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Expression and differential expression analysis of astrocytoma patient samples (WHO grades I and III) and primary glioblastoma (WHO grade IV)

ABSTRACT: Expression and differential expression analysis of astrocytoma patient samples (WHO grades I and III) and primary glioblastoma (WHO grade IV). Expression and differential expression was assessed by using an Agilent custom microarray (244K). The custom array contains probes for genomic regions that have been found to be differentially expressed (i) throughout cell cycle progression, (ii) in response to the anti-proliferative and pro-apoptotic p53 pathway, and (iii) the anti-apoptotic and pro-proliferative STAT-3 pathway by employing TAS (Kampa et al. "Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22". Genome Research, 14:331-42, 2004). In addition, the Agilent custom array (244K) interrogates probes for genomic regions predicted to contain a conserved secondary structure identified by RNAz (Washietl et al. "Fast and reliable prediction of noncoding RNAs." Proc Natl Acad Sci USA. 102:2454-9, 2005.) or Evofold (Pedersen et al. "Identification and classification of conserved RNA secondary structures in the human genome." PLoS Comput Biol. 2:e33, 2006.), as well as known non-coding RNAs from public databases, and the Agilent mRNA probe set 014850. We analyzed four arrays each for astrocytoma patient samples of grade I, grade III and grade IV.

ORGANISM(S): Homo sapiens

SUBMITTER: Reiche Kristin

PROVIDER: S-ECPF-GEOD-43911 | biostudies-other |

REPOSITORIES: biostudies-other

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Project description:Expression and differential expression analysis of breast cancer patient samples and normal samples from breast reduction operations. Fresh frozen tumor biopsies from early breast cancer cases were collected from 920 patients included in the Oslo Micrometastasis (MicMa) Study -- Oslo I from various hospitals between 1995 and 1998 (Naume et al. "Presence of bone marrow micrometastasis is associated with different recurrence risk within molecular subtypes of breast cancer." Mol Oncol 2007, 1: 160-171; Wiedswang et al. "Detection of isolated tumor cells in bone marrow is an independent prognostic factor in breast cancer." J Clin Oncol 2003, 21: 3469-3478.). Breast tissue samples from breast reduction operations were provided from the Colosseum Clinic, Oslo in co-operation with Akershus University Hospital, Lørenskog and are referred to as normal tissue. Expression and differential expression was assessed by using an Agilent custom microarray (244K, nONCOchip). The custom array contains probes for genomic regions that have been found to be differentially expressed (i) throughout cell cycle progression, (ii) in response to the anti-proliferative and pro-apoptotic p53 pathway, and (iii) the anti-apoptotic and pro-proliferative STAT-3 pathway by employing TAS (Kampa et al. "Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22". Genome Research, 14:331-42, 2004). In addition, the Agilent custom array (244K) interrogates probes for genomic regions predicted to contain a conserved secondary structure identified by RNAz (Washietl et al. "Fast and reliable prediction of noncoding RNAs." Proc Natl Acad Sci USA. 102:2454-9, 2005.) or Evofold (Pedersen et al. "Identification and classification of conserved RNA secondary structures in the human genome." PLoS Comput Biol. 2:e33, 2006.), as well as known non-coding RNAs from public databases, and the Agilent mRNA probe set 014850. We analyzed 5 to 6 arrays each for breast cancer patient samples and normal samples.

Project description:IntroductionHypertensive retinopathy describes a spectrum of retinal changes in patients with elevated blood pressure (BP). It is unknown why some patients are more likely to develop acute ocular end-organ damage than others with similar BP. We examined risk factors for grade III/IV hypertensive retinopathy among patients with hypertensive urgency in the emergency department (ED) and compared healthcare utilization and mortality between patients with and without grade III/IV hypertensive retinopathy.MethodsA preplanned subanalysis of patients who presented to a university hospital ED with diastolic BP ? 120 mmHg and who enrolled in the Fundus Photography versus Ophthalmoscopy Trial Outcomes in the ED study was performed. Bilateral nonmydriatic ocular fundus photographs, vital signs, and demographics were obtained at presentation. Past medical history, laboratory values, healthcare utilization, and mortality were ascertained from medical record review at least 8 months after initial ED visit.ResultsTwenty-one patients with diastolic BP ? 120 mmHg, 7 of whom (33%) had grade III/IV hypertensive retinopathy, were included. Patients with retinopathy were significantly younger than those without (median 33 vs 50 years, P= 0.02). Mean arterial pressure (165 vs 163 mmHg) was essentially equal in the 2 groups. Patients with retinopathy had substantially increased but nonsignificant rates of ED revisit (57% vs 29%, P = 0.35) and hospital admission after ED discharge (43% vs 14%, P = 0.28). One of the patients with retinopathy died, but none without.ConclusionYounger patients may be at higher risk for grade III/IV hypertensive retinopathy among patients with hypertensive urgency. Chronic compensatory mechanisms may have not yet developed in these younger patients. Alternatively, older patients with retinopathy may be underrepresented secondary to increased mortality among these patients at a younger age (survivorship bias). Further research is needed to validate these preliminary findings.

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Expression and differential expression analysis of astrocytoma patient samples (WHO grades I and III) and primary glioblastoma (WHO grade IV)

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