A gene expression profile for non-smoking and non-drinking patients with head and neck cancer

Oral Diseases (2012) 18 , 178–183 Objective: A small subset of patients with head and neck squamous cell carcinoma are non‐smoking and non‐drinking and have distinct clinical characteristics. We aimed to identify a possible different genetic profile for these patients when compared with their smoking and drinking counterparts. Materials and Methods: The gene expression data previously detected from primary tumors located in the oral cavity and oropharynx, using DNA microarray was analyzed for their differential expression between non‐smoking and non‐drinking patients (n = 15) and smoking and drinking patients (n = 89). Student’s T‐test (P < 0.05) and 10‐fold cross‐validation procedure (100 times repeated) were performed to determine differentially expressed genes. Results: Non‐smoking and non‐drinking patients were older, mostly female and had oral cavity‐localized tumors, whereas smoking and drinking patients were younger male patients with 81% oral cavity and 19% oropharynx tumors. A set of 49 differentially expressed genes were detected. Among others, seven genes related to interferon‐γ were upregulated and two genes linked to NFKB pathway were downregulated. Conclusions: Differentially expressed genes in non‐smoking and non‐drinking patients possibly indicate the presence of a different cellular response to carcinogenic events in these patients. Further studies are warranted to validate this gene set and explore possible therapeutic implications to improve prognosis for these patients.     

Regulation of immune-modulatory genes in left superior temporal cortex of schizophrenia patients: a genome-wide microarray study

Abstract

Objectives. The role of neuroinflammation in schizophrenia has been an issue for long time. There are reports supporting the hypothesis of ongoing inflammation and others denying it. This may be partly ascribed to the origin of the materials (CSF, blood, brain tissue) or to the genes selected for the respective studies. Moreover, in some locations, inflammatory genes may be up-regulated, others may be down-regulated. Methods. Genome-wide microarrays have been used for expression profiling in post-mortem brains of schizophrenia patients. Array data have been analyzed by gene set enrichment analysis (GSEA) and further confirmed with selected genes by real-time PCR. Results. In Brodman Area 22 of left superior temporal cortex, at least 70 genes (19%) out of 369 down-regulated genes (P < 0.05) belonged to the immune system. 23 from those 70 genes were randomly selected for real-time PCR. Six reached significance level at P < 0.05. Conclusions. The present data support a brain-specific view of the role immune-modulatory genes may play in the left superior temporal cortex in schizophrenia, because immune functions in the patients are not disturbed. In keeping with comparable, previous studies supporting the notion that schizophrenia is a disease of the synapse, we hypothesize that dysregulation of immune-related genes modifies synaptic functions and stability in this region.     

The psychological impact of cryptic chromosomal abnormalities diagnosis announcement

This qualitative study aims to describe the psychological impact of the diagnosis announcement of pathogenic Copy Number Variations (pCNVs). We performed semi-structured interviews of 60 parents of 41 affected children and 5 geneticists who announced the diagnoses. The diagnosis of the best characterized microdeletion syndromes, often defined by patronymic names (e.g. Williams syndrome), is generally made on a clinical basis by geneticists and confirmed by fluorescence in situ hybridization analysis. Chromosomal microarray, on the contrary, can allow the disclosure of rare pCNVs named after cytogenetic formulas, with poorly known clinical consequences: this makes doctors feel less confident with these diagnosis announcements. The disclosure of pCNVs named after cytogenetic formulas does not facilitate the parental mental representation of the disease, leading some parents to call into question the genotype-phenotype correlation or the very notion of a diagnosis. The announcement of inherited pCNVs can increase the feeling of parental guilt; the disclosure of de novo pCNVs can induce a feeling of “breakage” in the mental representation of the parent-child vertical transmission. In conclusion, our study shows that the disclosure of pCNVs has a significant psychological impact: a multidisciplinary approach to the diagnosis announcement, including a psychological support, should be systematically warranted.     

Profiling of differentially expressed genes in haemophilia A with inhibitor

Inhibitor development is the most significant complication in the therapy of haemophilia A (HA) patients. In spite of many studies, not much is known regarding the mechanism underlying inhibitor development. To understand the mechanism, we analysed profiles of differentially expressed genes (DEGs) between inhibitor and non-inhibitor HA via a microarray technique. Twenty unrelated Korean HAs were studied: 11 were non-inhibitor and nine were HA with inhibitor (≥5 BU mL(-1)). Microarray analysis was conducted using a Human Ref-8 expression Beadchip system (Illumina) and the data were analysed using Beadstudio software. We identified 545 DEGs in inhibitor HA as compared with the non-inhibitor patients; 384 genes were up-regulated and 161 genes were down-regulated. Among them, 75 genes whose expressions were altered by at least two-fold (>+2 or <-2) were selected and classified via the PANTHER classification method. The expressions of signal transduction and immunity-related genes differed significantly in the two groups. For validation of the DEGs, semi-quantitative RT-PCR (semi-qRT-PCR) was conducted with the six selected DEGs. The results corresponded to the microarray data, with the exception of one gene. We also examined the expression of the genes associated with the antigen presentation process via real-time PCR. The average levels of IL10, CTLA4 and TNFα slightly reduced, whereas that of IFNγ increased in the inhibitor HA group. We are currently unable to explain whether this phenomenon is a function of the inhibitor-inducing factor or is an epiphenomenon of antibody production. Nevertheless, our results provide a possible explanation for inhibitor development.     

利用凝集素芯片检测多囊肾病特异iPS细胞表面糖谱的研究

目的:建立一套凝集素芯片检测活体iPS细胞表面糖谱的方法。方法:以ADPKD-iPS为对象,运用不同活细胞染料,尝试不同的染色时间,找到最佳的iPS细胞与凝集素芯片结合的实验方案。结果:利用SYBR green,染色30min可以获得最佳的信号强度和信噪比。结论:已成功建立了一套利用凝集素芯片对活体iPS细胞进行表面糖谱检测的方法。     

The effect of cyclic mechanical strain on the expression of adhesion-related genes by periodontal ligament cells in two-dimensional culture

Saminathan A, Vinoth KJ, Wescott DC, Pinkerton MN, Milne TJ, Cao T, Meikle MC. The effect of cyclic mechanical strain on the expression of adhesion‐related genes by periodontal ligament cells in two‐dimensional culture. J Periodont Res 2012; 47: 212–221. © 2011 John Wiley & Sons A/S Background and Objective: Cell adhesion plays important roles in maintaining the structural integrity of connective tissues and sensing changes in the biomechanical environment of cells. The objective of the present investigation was to extend our understanding of the effect of cyclic mechanical strain on the expression of adhesion‐related genes by human periodontal ligament cells. Material and Methods: Cultured periodontal ligament cells were subjected to a cyclic in‐plane tensile deformation of 12% for 5 s (0.2 Hz) every 90 s for 6–24 h in a Flexercell FX‐4000 Strain Unit. The following parameters were measured: (i) cell viability by the MTT assay; (ii) caspase‐3 and ‐7 activity; and (iii) the expression of 84 genes encoding adhesion‐related molecules using real‐time RT‐PCR microarrays. Results: Mechanical stress reduced the metabolic activity of deformed cells at 6 h, and caspase‐3 and ‐7 activity at 6 and 12 h. Seventy‐three genes were detected at critical threshold values < 35. Fifteen showed a significant change in relative expression: five cell adhesion molecules (ICAM1, ITGA3, ITGA6, ITGA8 and NCAM1), three collagen α‐chains (COL6A1, COL8A1 and COL11A1), four MMPs (ADAMTS1, MMP8, MMP11 and MMP15), plus CTGF, SPP1 and VTN. Four genes were upregulated (ADAMTS1, CTGF, ICAM1 and SPP1) and 11 downregulated, with the range extending from a 1.76‐fold induction of SPP1 at 12 h to a 2.49‐fold downregulation of COL11A1 at 24 h. Conclusion: The study has identified several mechanoresponsive adhesion‐related genes, and shown that onset of mechanical stress was followed by a transient reduction in overall cellular activity, including the expression of two apoptosis ‘executioner’ caspases.