Multiple sclerosis susceptibility-associated SNPs do not influence disease severity measures in a cohort of Australian MS patients

Recent association studies in multiple sclerosis (MS) have identified and replicated several single nucleotide polymorphism (SNP) susceptibility loci including CLEC16A, IL2RA, IL7R, RPL5, CD58, CD40 and chromosome 12q13–14 in addition to the well established allele HLA-DR15. There is potential that these genetic susceptibility factors could also modulate MS disease severity, as demonstrated previously for the MS risk allele HLA-DR15. We investigated this hypothesis in a cohort of 1006 well characterised MS patients from South-Eastern Australia. We tested the MS-associated SNPs for association with five measures of disease severity incorporating disability, age of onset, cognition and brain atrophy. We observed trends towards association between the RPL5 risk SNP and time between first demyelinating event and relapse, and between the CD40 risk SNP and symbol digit test score. No associations were significant after correction for multiple testing. We found no evidence for the hypothesis that these new MS disease risk-associated SNPs influence disease severity.

Genome-wide association study identifies new multiple sclerosis susceptibility loci on chromosomes 12 and 20

To identify multiple sclerosis (MS) susceptibility loci, we conducted a genome-wide association study (GWAS) in 1,618 cases and used shared data for 3,413 controls. We performed replication in an independent set of 2,256 cases and 2,310 controls, for a total of 3,874 cases and 5,723 controls. We identified risk-associated SNPs on chromosome 12q13-14 (rs703842, P = 5.4 x 10(-11); rs10876994, P = 2.7 x 10(-10); rs12368653, P = 1.0 x 10(-7)) and upstream of CD40 on chromosome 20q13 (rs6074022, P = 1.3 x 10(-7); rs1569723, P = 2.9 x 10(-7)). Both loci are also associated with other autoimmune diseases. We also replicated several known MS associations (HLA-DR15, P = 7.0 x 10(-184); CD58, P = 9.6 x 10(-8); EVI5-RPL5, P = 2.5 x 10(-6); IL2RA, P = 7.4 x 10(-6); CLEC16A, P = 1.1 x 10(-4); IL7R, P = 1.3 x 10(-3); TYK2, P = 3.5 x 10(-3)) and observed a statistical interaction between SNPs in EVI5-RPL5 and HLA-DR15 (P = 0.001).

Cytogenetics of melanoma and nonmelanoma skin cancer

Cytogenetic analysis of melanoma and nonmelanoma skin cancers has revealed recurrent aberrations, the frequency of which is reflective of malignant potential. Highly aberrant karyotypes are seen in melanoma, squamous cell carcinoma, solar keratosis and Merkel cell carcinoma with more stable karyotypes seen in basal cell carcinoma, keratoacanthoma, Bowen’s disease, dermatofibrosarcomarotuberans and cutaneous lymphomas. Some aberrations were common amongst a number of skin cancer types including rearrangements and numerical abnormalities of chromosome 1, −3p, +3q, partial or entire trisomy 6, trisomy 7, +8q, −9p, +9q, partial or entire loss of chromosome 10, −17p, + 17q and partial or entire gain of chromosome 20. Combination of cytogenetic analysis with other molecular genetic techniques has enabled the identification of not only aberrant chromosomal regions, but also the genes that contribute to a malignant phenotype. This review provides a comprehensive summary of the pertinent cytogenetic aberrations associated with a variety of melanoma and nonmelanoma skin cancers.

Cytogenetic alterations in nonmelanoma skin cancer : a review

Since the advent of cytogenetic analysis, knowledge about fundamental aspects of cancer biology has increased, allowing the processes of cancer development and progression to be more fully understood and appreciated. Classical cytogenetic analysis of solid tumors had been considered difficult, but new advances in culturing techniques and the addition of new cytogenetic technologies have enabled a more comprehensive analysis of chromosomal aberrations associated with solid tumors. Our purpose in this review is to discuss the cytogenetic findings on a number of nonmelanoma skin cancers, including squamous- and basal cell carcinomas, keratoacanthoma, squamous cell carcinoma in situ (Bowen's disease), and solar keratosis. Through classical cytogenetic techniques, as well as fluorescence-based techniques such as fluorescence in situ hybridization and comparative genomic hybridization, numerous chromosomal alterations have been identified. These aberrations may aid in further defining the stages and classifications of nonmelanoma skin cancer and also may implicate chromosomal regions involved in progression and metastatic potential. This information, along with the development of newer technologies (including laser capture microdissection and comparative genomic hybridization arrays) that allow for more refined analysis, will continue to increase our knowledge about the role of chromosomal events at all stages of cancer development and progression and, more specifically, about how they are associated with nonmelanoma skin cancer.

The GSTM1 null genotype confers an increased risk for Solar Keratosis Development in an Australian Caucasian Population

Solar keratoses affect approximately 50% of Australian Caucasians aged over 40 y. Solar keratoses can undergo malignant transformation into squamous cell carcinoma followed by possible metastasis and are risk factors for basal cell carcinoma, melanoma, and squamous cell carcinoma. The glutathione-S-transferase genes play a part in detoxification of carcinogens and mutagens, including some produced by ultraviolet radiation. This study examined the role of glutathione-S-transferase M1, T1, P1, and Z1 gene polymorphisms in susceptibility to solar keratoses development. Using DNA samples from volunteers involved in the Nambour Skin Cancer Prevention Trial, allele and genotype frequencies were determined using polymerase chain reaction and restriction enzyme digestion. No significant differences were detected in glutathione-S-transferase P1 and glutathione-S-transferase Z1 allele or genotype frequencies; however, a significant association between glutathione-S-transferase M1 genotypes and solar keratoses development was detected (p=0.003) with null individuals having an approximate 2-fold increase in risk for solar keratoses development (odds ratio: 2.1; confidence interval: 1.3-3.5) and a significantly higher increase in risk in conjunction with high outdoor exposure (odds ratio: 3.4; confidence interval: 1.9-6.3). Also, a difference in glutathione-S-transferase T1 genotype frequencies was detected (p=0.039), although considering that multiple testing was undertaken, this was found not to be significant. Fair skin and inability to tan were found to be highly significant risk factors for solar keratoses development with odds ratios of 18.5 (confidence interval: 5.7-59.9) and 7.4 (confidence interval: 2.6-21.0), respectively. Overall, glutathione-S-transferase M1 conferred a significant increase in risk of solar keratoses development, particularly in the presence of high outdoor exposure and synergistically with known phenotypic risk factors of fair skin and inability to tan.

Association analysis of somatostatin receptor (SSTR1 and SSTR2) polymorphisms in breast cancer and solar keratosis

The presence of somatostatin receptors (SSTR1-5) in tumour cells indicates a potential for somatostatin to bind and suppress growth, as well as allowing for therapeutic treatment with somatostatin analogues. The genes for SSTR1 and SSTR2 have been shown to contain dinucleotide repeat polymorphisms. We have performed association studies on breast cancer and solar keratosis populations to determine whether these genes play a role in the development of these conditions. Results showed that there was no significant difference between SSTR1 and SSTR2 polymorphism frequencies in the tested breast cancer population (P = 0.59 and P = 0.54, respectively) nor the solar keratosis population (P = 0.10 and P = 0.883, respectively) as compared to unaffected populations. Hence, these studies do not support a role for these receptor genes in either breast cancer or solar keratosis lesions.

Cytogenetics of basal cell carcinoma and squamous cell carcinomas

Cytogenetic analysis is a powerful tool that allows analysis of chromosomal aberrations associated with diseased states. In particular, a combination of cytogenetic techniques has allowed the identification of aberrations associated with cancer development, including cancers of the skin. This chapter provides a comprehensive overview of cytogenetic alterations in basal and squamous cell carcinomas of the skin. These two distinct lesions have altered karyotypes that are consistent with their malignant potential. Basal cell carcinomas, although relatively stable lesions, are highly associated with recurrent aberrations of chromosomes 6, 7, 9 and X, as detected by a number of cytogenetic techniques. Squamous cell carcinomas, on the other hand are associated with a much higher degree of instability, involving aberrations of chromosomes 3, 7, 8, 11, 13, 17 and 18, as detected using a number of cytogenetic techniques. Overall, the numbers and types of aberrations associated with basal and squamous cell carcinoma, define the characteristic behaviour associated with these lesions and identification of these aberrations may aid in the understanding of malignant potential, prognosis and treatment of these skin cancers.

Analysis of androgen and anti-androgen regulation of KLK-related peptidase 2, 3, and 4 alternative transcripts in prostate cancer

We assessed whether alternative transcripts (using KLK2, KLK3 and KLK4 as models) are differentially regulated by androgens and anti-androgens as an indicator of prostate cancers as they acquire treatment resistance. Using RNAseq of LNCaP cells treated with dihydrotestosterone, bicalutamide and enzalutamide, we show that the expression of variant KLK transcripts is markedly different to other variant transcripts at those loci. We also reveal that KLK variants are also over 2-fold more highly expressed in prostate cancers compared to their corresponding normal prostate. We propose that androgens and anti-androgens can activate specific variant transcripts of critical prostate cancer genes during treatment resistance

The duration of Chlamydia muridarum genital tract infection and associated chronic pathological changes are reduced in IL-17 knockout mice but protection is not increased further by immunization

IL-17 is believed to be important for protection against extracellular pathogens, where clearance is dependent on neutrophil recruitment and local activation of epithelial cell defences. However, the role of IL-17 in protection against intracellular pathogens such as Chlamydia is less clear. We have compared (i) the course of natural genital tract C. muridarum infection, (ii) the development of oviduct pathology and (iii) the development of vaccine-induced immunity against infection in wild type (WT) BALB/c and IL-17 knockout mice (IL-17-/-) to determine if IL-17-mediated immunity is implicated in the development of infection-induced pathology and/or protection. Both the magnitude and duration of genital infection was significantly reduced in IL-17-/- mice compared to BALB/c. Similarly, hydrosalpinx was also greatly reduced in IL-17-/- mice and this correlated with reduced neutrophil and macrophage infiltration of oviduct tissues. Matrix metalloproteinase (MMP) 9 and MMP2 were increased in WT oviducts compared to IL-17-/- animals at day 7 post-infection. In contrast, oviducts from IL-17-/- mice contained higher MMP9 and MMP2 at day 21. Infection also elicited higher levels of Chlamydia-neutralizing antibody in serum of IL-17-/- mice than WT mice. Following intranasal immunization with C. muridarum Major Outer Membrane Protein (MOMP) and cholera toxin plus CpG adjuvants, significantly higher levels of chlamydial MOMP-specific IgG and IgA were found in serum and vaginal washes of IL-17-/- mice. T cell proliferation and IFNγ production by splenocytes was greater in WT animals following in vitro re-stimulation, however vaccination was only effective at reducing infection in WT, not IL-17-/- mice. Intranasal or transcutaneous immunization protected WT but not IL-17-/- mice against hydrosalpinx development. Our data show that in the absence of IL-17, the severity of C. muridarum genital infection and associated oviduct pathology are significantly attenuated, however neither infection or pathology can be reduced further by vaccination protocols that effectively protect WT mice.

Saliva-derived DNA performs well in large-scale, high-density single-nucleotide polymorphism microarray studies

As of June 2009, 361 genome-wide association studies (GWAS) had been referenced by the HuGE database. GWAS require DNA from many thousands of individuals, relying on suitable DNA collections. We recently performed a multiple sclerosis (MS) GWAS where a substantial component of the cases (24%) had DNA derived from saliva. Genotyping was done on the Illumina genotyping platform using the Infinium Hap370CNV DUO microarray. Additionally, we genotyped 10 individuals in duplicate using both saliva- and blood-derived DNA. The performance of blood- versus saliva-derived DNA was compared using genotyping call rate, which reflects both the quantity and quality of genotyping per sample and the “GCScore,” an Illumina genotyping quality score, which is a measure of DNA quality. We also compared genotype calls and GCScores for the 10 sample pairs. Call rates were assessed for each sample individually. For the GWAS samples, we compared data according to source of DNA and center of origin. We observed high concordance in genotyping quality and quantity between the paired samples and minimal loss of quality and quantity of DNA in the saliva samples in the large GWAS sample, with the blood samples showing greater variation between centers of origin. This large data set highlights the usefulness of saliva DNA for genotyping, especially in high-density single-nucleotide polymorphism microarray studies such as GWAS.

Kaleidoscope : Reframing learning and teaching evaluation through a shared stakeholder lens

Sector wide interest in Reframe: QUT’s Evaluation Framework continues with a number of institutions requesting finer details as QUT embeds the new approach to evaluation across the university in 2013. This interest, both nationally and internationally has warranted QUT’s collegial response to draw upon its experiences from developing Reframe into distilling and offering Kaleidoscope back to the sector. The word Reframe is a relevant reference for QUT’s specific re-evaluation, reframing and adoption of a new approach to evaluation; whereas Kaleidoscope reflects the unique lens through which any other institution will need to view their own cultural specificity and local context through an extensive user-led stakeholder engagement approach when introducing new approaches to learning and teaching evaluation. Kaleidoscope’s objectives are for QUT to develop its research-based stakeholder approach to distil the successful experience exhibited in the Reframe Project into a transferable set of guidelines for use by other tertiary institutions across the sector. These guidelines will assist others to design, develop, and deploy, their own culturally specific widespread organisational change informed by stakeholder engagement and organisational buy-in. It is intended that these guidelines will promote, support and enable other tertiary institutions to embark on their own evaluation projects and maximise impact. Kaleidoscope offers an institutional case study of widespread organisational change underpinned by Reframe’s (i) evidence-based methodology; (ii) research including published environmental scan, literature review (Alderman, et al., 2012), development of a conceptual model (Alderman, et al., in press 2013), project management principles (Alderman & Melanie, 2012) and national conference peer reviews; and (iii) year-long strategic project with national outreach to collaboratively engage the development of a draft set of National Guidelines. Kaleidoscope’s aims are to inform Higher Education evaluation policy development through national stakeholder engagement, the finalisation of proposed National Guidelines. In correlation with the conference paper, the authors will present a Draft Guidelines and Framework ready for external peer review by evaluation practitioners from the Higher Education sector, as part of Kaleidoscope’s dissemination strategy (Hinton & Gannaway, 2011) applying illuminative evaluation theory (Parlett & Hamilton, 1976), through conference workshops and ongoing discussions (Shapiro, et al., 1983; Jacobs, 2000). The initial National Guidelines will be distilled from the Reframe: QUT’s Evaluation Framework’s Policy, Protocols, and incorporated Business Rules. It is intended that the outcomes of Kaleidoscope are owned by and reflect sectoral engagement, including iterative evaluation through multiple avenues of dissemination and collaboration including the Higher Education sector. The dissemination strategy with the inclusion of Illuminative Evaluation methodology provides an inclusive opportunity for other institutions and stakeholders across the Higher Education sector to give voice through the information-gathering component of evaluating the draft Guidelines, providing a comprehensive understanding of the complex realities experienced across the Higher Education sector, and thereby ‘illuminating’ both the shared and unique lenses and contexts. This process will enable any final guidelines developed to have broader applicability, greater acceptance, enhanced sustainability and additional relevance benefiting the Higher Education sector, and the adoption and adaption by any single institution for their local contexts.

Kaleidoscope : shaping a better future through a stakeholder approach to widespread organisational change

The main focus of ‘Kaleidoscope: Reframing evaluation through a stakeholder approach to sustainable, cultural change in Higher Education’ is to develop a set of principles to guide user-led engagement in widespread organisational change and maximise its impact. The word kaleidoscope represents the unique lens through which each institution will need to view their cultural specificity and local context through an extensive process of collaboration and engagement, followed by communication and dissemination. Kaleidoscope has particular relevance when new approaches to learning and teaching evaluation are introduced by tertiary institutions. Building on the Reframe Project, which involved three years of user-led consultation and was designed to meet stakeholders’ needs, QUT successfully introduced a new evaluation framework in 2013 across the university. Reframe was evidence based, involved scholarly reflection and was founded on a strong theoretical framework. The evolution of the evaluation framework included analysis of scholarly literature and environmental scans across the higher education sector (Alderman, et al., 2012), researched development of conceptual theory (Alderman, et al., in press 2013), incorporated the stakeholder voice and framed within project management principles (Alderman & Melanie, 2012). Kaleidoscope’s objectives are for QUT to develop its research-based stakeholder approach to distil the successful experience exhibited in the Reframe Project into a transferable set of guidelines for use by other tertiary institutions across the sectors. These guidelines will assist others to design, develop, and deploy, their own culturally specific widespread organisational change informed by stakeholder engagement and organisational buy-in. It is intended that these guidelines will promote, support and enable other tertiary institutions to embark on their own projects and maximise the impact. In correlation with a our conference paper, this round table presents the Draft Guidelines and Framework ready for external peer review by evaluation practitioners, as part of Kaleidoscope’s dissemination (Hinton & Gannaway, 2011) applying illuminative evaluation theory (Parlett & Hamilton, 1976), through conference workshops and linked round table discussions (Shapiro, et al., 1983; Jacobs, 2000).

How to meet stakeholders' expectations, not manage them?

Evaluation practices in the higher education sector have been criticised for having unclear purpose and principles; ignoring the complexity and changing nature of learning and teaching and the environments in which they occur; relying almost exclusively on student ratings of teachers working in classroom settings; lacking reliability and validity; using data for inappropriate purposes; and focusing on accountability and marketing rather than the improvement of learning and teaching. In response to similar criticism from stakeholders, in 2011 Queensland University of Technology began a project, entitled REFRAME, to review its approach to evaluation, particularly the student survey system it had been using for the past five years. This presentation will outline the scholarly, evidence based methodology used to undertake institution-wide change, meet the needs of stakeholders suitable to the cultural needs of the institution. It is believed that this approach is broadly applicable to other institutions contemplating change with regard to evaluation of learning and teaching.

REFRAME: a new approach to evaluation in higher education

Evaluation practices in the higher education sector have been criticised for having unclear purpose and principles; ignoring the complexity and changing nature of learning and teaching and the environments in which they occur; relying almost exclusively on student ratings of teachers working in classroom settings; lacking reliability and validity; using data for inappropriate purposes; and focusing on accountability and marketing rather than the improvement of learning and teaching. In response to similar criticism from stakeholders, in 2011 Queensland University of Technology began a project, entitled REFRAME, to review its approach to evaluation, particularly the student survey system it had been using for the past five years. This presentation will outline the scholarly, evidence based methodology used to undertake institution-wide change, meet the needs of stakeholders suitable to the cultural needs of the institution. It is believed that this approach is broadly applicable to other institutions contemplating change with regard to evaluation of learning and teaching.

Kaleidoscope : illuminating learning and teaching evaluation for a shared stakeholder lens

Within the Australian higher education sector, institutions are required to evaluate teaching, units and courses to assure the quality of the student learning experience, however with hardly any regulatory parameters guiding institutions, and with disparate practices, there are few opportunities to benchmakr across institutions or the sector. QUT has received interest and requests from national and international universities on accessing Reframe: QUT's Evaluation Framework.