Molecular biomarkers in non-small-cell lung cancer : a retrospective analysis of data from the phase 3 FLEX study

Background: Findings from the phase 3 FLEX study showed that the addition of cetuximab to cisplatin and vinorelbine significantly improved overall survival, compared with cisplatin and vinorelbine alone, in the first-line treatment of EGFR-expressing, advanced non-small-cell lung cancer (NSCLC). We investigated whether candidate biomarkers were predictive for the efficacy of chemotherapy plus cetuximab in this setting. Methods: Genomic DNA extracted from formalin-fixed paraffin-embedded (FFPE) tumour tissue of patients enrolled in the FLEX study was screened for KRAS codon 12 and 13 and EGFR kinase domain mutations with PCR-based assays. In FFPE tissue sections, EGFR copy number was assessed by dual-colour fluorescence in-situ hybridisation and PTEN expression by immunohistochemistry. Treatment outcome was investigated according to biomarker status in all available samples from patients in the intention-to-treat population. The primary endpoint in the FLEX study was overall survival. The FLEX study, which is ongoing but not recruiting participants, is registered with ClinicalTrials.gov, number NCT00148798. Findings: KRAS mutations were detected in 75 of 395 (19%) tumours and activating EGFR mutations in 64 of 436 (15%). EGFR copy number was scored as increased in 102 of 279 (37%) tumours and PTEN expression as negative in 107 of 303 (35%). Comparisons of treatment outcome between the two groups (chemotherapy plus cetuximab vs chemotherapy alone) according to biomarker status provided no indication that these biomarkers were of predictive value. Activating EGFR mutations were identified as indicators of good prognosis, with patients in both treatment groups whose tumours carried such mutations having improved survival compared with those whose tumours did not (chemotherapy plus cetuximab: median 17·5 months [95% CI 11·7-23·4] vs 8·5 months [7·1-10·8], hazard ratio [HR] 0·52 [0·32-0·84], p=0·0063; chemotherapy alone: 23·8 months [15·2-not reached] vs 10·0 months [8·7-11·0], HR 0·35 [0·21-0·59], p<0·0001). Expression of PTEN seemed to be a potential indicator of good prognosis, with patients whose tumours expressed PTEN having improved survival compared with those whose tumours did not, although this finding was not significant (chemotherapy plus cetuximab: median 11·4 months [8·6-13·6] vs 6·8 months [5·9-12·7], HR 0·80 [0·55-1·16], p=0·24; chemotherapy alone: 11·0 months [9·2-12·6] vs 9·3 months [7·6-11·9], HR 0·77 [0·54-1·10], p=0·16). Interpretation: The efficacy of chemotherapy plus cetuximab in the first-line treatment of advanced NSCLC seems to be independent of each of the biomarkers assessed. Funding: Merck KGaA. © 2011 Elsevier Ltd.

Genome stability pathways in head and neck cancers

Genomic instability underlies the transformation of host cells toward malignancy, promotes development of invasion and metastasis and shapes the response of established cancer to treatment. In this review, we discuss recent advances in our understanding of genomic stability in squamous cell carcinoma of the head and neck (HNSCC), with an emphasis on DNA repair pathways. HNSCC is characterized by distinct profiles in genome stability between similarly staged cancers that are reflected in risk, treatment response and outcomes. Defective DNA repair generates chromosomal derangement that can cause subsequent alterations in gene expression, and is a hallmark of progression toward carcinoma. Variable functionality of an increasing spectrum of repair gene polymorphisms is associated with increased cancer risk, while aetiological factors such as human papillomavirus, tobacco and alcohol induce significantly different behaviour in induced malignancy, underpinned by differences in genomic stability. Targeted inhibition of signalling receptors has proven to be a clinically-validated therapy, and protein expression of other DNA repair and signalling molecules associated with cancer behaviour could potentially provide a more refined clinical model for prognosis and treatment prediction. Development and expansion of current genomic stability models is furthering our understanding of HNSCC pathophysiology and uncovering new, promising treatment strategies. © 2013 Glenn Jenkins et al.

Illness behaviour of patients with chronic fatigue syndrome

The study examines the illness behaviour of patients with Chronic Fatigue Syndrome (CFS). The Illness Behaviour Questionnaire (IBQ) the twenty-eight version of the General Health Questionnaire (GBQ-28), and the Beck Depression Inventory (BDI) were administered to forty patients with a diagnosis of CFS. The results revealed that CFS patients in comparison with general practice patients, scored significantly higher on the IBQ sub-scales of General Hypochonriasis, t(188) = 5.2, p < 0.001 and Disease Conviction, t(188) = 13.28, p < 0.001 but lower on the Psychological/Somatic sub-scale, t(188) = -5.88, p < 0.001. The CFS and psychiatric patients did not differ significantly on the general hypochondriasis sub-scale. Results of the GHQ-28 revealed 66.7% of the CFS patients scored above the cut-off for psychiatric morbidity. In comparison to a previous study of CFS patients [1], the current findings indicate a significantly higher score on general hypochondriasis. The implications of these findings are discussed.

Psychological maladjustment among homeless adolescents

The prevalence of psychological maladjustment in homeless adolescents (n = 54) was compared to control group (n 58) in Brisbane, Australia using the Youth Self-Report Scale [1]. Overall, 74% of the homeless group and 22.4% of the control group scored within the clinical range on one or more of the clinical subscales. There was considerable diversity of symptomatology in the homeless group. Less than half of the homeless group were within the clinical range on both the delinquent subscale and the thought disorder subscale. Depressive, Aggressive and Somatic Complaints were also prevalent. The study challenges preconceived notions of simple relationship between adolescent homelessness and delinquency, and draws attention to the psychological needs of this group of adolescents.

Disclose

Table of Contents “your darkness also/rich and beyond fear”: Community Performance, Somatic Poetics and the Vessels of Self and Other - Petra Kuppers. "So what will you do on the plinth?”: A Personal Experience of Disclosure during Antony Gormley’s "One & Other" Project - Jill Francesca Dowse. Food Confessions: Disclosing the Self through the Performance of Food - Jenny Lawson Participation Cartography: The Presentation of Self in Spatio-Temporal Terms - Luis Carlos Sotelo-Castro Disclosure in Biographically-Based Fiction: The Challenges of Writing Narratives Based on True Life Stories - Donna Lee Brien. Closure through Mock-Disclosure in Bret Easton Ellis’s Lunar Park - Jennifer Anne Phillips. Disclosing the Ethnographic Self - Christine Lohmeier Celebrity Twitter: Strategies of Intrusion and Disclosure in the Age of Technoculture - Nick Muntean, Anne Helen Petersen. “Just Emotional People”? Emo Culture and the Anxieties of Disclosure - Michelle Phillipov.

Langerhans cells in the cornea of diabetic patients : relevance to diabetic neuropathy

Purpose The presence of a lymphocytic infiltration in autonomic ganglia and an increased prevalence of autoantibodies and iritis in diabetic patients with autonomic neuropathy suggests a role for autoimmune mechanisms in the development of diabetic and perhaps somatic neuropathy. Corneal Langerhans cells are antigenpresenting cells which can be identified in corneal immunologic conditions using in-vivo confocal microscopy. The aim of this study was to assess the presence and density of Langerhans cells (LCs) in Bowman’s layer of the cornea in diabetic patients with varying degrees of neuropathy compared to healthy control subjects. Method 128 diabetic patients aged 58±1 years with differing severity of neuropathy (NDS – 4.7±0.28) and 26 control subjects aged 53±3 years were examined with in-vivo corneal confocal microscopy to quantify the density of “Langerhans cells” (LCs). Results LCs were observed more often in diabetic patients (73.8%) compared to control subjects (46.1%), P = 0.001. The LC density (number/mm2) was also significantly increased in diabetic patients (17.73±1.45) compared to control subjects (6.94±1.58, P = 0.001). There was a significant correlation between the density of LCs with age (r = 0.162, P = 0.047) and severity of neuropathy assessed by NDS (r =−0.202, P = 0.02). Conclusions In vivo corneal confocal microscopy enables quantification of Langerhans cells in Bowman’s layer of the cornea. There is a relationship between density of LCs and the degree of nerve damage. Corneal confocal microscopy could be a valuable tool to establish the role of immune mediated corneal nerve damage and provide insights into the pathogenesis of diabetic neuropathy.

Reconstruction of the ancestral marsupial karyotype from comparative gene maps

BACKGROUND: The increasing number of assembled mammalian genomes makes it possible to compare genome organisation across mammalian lineages and reconstruct chromosomes of the ancestral marsupial and therian (marsupial and eutherian) mammals. However, the reconstruction of ancestral genomes requires genome assemblies to be anchored to chromosomes. The recently sequenced tammar wallaby (Macropus eugenii) genome was assembled into over 300,000 contigs. We previously devised an efficient strategy for mapping large evolutionarily conserved blocks in non-model mammals, and applied this to determine the arrangement of conserved blocks on all wallaby chromosomes, thereby permitting comparative maps to be constructed and resolve the long debated issue between a 2n=14 and 2n=22 ancestral marsupial karyotype. RESULTS: We identified large blocks of genes conserved between human and opossum, and mapped genes corresponding to the ends of these blocks by fluorescence in situ hybridization (FISH). A total of 242 genes was assigned to wallaby chromosomes in the present study, bringing the total number of genes mapped to 554 and making it the most densely cytogenetically mapped marsupial genome. We used these gene assignments to construct comparative maps between wallaby and opossum, which uncovered many intrachromosomal rearrangements, particularly for genes found on wallaby chromosomes X and 3. Expanding comparisons to include chicken and human permitted the putative ancestral marsupial (2n=14) and therian mammal (2n=19) karyotypes to be reconstructed. CONCLUSIONS: Our physical mapping data for the tammar wallaby has uncovered the events shaping marsupial genomes and enabled us to predict the ancestral marsupial karyotype, supporting a 2n=14 ancestor. Futhermore, our predicted therian ancestral karyotype has helped to understand the evolution of the ancestral eutherian genome.

Molecular characterization of "Candidatus Similichlamydia latridicola" gen. nov., sp. nov. (Chlamydiales: "Candidatus Parilichlamydiaceae"), a novel Chlamydia-like epitheliocystis agent in the striped trumpeter, Latris lineata (Forster)

Histological analysis of gill samples taken from individuals of Latris lineata reared in aquaculture in Tasmania, Australia, and those sampled from the wild revealed the presence of epitheliocystis-like basophilic inclusions. Subsequent morphological, in situ hybridization, and molecular analyses were performed to confirm the presence of this disease and discovered a Chlamydia-like organism associated with this condition, and the criteria set by Fredericks and Relman's postulates were used to establish disease causation. Three distinct 16S rRNA genotypes were sequenced from 16 fish, and phylogenetic analyses of the nearly full-length 16S rRNA sequences generated for this bacterial agent indicated that they were nearly identical novel members of the order Chlamydiales. This new taxon formed a well-supported clade with "Candidatus Parilichlamydia carangidicola" from the yellowtail kingfish (Seriola lalandi). On the basis of sequence divergence over the 16S rRNA region relative to all other members of the order Chlamydiales, a new genus and species are proposed here for the Chlamydia-like bacterium from L. lineata, i.e., "Candidatus Similichlamydia latridicola" gen. nov., sp. nov.

Expression, regulation and putative nutrient-sensing function of taste GPCRs in the heart

G protein-coupled receptors (GPCRs) are critical for cardiovascular physiology. Cardiac cells express >100 nonchemosensory GPCRs, indicating that important physiological and potential therapeutic targets remain to be discovered. Moreover, there is a growing appreciation that members of the large, distinct taste and odorant GPCR families have specific functions in tissues beyond the oronasal cavity, including in the brain, gastrointestinal tract and respiratory system. To date, these chemosensory GPCRs have not been systematically studied in the heart. We performed RT-qPCR taste receptor screens in rodent and human heart tissues that revealed discrete subsets of type 2 taste receptors (TAS2/Tas2) as well as Tas1r1 and Tas1r3 (comprising the umami receptor) are expressed. These taste GPCRs are present in cultured cardiac myocytes and fibroblasts, and are enriched in myocytes, which we corroborated using in situ hybridization. Tas1r1 gene-targeted mice (Tas1r1Cre/Rosa26tdRFP) strikingly recapitulated these data. In vivo taste receptor expression levels were developmentally regulated in the postnatal period. Intriguingly, several Tas2rs were upregulated in cultured rat myocytes and in mouse heart in vivo following starvation. The discovery of taste GPCRs in the heart opens an exciting new field of cardiac research. We predict that these taste receptors may function as nutrient sensors in the heart.

Socio-demographic characteristics, modifiable lifestyle factors, and health as predictors of mental health in midlife and older Australian women: a multilevel investigation

Background Poor mental health is a significant cause of morbidity and mortality, yet debate continues about factors most likely to predict poor mental health outcomes. Objective This cohort study examines the influence of modifiable lifestyle factors, menopausal symptoms, and physical health on the mental health of midlife and older Australian women. Methods: Random sampling was used to recruit women aged 40-55, from rural and urban areas of Queensland, Australia. Overall, 340 women completed mailed surveys on socio-demographic characteristics, midlife symptoms (Greene Climacteric Scale©), modifiable lifestyle factors, and mental health (SF-12©) in 2001, 2004 and 2011. Hierarchical repeated-measure models were used to explore the correlates of poor mental health over time. Results The mean age [SD] at baseline was 55 [2.7] years, most were married (73%, n=248) and 18% were pre-menopausal. The model suggested that variance in mental health widened and showed a non-linear increase with age. Decrements in mental health were associated with an increase in midlife symptoms (Greene psychological scale, P <0.01; Greene somatic scale, P <0.05), time (P <0.01), poor physical health (P <0.01) and individual variance (P <0.01). Socio-demographics and lifestyle factors had little influence on mental health over time. Conclusion Findings suggest that while women’s mental health may decline during midlife, the effect is temporary; in older women, physical health and individual factors seem to be increasingly significant. This research highlights the importance of active health promotion as a means of enhancing both physical and mental health in midlife women.

Use of genetically modified muscle and fat grafts to repair defects in bone and cartilage

We report a novel technology for the rapid healing of large osseous and chondral defects, based upon the genetic modification of autologous skeletal muscle and fat grafts. These tissues were selected because they not only possess mesenchymal progenitor cells and scaffolding properties, but also can be biopsied, genetically modified and returned to the patient in a single operative session. First generation adenovirus vector carrying cDNA encoding human bone morphogenetic protein-2 (Ad.BMP-2) was used for gene transfer to biopsies of muscle and fat. To assess bone healing, the genetically modified (“gene activated”) tissues were implanted into 5mm-long critical size, mid-diaphyseal, stabilized defects in the femora of Fischer rats. Unlike control defects, those receiving gene-activated muscle underwent rapid healing, with evidence of radiologic bridging as early as 10 days after implantation and restoration of full mechanical strength by 8 weeks. Histologic analysis suggests that the grafts rapidly differentiated into cartilage, followed by efficient endochondral ossification. Fluorescence in situ hybridization detection of Y-chromosomes following the transfer of male donor muscle into female rats demonstrated that at least some of the osteoblasts of the healed bone were derived from donor muscle. Gene activated fat also healed critical sized defects, but less quickly than muscle and with more variability. Anti-adenovirus antibodies were not detected. Pilot studies in a rabbit osteochondral defect model demonstrated the promise of this technology for healing cartilage defects. Further development of these methods should provide ways to heal bone and cartilage more expeditiously, and at lower cost, than is presently possible.

Determining epithelial contribution to in vivo mesenchymal tumour expression signature using species-specific microarray profiling analysis of xenografts

Gene expression profiling using microarrays and xenograft transplants of human cancer cell lines are both popular tools to investigate human cancer. However, the undefined degree of cross hybridization between the mouse and human genomes hinders the use of microarrays to characterize gene expression of both the host and the cancer cell within the xenograft. Since an increasingly recognized aspect of cancer is the host response (or cancer-stroma interaction), we describe here a bioinformatic manipulation of the Affymetrix profiling that allows interrogation of the gene expression of both the mouse host and the human tumour. Evidence of microenvironmental regulation of epithelial mesenchymal transition of the tumour component in vivo is resolved against a background of mesenchymal gene expression. This tool could allow deeper insight to the mechanism of action of anti-cancer drugs, as typically novel drug efficacy is being tested in xenograft systems.

Repeated sequences as genetic markers in pooled tissue samples

We show, using the PDR1 element of pea, that dispersed repeated sequences of moderate copy number can be used simply and efficiently to generate markers linked to a trait of interest. Inspection of hybridization patterns of repeated sequences to DNA mixtures of pooled genotypes is a sensitive way of detecting such markers. The large number of bands in tracks of digests of these mixtures allows the simultaneous sampling of loci at many places in the genome, and the many unlinked loci serve as internal controls. It is also shown that intensity ratios calculated from these band differences can be used to give a rough estimate of linkage distance.

Inheritance of qualitative and quantitative trypsin inhibitor variants in Pisum

A trypsin inhibitor locus (Tri) has been mapped close to Vc-2 on Pisum (pea) linkage group 5 using recombinant inbred lines derived from crosses of genotypes showing qualitative variation in seed trypsin inhibitors. F2 seed populations derived from crosses between lines showing qualitative variation in trypsin inhibitors as well as quantitative variation in inhibitor activity showed an association between the segregation of the structural variation and relative activity levels. Clones complementary to Pisum trypsin inhibitor mRNA were used in hybridization analyses which showed that the segregation of protein polymorphisms reflected directly the segregation of polymorphisms associated with the structural genes.

Quantitative stem-loop RT-PCR for detection of microRNAs

Plant microRNAs (miRNAs) are a class of endogenous small RNAs that are essential for plant development and survival. They arise from larger precursor RNAs with a characteristic hairpin structure and regulate gene activity by targeting mRNA transcripts for cleavage or translational repression. Efficient and reliable detection and quantification of miRNA expression has become an essential step in understanding their specific roles. The expression levels of miRNAs can vary dramatically between samples and they often escape detection by conventional technologies such as cloning, northern hybridization and microarray analysis. The stem-loop RT-PCR method described here is designed to detect and quantify mature miRNAs in a fast, specific, accurate and reliable manner. First, a miRNA-specific stem-loop RT primer is hybridized to the miRNA and then reverse transcribed. Next, the RT product is amplified and monitored in real time using a miRNA-specific forward primer and the universal reverse primer. This method enables miRNA expression profiling from as little as 10 pg of total RNA and is suitable for high-throughput miRNA expression analysis.