Comprehensive genomic analysis of Oesophageal Squamous Cell Carcinoma reveals clinical relevance

Abstract Oesophageal carcinoma is the fourth leading cause of cancer-related death in China, and more than 90% of these tumours are oesophageal squamous cell carcinoma (ESCC). Although several ESCC genomic sequencing studies have identified mutated somatic genes, the number of samples in each study was relatively small, and the molecular basis of ESCC has not been fully elucidated. Here, we performed an integrated analysis of 490 tumours by combining the genomic data from 7 previous ESCC projects. We identified 18 significantly mutated genes (SMGs). PTEN, DCDC1 and CUL3 were first reported as SMGs in ESCC. Notably, the AJUBA mutations and mutational signature4 were significantly correlated with a poorer survival in patients with ESCC. Hierarchical clustering analysis of the copy number alteration (CNA) of cancer gene census (CGC) genes in ESCC patients revealed three subtypes, and subtype3 exhibited more CNAs and marked for worse prognosis compared with subtype2. Moreover, database annotation suggested that two significantly differential CNA genes (PIK3CA and FBXW7) between subtype3 and subtype2 may serve as therapeutic drug targets. This study has extended our knowledge of the genetic basis of ESCC and shed some light into the clinical relevance, which would help improve the therapy and prognosis of ESCC patients

Developing high throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in rice (<it>Oryza sativa </it>L.)

Abstract Background Genetic populations provide the basis for a wide range of genetic and genomic studies and have been widely used in genetic mapping, gene discovery and genomics-assisted breeding. Chromosome segment substitution lines (CSSLs) are the most powerful tools for the detection and precise mapping of quantitative trait loci (QTLs), for the analysis of complex traits in plant molecular genetics. Results In this study, a wide population consisting of 128 CSSLs was developed, derived from the crossing and back-crossing of two sequenced rice cultivars: 9311, an elite indica cultivar as the recipient and Nipponbare, a japonica cultivar as the donor. First, a physical map of the 128 CSSLs was constructed on the basis of estimates of the lengths and locations of the substituted chromosome segments using 254 PCR-based molecular markers. From this map, the total size of the 142 substituted segments in the population was 882.2 Mb, was 2.37 times that of the rice genome. Second, every CSSL underwent high-throughput genotyping by whole-genome re-sequencing with a 0.13× genome sequence, and an ultrahigh-quality physical map was constructed. This sequencing-based physical map indicated that 117 new segments were detected; almost all were shorter than 3 Mb and were not apparent in the molecular marker map. Furthermore, relative to the molecular marker-based map, the sequencing-based map yielded more precise recombination breakpoint determination and greater accuracy of the lengths of the substituted segments, and provided more accurate background information. Third, using the 128 CSSLs combined with the bin-map converted from the sequencing-based physical map, a multiple linear regression QTL analysis mapped nine QTLs, which explained 89.50% of the phenotypic variance for culm length. A large-effect QTL was located in a 791,655 bp region that contained the rice 'green revolution' gene. Conclusions The present results demonstrated that high throughput genotyped CSSLs combine the advantages of an ultrahigh-quality physical map with high mapping accuracy, thus being of great potential value for gene discovery and genetic mapping. These CSSLs may provide powerful tools for future whole genome large-scale gene discovery in rice and offer foundations enabling the development of superior rice varieties.</p

Regulating Surface Facets of Metallic Aerogel Electrocatalysts by Size-Dependent Localized Ostwald Ripening

It is well known that the activity and stability of electrocatalysts are largely dependent on their surface facets. In this work, we have successfully regulated surface facets of three-dimensional (3D) metallic Au^{<i>m</i>‑<i>n</i>} aerogels by salt-induced assembly of citrate-stabilized gold nanoparticles (Au NPs) of two different sizes and further size-dependent localized Ostwald ripening at controlled particle number ratios, where <i>m</i> and <i>n</i> represent the size of Au NPs. In addition, 3D Au^{<i>m</i>‑<i>n</i>}–Pd aerogels were further synthesized on the basis of Au^{<i>m</i>‑<i>n</i>} aerogels and also bear controlled surface facets because of the formation of ultrathin Pd layers on Au^{<i>m</i>‑<i>n</i>} aerogels. Taking the electrooxidation of small organic molecules (such as methanol and ethanol) by the resulting Au^{<i>m</i>‑<i>n</i>} and Au^{<i>m</i>‑<i>n</i>}–Pd aerogels as examples, it is found that surface facets of metallic aerogels with excellent performance can be regulated to realize preferential surface facets for methanol oxidation and ethanol oxidation, respectively. Moreover, they also indeed simultaneously bear high activity and excellent stability. Furthermore, their activities and stability are also highly dependent on the area ratio of active facets and inactive facets on their surfaces, respectively, and these ratios are varied via the mismatch of sizes of adjacent NPs. Thus, this work not only demonstrates the realization of the regulation of the surface facets of metallic aerogels by size-dependent localized Ostwald ripening but also will open up a new way to improve electrocatalytic performance of 3D metallic aerogels by surface regulation