WTAP facilitates progression of hepatocellular carcinoma via m6A-HuR-dependent epigenetic silencing of ETS1

Background

N6-methyladenosine (m6A) methylation, a well-known modification with new epigenetic functions, has been reported to participate in the tumorigenesis of hepatocellular carcinoma (HCC), providing novel insights into the molecular pathogenesis of this disease. However, as the key component of m6A methylation, Wilms tumor 1-associated protein (WTAP) has not been well studied in HCC. Here we investigated the biological role and underlying mechanism of WTAP in liver cancer.

Methods

We determined the expression of WTAP and its correlation with clinicopathological features using tissue microarrays and the Cancer Genome Atlas (TCGA) dataset. And we clarified the effects of WTAP on HCC cells using cell proliferation assay, colony formation, Edu assay and subcutaneous xenograft experiments. We then applied RNA sequencing combined with gene expression omnibus (GEO) data to screen candidate targets of WTAP. Finally, we investigated the regulatory mechanism of WTAP in HCC by m6A dot blot assay, methylated RNA immunoprecipitation (MeRIP) assay, dual luciferase reporter assay, RNA immunoprecipitation (RIP) assay and Chromatin immunoprecipitation (ChIP) assay.

Results

We demonstrated that WTAP was highly expressed in HCC which indicated the poor prognosis, and that WTAP expression served as an independent predictor of HCC survival. Functionally, WTAP promoted the proliferation capability and tumor growth of HCC cells in vitro and in vivo. Furthermore, ETS proto-oncogene 1 (ETS1) was identified as the downstream effector of WTAP. The m6A modification regulated by WTAP led to post-transcriptional suppression of ETS1, with the implication of Hu-Antigen R (HuR) as an RNA stabilizer. Then ETS1 was found to inhibit the progression of HCC and could rescue the phenotype induced by WTAP deficiency. Moreover, WTAP modulated the G2/M phase of HCC cells through a p21/p27-dependent pattern mediated by ETS1.

Conclusion

We have identified that WTAP is significantly up-regulated in HCC and promotes liver cancer development. WTAP-guided m6A modification contributes to the progression of HCC via the HuR-ETS1-p21/p27 axis. Our study is the first to report that WTAP-mediated m6A methylation has a crucial role in HCC oncogenesis, and highlights WTAP as a potential therapeutic target of HCC treatment.

Electronic supplementary material

The online version of this article (10.1186/s12943-019-1053-8) contains supplementary material, which is available to authorized users.

Changes in forest biomass carbon storage in China between 1949 and 1998

The location and mechanisms responsible for the carbon sink in northern mid-latitude lands are uncertain. Here, we used an improved estimation method of forest biomass and a 50-year national forest resource inventory in China to estimate changes in the storage of living biomass between 1949 and 1998. Our results suggest that Chinese forests released about 0.68 petagram of carbon between 1949 and 1980, for an annual emission rate of 0.022 petagram of carbon. Carbon storage increased significantly after the late 1970s from 4.38 to 4.75 petagram of carbon by 1998, for a mean accumulation rate of 0.021 petagram of carbon per year, mainly due to forest expansion and regrowth. Since the mid-1970s, planted forests (afforestation and reforestation) have sequestered 0.45 petagram of carbon, and their average carbon density increased from 15.3 to 31.1 megagrams per hectare, while natural forests have lost an additional 0.14 petagram of carbon, suggesting that carbon sequestration through forest management practices addressed in the Kyoto Protocol could help offset industrial carbon dioxide emissions.

Role of human immunodeficiency virus type 1-specific protease in core protein maturation and viral infectivity

It is generally believed that the gag gene product of human immunodeficiency virus type 1 (HIV-1) is processed into several core proteins by a virus-specific protease. We used deletion mutation analysis to study the role of HIV-specific protease in the processing of core proteins and its requirement for viral infectivity. Several mutant genomes with deletions in the protease gene were constructed. A mammalian cell line, COS-M6, transfected with the wild-type viral genome was shown to produce virions containing processed core proteins, while COS-M6 cells transfected with two mutated genomes could express only the core protein precursor, Pr56gag. The wild-type transfectant produced infectious virus; both transfectants expressing the mutated genomes also produced virions, and one of them still retained reverse transcriptase activity. However, the mutant viral particles were devoid of infectivity. Virions with a distinct central core and an electron-dense nucleoid budded out from the plasma membrane of COS-M6 cells transfected with the wild-type genome. In contrast, noninfectious virions that budded either into cytoplasmic vacuoles or out from the plasma membrane of COS-M6 cells transfected with mutant genomes contained ring-shaped nucleoids. These results indicate that the HIV-1 protease plays a role not only in the maturation of the core proteins but also in the assembly of the virus and thus is required for viral infectivity.

MicroRNA miR-93 promotes tumor growth and angiogenesis by targeting integrin-β8

It has been reported that the miR-106b∼25 cluster, a paralog of the miR-17∼92 cluster, possesses oncogenic activities. However, the precise role of each microRNA (miRNA) in the miR-106b∼25 cluster is not yet known. In this study, we examined the function of miR-93, one of the microRNAs within the miR-106b∼25 cluster, in angiogenesis and tumor formation. We found that miR-93 enhanced cell survival, promoted sphere formation and augmented tumor growth. Most strikingly, when miR-93-overexpressing U87 cells were co-cultured with endothelial cells, they supported endothelial cell spreading, growth, migration and tube formation. In vivo studies revealed that miR-93-expressing cells induced blood vessel formation, allowing blood vessels to extend to tumor tissues in high densities. Angiogenesis promoted by miR-93 in return facilitated cell survival, resulting in enhanced tumor growth. We further showed that integrin-β8 is a target of miR-93. Higher levels of integrin-β8 are associated with cell death in tumor mass and in human glioblastoma. Silencing of integrin-β8 expression using small interfering RNA promoted cell proliferation, whereas ectopic expression of integrin-β8 decreased cell growth. These findings showed that miR-93 promotes tumor growth and angiogenesis by suppressing, at least in part, integrin-β8 expression. Our results suggest that inhibition of miR-93 function may be a feasible approach to suppress angiogenesis and tumor growth.

Upregulation of long noncoding RNA ZEB1-AS1 promotes tumor metastasis and predicts poor prognosis in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related mortality worldwide. Despite progress in diagnostics and treatment of HCC, its prognosis remains poor. Emerging studies showed that long noncoding RNAs (lncRNAs) have crucial regulatory roles in cancer biology. In the current study, differentially expressed lncRNAs between HCC and paired non-tumor tissues were identified using microarrays. The effects of a specific differentially expressed lncRNA (termed ZEB1-AS1) on tumor progression were investigated in vitro and in vivo. We found that ZEB1-AS1 is frequently upregulated in HCC samples, especially in metastatic tumor tissues. DNA methylation analysis shows a tumor-specific ZEB1-AS1 promoter hypomethylation. Aberrant methylation is tightly correlated with overexpression of ZEB1-AS1 in HCC. Patients with ZEB1-AS1 hypomethylation or with high ZEB1-AS1 expression have poor recurrence-free survival. Functionally, ZEB1-AS1 promotes tumor growth and metastasis, acts as an oncogene in HCC. The ZEB1-AS1 gene is located in physical contiguity with ZEB1 and positively regulates the ZEB1 expression. ZEB1 inhibition partially abrogates ZEB1-AS1-induced epithelial to mesenchymal transition (EMT) and cancer metastasis. Our results provide novel insights into the function of lncRNA-driven hepatocarcinogenesis, highlight the important role of ZEB1-AS1 and ZEB1 in HCC progression, and indicate that ZEB1-AS1 may be served as a valuable prognostic biomarker for HCC.

Glycoprotein D of herpes simplex virus (HSV) binds directly to HVEM, a member of the tumor necrosis factor receptor superfamily and a mediator of HSV entry

Glycoprotein D (gD) is a structural component of the herpes simplex virus (HSV) envelope which is essential for virus entry into host cells. Chinese hamster ovary (CHO-K1) cells are one of the few cell types which are nonpermissive for the entry of many HSV strains. However, when these cells are transformed with the gene for the herpesvirus entry mediator (HVEM), the resulting cells, CHO-HVEM12, are permissive for many HSV strains, such as HSV-1(KOS). By virtue of its four cysteine-rich pseudorepeats, HVEM is a member of the tumor necrosis factor receptor superfamily of proteins. Recombinant forms of gD and HVEM, gD-1(306t) and HVEM(200t), respectively, were used to demonstrate a specific physical interaction between these two proteins. This interaction was dependent on native gD conformation but independent of its N-linked oligosaccharides, as expected from previous structure-function studies. Recombinant forms of gD derived from HSV-1(KOS)rid1 and HSV-1(ANG) did not bind to HVEM(200t), explaining the inability of these viruses to infect CHO-HVEM12 cells. A variant gD protein, gD-1(delta290-299t), showed enhanced binding to HVEM(200t) relative to the binding of gD-1(306t). Competition studies showed that gD-1(delta290-299t) and gD-1(306t) bound to the same region of HVEM(200t), suggesting that the differences in binding to HVEM are due to differences in affinity. These differences were also reflected in the ability of gD-1(delta290-299t) but not gD-1(306t) to block HSV type 1 infection of CHO-HVEM12 cells. By gel filtration chromatography, the complex between gD-1(delta290-299t) and HVEM(200t) had a molecular mass of 113 kDa and a molar ratio of 1:2. We conclude that HVEM interacts directly with gD, suggesting that HVEM is a receptor for virion gD and that the interaction between these proteins is a step in HSV entry into HVEM-expressing cells.

Maturation of gait dynamics: stride-to-stride variability and its temporal organization in children

In very young children, immature control of posture and gait results in unsteady locomotion. In children of approximately 3 yr of age, gait appears relatively mature; however, it is unknown whether the dynamics of walking change beyond this age. Because stride dynamics depend on neural control, we hypothesized that motor control would continue to develop beyond age 3. To test this hypothesis, we measured the gait cycle duration on a stride-by-stride basis in 50 healthy 3- to 14-yr-old children (25 girls). Measurements of stride-to-stride variability were significantly larger both in the 3- and 4-yr-old children, compared with the 6- and 7-yr-old children, and in the 6- and 7-yr-old children, compared with the 11- to 14-yr-old children. Measurements of the temporal organization of gait also revealed significant age-dependent changes. The effects of age persisted even after adjusting for height. These findings indicate that mature stride dynamics may not be completely developed even in healthy 7-yr-old children and that different aspects of stride dynamics mature at different ages.

ALKBH5 suppresses malignancy of hepatocellular carcinoma via m6A-guided epigenetic inhibition of LYPD1

Background

N6-methyladenosine (m⁶A) modification is an emerging layer of epigenetic regulation which is widely implicated in the tumorigenicity of hepatocellular carcinoma (HCC), offering a novel perspective for investigating molecular pathogenesis of this disease. The role of AlkB homolog 5 (ALKBH5), one of the m⁶A demethylases, has not been fully explored in HCC. Here we clarify the biological profile and potential mechanisms of ALKBH5 in HCC.

Methods

Expression of ALKBH5 and its correlation with clinicopathological characteristics of HCC were evaluated using tissue microarrays and online datasets. And biological effects of ALKBH5 in HCC were determined in vitro and in vivo. Subsequently, methylated RNA immunoprecipitation sequencing (MeRIP-seq) combined with RNA sequencing (RNA-seq), and following m⁶A dot blot, MeRIP-qPCR, RIP-qPCR or dual luciferase reporter assays were employed to screen and validate the candidate targets of ALKBH5.

Results

We demonstrated that ALKBH5 was down-regulated in HCC, and decreased ALKBH5 expression was an independent prognostic factor of worse survival in HCC patients. Functionally, ALKBH5 suppressed the proliferation and invasion capabilities of HCC cells in vitro and in vivo. Mechanistically, ALKBH5-mediated m⁶A demethylation led to a post-transcriptional inhibition of LY6/PLAUR Domain Containing 1 (LYPD1), which could be recognized and stabilized by the m⁶A effector IGF2BP1. In addition, we identified that LYPD1 induced oncogenic behaviors of tumors in contrast to ALKBH5. Dysregulation of ALKBH5/LYPD1 axis impelled the progression of HCC.

Conclusion

Our study reveals that ALKBH5, characterized as a tumor suppressor, attenuates the expression of LYPD1 via an m⁶A-dependent manner in HCC cells. Our findings enrich the landscape of m⁶A-modulated tumor malignancy, and provide new insights into potential biomarkers and therapeutic targets of HCC treatment.

The hygroscopic properties of dicarboxylic and multifunctional acids: measurements and UNIFAC predictions

The role of water-soluble organic compounds on the hygroscopic properties of atmospheric aerosols has recently been the subject of many studies. In particular, low molecular weight dicarboxylic acids and some multifunctional organic acids have been found or are expected to exist in atmospheric aerosols in urban, semiurban, rural, and remote sites. Unlike for their inorganic counterparts, the hygroscopic properties of organic acids have not been well characterized. In this study, the hygroscopic properties of selected water-soluble dicarboxylic acids (oxalic acid, malonic acid, succinic acid, and glutaric acid) and multifunctional acids (citric acid, DL-malic acid, and L-(+)-tartaric acid) were studied using single droplets levitated in an electrodynamic balance at 25 degrees C. The water activities of bulk samples of dilute solutions were also measured. Solute evaporation was observed in the dicarboxylic acids but not in the multifunctional acids. Oxalic acid, succinic acid, and glutaric acid droplets crystallize upon evaporation of water, but, except for glutaric acid droplets, do not deliquesce even at 90% relative humidity (RH). Mass transfer limitation of the deliquescence process was observed in glutaric acid. Neither crystallization nor deliquescence was observed in malonic acid, citric acid, DL-malic acid, or L-(+)-tartaric acid. Malonic acid and these three hydroxy-carboxylic acids absorb water even at RH much lower than their respective deliquescence RH. The growth factor (Gf), defined as the ratio of the particle diameter at RH = 10% to that at RH = 90%, of oxalic acid and succinic acid was close to unity, indicating no hygroscopicity in this range. The remaining acids (malonic acid, glutaric acid, citric acid, malic acid, and tartaric acid) showed roughly similar hygroscopicity of a Gf of 1.30-1.53, which is similar to that of "more hygroscopic" aerosols in field measurements reported in the literature. A generalized equation for these four acids, Gf = (1-aw)-0.163, was developed to represent the hygroscopicity of these acids. Water activity predictions from calculations using the UNIFAC model were found to agree with the measured water activity data to within 40% for most of the acids but the deviations were as large as about 100% for malic acid and tartaric acid. We modified the functional group interaction parameters of the COOH(-H20, OH-H20, and OH-COOH pairs by fitting the UNIFAC model with the measured data. The modified UNIFAC model improves the agreement of predictions and measurements to within 38% for all the acids studied.

Interaction of herpes simplex virus glycoprotein gC with mammalian cell surface molecules

The entry of herpes simplex virus (HSV) into mammalian cells is a multistep process beginning with an attachment step involving glycoproteins gC and gB. A second step requires the interaction of glycoprotein gD with a cell surface molecule. We explored the interaction between gC and the cell surface by using purified proteins in the absence of detergent. Truncated forms of gC and gD, gC1(457t), gC2(426t), and gD1(306t), lacking the transmembrane and carboxyl regions were expressed in the baculovirus system. We studied the ability of these proteins to bind to mammalian cells, to bind to immobilized heparin, to block HSV type 1 (HSV-1) attachment to cells, and to inhibit plaque formation by HSV-1. Each of these gC proteins bound to conformation-dependent monoclonal antibodies and to human complement component C3b, indicating that they maintained the same conformation of gC proteins expressed in mammalian cells. Biotinylated gC1(457t) and gC2(426t) each bind to several cell lines. Binding was inhibited by an excess of unlabeled gC but not by gD, indicating specificity. The attachment of gC to cells involves primarily heparan sulfate proteoglycans, since heparitinase treatment of cells reduced gC binding by 50% but had no effect on gD binding. Moreover, binding of gC to two heparan sulfate-deficient L-cell lines, gro2C and sog9, both of which are mostly resistant to HSV infection, was markedly reduced. Purified gD1 (306t), however, bound equally well to the two mutant cell lines. In contrast, saturating amounts of gC1(457t) interfered with HSV-1 attachment to cells but failed to block plaque formation, suggesting a role for gC in attachment but not penetration. A mutant form of gC lacking residues 33 to 123, gC1(delta 33-123t), expressed in the baculovirus system, bound significantly less well to cells than did gC1(457t) and competed poorly with biotinylated gC1(457t) for binding. These results suggest that residues 33 to 123 are important for gC attachment to cells. In contrast, both the mutant and wild-type forms of gC bound to immobilized heparin, indicating that binding of these proteins to the cell surface involves more than a simple interaction with heparin. To determine that the contribution of the N-terminal region of gC is important for HSV attachment, we compared several properties of a mutant HSV-1 which contains gC lacking amino acids 33 to 123 to those of its parental virus, which contains full-length gC. The mutant bound less well to cells than the parental virus but exhibited normal growth properties.(ABSTRACT TRUNCATED AT 400 WORDS)

ACSL4 reprograms fatty acid metabolism in hepatocellular carcinoma via c-Myc/SREBP1 pathway

Lipid metabolic reprogramming plays a pivotal role in hepatocellular carcinoma (HCC) development, but the underlying mechanisms are incompletely characterized. Long chain acyl CoA synthetase 4 (ACSL4), a member of acyl-CoA synthetases (ACS) family, has been identified as a novel marker of alpha-fetoprotein-high subtype HCC and as an oncogene. Here, we identified a new function of ACSL4 in HCC lipid metabolism. ACSL4 can modulate de novo lipogenesis by accumulating intracellular triglycerides, cholesterols, and lipid droplets in HCC. Mechanistically, ACSL4 upregulates the master lipogenesis regulator sterol regulatory element binding protein 1 (SREBP1) and its downstream lipogenic enzymes in HCC cells via c-Myc. Moreover, SREBP1 is crucial for ACSL4-mediated regulation of lipogenesis as well as HCC cell proliferation and metastasis, as SREBP1 overexpression rescues lipogenic deficiency and decreased oncogenic capabilities associated with ACSL4 suppression in vitro and in vivo. Clinically, our data showed that the expression of ACSL4 was positively correlated with that of SREBP1 in HCC patients, and the combinational biomarkers showed strong predictive value for HCC. Together, our findings uncover a new mechanism by which ACSL4 modulates aberrant lipid metabolism and promotes the progression of HCC.

Panagiotopoulou E, Panagoulias I, Pandini CE, Panduro Vazquez JG, Pani P, Panitkin S, Pantea D, Paolozzi L, Papadopoulou TD, Papageorgiou K, Paramonov A, Paredes Hernandez D, Parker AJ, Parker MA, Parker KA, Parodi F, Parsons JA, Parzefall U, Pascuzzi VR, Pasqualucci E, Passaggio S, Pastore F, Pásztor G, Pataraia S, Pater JR, Pauly T, Pearce J, Pearson B, Pedersen LE, Pedersen M, Pedraza Lopez S, Pedro R, Peleganchuk SV, Penc O, Peng C, Peng H, Penwell J, Peralva BS, Perego MM, Perepelitsa DV, Perez Codina E, Perini L, Pernegger H, Perrella S, Peschke R, Peshekhonov VD, Peters K, Peters RFY, Petersen BA, Petersen TC, Petit E, Petridis A, Petridou C, Petroff P, Petrolo E, Petrov M, Petrucci F, Pettersson NE, Peyaud A, Pezoa R, Phillips PW, Piacquadio G, Pianori E, Picazio A, Piccaro E, Piccinini M, Pickering MA, Piegaia R, Pilcher JE, Pilkington AD, Pin AWJ, Pinamonti M, Pinfold JL, Pingel A, Pires S, Pirumov H, Pitt M, Plazak L, Pleier MA, Pleskot V, Plotnikova E, Pluth D, Poettgen R, Poggioli L, Pohl D, Polesello G, Poley A, Policicchio A, Polifka R, Polini A, Pollard CS, Polychronakos V, Pommès K, Pontecorvo L, Pope BG, Popeneciu GA, Poppleton A, Pospisil S, Potamianos K, Potrap IN, Potter CJ, Potter CT, Poulard G, Poveda J, Pozdnyakov V, Pozo Astigarraga ME, Pralavorio P, Pranko A, Prell S, Price D, Price LE, Primavera M, Prince S, Prokofiev K, Prokoshin F, Protopopescu S, Proudfoot J, Przybycien M, Puddu D, Purohit M, Puzo P, Qian J, Qin G, Qin Y, Quadt A, Quayle WB, Queitsch-Maitland M, Quilty D, Raddum S, Radeka V, Radescu V, Radhakrishnan SK, Radloff P, Rados P, Ragusa F, Rahal G, Raine JA, Rajagopalan S, Rammensee M, Rangel-Smith C, Ratti MG, Rauch DM, Rauscher F, Rave S, Ravenscroft T, Ravinovich I, Raymond M, Read AL, Readioff NP, Reale M, Rebuzzi DM, Redelbach A, Redlinger G, Reece R, Reed RG, Reeves K, Rehnisch L, Reichert J, Reiss A, Rembser C, Ren H, Rescigno M, Resconi S, Rezanova OL, Reznicek P, Rezvani R, Richter R, Richter S, Richter-Was E, Ricken O, Ridel M, Rieck P, Riegel CJ, Rieger J, Rifki O, Rijssenbeek M, Rimoldi A, Rimoldi M, Rinaldi L, Ristić B, Ritsch E, Riu I, Rizatdinova F, Rizvi E, Rizzi C, Robertson SH, Robichaud-Veronneau A, Robinson D, Robinson JEM, Robson A, Roda C, Rodina Y, Rodriguez Perez A, Rodriguez Rodriguez D, Roe S, Rogan CS, Røhne O, Roloff J, Romaniouk A, Romano M, Romano Saez SM, Romero Adam E, Rompotis N, Ronzani M, Roos L, Ros E, Rosati S, Rosbach K, Rose P, Rosien NA, Rossetti V, Rossi E, Rossi LP, Rosten JHN, Rosten R, Rotaru M, Roth I, Rothberg J, Rousseau D, Rozanov A, Rozen Y, Ruan X, Rubbo F, Rudolph MS, Rühr F, Ruiz-Martinez A, Rurikova Z, Rusakovich NA, Ruschke A, Russell HL, Rutherfoord JP, Ruthmann N, Ryabov YF, Rybar M, Rybkin G, Ryu S, Ryzhov A, Rzehorz GF, Saavedra AF, Sabato G, Sacerdoti S, Sadrozinski HFW, Sadykov R, Safai Tehrani F, Saha P, Sahinsoy M, Saimpert M, Saito T, Sakamoto H, Sakurai Y, Salamanna G, Salamon A, Salazar Loyola JE, Salek D, Sales De Bruin PH, Salihagic D, Salnikov A, Salt J, Salvatore D, Salvatore F, Salvucci A, Salzburger A, Sammel D, Sampsonidis D, Sánchez J, Sanchez Martinez V, Sanchez Pineda A, Sandaker H, Sandbach RL, Sandhoff M, Sandoval C, Sankey DPC, Sannino M, Sansoni A, Santoni C, Santonico R, Santos H, Santoyo Castillo I, Sapp K, Sapronov A, Saraiva JG, Sarrazin B, Sasaki O, Sato K, Sauvan E, Savage G, Savard P, Savic N, Sawyer C, Sawyer L, Saxon J, Sbarra C, Sbrizzi A, Scanlon T, Scannicchio DA, Scarcella M, Scarfone V, Schaarschmidt J, Schacht P, Schachtner BM, Schaefer D, Schaefer L, Schaefer R, Schaeffer J, Schaepe S, Schaetzel S, Schäfer U, Schaffer AC, Schaile D, Schamberger RD, Scharf V, Schegelsky VA, Scheirich D, Schernau M, Schiavi C, Schier S, Schillo C, Schioppa M, Schlenker S, Schmidt-Sommerfeld KR, Schmieden K, Schmitt C, Schmitt S, Schmitz S, Schneider B, Schnoor U, Schoeffel L, Schoening A, Schoenrock BD, Schopf E, Schott M, Schouwenberg JFP, Schovancova J, Schramm S, Schreyer M, Schuh N, Schulte A, Schultens MJ, Schultz-Coulon HC, Schulz H, Schumacher M, Schumm BA, Schune P, Schwartzman A, Schwarz TA, Schweiger H, Schwemling P, Schwienhorst R, Schwindling J, Schwindt T, Sciolla G, Scuri F, Scutti F, Searcy J, Seema P, Seidel SC, Seiden A, Seifert F, Seixas JM, Sekhniaidze G, Sekhon K, Sekula SJ, Seliverstov DM, Semprini-Cesari N, Serfon C, Serin L, Serkin L, Sessa M, Seuster R, Severini H, Sfiligoj T, Sforza F, Sfyrla A, Shabalina E, Shaikh NW, Shan LY, Shang R, Shank JT, Shapiro M, Shatalov PB, Shaw K, Shaw SM, Shcherbakova A, Shehu CY, Sherwood P, Shi L, Shimizu S, Shimmin CO, Shimojima M, Shirabe S, Shiyakova M, Shmeleva A, Shoaleh Saadi D, Shochet MJ, Shojaii S, Shope DR, Shrestha S, Shulga E, Shupe MA, Sicho P, Sickles AM, Sidebo PE, Sideras Haddad E, Sidiropoulou O, Sidorov D, Sidoti A, Siegert F, Sijacki D, Silva J, Silverstein SB, Simak V, Simic L, Simion S, Simioni E, Simmons B, Simon D, Simon M, Sinervo P, Sinev NB, Sioli M, Siragusa G, Sivoklokov SY, Sjölin J, Skinner MB, Skottowe HP, Skubic P, Slater M, Slavicek T, Slawinska M, Sliwa K, Slovak R, Smakhtin V, Smart BH, Smestad L, Smiesko J, Smirnov SY, Smirnov Y, Smirnova LN, Smirnova O, Smith JW, Smith MNK, Smith RW, Smizanska M, Smolek K, Snesarev AA, Snyder IM, Snyder S, Sobie R, Socher F, Soffer A, Soh DA, Sokhrannyi G, Solans Sanchez CA, Solar M, Soldatov EY, Soldevila U, Solodkov AA, Soloshenko A, Solovyanov OV, Solovyev V, Sommer P, Son H, Song HY, Sood A, Sopczak A, Sopko V, Sorin V, Sosa D, Sotiropoulou CL, Soualah R, Soukharev AM, South D, Sowden BC, Spagnolo S, Spalla M, Spangenberg M, Spanò F, Sperlich D, Spettel F, Spieker TM, Spighi R, Spigo G, Spiller LA, Spousta M, St. Denis RD, Stabile A, Stamen R, Stamm S, Stanecka E, Stanek RW, Stanescu C, Stanescu-Bellu M, Stanitzki MM, Stapnes S, Starchenko EA, Stark GH, Stark J, Staroba P, Starovoitov P, Stärz S, Staszewski R, Steinberg P, Stelzer B, Stelzer HJ, Stelzer-Chilton O, Stenzel H, Stewart GA, Stillings JA, Stockton MC, Stoebe M, Stoicea G, Stolte P, Stonjek S, Stradling AR, Straessner A, Stramaglia ME, Strandberg J, Strandberg S, Strandlie A, Strauss M, Strizenec P, Ströhmer R, Strom DM, Stroynowski R, Strubig A, Stucci SA, Stugu B, Styles NA, Su D, Su J, Suchek S, Sugaya Y, Suk M, Sulin VV, Sultansoy S, Sumida T, Sun S, Sun X, Sundermann JE, Suruliz K, Suster CJE, Sutton MR, Suzuki S, Svatos M, Swiatlowski M, Swift SP, Sykora I, Sykora T, Ta D, Taccini C, Tackmann K, Taenzer J, Taffard A, Tafirout R, Taiblum N, Takai H, Takashima R, Takeshita T, Takubo Y, Talby M, Talyshev AA, Tan KG, Tanaka J, Tanaka M, Tanaka R, Tanaka S, Tanioka R, Tannenwald BB, Tapia Araya S, Tapprogge S, Tarem S, Tartarelli GF, Tas P, Tasevsky M, Tashiro T, Tassi E, Tavares Delgado A, Tayalati Y, Taylor AC, Taylor GN, Taylor PTE, Taylor W, Teischinger FA, Teixeira-Dias P, Temming KK, Temple D, Ten Kate H, Teng PK, Teoh JJ, Tepel F, Terada S, Terashi K, Terron J, Terzo S, Testa M, Teuscher RJ, Theveneaux-Pelzer T, Thomas JP, Thomas-Wilsker J, Thompson PD, Thompson AS, Thomsen LA, Thomson E, Tibbetts MJ, Ticse Torres RE, Tikhomirov VO, Tikhonov YA, Timoshenko S, Tipton P, Tisserant S, Todome K, Todorov T, Todorova-Nova S, Tojo J, Tokár S, Tokushuku K, Tolley E, Tomlinson L, Tomoto M, Tompkins L, Toms K, Tong B, Tornambe P, Torrence E, Torres H, Torró Pastor E, Toth J, Touchard F, Tovey DR, Trefzger T, Tricoli A, Trigger IM, Trincaz-Duvoid S, Tripiana MF, Trischuk W, Trocmé B, Trofymov A, Troncon C, Trottier-McDonald M, Trovatelli M, Truong L, Trzebinski M, Trzupek A, Tseng JCL, Tsiareshka PV, Tsipolitis G, Tsirintanis N, Tsiskaridze S, Tsiskaridze V, Tskhadadze EG, Tsui KM, Tsukerman II, Tsulaia V, Tsuno S, Tsybychev D, Tu Y, Tudorache A, Tudorache V, Tulbure TT, Tuna AN, Tupputi SA, Turchikhin S, Turgeman D, Turk Cakir I, Turra R, Tuts PM, Ucchielli G, Ueda I, Ughetto M, Ukegawa F, Unal G, Undrus A, Unel G, Ungaro FC, Unno Y, Unverdorben C, Urban J, Urquijo P, Urrejola P, Usai G, Usui J, Vacavant L, Vacek V, Vachon B, Valderanis C, Valdes Santurio E, Valencic N, Valentinetti S, Valero A, Valery L, Valkar S, Valls Ferrer JA, Van Den Wollenberg W, Van Der Deijl PC, van der Graaf H, van Eldik N, van Gemmeren P, Van Nieuwkoop J, van Vulpen I, van Woerden MC, Vanadia M, Vandelli W, Vanguri R, Vaniachine A, Vankov P, Vardanyan G, Vari R, Varnes EW, Varol T, Varouchas D, Vartapetian A, Varvell KE, Vasquez JG, Vasquez GA, Vazeille F, Vazquez Schroeder T, Veatch J, Veeraraghavan V, Veloce LM, Veloso F, Veneziano S, Ventura A, Venturi M, Venturi N, Venturini A, Vercesi V, Verducci M, Verkerke W, Vermeulen JC, Vest A, Vetterli MC, Viazlo O, Vichou I, Vickey T, Vickey Boeriu OE, Viehhauser GHA, Viel S, Vigani L, Villa M, Villaplana Perez M, Vilucchi E, Vincter MG, Vinogradov VB, Vittori C, Vivarelli I, Vlachos S, Vlasak M, Vogel M, Vokac P, Volpi G, Volpi M, von der Schmitt H, von Toerne E, Vorobel V, Vorobev K, Vos M, Voss R, Vossebeld JH, Vranjes N, Vranjes Milosavljevic M, Vrba V, Vreeswijk M, Vuillermet R, Vukotic I, Wagner P, Wagner W, Wahlberg H, Wahrmund S, Wakabayashi J, Walder J, Walker R, Walkowiak W, Wallangen V, Wang C, Wang C, Wang F, Wang H, Wang H, Wang J, Wang J, Wang K, Wang R, Wang SM, Wang T, Wang W, Wanotayaroj C, Warburton A, Ward CP, Wardrope DR, Washbrook A, Watkins PM, Watson AT, Watson MF, Watts G, Watts S, Waugh BM, Webb S, Weber MS, Weber SW, Weber SA, Webster JS, Weidberg AR, Weinert B, Weingarten J, Weiser C, Weits H, Wells PS, Wenaus T, Wengler T, Wenig S, Wermes N, Werner MD, Werner P, Wessels M, Wetter J, Whalen K, Whallon NL, Wharton AM, White A, White MJ, White R, Whiteson D, Wickens FJ, Wiedenmann W, Wielers M, Wiglesworth C, Wiik-Fuchs LAM, Wildauer A, Wilk F, Wilkens HG, Williams HH, Williams S, Willis C, Willocq S, Wilson JA, Wingerter-Seez I, Winklmeier F, Winston OJ, Winter BT, Wittgen M, Wolf TMH, Wolff R, Wolter MW, Wolters H, Worm SD, Wosiek BK, Wotschack J, Woudstra MJ, Wozniak KW, Wu M, Wu M, Wu SL, Wu X, Wu Y, Wyatt TR, Wynne BM, Xella S, Xi Z, Xu D, Xu L, Yabsley B, Yacoob S, Yamaguchi D, Yamaguchi Y, Yamamoto A, Yamamoto S, Yamanaka T, Yamauchi K, Yamazaki Y, Yan Z, Yang H, Yang H, Yang Y, Yang Z, Yao WM, Yap YC, Yasu Y, Yatsenko E, Yau Wong KH, Ye J, Ye S, Yeletskikh I, Yildirim E, Yorita K, Yoshida R, Yoshihara K, Young C, Young CJS, Youssef S, Yu DR, Yu J, Yu JM, Yu J, Yuan L, Yuen SPY, Yusuff I, Zabinski B, Zacharis G, Zaidan R, Zaitsev AM, Zakharchuk N, Zalieckas J, Zaman A, Zambito S, Zanello L, Zanzi D, Zeitnitz C, Zeman M, Zemla A, Zeng JC, Zeng Q, Zenin O, Ženiš T, Zerwas D, Zhang D, Zhang F, Zhang G, Zhang H, Zhang J, Zhang L, Zhang L, Zhang M, Zhang R, Zhang R, Zhang X, Zhang Z, Zhao X, Zhao Y, Zhao Z, Zhemchugov A, Zhong J, Zhou B, Zhou C, Zhou L, Zhou L, Zhou M, Zhou N, Zhu CG, Zhu H, Zhu J, Zhu Y, Zhuang X, Zhukov K, Zibell A, Zieminska D, Zimine NI, Zimmermann C, Zimmermann S, Zinonos Z, Zinser M, Ziolkowski M, Živković L, Zobernig G, Zoccoli A, zur Nedden M, Zwalinski L. Performance of the ATLAS trigger system in 2015

During 2015 the ATLAS experiment recorded [Formula: see text] of proton-proton collision data at a centre-of-mass energy of [Formula: see text]. The ATLAS trigger system is a crucial component of the experiment, responsible for selecting events of interest at a recording rate of approximately 1 kHz from up to 40 MHz of collisions. This paper presents a short overview of the changes to the trigger and data acquisition systems during the first long shutdown of the LHC and shows the performance of the trigger system and its components based on the 2015 proton-proton collision data.

5' upstream DNA sequence of the rat tyrosine hydroxylase gene directs high-level and tissue-specific expression to catecholaminergic neurons in the central nervous system of transgenic mice

Tyrosine hydroxylase (TH), the first and rate-limiting enzyme in the biosynthesis of catecholamine neurotransmitters, is expressed within central and peripheral catecholaminergic cells. To delineate DNA sequences necessary for tissue-specific expression of the rat TH gene, transgenic mice were produced containing 0.15 kb, 2.4 kb, and 9.0 kb of 5' flanking sequence fused to the E. coli lacZ (beta-galactosidase) reporter gene. The reporter gene expression in the transgenic animals was monitored by both X-gal histochemical staining and beta-galactosidase immunohistochemistry and compared to TH mRNA and protein expression. Transgenic mice bearing 9.0 kb, but not the smaller constructs with either 2.4 kb or 0.15 kb of 5' flanking sequence, fused to lacZ were able to direct high level expression of beta-galactosidase at levels equivalent to the endogenous TH in central catecholaminergic cells, and to a lesser degree to adrenal gland. Previously, 4.8 kb of 5' flanking region was reported to contain some tissue-specific element(s) determined by chloramphenicol acetyltransferase (CAT) assay using regional brain dissections and was not able to demonstrate cellular localization of the CAT expression [2]. Using histological procedures which allow for spatial resolution, this study demonstrated that the crucial catecholaminergic neuron-specific DNA element(s) resides between -9 kb and -2.4 kb of the 5' flanking region of the rat TH gene; this assertion is substantiated by the high-level of tissue-specific expression of lacZ in catecholaminergic cells.

Long non-coding RNA PVT1 is associated with tumor progression and predicts recurrence in hepatocellular carcinoma patients

PVT1, which maps to chromosome 8q24, is a copy number amplification-associated long non-coding RNA. Overexpression of PVT1 is a powerful predictor of tumor progression and patient survival in a diverse range of cancer types. However, the association between PVT1 and hepatocellular carcinoma (HCC) remains unclear. The aim of the present study was to examine the expression pattern of PVT1, and its clinical significance in HCC. Between 2003 and 2012, reverse transcription-quantitative polymerase chain reaction was used to determine the expression levels of PVT1 in two independent cohorts: Cohort one, 58 HCC resection samples; and cohort 2, 214 HCC transplant samples. Additionally, the correlation between PVT1 expression levels and clinical parameters and outcomes was analyzed. The relative expression levels of PVT1 were significantly higher in cancerous tissues compared with the corresponding non-cancerous tissues (cohort one, P=0.0016; cohort two, P=0.0274). Furthermore, overexpression of PVT1 was associated with a higher serum α-fetoprotein expression level (P=0.011) and a higher recurrence rate (P=0.004). Kaplan-Meier analysis indicated that the patients with high PVT1 expression exhibited poor recurrence-free survival (P=0.021), and multivariate analysis demonstrated that high levels of PVT1 expression are an independent predictor for HCC recurrence (P=0.042; hazard ratio, 1.653). Thus, the high expression levels of PVT1 in HCC may serve as a novel biomarker for predicting tumor recurrence in HCC patients, and as a potential therapeutic target.

Expression and regulation of gonadotropin-releasing hormone (GnRH) and GnRH receptor messenger ribonucleic acids in human granulosa-luteal cells

The present study investigated the expression and regulation of GnRH and GnRH receptor (GnRHR) messenger RNAs (mRNAs) in human granulosa-luteal cells using reverse transcription-polymerase chain reaction (RT-PCR). Granulosa-luteal cells were aspirated from preovulatory follicles obtained from women undergoing in vitro fertilization. Two sets of primers derived from human hypothalamic GnRHR complementary DNA (cDNA) were used to amplify cDNAs from granulosa-luteal cells. PCR products corresponding to the expected sizes of GnRH were obtained from granulosa-luteal cells as well as the brain, but not from skeletal muscle cDNA. The authenticity of the PCR products was confirmed by Southern blot hybridization with internal oligonucleotide probes and by subsequent cloning and sequencing. Similarly, using four sets of primers specific for the human pituitary GnRHR cDNA, PCR products with the expected sizes were detected from both brain and granulosa-luteal cells, but not from skeletal muscle. PCR products were subsequently confirmed by Southern blot hybridization using an internal oligonucleotide probe or a cDNA probe which was obtained from screening a human pituitary cDNA library. Cloning and sequencing of the PCR product in the 3'-untranslated region revealed identical sequence with the reported human pituitary GnRHR cDNA sequence. RNA samples obtained from cells immediately after dissociation or after 2, 5, and 8 days of culture were analyzed by RT-PCR, and in all cases, both GnRH and GnRHR mRNA were detected. To investigate how gene expression of GnRH and GnRHR is regulated, we examined the effect of GnRH and hCG on GnRH and GnRHR mRNA levels in cultured human granulosa-luteal cells. Treatment with different concentrations of GnRH induced biphasic responses. Both GnRH and GnRHR mRNA were significantly increased by 1 nM, but slightly decreased by 1 microM GnRH; 1 nM GnRH also significantly inhibited progesterone production, whereas higher doses had no effect. Treatment with hCG (1 IU/ml) decreased GnRHR mRNA levels without altering the expression of the GnRH gene. These results demonstrate for the first time that 1) both GnRH and GnRHR mRNAs are expressed in human granulosa-luteal cells; 2) GnRH mRNA levels are autoregulated by GnRH; and 3) GnRHR gene expression is up-regulated by GnRH, but down-regulated by hCG. These findings provide strong evidence that GnRH is an autocrine regulator in the human ovary.

High-level expression and purification of secreted forms of herpes simplex virus type 1 glycoprotein gD synthesized by baculovirus-infected insect cells

Two forms of herpes simplex virus glycoprotein gD were recombined into Autographa californica nuclear polyhedrosis virus (baculovirus) and expressed in infected Spodoptera frugiperda (Sf9) cells. Each protein was truncated at residue 306 of mature gD. One form, gD-1(306t), contains the coding sequence of Patton strain herpes simplex virus type 1 gD; the other, gD-1(QAAt), contains three mutations which eliminate all signals for addition of N-linked oligosaccharides. Prior to recombination, each gene was cloned into the baculovirus transfer vector pVT-Bac, which permits insertion of the gene minus its natural signal peptide in frame with the signal peptide of honeybee melittin. As in the case with many other baculovirus transfer vectors, pVT-Bac also contains the promoter for the baculovirus polyhedrin gene and flanking sequences to permit recombination into the polyhedrin site of baculovirus. Each gD gene was engineered to contain codons for five additional histidine residues following histidine at residue 306, to facilitate purification of the secreted protein on nickel-containing resins. Both forms of gD-1 were abundantly expressed and secreted from infected Sf9 cells, reaching a maximum at 96 h postinfection for gD-1(306t) and 72 h postinfection for gD-1(QAAt). Secretion of the latter protein was less efficient than gD-1(306t), possibly because of the absence of N-linked oligosaccharides from gD-1(QAAt). Purification of the two proteins by a combination of immunoaffinity chromatography, nickel-agarose chromatography, and gel filtration yielded products that were > 99% pure, with excellent recovery. We are able to obtain 20 mg of purified gD-1(306t) and 1 to 5 mg of purified gD-1(QAAt) per liter of infected insect cells grown in suspension. Both proteins reacted with monoclonal antibodies to discontinuous epitopes, indicating that they retain native structure. Use of this system for gD expression makes crystallization trials feasible.

Examination of the kinetics of herpes simplex virus glycoprotein D binding to the herpesvirus entry mediator, using surface plasmon resonance

Previously, we showed that truncated soluble forms of herpes simplex virus (HSV) glycoprotein D (gDt) bound directly to a truncated soluble form of the herpesvirus entry mediator (HveAt, formerly HVEMt), a cellular receptor for HSV. The purpose of the present study was to determine the affinity of gDt for HveAt by surface plasmon resonance and to compare and contrast the kinetics of an expanded panel of gDt variants in binding to HveAt in an effort to better understand the mechanism of receptor binding and virus entry. Both HveAt and gDt are dimers in solution and interact with a 2:1 stoichiometry. With HveAt, gD1(306t) (from the KOS strain of HSV-1) had a dissociation constant (KD) of 3.2 x 10(-6) M and gD2(306t) had a KD of 1.5 x 10(-6) M. The interaction between gDt and HveAt fits a 1:1 Langmuir binding model, i.e., two dimers of HveAt may act as one binding unit to interact with one dimer of gDt as the second binding unit. A gD variant lacking all signals for N-linked oligosaccharides had an affinity for HveAt similar to that of gD1(306t). A variant lacking the bond from cysteine 1 to cysteine 5 had an affinity for HveAt that did not differ from that of the wild type. However, variants with double cysteine mutations that eliminated either of the other two disulfide bonds showed decreased affinity for HveAt. This result suggests that two of the three disulfide bonds of gD are important for receptor binding. Four nonfunctional gDt variants, each representing one functional domain of gD, were also studied. Mutations in functional regions I and II drastically decreased the affinity of gDt for HveAt. Surprisingly, a variant with an insertion in functional region III had a wild-type level of affinity for HveAt, suggesting that this domain may function in virus entry at a step other than receptor binding. A variant with a deletion in functional region IV [gD1(Delta290-299t)] exhibited a 100-fold enhancement in affinity for HveAt (KD = 3.3 x 10(-8) M) due mainly to a 40-fold increase in its kinetic on rate. This agrees with the results of other studies showing the enhanced ability of gD1(Delta290-299t) to block infection. Interestingly, all the variants with decreased affinities for HveAt exhibited decreased kinetic on rates but only minor changes in their kinetic off rates. The results suggest that once the complex between gDt and HveAt forms, its stability is unaffected by a variety of changes in gD.

Activin, inhibin, and follistatin in zebrafish ovary: expression and role in oocyte maturation

Activins, inhibins, and follistatins are important regulators of mammalian reproduction. However, their roles in lower vertebrates are poorly understood. In this study, we examined the expression of activin A, inhibin A, and follistatins in the zebrafish ovary and determined their role in final oocyte maturation. Using reverse transcription-polymerase chain reaction with primers specific for activin/inhibin beta(A) subunit and for follistatins, we detected DNA fragments of the expected size, which, upon sequencing, conformed to activin/inhibin beta(A) and follistatin. Western blot analysis using an antibody against activin/inhibin beta(A) subunit revealed two bands with sizes similar to those of activin A and inhibin A. The expression of follistatins was also confirmed by Western blot analysis. These results suggest that activin A, an inhibin A-like molecule, and follistatins are expressed in the zebrafish ovary. In cultured zebrafish follicles, activin A and inhibin A both induced final oocyte maturation in a dose-dependent manner. The effects of activin A and inhibin A were blocked by their binding protein, follistatin-288. Interestingly, follistatin-288 also inhibited final oocyte maturation induced by gonadotropin and by maturation-inducing hormone (MIH), suggesting that activin A and/or inhibin A may be local regulators mediating gonadotropin- and MIH-induced final oocyte maturation. Taken together, these findings suggest that activin A and inhibin A are paracrine regulators of ovarian functions in fish.

Roles of NLRP3 inflammasome in intervertebral disc degeneration

Intervertebral disc degeneration (IVDD) is one of the leading causes of low back pain and one of the most common health problems in the world. The nucleotide-binding oligomerization domain-like receptor family pyrin domain-containing-3 (NLRP3) inflammasome, as a pattern recognition receptor, has been shown to be associated with the pathological processes of many diseases in recent years. With the exploration of the mechanism of IVDD, recent studies have shown that activation of the NLRP3 inflammasome is associated with intervertebral disc (IVD) inflammation, pyroptosis, extracellular matrix degradation and apoptosis of IVD cells. In this review, we summarize the structural characteristics of NLRP3 inflammasome and the activation signalling mechanisms. We also describe the role of the NLRP3 inflammasome in the pathological process of IVDD and the application of the targeting the NLRP3 inflammasome in IVDD treatment.