Transcriptomic analysis of <i>Crassostrea sikamea</i> × <i>Crassostrea angulata</i> hybrids in response to low salinity stress

<div><p>Hybrid oysters often show heterosis in growth rate, weight, survival and adaptability to extremes of salinity. Oysters have also been used as model organisms to study the evolution of host-defense system. To gain comprehensive knowledge about various physiological processes in hybrid oysters under low salinity stress, we performed transcriptomic analysis of gill tissue of <i>Crassostrea sikamea</i> ♀ × <i>Crassostrea angulata</i>♂ hybrid using the deep-sequencing platform Illumina HiSeq. We exploited the high-throughput technique to delineate differentially expressed genes (DEGs) in oysters maintained in hypotonic conditions. A total of 199,391 high quality unigenes, with average length of 644 bp, were generated. Of these 35 and 31 genes showed up- and down-regulation, respectively. Functional categorization and pathway analysis of these DEGs revealed enrichment for immune mechanism, apoptosis, energy metabolism and osmoregulation under low salinity stress. The expression patterns of 41 DEGs in hybrids and their parental species were further analyzed by quantitative real-time PCR (qRT-PCR). This study will serve as a platform for subsequent gene expression analysis regarding environmental stress. Our findings will also provide valuable information about gene expression to better understand the immune mechanism, apoptosis, energy metabolism and osmoregulation in hybrid oysters under low salinity stress.</p></div

Length distribution of unigenes and transcripts.

<p>Length distribution of unigenes and transcripts.</p

Seasonal variations of aboveground litterfall (a), floor mass (b) in the perennial grasses and the shrubs from April to October 2010 at monthly intervals.

<p>Litterfall mass remained (% of original) (c) in the perennial grasses and the shrubs during more than one year period. Vertical bars indicate standard errors of means (n = 3).</p

Cluster analysis of DEGs in SS, SA and AA oysters based on their relative expression level as determined by qRT-PCR.

<p>Blue represents lower expression, and red represents higher expression. Each column represents a comparison between low salinity samples and control samples for each species. Each row represents a gene. The yellow square represents immune- or apoptosis-related gene, the green square represents genes involved in osmotic regulation, and the purple square represents genes involved in energy regulation. The 41genes were classified into five groups.</p

Mean annual decay constant (k) of aboveground litterfall in the perennial grasses and the shrubs.

<p>Values in the parentheses indicate standard error (n = 3). Difference letters indicate statistically significant differences (P<0.05).</p

Soil pH, bulk density and texture of this study.

<p>Values in the parentheses indicate standard error (n = 3). Difference letters indicate statistically significant differences (P<0.05), and absence of letters implies that no significant differences were detected.</p

All enrichment pathways.

<p>All enrichment pathways.</p

Soil microbial biomass carbon (a), soil microbial activity (b) and <i>q</i>CO₂ (c) in the perennial grasses and the shrubs in May, July and September in 2010.

<p>Vertical bars indicate standard errors of means (n = 3). Difference letters indicate statistically significant differences (P<0.05), and absence of letters implies that no significant differences were detected.</p

Seasonal variations of fine root biomass (a, c) and necromass (b, d) in the perennial grasses (a, b) and the shrubs (c, d) from April to September 2010 for soil layers 0–10, 10–20, and 20–30 cm.

<p>Vertical bars indicate standard errors of means (n = 3).</p

Image_2_Multi-omics profiles refine L-dopa decarboxylase (DDC) as a reliable biomarker for prognosis and immune microenvironment of clear cell renal cell carcinoma.tif

BackgroundIncreasing evidence indicates that L-dopa decarboxylase (DDC), which mediates aberrant amino acid metabolism, is significantly associated with tumor progression. However, the impacts of DDC are not elucidated clearly in clear cell renal cell carcinoma (ccRCC). This study aimed to evaluate DDC prognostic value and potential mechanisms for ccRCC patients.MethodsTranscriptomic and proteomic expressions of and clinical data including 532 patients with ccRCC (The Cancer Genome Atlas RNA-seq data), 226 ccRCC samples (Gene Expression Omnibus), 101 ccRCC patients from the E-MTAB-1980 cohort, and 232 patients with ccRCC with proteogenomic data (Fudan University Shanghai Cancer Center) were downloaded and analyzed to investigate the prognostic implications of DDC expression. Cox regression analyses were implemented to explore the effect of DDC expression on the prognosis of pan-cancer. The "limma" package identified the differentially expressed genes (DEGs) between high DDC subgroups and low DDC groups. Functional enrichments were performed based DEGs between DDC subgroups. The differences of immune cell infiltrations and immune checkpoint genes between DDC subgroups were analyzed to identify potential influence on immune microenvironment.ResultsWe found significantly decreased DDC expression in ccRCC tissues compared with normal tissues from multiple independent cohorts based on multi-omics data. We also found that DDC expression was correlated with tumor grades and stages.The following findings revealed that lower DDC expression levels significantly correlated with shorter overall survival (P ConclusionThe present study is the first to our knowledge to indicate that decreased DDC expression is significantly associated with poor survival and an immune-suppressive tumor microenvironment in ccRCC. These findings suggest that DDC could serve as a biomarker for guiding molecular diagnosis and facilitating the development of novel individual therapeutic strategies for patients with advanced ccRCC.</p