Cell cycle and aging, morphogenesis, and response to stimuli genes are individualized biomarkers of glioblastoma progression and survival

Background

Glioblastoma is a complex multifactorial disorder that has swift and devastating consequences. Few genes have been consistently identified as prognostic biomarkers of glioblastoma survival. The goal of this study was to identify general and clinical-dependent biomarker genes and biological processes of three complementary events: lifetime, overall and progression-free glioblastoma survival.

Methods

A novel analytical strategy was developed to identify general associations between the biomarkers and glioblastoma, and associations that depend on cohort groups, such as race, gender, and therapy. Gene network inference, cross-validation and functional analyses further supported the identified biomarkers.

Results

A total of 61, 47 and 60 gene expression profiles were significantly associated with lifetime, overall, and progression-free survival, respectively. The vast majority of these genes have been previously reported to be associated with glioblastoma (35, 24, and 35 genes, respectively) or with other cancers (10, 19, and 15 genes, respectively) and the rest (16, 4, and 10 genes, respectively) are novel associations. Pik3r1, E2f3, Akr1c3, Csf1, Jag2, Plcg1, Rpl37a, Sod2, Topors, Hras, Mdm2, Camk2g, Fstl1, Il13ra1, Mtap and Tp53 were associated with multiple survival events. Most genes (from 90 to 96%) were associated with survival in a general or cohort-independent manner and thus the same trend is observed across all clinical levels studied. The most extreme associations between profiles and survival were observed for Syne1, Pdcd4, Ighg1, Tgfa, Pla2g7, and Paics. Several genes were found to have a cohort-dependent association with survival and these associations are the basis for individualized prognostic and gene-based therapies. C2, Egfr, Prkcb, Igf2bp3, and Gdf10 had gender-dependent associations; Sox10, Rps20, Rab31, and Vav3 had race-dependent associations; Chi3l1, Prkcb, Polr2d, and Apool had therapy-dependent associations. Biological processes associated glioblastoma survival included morphogenesis, cell cycle, aging, response to stimuli, and programmed cell death.

Conclusions

Known biomarkers of glioblastoma survival were confirmed, and new general and clinical-dependent gene profiles were uncovered. The comparison of biomarkers across glioblastoma phases and functional analyses offered insights into the role of genes. These findings support the development of more accurate and personalized prognostic tools and gene-based therapies that improve the survival and quality of life of individuals afflicted by glioblastoma multiforme.     

Using quantum dots to visualize clathrin associations

Our current understanding of clathrin-mediated endocytosis proposes that the process is initiated at a specialized anatomical structure called a coated pit. Electron microscopy has been required for elucidation of the morphology of coated pits and the vesicles produced therein, and the presence of a bristle coat has been taken as suggestive of clathrin surrounding these vesicles. More recently, immunocytochemical methods have confirmed that endocytic vesicles are surrounded by clathrin and its adaptor proteins, but there is a need to identify precisely and to follow the fate of the cellular organelles seen by fluorescence microscopy. We used quantum immune-electron microscopy to localize clathrin in a human adrenal cortical cell line (SW-13). Clathrin was shown to associate with a variety of vesicle types including the classic clathrin-coated vesicles and pits used in receptor internalization, pentilaminar annular gap junction vesicles, and multivesicular bodies. The images obtained with quantum dot technology allow accurate and specific localization of clathrin and the clathrin adaptor protein, AP-2, with cellular organelles and suggest that some of the structures classified as typical coated vesicles by immunocytochemical light microscopic techniques actually may be membrane bound pits.     

The karyotype of Axarus festivus (Say) and a comparison with species of Lipiniella (Chironomidae: Diptera)

Larvae of Axarus andLipiniella share several apparantly apomorphic features of the mouth-part structure, however adults ofLipiniella show possible relationships toDemeijerea andChironomus. In order to assist in refining the relationships ofAxarus toLipiniella the karyotype ofAxarus festivus was determined and compared to the karyotypes ofLipiniella arenicola andL. moderata. Larvae ofA. festivus from a population in Kansas were monomorphous, with 2n=8, the Ist, IInd and IIIrd chromosomes metacentric, and IVth acrocentric.Axarus festivus therefore differs fromL. arenicola in chromosome number (2n=6), however homologous sections of all chromosomes were identified. Inversions were detected in the Ist, IInd and IIIrd chromosomes ofA. festivus relative toL. arenicola. It was determined that both species have high functional activity, as indicated by the presence of three Balbiani rings, and more than one nucleolus per genome. Differing degrees of polyteny, a feature previously described forL. arenicola, were observed in the salivary glands, with highest degrees of polyteny in cells near the salivary duct. These similarities of chromosome structure indicate close genetic relationships betweenA. festivus andL. arenicola. However, we did not find evidence for similarity ofA. festivus toL. moderata, which supports the previous conclusions byKiknadze et al. (1989) regardingL. arenicola andL. moderata.     

Gel filtration of bacterial cell extract

Так как от остатков гомогенизированных клеток легко отделить растительные вирусы (Steere и Qckers, 1962; ?ech, 1962) и митохондрии (Hjertén, 1962), мы сделали попытку использовать этот простой метод и для отделения рибосом. Надосадок гомогената растущих клеток Bacillus megaterium 110 наносили на столбец 3% гранулированного агара (Polson, 1961) и промывали 66 мл буферного раствора Tris (pH 7,72, 0,005 M с 0,01 M?MgCl₂) в течение часа при комнатной температуре. В элюате определяли абсорбцию при 260 мμ и белки (рис. 1). При ультрацентрифугировании образца были обнаружены рибосомы с S ₂₀ ⁰ 107, 71, 5, 45 и 30S (рис. 2). Ультрацентрифугированием фракции № 10 были с помощью адсорбции в УФ лучах найдены рибосомы с s ₂₀ ⁰ 107 и 44,6S (рис. 3). Группа 100S перекрывалась абсорбцией рибосом 70S, группа 30 не была обнаружена. Отделение рибосом как самостоятельной вершины не было получено. Однако, судя по соотношению нуклеиновых кислот и белков во главе вымываемой плазмы (где присутствует только РНК), здесь имела место концентрация практически чистых рибосом, как подтверждает и седиментация. ДНК удавалось определить только во фракциях второй половины элюата плазмы (рис. 4).     

Sequence variation in the guillemot (Alcidae: Cepphus) mitochondrial control region and its nuclear homolog

We describe sequence variation in the mitochondrial control region and its nuclear homolog in three species and seven subspecies of guillemots (Cepphus spp.). Nuclear homologs of the 5' end of the control region were found in all individuals. Nuclear sequences were approximately 50% divergent from their mitochondrial counterparts and formed a distinct phylogenetic clade; the mitochondrial-nuclear introgression event must have predated the radiation of Cepphus. As in other vertebrates, the guillemot control region has a relatively conserved central block flanked by hypervariable 5' and 3' ends. Mean pairwise interspecific divergence values among control regions were lower than those in other birds. All individuals were heteroplasmic for the number of simple tandem nucleotide repeats (A(n)C) at the 3' end of the control region. Phylogenetic analyses suggest that black guillemots are basal to pigeon and spectacled guillemots, but evolutionary relationships among subspecies remain unresolved, possibly due to incomplete lineage sorting. Describing molecular variation in nuclear homologs of mitochondrial genes is of general interest in phylogenetics because, if undetected, the homologs may confound interpretations of mitochondrial phylogenies.      

Implications from predictions of HLA-DRB1 binding peptides in the membrane proteins of Corynebacterium diphtheriae

The aerobic gram positive bacterium Corynebacterium diphtheriae causes diphtheria, a respiratory tract illness characterized by symptoms such as sore throat, low fever, and an adherent membrane on the tonsils, pharynx, and/or nasal cavity. Therefore, it is important to develop preventive vaccines for diphtheria. The availability of the 2,488,635 bp long complete sequence for the C. diphtheriae genome provides an opportunity to understand cell mediated immune response using Computational Biology tools from the bacterial proteome sequence data. We selected 355 membrane proteins from the C. diphtheriae proteome using annotation data to identify potential HLA-DRB1 binding short peptide using modeling, simulations and predictions. This exercise identified 30 short peptides in membrane proteins showing binding capability to HLA-DRB1 alleles. These peptides serve as outline for the understanding of cell mediated immune response to C. diphtheriae. It should be noted that the predicted data to be verified using binding assays for further consideration.