Cellular retinaldehyde-binding protein-like (CRALBPL), a novel human Sec14p-like gene that is upregulated in human hepatocellular carcinomas, may be used as a marker for human hepatocellular carcinomas

Saccharomyces cerevisiae-like 1 (SEC14L1) is a prognostic factor in breast cancer associated with lymphovascular invasion

Lymphovascular invasion is strongly related to breast cancer metastasis. However, the underlying mechanisms of lymphovascular invasion and its driver molecules in breast cancer remain to be defined. In this study, we explore differential expression of genes in large molecularly characterized and clinically annotated datasets of invasive breast cancer patients (n = 8056) coupled with histological review and strict definition for lymphovascular invasion status. The METABRIC series was used to identify genes associated with lymphovascular invasion, as defined using hematoxylin and eosin staining supplemented by immunohistochemistry, at the genomic/transcriptomic levels. Saccharomyces cerevisiae-like 1 (SEC14L1) was identified as one of the most significant genes associated with lymphovascular invasion. The prognostic significance of SEC14L1 gene copy number and mRNA expression was further investigated in the METABRIC series and externally validated using the Breast Cancer Gene-Expression Miner v4.0. Protein expression of SEC14L1 was also assessed using immunohistochemistry in series of early stage breast cancer using tissue microarrays. SEC14L1 gene copy number gain was significantly associated with high histological grade and poor outcome. SEC14L1 mRNA expression showed positive association with higher grade, lymph node metastasis, and poor outcome. SEC14L1 protein overexpression was significantly associated with lymphovascular invasion (p < 0.0001), higher grade (p = 0.011), HER2 positivity (p = 0.036), and shorter survival (p = 0.00075). Our findings specify SEC14L1 as an independent prognostic factor in breast cancer. Its association, at both transcriptome and protein expression levels, with lymphovascular invasion and outcome could imply an important role in tumor progression. A further mechanistic insight into its molecular roles including potential therapeutic utility is warranted.

Genomic and Epigenomic Aberrations in Esophageal Squamous Cell Carcinoma and Implications for Patients

Esophageal squamous cell carcinoma (ESCC) is a common malignancy without effective therapy. The exomes of more than 600 ESCCs have been sequenced in the past 4 years, and numerous key aberrations have been identified. Recently, researchers reported both inter- and intratumor heterogeneity. Although these are interesting observations, their clinical implications are unclear due to the limited number of samples profiled. Epigenomic alterations, such as changes in DNA methylation, histone acetylation, and RNA editing, also have been observed in ESCCs. However, it is not clear what proportion of ESCC cells carry these epigenomic aberrations or how they contribute to tumor development. We review the genomic and epigenomic characteristics of ESCCs, with a focus on emerging themes. We discuss their clinical implications and future research directions.

Identification of the secreted watery saliva proteins of the rice brown planthopper, Nilaparvata lugens (Stål) by transcriptome and Shotgun LC-MS/MS approach

The rice brown planthopper, Nilaparvata lugens (Stål), a major rice insect pest in Asia, is a vascular bundle-feeder that ejects gelling and watery saliva during the feeding process. Although major proteins in the salivary glands of N. lugens have been identified using 2D PAGE, very little is known about the secreted saliva of this insect. In this study, we identified the major proteins in the secreted watery saliva of N. lugens, via collecting from a sucrose diet that adult planthoppers had fed upon through a membrane of stretched parafilm, and using shotgun LC-MS/MS analysis with reference to transcriptome database of salivary glands of N. lugens. A total of 107 proteins were identified in the watery saliva of N. lugens, over 80% of which showed significant similarity to known proteins. When annotated by the Blast2GO suite, 29 proteins had catalytic activity and 24 proteins were binding proteins. The saliva enzymes included oxidoreductases, hydrolases, phosphatases, peptidases (proteases), kinases, transferases, and lyases. Binding proteins in N. lugens watery saliva included ATP-binding, lipophorin, calcium-binding, actin-binding and DNA-, RNA-, and chromatin-binding proteins. Other non-enzymatic proteins, such as ubiquitins, heat shock proteins, ribosomal proteins, and immunoglobulin proteins were also found in N. lugens watery saliva. This is the first study to identify, characterize and list the proteins in watery saliva of N. lugens, which might be involved in planthopper-rice interactions.

Whole-Genome Sequencing Reveals Diverse Models of Structural Variations in Esophageal Squamous Cell Carcinoma

Comprehensive identification of somatic structural variations (SVs) and understanding their mutational mechanisms in cancer might contribute to understanding biological differences and help to identify new therapeutic targets. Unfortunately, characterization of complex SVs across the whole genome and the mutational mechanisms underlying esophageal squamous cell carcinoma (ESCC) is largely unclear. To define a comprehensive catalog of somatic SVs, affected target genes, and their underlying mechanisms in ESCC, we re-analyzed whole-genome sequencing (WGS) data from 31 ESCCs using Meerkat algorithm to predict somatic SVs and Patchwork to determine copy-number changes. We found deletions and translocations with NHEJ and alt-EJ signature as the dominant SV types, and 16% of deletions were complex deletions. SVs frequently led to disruption of cancer-associated genes (e.g., CDKN2A and NOTCH1) with different mutational mechanisms. Moreover, chromothripsis, kataegis, and breakage-fusion-bridge (BFB) were identified as contributing to locally mis-arranged chromosomes that occurred in 55% of ESCCs. These genomic catastrophes led to amplification of oncogene through chromothripsis-derived double-minute chromosome formation (e.g., FGFR1 and LETM2) or BFB-affected chromosomes (e.g., CCND1, EGFR, ERBB2, MMPs, and MYC), with approximately 30% of ESCCs harboring BFB-derived CCND1 amplification. Furthermore, analyses of copy-number alterations reveal high frequency of whole-genome duplication (WGD) and recurrent focal amplification of CDCA7 that might act as a potential oncogene in ESCC. Our findings reveal molecular defects such as chromothripsis and BFB in malignant transformation of ESCCs and demonstrate diverse models of SVs-derived target genes in ESCCs. These genome-wide SV profiles and their underlying mechanisms provide preventive, diagnostic, and therapeutic implications for ESCCs.

Salivary proteins of plant-feeding hemipteroids - implication in phytophagy

Many hemipteroids are major pests and vectors of microbial pathogens, infecting crops. Saliva of the hemipteroids is critical in enabling them to be voracious feeders on plants, including the economically important ones. A plethora of hemipteroid salivary enzymes is known to inflict stress in plants, either by degrading the plant tissue or by affecting their normal metabolism. Hemipteroids utilize one of the following three strategies of feeding behaviour: salivary sheath feeding, osmotic-pump feeding and cell-rupture feeding. The last strategy also includes several different tactics such as lacerate-and-flush, lacerate-and-sip and macerate-and-flush. Understanding hemipteroid feeding mechanisms is critical, since feeding behaviour directs salivary composition. Saliva of the Heteroptera that are specialized as fruit and seed feeders, includes cell-degrading enzymes, auchenorrhynchan salivary composition also predominantly consists of cell-degrading enzymes such as amylase and protease, whereas that of the Sternorhyncha includes a variety of allelochemical-detoxifying enzymes. Little is known about the salivary composition of the Thysanoptera. Cell-degrading proteins such as amylase, pectinase, cellulase and pectinesterase enable stylet entry into the plant tissue. In contrast, enzymes such as glutathione peroxidase, laccase and trehalase detoxify plant chemicals, enabling the circumvention of plant-defence mechanisms. Salivary enzymes such as M1-zinc metalloprotease and CLIP-domain serine protease as in Acyrthosiphon pisum (Aphididae), and non-enzymatic proteins such as apolipophorin, ficolin-3-like protein and 'lava-lamp' protein as in Diuraphis noxia (Aphididae) have the capacity to alter host-plant-defence mechanisms. A majority of the hemipteroids feed on phloem, hence Ca++-binding proteins such as C002 protein, calreticulin-like isoform 1 and calmodulin (critical for preventing sieve-plate occlusion) are increasingly being recognized in hemipteroid-plant interactions. Determination of a staggering variety of proteins shows the complexity of hemipteroid saliva: effector proteins localized in hemipteran saliva suggest a similarity to the physiology of pathogen-plant interactions.

A 12-gene expression signature is associated with aggressive histological in prostate cancer: SEC14L1 and TCEB1 genes are potential markers of progression

The main challenge for clinical management of prostate cancer is to distinguish tumors that will progress faster and will show a higher tendency to recur from the more indolent ones. We have compared expression profiles of 18 prostate cancer samples (seven with a Gleason score of 6, eight with a Gleason score of 7, and three with a Gleason score of ≥8) and five nonneoplastic prostate samples, using the Affymetrix Human Array GeneChip Exon 1.0 ST. Microarray analysis revealed 99 genes showing statistically significant differences among tumors with Gleason scores of 6, 7, and ≥8. In addition, mRNA expression of 29 selected genes was analyzed by real-time quantitative RT-PCR with microfluidic cards in an extended series of 30 prostate tumors. Of the 29 genes, 18 (62%) were independently confirmed in the extended series by quantitative RT-PCR: 14 were up-regulated and 4 were down-regulated in tumors with a higher Gleason score. Twelve of these genes were differentially expressed in tumors with a Gleason score of 6 to 7 versus ≥8. Finally, IHC validation of the protein levels of two genes from the 12-gene signature (SEC14L1 and TCEB1) showed strong protein expression levels of both genes, which were statistically associated with a high combined Gleason score, advanced stage, and prostate-specific antigen progression. This set of genes may contribute to a better understanding of the molecular basis of prostate cancer. TCEB1 and SELC14L1 are good candidate markers for predicting prognosis and progression of prostate cancer.

Mammalian diseases of phosphatidylinositol transfer proteins and their homologs

Inositol and phosphoinositide signaling pathways represent major regulatory systems in eukaryotes. The physiological importance of these pathways is amply demonstrated by the variety of diseases that involve derangements in individual steps in inositide and phosphoinositide production and degradation. These diseases include numerous cancers, lipodystrophies and neurological syndromes. Phosphatidylinositol transfer proteins (PITPs) are emerging as fascinating regulators of phosphoinositide metabolism. Recent advances identify PITPs (and PITP-like proteins) to be coincidence detectors, which spatially and temporally coordinate the activities of diverse aspects of the cellular lipid metabolome with phosphoinositide signaling. These insights are providing new ideas regarding mechanisms of inherited mammalian diseases associated with derangements in the activities of PITPs and PITP-like proteins.

Identification of candidate growth promoting genes in ovarian cancer through integrated copy number and expression analysis

Ovarian cancer is a disease characterised by complex genomic rearrangements but the majority of the genes that are the target of these alterations remain unidentified. Cataloguing these target genes will provide useful insights into the disease etiology and may provide an opportunity to develop novel diagnostic and therapeutic interventions. High resolution genome wide copy number and matching expression data from 68 primary epithelial ovarian carcinomas of various histotypes was integrated to identify genes in regions of most frequent amplification with the strongest correlation with expression and copy number. Regions on chromosomes 3, 7, 8, and 20 were most frequently increased in copy number (>40% of samples). Within these regions, 703/1370 (51%) unique gene expression probesets were differentially expressed when samples with gain were compared to samples without gain. 30% of these differentially expressed probesets also showed a strong positive correlation (r≥0.6) between expression and copy number. We also identified 21 regions of high amplitude copy number gain, in which 32 known protein coding genes showed a strong positive correlation between expression and copy number. Overall, our data validates previously known ovarian cancer genes, such as ERBB2, and also identified novel potential drivers such as MYNN, PUF60 and TPX2.