Prognostic CpG Methylation Biomarkers Identified by Methylation Array in Esophageal Squamous Cell Carcinoma Patients

Background: Esophageal squamous cell carcinoma (ESCC) is an aggressive cancer with poor prognosis. We aimed to identify a panel of CpG methylation biomarkers for prognosis prediction of ESCC patients.Methods: Illumina''s GoldenGate methylation array, supervised principal components, Kaplan-Meier survival analyses and Cox regression model were conducted on dissected tumor tissues from a training cohort of 40 ESCC patients to identify potential CpG methylation biomarkers. Pyrosequencing quantitative methylation assay were performed to validate prognostic CpG methylation biomarkers in 61 ESCC patients. The correlation between DNA methylation and RNA expression of a validated marker, SOX17, was examined in a validation cohort of 61 ESCC patients.Results: We identified a panel of nine CpG methylation probes located at promoter or exon1 region of eight genes including DDIT3, FES, FLT3, NTRK3, SEPT5, SEPT9, SOX1, and SOX17, for prognosis prediction in ESCC patients. Risk score calculated using the eight-gene panel statistically predicted poor outcome for patients with high risk score. These eight-gene also showed a significantly higher methylation level in tumor tissues than their corresponding normal samples in all patients analyzed. In addition, we also detected an inverse correlation between CpG hypermethylation and the mRNA expression level of SOX17 gene in ESCC patients, indicating that DNA hypermethylation was responsible for decreased expression of SOX17.Conclusions: This study established a proof-of-concept CpG methylation biomarker panel for ESCC prognosis that can be further validated by multiple cohort studies. Functional characterization of the eight prognostic methylation genes in our biomarker panel could help to dissect the mechanism of ESCC tumorigenesis.     

Fifty million years of beetle evolution along the Antarctic Polar Front

Global cooling and glacial–interglacial cycles since Antarctica’s isolation have been responsible for the diversification of the region’s marine fauna. By contrast, these same Earth system processes are thought to have played little role terrestrially, other than driving widespread extinctions. Here, we show that on islands along the Antarctic Polar Front, paleoclimatic processes have been key to diversification of one of the world’s most geographically isolated and unique groups of herbivorous beetles—Ectemnorhinini weevils. Combining phylogenomic, phylogenetic, and phylogeographic approaches, we demonstrate that these weevils colonized the sub-Antarctic islands from Africa at least 50 Ma ago and repeatedly dispersed among them. As the climate cooled from the mid-Miocene, diversification of the beetles accelerated, resulting in two species-rich clades. One of these clades specialized to feed on cryptogams, typical of the polar habitats that came to prevail under Miocene conditions yet remarkable as a food source for any beetle. This clade’s most unusual representative is a marine weevil currently undergoing further speciation. The other clade retained the more common weevil habit of feeding on angiosperms, which likely survived glaciation in isolated refugia. Diversification of Ectemnorhinini weevils occurred in synchrony with many other Antarctic radiations, including penguins and notothenioid fishes, and coincided with major environmental changes. Our results thus indicate that geo-climatically driven diversification has progressed similarly for Antarctic marine and terrestrial organisms since the Miocene, potentially constituting a general biodiversity paradigm that should be sought broadly for the region’s taxa.

Antarctica’s isolation, cooling, and glacial–interglacial cycles over the Cenozoic have resulted in the remarkable diversification of a unique marine fauna (1, 2). The investigation of marine radiations in Antarctica has reshaped modern understanding of biodiversity processes, for example, by revealing a surprising inverse latitudinal gradient in diversification rates for fish and brittle stars (3–5). In contrast, Antarctica’s paleoclimatic legacy for terrestrial communities has long been considered one of widespread extinction due to glaciation. Evidence of terrestrial species surviving in Antarctic glacial refugia (6) and discoveries of substantial endemic diversity and biogeographic structuring in some groups (7, 8) is changing this narrative, indicating extended evolutionary histories on land. Yet, such evolutionary histories remain obscured by a lack of large-scale molecular phylogenetic work, with most Antarctic terrestrial research focused on small subsets of species or populations (9, 10). The few studies that have taken a multilocus phylogenetic approach have uncovered hidden terrestrial diversity and signals of long-term allopatric divergence (e.g., refs. 11 and 12), hinting that Cenozoic climatic processes may have driven terrestrial diversification in ways similar to that for marine life.The hypothesis that diversification has proceeded similarly in Antarctic marine and terrestrial groups has not been tested. While the extinction of a diverse continental Antarctic biota is well established (13), mounting evidence of significant and biogeographically structured Antarctic terrestrial diversity (8, 14, 15) with a long evolutionary history (6, 16) suggests the possibility of broadly similar diversification processes across marine and terrestrial Antarctic systems. If valid for some taxa, further tests should then be sought across a wider variety of organisms. Here, we therefore evaluate the terrestrial applicability of the paradigm emerging for Antarctic marine biodiversity—that a major cooling phase from the mid-Miocene climatic transition (14 Ma) onwards, and subsequent habitat restructuring, have led to significant and ongoing diversification for many taxa, including those with much older origins in the region (2, 4, 17). We do so by using one of the most well-known and speciose groups from the sub-Antarctic, the herbivorous Ectemnorhinini weevils (Coleoptera: Curculionidae) (18–20).Preliminary molecular studies indicate that the Ectemnorhinini, along with numerous other terrestrial taxa, have long histories in the sub-Antarctic, extending to the Miocene or earlier [e.g., beetles (21), midges (22), and springtails (11)]. This enables a comparison of their evolution throughout the same periods of environmental change that drove the diversification of Antarctic marine taxa. Moreover, the sub-Antarctic islands overlap spatially with the Southern Ocean, with climates that reflect oceanic conditions both past and present (23, 24). While in some respects quite different to the continental Antarctic, the islands are in other ways quite similar, providing a window into diversification processes that might be sought for continental groups, especially given their age and biogeographic structuring. Both regions share many higher taxa (e.g., ref. 25), a dynamic geo-climatic history (6, 26), a profound degree of isolation, and indications that climatic events likely structured their biota (6, 8, 27). The terrestrial habitat on the continent and its surrounding islands is fragmented by large expanses of ice or ocean, respectively, and has been further isolated by the Antarctic Circumpolar Current for at least 34 Ma (28, 29). Cyclic growth and contraction of ice sheets throughout the Plio–Pleistocene, though typically associated with the continent, has also had extensive impacts on the sub-Antarctic islands (26). The more intensively surveyed sub-Antarctic faunas thus provide an opportunity to investigate terrestrial diversification processes for the wider Antarctic while recognizing that for many groups on the continent, the main legacy of change has been extinction.To test the hypothesis that a major phase of cooling from the mid-Miocene onwards and subsequent habitat restructuring has led to the diversification of Antarctic terrestrial taxa, we integrate three tiers of molecular data to reveal a comprehensive evolutionary history for the Ectemnorhinini weevils. This additionally allows us to resolve the geographic, taxonomic, and temporal origins of the Ectemnorhinini and the role of dispersal and colonization in the development of the region’s biogeography. We first resolve the controversial origins of these weevils (19, 30) with a phylogenomic approach using anchored hybrid enrichment (AHE) for up to 515 genes across 12 representative species of Ectemnorhinini and a worldwide sample of 87 species of putative relatives and known outgroups, mostly from the beetle subfamily Entiminae (18, 30, 31). We then build on these outcomes by exploring the timing and patterns of taxonomic diversification, including divergence times and proposed dispersal events, using a multilocus phylogenetic dataset (three mitochondrial and two nuclear genes) for an extensive sample of Ectemnorhinini from each archipelago on which they are known to occur. Finally, we reveal contemporary limits to gene flow and examine the population structure of the littoral-dwelling ectemnorhinine weevil Palirhoeus eatoni using phylogeographic methods applied to a library of 5,859 genome-wide single-nucleotide polymorphisms (SNPs). This unusually widespread species is found on all four archipelagos of the Kerguelen Province known to host Ectemnorhinini: Crozet, Kerguelen, Prince Edward Islands (PEI), and Heard Island and McDonald Islands (HIMI).     

胞嘧啶鸟嘌呤二核苷酸-脱氧寡核苷酸抑制疟原虫红前期发育

目的 观察胞嘧啶鸟嘌呤二核苷酸-脱氧寡核苷酸（cytidine-phosphate-guanosine oligodeoxynucleotide,CpG ODN）对疟原虫红前期发育的影响。 方法 通过构建约氏疟原虫BY265株18S rRNA外标准品质粒,与小鼠三磷酸甘油醛脱氢酶（GAPDH）内标准品共同组成TaqMan RT-PCR分析模型。用不同剂量（0.05×10⁵ 、0.1×10⁵、0.5×10⁵、1×10⁵和2×10⁵个）约氏疟原虫唾液腺子孢子感染BALB/c小鼠,42 h后处死小鼠取其肝脏,制备约氏疟原虫cDNA进行TaqMan RT-PCR反应,以小鼠肝脏虫荷指标检验模型的有效性。将12只BALB/c小鼠随机均分为CpG组、CpG对照组和PBS对照组,CpG组和CpG对照组小鼠分别尾静脉注射脱氧寡核苷酸1826（ODN1826）及其对照（ODN1826 control）各30 μg,PBS对照组注射0.01 mol/L PBS溶液 200 μl。24 h后各组每鼠感染100个子孢子,于感染后42 h处死小鼠取肝脏,制备约氏疟原虫cDNA进行TaqMan RT-PCR,定量分析感染疟原虫24 h前CpG ODN预处理小鼠肝脏虫荷的变化。 结果 构建的约氏疟原虫外标准品质粒所插入的BY265株18S rRNA基因与17XNL株18S rRNA基因相似性为98%,它与小鼠GAPDH内标准品共同组成的TaqMan RT-PCR分析模型能够正确反映小鼠肝脏虫荷与唾液腺子孢子感染量的正比关系。感染疟原虫24 h前给予CpG ODN处理,CpG组小鼠肝脏虫荷为CPG对照组的1/5（0.28/1.33）,两者差异有统计学意义（P<0.05）。 结论 本实验建立的TaqMan RT-PCR分析模型适用于红前期疟原虫（肝脏）虫荷指标的研究。CpG ODN能显著抑制红前期疟原虫的发育。     

CpG寡核苷酸作为黏膜佐剂的研究进展

含未甲基化的CpG二核苷酸的寡聚脱氧核苷酸模体(CpG ODN)具有很强的黏膜佐剂活性,已成为近年来的研究热点之一。应用CpG ODN与各种病毒和细菌抗原进行了大量实验研究,所涉及的黏膜免疫途径包括滴鼻、口服和生殖道。CpG ODN可与传统的黏膜佐剂CT和LT产生协同效应,对人体无毒副作用,是一种极具应用前景的黏膜佐剂。目前认为,CpG ODN的佐剂效应发挥与TLR9识别和后续的一系列信号转导密切相关。     

Phytoplankton species richness scales consistently from laboratory microcosms to the world's oceans

Species-area relationships have been observed for virtually all major groups of macroorganisms that have been studied to date but have not been explored for microscopic phytoplankton algae, which are the dominant producers in many freshwater and marine ecosystems. Our analyses of data from 142 different natural ponds, lakes, and oceans and 239 experimental ecosystems reveal a strong species-area relationship with an exponent that is invariant across ecosystems that span >15 orders of magnitude in spatial extent. A striking result is that the species-area relationship derived from small-scale experimental studies correctly scales up to natural aquatic ecosystems. These results significantly broaden our knowledge of the effects of island size on biodiversity and also confirm the relevance of experimentally derived data to the analysis and understanding of larger-scale ecological patterns. In addition, they confirm that patterns in microbial diversity are strongly consistent with those that have been repeatedly reported in the literature for macroorganisms.     

Insect-Specific Flavivirus Replication in Mammalian Cells Is Inhibited by Physiological Temperature and the Zinc-Finger Antiviral Protein

The genus Flavivirus contains pathogenic vertebrate-infecting flaviviruses (VIFs) and insect-specific flaviviruses (ISF). ISF transmission to vertebrates is inhibited at multiple stages of the cellular infection cycle, via yet to be elucidated specific antiviral responses. The zinc-finger antiviral protein (ZAP) in vertebrate cells can bind CpG dinucleotides in viral RNA, limiting virus replication. Interestingly, the genomes of ISFs contain more CpG dinucleotides compared to VIFs. In this study, we investigated whether ZAP prevents two recently discovered lineage II ISFs, Binjari (BinJV) and Hidden Valley viruses (HVV) from replicating in vertebrate cells. BinJV protein and dsRNA replication intermediates were readily observed in human ZAP knockout cells when cultured at 34 °C. In ZAP-expressing cells, inhibition of the interferon response via interferon response factors 3/7 did not improve BinJV protein expression, whereas treatment with kinase inhibitor C16, known to reduce ZAP’s antiviral function, did. Importantly, at 34 °C, both BinJV and HVV successfully completed the infection cycle in human ZAP knockout cells evident from infectious progeny virus in the cell culture supernatant. Therefore, we identify vertebrate ZAP as an important barrier that protects vertebrate cells from ISF infection. This provides new insights into flavivirus evolution and the mechanisms associated with host switching.     

Involvement of epigenetics and microRNA-29b in the urethane induced inception and establishment of mouse lung tumors

Epigenetic changes are correlated with tumor development showing aberrations in DNA methylation and histone modifications. To find the early changes, we evaluated the epigenetic events from early to late stage of the urethane induced lung tumor development in mouse model and tried to correlate the molecular events with the progression of tumor. We addressed the hypothesis by examining the tumor development, status of DNMTs, HDACs and MBDs, DNA methylation and expression of microRNA-29b during 1 to 36 weeks after urethane exposure that included the period before and after the tumor appearance. Tumors did not appear after 1 or 4 weeks but well defined tumors appeared after 12 weeks and larger tumors appeared at 36 weeks which was prevented by IP6. DNMT1, DNMT3a and DNMT3b were upregulated after urethane exposure at the time of no tumor till the tumor developed and showed its upregulated functional activity. DNMTs are shown to be the targets of microRNA-29b and we showed that microRNA-29b was downregulated in the line of DNMT upregulation. HDAC, the histone modifier, also showed progressive upregulation. Periodic increase in methyl binding proteins, MBD2, supported the expression of gene silencing pathways in terms of the downregulation of tumor suppressor genes, p16 and MLH1. All these molecular alterations were protected in the presence of IP6. Our results showed that the key steps of epigenetics, DNMTs, mir29b, and HDAC1, are altered both before and after the development of tumors.     

Identification of in-vivo induced genes of Streptococcus suis serotype 2 specially expressed in infected human

Streptococcus suis (S. suis) serotype 2 usually cause infection in swine. Recently, two large-scale outbreaks in China with severe streptococcal toxic shock syndrome (STSS) and high mortality raised worldwide concern to human S. suis infection. To reveal the molecular pathogenesis of S. suis 2 during human infection, in-vivo induced antigen technology (IVIAT) was applied to identify the in-vivo induced genes (ivi genes) of S. suis 05ZYH33. The ivi genes are specifically expressed or up-regulated in-vivo and always associated with the in-vivo survival and pathogenicity of pathogens. In present study, convalescent sera from S. suis 05ZYH33 infected patients were pooled and fully adsorbed with in-vitro grown S. suis 05ZYH33 and Escherichia coli BL21 (DE3). Genomic expression library of 05ZYH33 was repeatedly screened with colony immunoblot assay using adsorbed sera. Finally, 19 genes were assessed as ivi genes of 05ZYH33. Fifteen of 19 genes encode proteins with biological functions in substance transport and metabolism, cell structure biogenesis, cell cycle control, replication, translation and other functions. The 4 remaining genes encode proteins with unknown functions. Of the 19 ivi genes, five (SSU05_0247, 0437, 1577, 1664 and 2144) encode proteins with no immunoreactivity to control sera from healthy individuals never exposed to 05ZYH33. The successful identification of ivi genes not only sheds light on understanding the pathogenesis of S. suis 05ZYH33 during its human infection, but also provides potential targets for the developments of new vaccines, therapeutic drugs and diagnostic reagents against human S. suis infection.