59 research outputs found
Replicated effects of sex and genotype on gene expression in human lymphoblastoid cell lines
No full textCopyright © The Author 2006. Published by Oxford University Press. All rights reserved.The expression level for 15 887 transcripts in lymphoblastoid cell lines from 19 monozygotic twin pairs (10 male, 9 female) were analysed for the effects of genotype and sex. On an average, the effect of twin pairs explained 31% of the variance in normalized gene expression levels, consistent with previous broad sense heritability estimates. The effect of sex on gene expression levels was most noticeable on the X chromosome, which contained 15 of the 20 significantly differentially expressed genes. A high concordance was observed between the sex difference test statistics and surveys of genes escaping X chromosome inactivation. Notably, several autosomal genes showed significant differences in gene expression between the sexes despite much of the cellular environment differences being effectively removed in the cell lines. A publicly available gene expression data set from the CEPH families was used to validate the results. The heritability of gene expression levels as estimated from the two data sets showed a highly significant positive correlation, particularly when both estimates were close to one and thus had the smallest standard error. There was a large concordance between the genes significantly differentially expressed between the sexes in the two data sets. Analysis of the variability of probe binding intensities within a probe set indicated that results are robust to the possible presence of polymorphisms in the target sequences.Allan F. McRae, Nicholas A. Matigian, Lata Vadlamudi, John C. Mulley, Bryan Mowry, Nicholas G. Martin, Sam F. Berkovic, Nicholas K. Hayward and Peter M. Vissche
Loss of Usp9x disrupts cell adhesion, and components of the Wnt and Notch signaling pathways in neural progenitors
No full textDevelopment of neural progenitors depends upon the coordination of appropriate intrinsic responses to extrinsic signalling pathways. Here we show the deubiquitylating enzyme, Usp9x regulates components of both intrinsic and extrinsic fate determinants. Nestin-cre mediated ablation of Usp9x from embryonic neural progenitors in vivo resulted in a transient disruption of cell adhesion and apical-basal polarity and, an increased number and ectopic localisation of intermediate neural progenitors. In contrast to other adhesion and polarity proteins, levels of β-catenin protein, especially S33/S37/T41 phospho-β-catenin, were markedly increased in Usp9x -/Y embryonic cortices. Loss of Usp9x altered composition of the β-catenin destruction complex possibly impeding degradation of S33/S37/T41 phospho-β-catenin. Pathway analysis of transcriptomic data identified Wnt signalling as significantly affected in Usp9x -/Y embryonic brains. Depletion of Usp9x in cultured human neural progenitors resulted in Wnt-reporter activation. Usp9x also regulated components of the Notch signalling pathway. Usp9x co-localized and associated with both Itch and Numb in embryonic neocortices. Loss of Usp9x led to decreased Itch and Numb levels, and a concomitant increase in levels of the Notch intracellular domain as well as, increased expression of the Notch target gene Hes5. Therefore Usp9x modulates and potentially coordinates multiple fate determinants in neural progenitors.Susitha Premarathne, Mariyam Murtaza, Nicholas Matigian, Lachlan A. Jolly and Stephen A. Woo
Gene expression analysis in absence epilepsy using a monozygotic twin design
No full textDiscussion: Using a unique sample of discordant MZ twins, our study identified genes with altered expression, which suggests novel mechanisms in idiopathic absence epilepsy. Dysregulation of EGR1 and RCN2 is implicated in idiopathic absence epilepsy.
Methods: Genome-wide gene expression in lymphoblastoid cell lines (LCLs) was determined using microarrays derived from five discordant and four concordant MZ twin pairs with idiopathic absence epilepsies and five unaffected MZ twin pairs. Gene expression was analyzed using three strategies: discordant MZ twins were compared as matched pairs, MZ twins concordant for epilepsy were compared to control MZ twins, and a singleton design of affected versus unaffected MZ twin individuals was used irrespective of twin pairing. An overlapping gene list was generated from these analyses. Dysregulation of genes recognized from the microarray experiment was validated using quantitative real time PCR (qRT-PCR) in the twin sample and in an independent sample of 18 sporadic absence cases and 24 healthy controls.
Purpose: To identify genes involved in idiopathic absence epilepsies by analyzing gene expression using a monozygotic (MZ) twin design.Ingo Helbig, Nicholas A. Matigian, Lata Vadlamudi, Kate M. Lawrence, Marta A. Bayly, Sharon M. Bain, Dileepa Diyagama, Ingrid E. Scheffer, John C. Mulley, Andrew J. Holloway, Leanne M. Dibbens, Samuel F. Berkovic and Nicholas K. Haywar
Pathway dysregulation analysis of the nucleotide excision repair mechanisms reveals it is not a common feature of melanomas
No full textDear Editor,
Ultraviolet Radiation (UVR) is the major environmental mutagen driving the development of melanoma. The major UVR‐induced DNA lesions, 6–4 photoproducts and cyclobutane pyrimidine dimers are primarily repaired by Nucleotide Excision Repair (NER). The very high levels of UV signature mutations (USM; Signature 7 mutations) that are observed in melanomas are the direct outcome of unrepaired UV‐induced lesions (Alexandrov et al., 2013; Hodis et al., 2012), suggesting that there must be defects in the repair of these lesions, and thus potentially in NER. For further description of signature 7 mutations, please refer to (Alexandrov et al., 2013). To date, there have been contradictory reports on the efficiency of NER in melanomas. Most of these studies have used small numbers of melanoma cell lines (Belanger, Rajotte, & Drobetsky, 2014; Budden et al., 2016; Gaddameedhi et al., 2010). To address this question in a larger dataset, we have examined the relationship between the expression of a comprehensive panel of NER component genes (KEGG NER pathway, 47 genes; Supporting information Table S1) using The Cancer Genome Analysis (TCGA) melanoma dataset (Akbani et al., 2015) and USMs for each sample from (Alexandrov et al., 2013). Our analysis used “Pathifier” (Drier, Sheffer, & Domany, 2013), a validated tool developed to quantify pathway deregulation in gene expression data. Pathifier transforms gene‐level information into pathway‐level information to model a Pathway Deregulation Score (PDS) for each sample (Drier et al., 2013; Huang, Yee, Ching, Yu, & Garmire, 2014; Liu et al., 2016). We quantify the amount of dysregulation of a pathway in a sample by measuring the deviation of the sample from normal behaviour. More specifically, the expression data is used to construct a principal curve using the Hastie and Stuetzle's algorithm, onto which each sample is projected. The PDS represents the projected distance of the sample along the curve, with a larger deviation from normal expression levels indicating a higher PDS, and therefore more dysregulation in the pathway. In our study, the PDS for each sample was related to the number of S7 mutations, to determine strength of association between dysregulation of the pathway and USM load. The TCGA data was filtered to only include Malignant Melanoma NOS and Nodular Melanoma. A total of 353 samples with complete RNAseq and USM data, including 67 primary melanomas was further analysed (Supporting information Table S2).No Full Tex
Induction of Reactive Bone Stromal Fibroblasts in 3D Models of Prostate Cancer Bone Metastases
No full textA dynamic interplay between prostate cancer (PCa) cells and reactive bone stroma modulates the growth of metastases within the bone microenvironment. Of the stromal cells, metastasis-associated fibroblasts (MAFs) are known to contribute but are the least studied cell type in PCa tumour progression. It is the aim of the current study to establish a biologically relevant 3D in vitro model that mimics the cellular and molecular profiles of MAFs found in vivo. Using 3D in vitro cell culture models, the bone-derived fibroblast cell line, HS-5, was treated with conditioned media from metastatic-derived PCa cell lines, PC3 and MDA-PCa 2b, or mouse-derived fibroblasts 3T3. Two corresponding reactive cell lines were propagated: HS5-PC3 and HS5-MDA, and evaluated for alterations in morphology, phenotype, cellular behaviour, plus protein and genomic profiles. HS5-PC3 and HS5-MDA displayed distinct alterations in expression levels of N-Cadherin, non-functional E-Cadherin, alpha-smooth muscle actin (α-SMA), Tenascin C, and vimentin, along with transforming growth factor receptor expression (TGF β R1 and R2), consistent with subpopulations of MAFs reported in vivo. Transcriptomic analysis revealed a reversion of HS5-PC3 towards a metastatic phenotype with an upregulation in pathways known to regulate cancer invasion, proliferation, and angiogenesis. The exploitation of these engineered 3D models could help further unravel the novel biology regulating metastatic growth and the role fibroblasts play in the colonisation process
Validation of the Boston University staging system in AL amyloidosis
No full textObjectives: We aimed to externally validate Lilleness' et al. Boston University (BU) prognostic score that replaced NT-proBNP with brain natriuretic peptide (BNP), which will allow centres without access to NT-proBNP to accurately stage and prognosticate AL amyloidosis. Patients/methods: Forty-four were identified that had BNP, NTpro-BNP and TnI taken simultaneously, with a mean follow up of 7.3 years. Median age of the 44 patients was 67 years and 27% were female, with 61% having cardiac involvement, and 61% having renal involvement. Results: Using the BU BNP-based staging system, we identified 12/44 (27%) of patients as stage I, 18/44 (41%) of patients as stage II and 14/44 (31%) of patients as stage III. This correlated closely with stratification via the Mayo score, with only one patient miscategorised (97.7% agreement, k = 0.98). Median overall survival for our BU stage I was not reached, stage II was 40 months and stage III was 5 months (long rank p = .0012). Mayo 2004 median overall survival was identical for stages I, II and III. Conclusion: We have provided external validation of the BU staging system, a novel prognostic scoring system incorporating BNP, instead of NT-proBNP, for AL amyloidosis
Whole transcriptome profiling of placental pathobiology in SARS-CoV-2 pregnancies identifies placental dysfunction signatures
No full textOBJECTIVES: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus infection in pregnancy is associated with higher incidence of placental dysfunction, referred to by a few studies as a 'preeclampsia-like syndrome'. However, the mechanisms underpinning SARS-CoV-2-induced placental malfunction are still unclear. Here, we investigated whether the transcriptional architecture of the placenta is altered in response to SARS-CoV-2 infection. METHODS: We utilised whole-transcriptome, digital spatial profiling, to examine gene expression patterns in placental tissues from participants who contracted SARS-CoV-2 in the third trimester of their pregnancy (n = 7) and those collected prior to the start of the coronavirus disease 2019 (COVID-19) pandemic (n = 9). RESULTS: Through comprehensive spatial transcriptomic analyses of the trophoblast and villous core stromal cell subpopulations in the placenta, we identified SARS-CoV-2 to promote signatures associated with hypoxia and placental dysfunction. Notably, genes associated with vasodilation (NOS3), oxidative stress (GDF15, CRH) and preeclampsia (FLT1, EGFR, KISS1, PAPPA2) were enriched with SARS-CoV-2. Pathways related to increased nutrient uptake, vascular tension, hypertension and inflammation were also enriched in SARS-CoV-2 samples compared to uninfected controls. CONCLUSIONS: Our findings demonstrate the utility of spatially resolved transcriptomic analysis in defining the underlying pathogenic mechanisms of SARS-CoV-2 in pregnancy, particularly its role in placental dysfunction. Furthermore, this study highlights the significance of digital spatial profiling in mapping the intricate crosstalk between trophoblasts and villous core stromal cells, thus shedding light on pathways associated with placental dysfunction in pregnancies with SARS-CoV-2 infection.Nataly Stylianou, Ismail Sebina, Nicholas Matigian, James Monkman, Hadeel Doehler, Joan Rohl, Mark Allenby, Andy Nam, Liuliu Pan, Anja Rockstroh, Habib Sadeghirad, Kimberly Chung, Thais Sobanski, Ken O, Byrne, Ana Clara Simoes Florido Almeida, Patricia Zadorosnei Rebutini, Cleber Machado-Souza, Emanuele Therezinha Schueda Stonoga, Majid E Warkiani, Carlos Salomon, Kirsty Short, Lana McClements, Lucia de Noronha, Ruby Huang, Gabrielle T Belz, Fernando Souza-Fonseca-Guimaraes, Vicki Clifton, Arutha Kulasingh
NRF2 activation restores disease related metabolic deficiencies in olfactory neurosphere-derived cells from patients with sporadic Parkinson's Disease
No full textExtent: 14p.Background: Without appropriate cellular models the etiology of idiopathic Parkinson’s disease remains unknown. We recently reported a novel patient-derived cellular model generated from biopsies of the olfactory mucosa (termed olfactory neurosphere-derived (hONS) cells) which express functional and genetic differences in a disease-specific manner. Transcriptomic analysis of Patient and Control hONS cells identified the NRF2 transcription factor signalling pathway as the most differentially expressed in Parkinson’s disease. Results: We tested the robustness of our initial findings by including additional cell lines and confirmed that hONS cells from Patients had 20% reductions in reduced glutathione levels and MTS [3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)- 2-(4-sulfophenyl)-2H-tetrazolium, inner salt] metabolism compared to cultures from healthy Control donors. We also confirmed that Patient hONS cells are in a state of oxidative stress due to higher production of H2O2 than Control cultures. siRNA-mediated ablation of NRF2 in Control donor cells decreased both total glutathione content and MTS metabolism to levels detected in cells from Parkinson’s Disease patients. Conversely, and more importantly, we showed that activation of the NRF2 pathway in Parkinson’s disease hONS cultures restored glutathione levels and MTS metabolism to Control levels. Paradoxically, transcriptomic analysis after NRF2 pathway activation revealed an increased number of differentially expressed mRNAs within the NRF2 pathway in L-SUL treated Patient-derived hONS cells compared to L-SUL treated Controls, even though their metabolism was restored to normal. We also identified differential expression of the PI3K/AKT signalling pathway, but only post-treatment. Conclusions: Our results confirmed NRF2 as a potential therapeutic target for Parkinson’s disease and provided the first demonstration that NRF2 function was inducible in Patient-derived cells from donors with uniquely varied genetic backgrounds. However, our results also demonstrated that the response of PD patient-derived cells was not co-ordinated in the same way as in Control cells. This may be an important factor when developing new therapeutics.Anthony L. Cook, Alejandra M. Vitale, Sugandha Ravishankar, Nicholas Matigian, Greg T. Sutherland, Jiangou Shan, Ratneswary Sutharsan, Chris Perry, Peter A. Silburn, George D. Mellick, Murray L. Whitelaw, Christine A. Wells, Alan Mackay-Sim and Stephen A. Woo
The relationship between cognitive inhibition and extraversion/introversion
No full textThe purpose of this study was to analyze the visual and textual content presented on the covers of Seventeen magazines published between 1997 and 2007. Seventeen is the most widely read magazine among adolescent females today (SRDS, 2002); research suggests that young readers look to this publication for ideas about who to be and how to look (Duffy and Gotcher, 1996). Covers were chosen for analysis because they represent an index to the information included within the magazine and serve as an advertisement for the sale of the publication. Since young people look to Seventeen magazine for insight on how to look and act, it is important to be aware of what they are being told and shown.College Honors
Management of isoniazid-monoresistant tuberculosis (Hr-TB) in Queensland, Australia: a retrospective case series
No full textObjectives: Drug-resistance represents a major threat in the fight against tuberculosis. Globally, isoniazid-monoresistant tuberculosis (Hr-TB) is twice as common as multidrug/rifampicin-resistant (MDR/RR)-TB. Recently updated WHO guidelines now recommend treatment of Hr-TB with rifampicin, ethambutol, pyrazinamide and levofloxacin for at least six months. Our primary objective was to define the frequency, treatment and outcomes for Hr-TB in Queensland, Australia. We also sought to determine the frequency of fluoroquinolone use and whether its inclusion improved outcomes. Methods: Retrospective case series of tuberculosis notifications in Queensland between 2000 and 2017 with at least low-level isoniazid resistance and preserved susceptibility to other first-line oral agents. Results: Hr-TB was identified in 7.2% of all notifications. Where outcomes were assessable (163/198), 76.1% were treated with first-line agents only and 11.0% received at least six months of a fluoroquinolone-containing regimen (consistent with recent WHO guidelines). Favourable outcomes were achieved in 95.7%, comparable to fully susceptible disease (94.9%). Inclusion of a fluoroquinolone did not significantly improve outcomes compared with a regimen containing first-line agents only, although these cases were more likely to have high-level resistance. Previous treatment made an unfavourable outcome more likely. Conclusions: Hr-TB is prevalent in Queensland. Treatment outcomes in our cohort were comparable to fully susceptible disease. The current WHO-recommended regimen did not confer advantage over an appropriately constructed regimen containing first-line agents only. Our findings suggest that, in a well-resourced setting with good programmatic management, the addition of a fluoroquinolone may not substantially improve outcomes – potentially allowing these agents to be reserved for more extensively resistant disease
- …
