazilian Amazon. The mean number of alleles per locus was 8.8, the mean observed heterozygosity was 0.76, and the combined power of discrimination and the combined power of exclusion were 0.99999999999999993 and 0.999991762, respectively. We observed no significant deviation from Hardy-Weinberg equilibrium in this population. All amplified alleles were clearly typed, and easily interpretable results were obtained. This method will be useful for paternity analysis, population genetics and conservation studies, as well as for selective breeding programs for C. macropomum.

ABStRACt. The aim of the present study was the development of a multiplex genotyping panel of eight microsatellite markers of Arapaima gigas, previously described. Specific primer pairs were developed, each one of them marked with either FAM-6, HEX or NED. The amplification conditions using the new primers were standardized for a single reaction. The results obtained demonstrate high heterozygosity (average of 0.69) in a Lower Amazon population. The multiplex system described can thus be considered a fast, efficient and inexpensive method for the investigation of genetic variability in Arapaima populations.