240 results on '"Christine A Wells"'
Search Results
2. A simple, scalable approach to building a cross-platform transcriptome atlas.
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Paul W Angel, Nadia Rajab, Yidi Deng, Chris M Pacheco, Tyrone Chen, Kim-Anh Lê Cao, Jarny Choi, and Christine A Wells
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Biology (General) ,QH301-705.5 - Abstract
Gene expression atlases have transformed our understanding of the development, composition and function of human tissues. New technologies promise improved cellular or molecular resolution, and have led to the identification of new cell types, or better defined cell states. But as new technologies emerge, information derived on old platforms becomes obsolete. We demonstrate that it is possible to combine a large number of different profiling experiments summarised from dozens of laboratories and representing hundreds of donors, to create an integrated molecular map of human tissue. As an example, we combine 850 samples from 38 platforms to build an integrated atlas of human blood cells. We achieve robust and unbiased cell type clustering using a variance partitioning method, selecting genes with low platform bias relative to biological variation. Other than an initial rescaling, no other transformation to the primary data is applied through batch correction or renormalisation. Additional data, including single-cell datasets, can be projected for comparison, classification and annotation. The resulting atlas provides a multi-scaled approach to visualise and analyse the relationships between sets of genes and blood cell lineages, including the maturation and activation of leukocytes in vivo and in vitro. In allowing for data integration across hundreds of studies, we address a key reproduciblity challenge which is faced by any new technology. This allows us to draw on the deep phenotypes and functional annotations that accompany traditional profiling methods, and provide important context to the high cellular resolution of single cell profiling. Here, we have implemented the blood atlas in the open access Stemformatics.org platform, drawing on its extensive collection of curated transcriptome data. The method is simple, scalable and amenable for rapid deployment in other biological systems or computational workflows.
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- 2020
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3. Discovery of NRG1-VII: the myeloid-derived class of NRG1
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Miguel A Berrocal-Rubio, Yair David Joseph Pawer, Marija Dinevska, Ricardo De Paoli-Iseppi, Samuel S. Widodo, Josie Gleeson, Nadia Rajab, Will De Nardo, Jeannette Hallab, Anran Li, Theo Mantamadiotis, Michael B. Clark, and Christine A. Wells
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NRG1 ,Myeloid ,Growth factor ,Isoforms ,Macrophages ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract The growth factor Neuregulin-1 (NRG1) has pleiotropic roles in proliferation and differentiation of the stem cell niche in different tissues. It has been implicated in gut, brain and muscle development and repair. Six isoform classes of NRG1 and over 28 protein isoforms have been previously described. Here we report a new class of NRG1, designated NRG1-VII to denote that these NRG1 isoforms arise from a myeloid-specific transcriptional start site (TSS) previously uncharacterized. Long-read sequencing was used to identify eight high-confidence NRG1-VII transcripts. These transcripts presented major structural differences from one another, through the use of cassette exons and alternative stop codons. Expression of NRG1-VII was confirmed in primary human monocytes and tissue resident macrophages and induced pluripotent stem cell-derived macrophages (iPSC-derived macrophages). Isoform switching via cassette exon usage and alternate polyadenylation was apparent during monocyte maturation and macrophage differentiation. NRG1-VII is the major class expressed by the myeloid lineage, including tissue-resident macrophages. Analysis of public gene expression data indicates that monocytes and macrophages are a primary source of NRG1. The size and structure of class VII isoforms suggests that they may be more diffusible through tissues than other NRG1 classes. However, the specific roles of class VII variants in tissue homeostasis and repair have not yet been determined.
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- 2024
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4. Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease.
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J Kenneth Baillie, Andrew Bretherick, Christopher S Haley, Sara Clohisey, Alan Gray, Lucile P A Neyton, Jeffrey Barrett, Eli A Stahl, Albert Tenesa, Robin Andersson, J Ben Brown, Geoffrey J Faulkner, Marina Lizio, Ulf Schaefer, Carsten Daub, Masayoshi Itoh, Naoto Kondo, Timo Lassmann, Jun Kawai, IIBDGC Consortium, Damian Mole, Vladimir B Bajic, Peter Heutink, Michael Rehli, Hideya Kawaji, Albin Sandelin, Harukazu Suzuki, Jack Satsangi, Christine A Wells, Nir Hacohen, Thomas C Freeman, Yoshihide Hayashizaki, Piero Carninci, Alistair R R Forrest, and David A Hume
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Biology (General) ,QH301-705.5 - Abstract
Genetic variants underlying complex traits, including disease susceptibility, are enriched within the transcriptional regulatory elements, promoters and enhancers. There is emerging evidence that regulatory elements associated with particular traits or diseases share similar patterns of transcriptional activity. Accordingly, shared transcriptional activity (coexpression) may help prioritise loci associated with a given trait, and help to identify underlying biological processes. Using cap analysis of gene expression (CAGE) profiles of promoter- and enhancer-derived RNAs across 1824 human samples, we have analysed coexpression of RNAs originating from trait-associated regulatory regions using a novel quantitative method (network density analysis; NDA). For most traits studied, phenotype-associated variants in regulatory regions were linked to tightly-coexpressed networks that are likely to share important functional characteristics. Coexpression provides a new signal, independent of phenotype association, to enable fine mapping of causative variants. The NDA coexpression approach identifies new genetic variants associated with specific traits, including an association between the regulation of the OCT1 cation transporter and genetic variants underlying circulating cholesterol levels. NDA strongly implicates particular cell types and tissues in disease pathogenesis. For example, distinct groupings of disease-associated regulatory regions implicate two distinct biological processes in the pathogenesis of ulcerative colitis; a further two separate processes are implicated in Crohn's disease. Thus, our functional analysis of genetic predisposition to disease defines new distinct disease endotypes. We predict that patients with a preponderance of susceptibility variants in each group are likely to respond differently to pharmacological therapy. Together, these findings enable a deeper biological understanding of the causal basis of complex traits.
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- 2018
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5. Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease.
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J Kenneth Baillie, Erik Arner, Carsten Daub, Michiel De Hoon, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Piero Carninci, Alistair R R Forrest, Yoshihide Hayashizaki, FANTOM Consortium, Geoffrey J Faulkner, Christine A Wells, Michael Rehli, Paul Pavli, Kim M Summers, and David A Hume
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Genetics ,QH426-470 - Abstract
The FANTOM5 consortium utilised cap analysis of gene expression (CAGE) to provide an unprecedented insight into transcriptional regulation in human cells and tissues. In the current study, we have used CAGE-based transcriptional profiling on an extended dense time course of the response of human monocyte-derived macrophages grown in macrophage colony-stimulating factor (CSF1) to bacterial lipopolysaccharide (LPS). We propose that this system provides a model for the differentiation and adaptation of monocytes entering the intestinal lamina propria. The response to LPS is shown to be a cascade of successive waves of transient gene expression extending over at least 48 hours, with hundreds of positive and negative regulatory loops. Promoter analysis using motif activity response analysis (MARA) identified some of the transcription factors likely to be responsible for the temporal profile of transcriptional activation. Each LPS-inducible locus was associated with multiple inducible enhancers, and in each case, transient eRNA transcription at multiple sites detected by CAGE preceded the appearance of promoter-associated transcripts. LPS-inducible long non-coding RNAs were commonly associated with clusters of inducible enhancers. We used these data to re-examine the hundreds of loci associated with susceptibility to inflammatory bowel disease (IBD) in genome-wide association studies. Loci associated with IBD were strongly and specifically (relative to rheumatoid arthritis and unrelated traits) enriched for promoters that were regulated in monocyte differentiation or activation. Amongst previously-identified IBD susceptibility loci, the vast majority contained at least one promoter that was regulated in CSF1-dependent monocyte-macrophage transitions and/or in response to LPS. On this basis, we concluded that IBD loci are strongly-enriched for monocyte-specific genes, and identified at least 134 additional candidate genes associated with IBD susceptibility from reanalysis of published GWA studies. We propose that dysregulation of monocyte adaptation to the environment of the gastrointestinal mucosa is the key process leading to inflammatory bowel disease.
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- 2017
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6. Australian researchers’ perceptions and experiences with stem cell registration
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Mengqi Hu, Dan Santos, Edilene Lopes, Dianne Nicol, Andreas Kurtz, Nancy Mah, Sabine Muller, Rachel A. Ankeny, and Christine A. Wells
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Pluripotent stem cell registration ,Researcher expectations ,Stem cell governance ,Open science ,Biology (General) ,QH301-705.5 - Abstract
The recently issued ISSCR standards in stem cell research recommend registration of human pluripotent stem cell lines (hPSCs). Registration is critical to establishing stem cell provenance and connecting cell lines to data derived on those lines. In this study, we sought to understand common barriers to registration by conducting interviews with forty-eight Australian stem cell stakeholders, including researchers, clinicians, and industry professionals. Australian stem cell researchers do not routinely register their lines, and only a third of those Australian lines captured by an international registry have fully completed the registration process. Most registered Australian cell lines lack complete information about their ethical provenance or key pluripotency characteristics. Incomplete registration is poorly aligned with the goals of open science on which registries are founded. Users also expressed concerns about the quality of the incomplete information provided to the resource. Registration was considered negatively, for instance as a hurdle or barrier to publication, which impacted on user perceptions of usefulness of registration and lowered the likelihood that they would engage with registries to find resources. Broader adoption of registration by journals, and continued advocacy by stem cell societies, will be important levers for awareness and engagement with registration. Although the Australian community represents a small fraction of potential registry users, the results of this study suggest ways for journals, registries, funders, and the international stem cell community to improve registration compliance.
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- 2024
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7. Variance of gene expression identifies altered network constraints in neurological disease.
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Jessica C Mar, Nicholas A Matigian, Alan Mackay-Sim, George D Mellick, Carolyn M Sue, Peter A Silburn, John J McGrath, John Quackenbush, and Christine A Wells
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Genetics ,QH426-470 - Abstract
Gene expression analysis has become a ubiquitous tool for studying a wide range of human diseases. In a typical analysis we compare distinct phenotypic groups and attempt to identify genes that are, on average, significantly different between them. Here we describe an innovative approach to the analysis of gene expression data, one that identifies differences in expression variance between groups as an informative metric of the group phenotype. We find that genes with different expression variance profiles are not randomly distributed across cell signaling networks. Genes with low-expression variance, or higher constraint, are significantly more connected to other network members and tend to function as core members of signal transduction pathways. Genes with higher expression variance have fewer network connections and also tend to sit on the periphery of the cell. Using neural stem cells derived from patients suffering from Schizophrenia (SZ), Parkinson's disease (PD), and a healthy control group, we find marked differences in expression variance in cell signaling pathways that shed new light on potential mechanisms associated with these diverse neurological disorders. In particular, we find that expression variance of core networks in the SZ patient group was considerably constrained, while in contrast the PD patient group demonstrated much greater variance than expected. One hypothesis is that diminished variance in SZ patients corresponds to an increased degree of constraint in these pathways and a corresponding reduction in robustness of the stem cell networks. These results underscore the role that variation plays in biological systems and suggest that analysis of expression variance is far more important in disease than previously recognized. Furthermore, modeling patterns of variability in gene expression could fundamentally alter the way in which we think about how cellular networks are affected by disease processes.
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- 2011
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8. attract: A method for identifying core pathways that define cellular phenotypes.
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Jessica C Mar, Nicholas A Matigian, John Quackenbush, and Christine A Wells
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Medicine ,Science - Abstract
attract is a knowledge-driven analytical approach for identifying and annotating the gene-sets that best discriminate between cell phenotypes. attract finds distinguishing patterns within pathways, decomposes pathways into meta-genes representative of these patterns, and then generates synexpression groups of highly correlated genes from the entire transcriptome dataset. attract can be applied to a wide range of biological systems and is freely available as a Bioconductor package and has been incorporated into the MeV software system.
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- 2011
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9. NRF2 activation restores disease related metabolic deficiencies in olfactory neurosphere-derived cells from patients with sporadic Parkinson's disease.
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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 Wood
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Medicine ,Science - Abstract
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.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 H(2)O(2) 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.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.
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- 2011
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10. A cross-study transcriptional analysis of Parkinson's disease.
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Greg T Sutherland, Nicholas A Matigian, Alistair M Chalk, Matthew J Anderson, Peter A Silburn, Alan Mackay-Sim, Christine A Wells, and George D Mellick
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Medicine ,Science - Abstract
The study of Parkinson's disease (PD), like other complex neurodegenerative disorders, is limited by access to brain tissue from patients with a confirmed diagnosis. Alternatively the study of peripheral tissues may offer some insight into the molecular basis of disease susceptibility and progression, but this approach still relies on brain tissue to benchmark relevant molecular changes against. Several studies have reported whole-genome expression profiling in post-mortem brain but reported concordance between these analyses is lacking. Here we apply a standardised pathway analysis to seven independent case-control studies, and demonstrate increased concordance between data sets. Moreover data convergence increased when the analysis was limited to the five substantia nigra (SN) data sets; this highlighted the down regulation of dopamine receptor signaling and insulin-like growth factor 1 (IGF1) signaling pathways. We also show that case-control comparisons of affected post mortem brain tissue are more likely to reflect terminal cytoarchitectural differences rather than primary pathogenic mechanisms. The implementation of a correction factor for dopaminergic neuronal loss predictably resulted in the loss of significance of the dopamine signaling pathway while axon guidance pathways increased in significance. Interestingly the IGF1 signaling pathway was also over-represented when data from non-SN areas, unaffected or only terminally affected in PD, were considered. Our findings suggest that there is greater concordance in PD whole-genome expression profiling when standardised pathway membership rather than ranked gene list is used for comparison.
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- 2009
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11. Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs.
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Norihiro Maeda, Takeya Kasukawa, Rieko Oyama, Julian Gough, Martin Frith, Pär G Engström, Boris Lenhard, Rajith N Aturaliya, Serge Batalov, Kirk W Beisel, Carol J Bult, Colin F Fletcher, Alistair R R Forrest, Masaaki Furuno, David Hill, Masayoshi Itoh, Mutsumi Kanamori-Katayama, Shintaro Katayama, Masaru Katoh, Tsugumi Kawashima, John Quackenbush, Timothy Ravasi, Brian Z Ring, Kazuhiro Shibata, Koji Sugiura, Yoichi Takenaka, Rohan D Teasdale, Christine A Wells, Yunxia Zhu, Chikatoshi Kai, Jun Kawai, David A Hume, Piero Carninci, and Yoshihide Hayashizaki
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Genetics ,QH426-470 - Abstract
The international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched cDNAs. The previous dataset, FANTOM2, comprised 60,770 full-length enriched cDNAs. Functional annotation revealed that this cDNA dataset contained only about half of the estimated number of mouse protein-coding genes, indicating that a number of cDNAs still remained to be collected and identified. To pursue the complete gene catalog that covers all predicted mouse genes, cloning and sequencing of full-length enriched cDNAs has been continued since FANTOM2. In FANTOM3, 42,031 newly isolated cDNAs were subjected to functional annotation, and the annotation of 4,347 FANTOM2 cDNAs was updated. To accomplish accurate functional annotation, we improved our automated annotation pipeline by introducing new coding sequence prediction programs and developed a Web-based annotation interface for simplifying the annotation procedures to reduce manual annotation errors. Automated coding sequence and function prediction was followed with manual curation and review by expert curators. A total of 102,801 full-length enriched mouse cDNAs were annotated. Out of 102,801 transcripts, 56,722 were functionally annotated as protein coding (including partial or truncated transcripts), providing to our knowledge the greatest current coverage of the mouse proteome by full-length cDNAs. The total number of distinct non-protein-coding transcripts increased to 34,030. The FANTOM3 annotation system, consisting of automated computational prediction, manual curation, and final expert curation, facilitated the comprehensive characterization of the mouse transcriptome, and could be applied to the transcriptomes of other species.
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- 2006
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12. A national sample of developmentally disabled adolescents with obesity and their utilization of preventive dental care services
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Nini C. Tran, Christine R. Wells, Kathryn A. Atchison, and Vinodh Bhoopathi
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developmental disabilities ,adolescents ,obesity ,dental sealants ,fluoride treatment ,dental cleanings ,Dentistry ,RK1-715 - Abstract
BackgroundPrevious literature indicates that adolescents with developmental disabilities and obesity may have more oral health complications than healthy adolescents. However, dental care utilization among adolescents with developmental disabilities (DDs) and obesity is unclear. We investigated the differences in the utilization of preventive dental services between this high-risk group of adolescents and those with no DDs or obesity.MethodsParent-reported data of adolescents 10–17 years (n = 68,942) from the 2016 to 2019 National Survey of Children's Health was used. In addition to descriptive and bivariate statistics, we ran three multiple logistic regression models guided by Andersen's Behavioral Model of Health Services Use, predicting the use of dental cleanings, fluoride treatments, and dental sealants.ResultsAmong adolescents with DDs and obesity, dental cleanings, fluoride treatments, and dental sealant utilization prevalence were 76%, 48%, and 21%, respectively. In comparison, adolescents with no DDs or obesity had a prevalence of 83%, 50%, and 19%, respectively. Multiple logistic regression analysis showed that adolescents with DDs and obesity did not significantly differ in their receipt of dental cleanings (p = .07), fluoride treatments (p = .55), and dental sealants (p = .23) compared to those with neither DDs nor obesity. Adolescents with DDs but no obesity were 22% and 30% more likely to receive fluoride treatments (p
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- 2023
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13. Stemformatics: visualize and download curated stem cell data.
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Jarny Choi, Chris M. Pacheco, Rowland Mosbergen, Othmar Korn, Tyrone Chen, Isha Nagpal, Steve Englart, Paul W. Angel, and Christine A. Wells
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- 2019
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14. Supplementary Figure 6 from Concordant Epigenetic Silencing of Transforming Growth Factor-β Signaling Pathway Genes Occurs Early in Breast Carcinogenesis
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Susan J. Clark, Roger R. Reddel, David A. Hume, Christine A. Wells, Timothy Ravasi, Bryce Vissel, Andrea Abdipranoto, Clare Stirzaker, John Melki, Lily I. Huschtscha, and Rebecca A. Hinshelwood
- Abstract
Supplementary Figure 6 from Concordant Epigenetic Silencing of Transforming Growth Factor-β Signaling Pathway Genes Occurs Early in Breast Carcinogenesis
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- 2023
15. Supplementary Figure 2 from Concordant Epigenetic Silencing of Transforming Growth Factor-β Signaling Pathway Genes Occurs Early in Breast Carcinogenesis
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Susan J. Clark, Roger R. Reddel, David A. Hume, Christine A. Wells, Timothy Ravasi, Bryce Vissel, Andrea Abdipranoto, Clare Stirzaker, John Melki, Lily I. Huschtscha, and Rebecca A. Hinshelwood
- Abstract
Supplementary Figure 2 from Concordant Epigenetic Silencing of Transforming Growth Factor-β Signaling Pathway Genes Occurs Early in Breast Carcinogenesis
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- 2023
16. Supplementary Figure 5 from Concordant Epigenetic Silencing of Transforming Growth Factor-β Signaling Pathway Genes Occurs Early in Breast Carcinogenesis
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Susan J. Clark, Roger R. Reddel, David A. Hume, Christine A. Wells, Timothy Ravasi, Bryce Vissel, Andrea Abdipranoto, Clare Stirzaker, John Melki, Lily I. Huschtscha, and Rebecca A. Hinshelwood
- Abstract
Supplementary Figure 5 from Concordant Epigenetic Silencing of Transforming Growth Factor-β Signaling Pathway Genes Occurs Early in Breast Carcinogenesis
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- 2023
17. Supplementary Figure 3 from Concordant Epigenetic Silencing of Transforming Growth Factor-β Signaling Pathway Genes Occurs Early in Breast Carcinogenesis
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Susan J. Clark, Roger R. Reddel, David A. Hume, Christine A. Wells, Timothy Ravasi, Bryce Vissel, Andrea Abdipranoto, Clare Stirzaker, John Melki, Lily I. Huschtscha, and Rebecca A. Hinshelwood
- Abstract
Supplementary Figure 3 from Concordant Epigenetic Silencing of Transforming Growth Factor-β Signaling Pathway Genes Occurs Early in Breast Carcinogenesis
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- 2023
18. Supplementary Table 1 from Concordant Epigenetic Silencing of Transforming Growth Factor-β Signaling Pathway Genes Occurs Early in Breast Carcinogenesis
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Susan J. Clark, Roger R. Reddel, David A. Hume, Christine A. Wells, Timothy Ravasi, Bryce Vissel, Andrea Abdipranoto, Clare Stirzaker, John Melki, Lily I. Huschtscha, and Rebecca A. Hinshelwood
- Abstract
Supplementary Table 1 from Concordant Epigenetic Silencing of Transforming Growth Factor-β Signaling Pathway Genes Occurs Early in Breast Carcinogenesis
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- 2023
19. Supplementary Figure 4 from Concordant Epigenetic Silencing of Transforming Growth Factor-β Signaling Pathway Genes Occurs Early in Breast Carcinogenesis
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Susan J. Clark, Roger R. Reddel, David A. Hume, Christine A. Wells, Timothy Ravasi, Bryce Vissel, Andrea Abdipranoto, Clare Stirzaker, John Melki, Lily I. Huschtscha, and Rebecca A. Hinshelwood
- Abstract
Supplementary Figure 4 from Concordant Epigenetic Silencing of Transforming Growth Factor-β Signaling Pathway Genes Occurs Early in Breast Carcinogenesis
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- 2023
20. Supplementary Methods and Materials from Concordant Epigenetic Silencing of Transforming Growth Factor-β Signaling Pathway Genes Occurs Early in Breast Carcinogenesis
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Susan J. Clark, Roger R. Reddel, David A. Hume, Christine A. Wells, Timothy Ravasi, Bryce Vissel, Andrea Abdipranoto, Clare Stirzaker, John Melki, Lily I. Huschtscha, and Rebecca A. Hinshelwood
- Abstract
Supplementary Methods and Materials from Concordant Epigenetic Silencing of Transforming Growth Factor-β Signaling Pathway Genes Occurs Early in Breast Carcinogenesis
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- 2023
21. Supplementary Figure 1 from Concordant Epigenetic Silencing of Transforming Growth Factor-β Signaling Pathway Genes Occurs Early in Breast Carcinogenesis
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Susan J. Clark, Roger R. Reddel, David A. Hume, Christine A. Wells, Timothy Ravasi, Bryce Vissel, Andrea Abdipranoto, Clare Stirzaker, John Melki, Lily I. Huschtscha, and Rebecca A. Hinshelwood
- Abstract
Supplementary Figure 1 from Concordant Epigenetic Silencing of Transforming Growth Factor-β Signaling Pathway Genes Occurs Early in Breast Carcinogenesis
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- 2023
22. Data from Concordant Epigenetic Silencing of Transforming Growth Factor-β Signaling Pathway Genes Occurs Early in Breast Carcinogenesis
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Susan J. Clark, Roger R. Reddel, David A. Hume, Christine A. Wells, Timothy Ravasi, Bryce Vissel, Andrea Abdipranoto, Clare Stirzaker, John Melki, Lily I. Huschtscha, and Rebecca A. Hinshelwood
- Abstract
Human mammary epithelial cells (HMEC) grown under standard cell culture conditions enter a growth phase referred to as selection, but a subpopulation is able to escape from arrest and continue to proliferate. These cells, called post-selection or variant HMECs, may be derived from progenitor cells found in normal mammary epithelium that subsequently acquire premalignant lesions, including p16INK4A promoter hypermethylation. Epigenetic silencing of tumor suppressor genes through DNA methylation and histone modification is an early event in tumorigenesis. A major challenge is to find genes or gene pathways that are commonly silenced to provide early epigenetic diagnostic and therapeutic cancer targets. To identify very early epigenetic events that occur in breast cancer, we used microarrays to screen for gene pathways that were suppressed in post-selection HMECs but reactivated after treatment with the demethylation agent 5-aza-2′-deoxycytidine. We found that several members of the transforming growth factor β (TGF-β) signaling pathway were consistently down-regulated in the post-selection HMEC populations, and this was associated with a marked decrease in Smad4 nuclear staining. Gene suppression was not associated with DNA methylation but with chromatin remodeling, involving a decrease in histone H3 lysine 27 trimethylation and an increase in histone H3 lysine 9 dimethylation and deacetylation. These results show for the first time that TGF-β2, its receptors TGF-βR1 and TGF-βR2, and activator thrombospondin-1 are concordantly suppressed early in breast carcinogenesis by histone modifications and indicate that the TGF-β signaling pathway is a novel target for gene activation by epigenetic therapy. [Cancer Res 2007;67(24):11517–27]
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- 2023
23. Discovery of NRG1-VII: a novel myeloid-derived class of NRG1 isoforms
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Miguel Ángel Berrocal-Rubio, Yair David Joseph Pawer, Marija Dinevska, Ricardo De Paoli-Iseppi, Samuel S. Widodo, Nadia Rajab, Will De Nardo, Jeannette C. Hallab, Anran Li, Theo Mantamadiotis, Michael B. Clark, and Christine A. Wells
- Abstract
Macrophages are a primary source of the growth factor Neuregulin-1 (NRG1), which has pleiotropic roles in proliferation and differentiation of the stem cell niche in different tissues, and has been implicated in gut, brain and muscle development and repair. Six isoform classes of NRG1 and over 28 protein isoforms have been previously described. Here we report a new class of NRG1, designated NRG1-VII to denote the start of this isoform class from a myeloid-specific transcriptional start site (TSS). Long-read sequencing identified up to nine different NRG1-VII transcripts that show major structural differences from one another due to use of cassette exons and alternative stop codons. Expression of NRG1-VII was confirmed in human monocytes and tissue resident macrophages. Isoform switching via cassette exon usage and alternate polyadenylation was apparent during monocyte maturation and macrophage differentiation. NRG1-VII is the major class expressed by the myeloid lineage, including tissue-resident macrophages. The size and structure of type VII isoforms suggests that they may be more diffusible than other NRG1 classes, however, the specific roles of type VII variants in tissue homeostasis and repair have not yet been determined.
- Published
- 2023
24. Ontology Challenges for the Stem Cell Community: Towards Integrative Data Mining in the Stemformatics Atlas.
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Chris Pacheco Rivera, Rowland Mosbergen, Othmar Korn, Tyrone Chen, Isha Nagpal, and Christine A. Wells
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- 2017
25. Discovery of NRG1-VII: A Myeloid-Derived Class of NRG1 Isoforms
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Miguel Angel Berrocal-Rubio, Yair D.J Prawer, Marija Dinevska, Ricardo De Paoli-Iseppi, Samuel S. Widodo, Nadia Rajab, William De Nardo, Jeannette C. Hallab, Anran Li, Theo Mantamadiotis, Michael B. Clark, and Christine A. Wells
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- 2023
26. A promoter-level mammalian expression atlas.
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The Fantom Consortium, RIKEN PMII, RIKEN CLST (DGT), Alistair R. R. Forrest, Hideya Kawaji, Michael Rehli, J. Kenneth Baillie, Michiel J. L. de Hoon, Vanja Haberle, Timo Lassmann, Ivan V. Kulakovskiy, Marina Lizio, Masayoshi Itoh, Robin Andersson, Christopher J. Mungall, Terrence F. Meehan, Sebastian Schmeier, Nicolas Bertin, Mette Jørgensen, Emmanuel Dimont, Erik Arner, Christian Schmidl, Ulf Schaefer, Yulia A. Medvedeva, Charles Plessy, Morana Vitezic, Jessica Severin, Colin A. M. Semple, Yuri Ishizu, Robert S. Young, Margherita Francescatto, Intikhab Alam, Davide Albanese, Gabriel M. Altschuler, Takahiro Arakawa, John A. C. Archer, Peter Arner, Magda Babina, Sarah Rennie, Piotr J. Balwierz, Anthony G. Beckhouse, Swati Pradhan-Bhatt, Judith A. Blake, Antje Blumenthal, Beatrice Bodega, Alessandro Bonetti, James Briggs, Frank Brombacher, A. Maxwell Burroughs, Andrea Califano, Carlo V. Cannistraci, Daniel Carbajo, Yun Chen, Marco Chierici, Yari Ciani, Hans Clevers, Emiliano Dalla, Carrie A. Davis, Michael Detmar, Alexander D. Diehl, Taeko Dohi, Finn Drabløs, Albert S. B. Edge, Matthias Edinger, Karl Ekwall, Mitsuhiro Endoh, Hideki Enomoto, Michela Fagiolini, Lynsey Fairbairn, Hai Fang, Mary C. Farach-Carson, Geoffrey J. Faulkner, Alexander V. Favorov, Malcolm E. Fisher, Martin C. Frith, Rie Fujita, Shiro Fukuda, Cesare Furlanello, Masaaki Furuno, Jun-ichi Furusawa, Teunis B. Geijtenbeek, Andrew P. Gibson, Thomas R. Gingeras, Daniel Goldowitz, Julian Gough, Sven Guhl, Reto Guler, Stefano Gustincich, Thomas J. Ha, Masahide Hamaguchi, Mitsuko Hara, Matthias Harbers, Jayson Harshbarger, Akira Hasegawa, Yuki Hasegawa, Takehiro Hashimoto, Meenhard Herlyn, Kelly J. Hitchens, Shannan J. Ho Sui, Oliver M. Hofmann, Ilka Hoof, Fumi Hori, Lukasz Huminiecki, Kei Iida, Tomokatsu Ikawa, Boris R. Jankovic, Hui Jia, Anagha Joshi, Giuseppe Jurman, Bogumil Kaczkowski, Chieko Kai, Kaoru Kaida, Ai Kaiho, Kazuhiro Kajiyama, Mutsumi Kanamori-Katayama, Artem S. Kasianov, Takeya Kasukawa, Shintaro Katayama, Sachi Kato, Shuji Kawaguchi, Hiroshi Kawamoto, Yuki I. Kawamura, Tsugumi Kawashima, Judith S. Kempfle, Tony J. Kenna, Juha Kere, Levon M. Khachigian, Toshio Kitamura, S. Peter Klinken, Alan J. Knox, Miki Kojima, Soichi Kojima, Naoto Kondo, Haruhiko Koseki, Shigeo Koyasu, Sarah Krampitz, Atsutaka Kubosaki, Andrew T. Kwon, Jeroen F. J. Laros, Weonju Lee, Andreas Lennartsson, Kang Li, Berit Lilje, Leonard Lipovich, Alan Mackay-Sim, Ri-ichiroh Manabe, Jessica Cara Mar, Benoit Marchand, Anthony Mathelier, Niklas Mejhert, Alison M. Meynert, Yosuke Mizuno, David A. de Lima Morais, Hiromasa Morikawa, Mitsuru Morimoto, Kazuyo Moro, Efthymios Motakis, Hozumi Motohashi, Christine Mummery, Mitsuyoshi Murata, Sayaka Nagao-Sato, Yutaka Nakachi, Fumio Nakahara, Toshiyuki Nakamura, Yukio Nakamura, Kenichi Nakazato, Erik van Nimwegen, Noriko Ninomiya, Hiromi Nishiyori, Shohei Noma, Tadasuke Nozaki, Soichi Ogishima, Naganari Ohkura, Hiroko Ohmiya, Hiroshi Ohno, Mitsuhiro Ohshima, Mariko Okada-Hatakeyama, Yasushi Okazaki, Valerio Orlando, Dmitry A. Ovchinnikov, Arnab Pain, Robert Passier, Margaret Patrikakis, Helena Persson, Silvano Piazza, James G. D. Prendergast, Owen J. L. Rackham, Jordan A. Ramilowski, Mamoon Rashid, Timothy Ravasi, Patrizia Rizzu, Marco Roncador, Sugata Roy, Morten B. Rye, Eri Saijyo, Antti Sajantila, Akiko Saka, Shimon Sakaguchi, Mizuho Sakai, Hiroki Sato, Hironori Sato, Suzana Savvi, Alka Saxena, Claudio Schneider, Erik A. Schultes, Gundula G. Schulze-Tanzil, Anita Schwegmann, Thierry Sengstag, Guojun Sheng, Hisashi Shimoji, Yishai Shimoni, Jay W. Shin, Christophe Simon, Daisuke Sugiyama, Takaaki Sugiyama, Masanori Suzuki, Naoko Suzuki, Rolf K. Swoboda, Peter A. C. 't Hoen, Michihira Tagami, Naoko Takahashi, Jun Takai, Hiroshi Tanaka, Hideki Tatsukawa, Zuotian Tatum, Mark Thompson 0002, Hiroo Toyoda, Tetsuro Toyoda, Eivind Valen, Marc van de Wetering, Linda M. van den Berg, Roberto Verardo, Dipti Vijayan, Ilya E. Vorontsov, Wyeth W. Wasserman, Shoko Watanabe, Christine A. Wells, Louise N. Winteringham, Ernst Wolvetang, Emily J. Wood, Yoko Yamaguchi, Masayuki Yamamoto, Misako Yoneda, Yohei Yonekura, Shigehiro Yoshida, Susan E. Zabierowski, Peter G. Zhang, Xiaobei Zhao, Silvia Zucchelli, Kim M. Summers, Harukazu Suzuki, Carsten O. Daub, Jun Kawai, Peter Heutink, Winston Hide, Tom C. Freeman, Boris Lenhard, Vladimir B. Bajic, Martin S. Taylor, Vsevolod J. Makeev, Albin Sandelin, David A. Hume, Piero Carninci, and Yoshihide Hayashizaki
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- 2014
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27. An integrated analysis of human myeloid cells identifies gaps in in vitro models of in vivo biology
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Mariola Kurowska-Stolarska, Chris M. Pacheco, Kim-Anh Lê Cao, Paul W. Angel, Vanta Jameson, Yidi Deng, Jennifer Gu, Christine A. Wells, Simon Milling, Andrew L. Laslett, Jarny Choi, Nadia Rajab, and Matt Rutar
- Subjects
Resource ,tissue-resident macrophage ,Pluripotent Stem Cells ,0301 basic medicine ,pluripotent stem cell–derived macrophage ,Myeloid ,dendritic cell ,microglia ,Kupffer cell ,macrophage ,Computational biology ,Biology ,Biochemistry ,Regenerative medicine ,Monocytes ,Cell Line ,Transcriptome ,03 medical and health sciences ,0302 clinical medicine ,Genetics ,medicine ,Humans ,Cells, Cultured ,hematopoietic progenitor ,monocyte-derived macrophage ,Microglia ,Gene Expression Profiling ,Macrophages ,Monocyte ,Cell Biology ,Dendritic cell ,Phenotype ,030104 developmental biology ,medicine.anatomical_structure ,monocyte ,Single-Cell Analysis ,030217 neurology & neurosurgery ,Developmental Biology - Abstract
Summary The Stemformatics myeloid atlas is an integrated transcriptome atlas of human macrophages and dendritic cells that systematically compares freshly isolated tissue-resident, cultured, and pluripotent stem cell–derived myeloid cells. Three classes of tissue-resident macrophage were identified: Kupffer cells and microglia; monocyte-associated; and tumor-associated macrophages. Culture had a major impact on all primary cell phenotypes. Pluripotent stem cell–derived macrophages were characterized by atypical expression of collagen and a highly efferocytotic phenotype. Myeloid subsets, and phenotypes associated with derivation, were reproducible across experimental series including data projected from single-cell studies, demonstrating that the atlas provides a robust reference for myeloid phenotypes. Implementation in Stemformatics.org allows users to visualize patterns of sample grouping or gene expression for user-selected conditions and supports temporary upload of your own microarray or RNA sequencing samples, including single-cell data, to benchmark against the atlas., Graphical abstract, Highlights • A reference transcriptome atlas for human macrophage biology • Culture alters primary myeloid phenotypes • Pluripotent stem cell–derived macrophages retain a common stromal signature • FLT3L-derived cord blood DCs lack expression of key pattern recognition receptors, In this article, Wells and colleagues describe an integrated myeloid transcriptome atlas. Analysis resulted in tissue-resident populations being categorized into three broad classes, with culture also found to impact primary cell phenotypes. Pluripotent stem cell–derived cells were compared with their in vivo counterparts, differing in maturation, efferocytosis capacity, and ectopic expression of extracellular matrix genes.
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- 2021
28. The Human Dendritic Cell Atlas: An Integrated Transcriptional Tool to Study Human Dendritic Cell Biology
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Zahra Elahi, Paul W. Angel, Suzanne K. Butcher, Nadia Rajab, Jarny Choi, Yidi Deng, Justine D. Mintern, Kristen Radford, and Christine A. Wells
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Systems Immunology ,Immunology ,Immunology and Allergy - Abstract
Dendritic cells (DCs) are functionally diverse and are present in most adult tissues, but deep understanding of human DC biology is hampered by relatively small numbers of these in circulation and their short lifespan in human tissues. We built a transcriptional atlas of human DCs by combining samples from 14 expression profiling studies derived from 10 laboratories. We identified significant gene expression variation of DC subset–defining markers across tissue type and upon viral or bacterial stimulation. We further highlight critical gaps between in vitro–derived DC subsets and their in vivo counterparts and provide evidence that monocytes or cord blood progenitor in vitro–differentiated DCs fail to capture the repertoire of primary DC subsets or behaviors. In constructing a reference DC atlas, we provide an important resource for the community wishing to identify and annotate tissue-specific DC subsets from single-cell datasets, or benchmark new in vitro models of DC biology.
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- 2022
29. Hospital emergency department visits made by developmentally disabled adolescents with oral complications
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Kathryn A. Atchison, Vinodh Bhoopathi, and Christine R. Wells
- Abstract
PurposeWe used Andersen's Behavioral Model in a cross-sectional study to determine the factors associated with utilization of the emergency department (ED), controlling for whether an adolescent has a developmental disability (DD) and one or more oral complications (toothaches, decayed teeth, bleeding gums, eating or swallowing problems).MethodsData from the 2016–2019 National Survey of Children's Health (NSCH) was used for this secondary data analysis study. We used frequencies and percentages to describe the sample characteristics. Chi-square tests were used for bivariate analyses. Multivariable logistic regression modeling was conducted to predict ED visits by adolescents aged 10–17 controlling for predisposing, enabling, and need variables.ResultsThe sample consisted of 68,942 adolescents who were primarily male, non-Hispanic White, and born in the U.S. Parents reported that 69% of the adolescents had neither a DD nor an oral complication; 10% had no DD but experienced one or more oral complication; 16% had a DD but no oral complication; and 5% had both DDs and one or more oral complication. Adolescents with both a DD and an oral complication reported the highest level of ED visits at 33%, compared to 14% of adolescents with neither DD nor oral complication. Regression analysis showed that adolescents with a DD and oral complication (OR: 2.0, 95% CI: 1.64–2.54, p < 0.0001), and those with DDs but no oral complications (OR: 1.45, 95% CI: 1.25–1.68, p < 0.0001) were at higher odds of having an ED visit compared to those with neither a DD nor an oral complication. Not having a Medical Home increased the likelihood of ED visits by 14% (p = 0.02). Those with private insurance (OR: 0.63, 95% CI: 0.53–0.75, p < 0.0001) and those from a family where the highest level of education was some college and above (OR: 0.85, 95% CI: 0.73–0.98, p = 0.03) were less likely than their counterparts to have had an ED visit.ConclusionAdolescents with DDs and oral complications utilize ED visits more frequently than those with neither DDs nor oral complications. Integrating the dental and medical health systems and incorporating concepts of a Patient-Centered Medical Home could improve overall health care and reduce ED visits for adolescents.
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- 2022
30. Proliferation drives quorum sensing of microbial products in human macrophage populations
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Nadia Rajab, Linden J. Gearing, Ruqian Lyu, Yair D.J. Prawer, Paul W. Angel, Sean M. Grimmond, Andrew L. Laslett, Davis J. McCarthy, and Christine A. Wells
- Abstract
Macrophages coordinate the initial host inflammatory response to tissue infection, as well as mediating the reparative phase, by producing growth factors that promote tissue repair. One model of this functional dichotomy is that peripherally recruited monocyte-derived macrophages drive acute inflammatory responses to infection, whereas tissue-resident macrophages are responsible for tissue repair. Alternatively, inflammation and repair may be inter-dependent molecular programs, such that both recruited and resident cells have equivalent capacity to contribute. Repeated exposure to pathogenic challenge results in innate tolerance, which may also alter the contributions of discrete macrophage populations to inflammation or repair. In this study a village model of tissue resident and recruited macrophages was created using induced pluripotent stem cell-derived macrophages and peripheral blood monocyte-derived macrophages, respectively. Population responses to repeated exposure to lipopolysaccharide were assessed with single-cell RNA sequencing and donors demultiplexed with Vireo. A subset of genes escaped classical tolerance programs in the iPSC, but not monocyte-derived macrophages, and this was associated with differences in their proliferative capacity. This suggests that targeting the proliferative resident macrophages would be most effective to limit inflammatory signaling.
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- 2022
31. Defining an informativeness metric for clustering gene expression data.
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Jessica Cara Mar, Christine A. Wells, and John Quackenbush
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- 2011
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32. Identifying Co-Regulating microRNA Groups.
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Jiyuan An, Kwok Pui Choi, Christine A. Wells, and Yi-Ping Phoebe Chen
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- 2010
- Full Text
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33. Multipotent RAG1+ progenitors emerge directly from haemogenic endothelium in human pluripotent stem cell-derived haematopoietic organoids
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Freya Bruveris, Jacqueline V. Schiesser, Andrew G. Elefanty, Tyrone Chen, Santhosh V. Kumar, Ali Motazedian, Elizabeth Ng, Christine A. Wells, Ann P. Chidgey, and Edouard G. Stanley
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0303 health sciences ,Cellular differentiation ,chemical and pharmacologic phenomena ,Cell Biology ,Biology ,Cell biology ,03 medical and health sciences ,Haematopoiesis ,0302 clinical medicine ,hemic and lymphatic diseases ,030220 oncology & carcinogenesis ,Hemangioblast ,CD90 ,Lymphopoiesis ,Stem cell ,Progenitor cell ,Induced pluripotent stem cell ,030304 developmental biology - Abstract
Defining the ontogeny of the human adaptive immune system during embryogenesis has implications for understanding childhood diseases including leukaemias and autoimmune conditions. Using RAG1:GFP human pluripotent stem cell reporter lines, we examined human T-cell genesis from pluripotent-stem-cell-derived haematopoietic organoids. Under conditions favouring T-cell development, RAG1+ cells progressively upregulated a cohort of recognized T-cell-associated genes, arresting development at the CD4+CD8+ stage. Sort and re-culture experiments showed that early RAG1+ cells also possessed B-cell, myeloid and erythroid potential. Flow cytometry and single-cell-RNA-sequencing data showed that early RAG1+ cells co-expressed the endothelial/haematopoietic progenitor markers CD34, VECAD and CD90, whereas imaging studies identified RAG1+ cells within CD31+ endothelial structures that co-expressed SOX17+ or the endothelial marker CAV1. Collectively, these observations provide evidence for a wave of human T-cell development that originates directly from haemogenic endothelium via a RAG1+ intermediate with multilineage potential.
- Published
- 2020
34. Defining the role of nuclear factor NF-κB p105 subunit in human macrophage by transcriptomic analysis of NFKB1 knockout THP-1 cells
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Fatma O. Kok, Domenico Somma, Christine A. Wells, Ruaidhrí J. Carmody, and David Kerrigan
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NFKB1 ,Monocyte ,Immunology ,Inflammation ,macrophage ,Biology ,RC581-607 ,NF-κB ,Cell biology ,THP1 cells ,Interleukin 10 ,transcriptomics ,medicine.anatomical_structure ,Immune system ,toll-like receptors ,medicine ,Immunology and Allergy ,Macrophage ,Tumor necrosis factor alpha ,medicine.symptom ,Immunologic diseases. Allergy ,Transcription factor - Abstract
Since its discovery over 30 years ago the NF-ĸB family of transcription factors has gained the status of master regulator of the immune response. Much of what we understand of the role of NF-ĸB in immune development, homeostasis and inflammation comes from studies of mice null for specific NF-ĸB subunit encoding genes. The role of inflammation in diseases that affect a majority of individuals with health problems globally further establishes NF-ĸB as an important pathogenic factor. More recently, genomic sequencing has revealed loss of function mutations in the NFKB1 gene as the most common monogenic cause of common variable immunodeficiencies in Europeans. NFKB1 encodes the p105 subunit of NF-ĸB which is processed to generate the NF-ĸB p50 subunit. NFKB1 is the most highly expressed transcription factor in macrophages, key cellular drivers of inflammation and immunity. Although a key role for NFKB1 in the control of the immune system is apparent from Nfkb1-/- mouse studies, we know relatively little of the role of NFKB1 in regulating human macrophage responses. In this study we use the THP1 monocyte cell line and CRISPR/Cas9 gene editing to generate a model of NFKB1-/- human macrophages. Transcriptomic analysis reveals that activated NFKB1-/- macrophages are more pro-inflammatory than wild type controls and express elevated levels of TNF, IL6, and IL1B, but also have reduced expression of co-stimulatory factors important for the activation of T cells and adaptive immune responses such as CD70, CD83 and CD209. NFKB1-/- THP1 macrophages recapitulate key observations in individuals with NFKB1 haploinsufficiency including decreased IL10 expression. These data supporting their utility as an in vitro model for understanding the role of NFKB1 in human monocytes and macrophages and indicate that of loss of function NFKB1 mutations in these cells is an important component in the associated pathology.
- Published
- 2021
35. Transcriptional Profiling of Stem Cells: Moving from Descriptive to Predictive Paradigms
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Christine A. Wells and Jarny Choi
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0301 basic medicine ,Transcription, Genetic ,RNA Splicing ,Review ,Computational biology ,single-cell sequencing ,Biology ,Biochemistry ,Transcriptome ,03 medical and health sciences ,0302 clinical medicine ,Single-cell analysis ,Genetics ,Humans ,Profiling (information science) ,pluripotent stem cell ,Induced pluripotent stem cell ,lcsh:QH301-705.5 ,lcsh:R5-920 ,Stem Cells ,Computational Biology ,reprogramming ,bioinformatics ,Cell Biology ,Models, Theoretical ,Chromatin ,030104 developmental biology ,lcsh:Biology (General) ,Single cell sequencing ,RNA ,Single-Cell Analysis ,Stem cell ,lcsh:Medicine (General) ,transcriptome ,Reprogramming ,030217 neurology & neurosurgery ,Developmental Biology - Abstract
Transcriptional profiling is a powerful tool commonly used to benchmark stem cells and their differentiated progeny. As the wealth of stem cell data builds in public repositories, we highlight common data traps, and review approaches to combine and mine this data for new cell classification and cell prediction tools. We touch on future trends for stem cell profiling, such as single-cell profiling, long-read sequencing, and improved methods for measuring molecular modifications on chromatin and RNA that bring new challenges and opportunities for stem cell analysis., In this review, Wells and Choi highlight developments in stem cell transcriptome profiling that are moving the field from descriptive to predictive modelling of stem cell biology. The authors review emergence of reference atlas databases for benchmarking new stem cell models, putting together a wish list for future technologies, including single-cell sequencing, that harmonise multi-scaled measurements of stem cell systems.
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- 2019
36. Stemformatics: visualize and download curated stem cell data
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Paul W. Angel, Christine A. Wells, Rowland Mosbergen, Tyrone Chen, Steve Englart, Isha Nagpal, Jarny Choi, Chris M. Pacheco, and Othmar Korn
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Cellular differentiation ,Computational biology ,Biology ,Transcriptome ,03 medical and health sciences ,0302 clinical medicine ,Databases, Genetic ,Genetics ,Database Issue ,Animals ,Humans ,Profiling (information science) ,Gene ,Data Curation ,030304 developmental biology ,0303 health sciences ,Genes, Essential ,Data curation ,Sequence Analysis, RNA ,Stem Cells ,Cell Differentiation ,Housekeeping gene ,Gene expression profiling ,Reprogramming ,Software ,030217 neurology & neurosurgery - Abstract
Stemformatics is an established gene expression data portal containing over 420 public gene expression datasets derived from microarray, RNA sequencing and single cell profiling technologies. Developed for the stem cell community, it has a major focus on pluripotency, tissue stem cells, and staged differentiation. Stemformatics includes curated ‘collections’ of data relevant to cell reprogramming, as well as hematopoiesis and leukaemia. Rather than simply rehosting datasets as they appear in public repositories, Stemformatics uses a stringent set of quality control metrics and its own pipelines to process handpicked datasets from raw files. This means that about 30% of datasets processed by Stemformatics fail the quality control metrics and never make it to the portal, ensuring that Stemformatics data are of high quality and have been processed in a consistent manner. Stemformatics provides easy-to-use and intuitive tools for biologists to visually explore the data, including interactive gene expression profiles, principal component analysis plots and hierarchical clusters, among others. The addition of tools that facilitate cross-dataset comparisons provides users with snapshots of gene expression in multiple cell and tissues, assisting the identification of cell-type restricted genes, or potential housekeeping genes. Stemformatics is freely available at stemformatics.org.
- Published
- 2018
37. Designer macrophages: Pitfalls and opportunities for modelling macrophage phenotypes from pluripotent stem cells
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Matt Rutar, Nadia Rajab, Christine A. Wells, and Andrew L. Laslett
- Subjects
Pluripotent Stem Cells ,0301 basic medicine ,Cancer Research ,Innate immune system ,Macrophages ,Cellular differentiation ,Induced Pluripotent Stem Cells ,Cell Differentiation ,Cell Biology ,Biology ,Regenerative medicine ,Immunity, Innate ,Monocytes ,Cell biology ,03 medical and health sciences ,030104 developmental biology ,Directed differentiation ,Immune system ,Humans ,Macrophage ,Induced pluripotent stem cell ,Molecular Biology ,Tissue homeostasis ,Developmental Biology - Abstract
Macrophages are phagocytic immune cells resident in every tissue that are not only important for host defence, but are also involved in tissue homeostasis, injury, and disease. Despite increasingly sophisticated methods for in vitro macrophage isolation, expansion and activation over the past three decades, these have largely been restricted to modelling bone-marrow or blood-derived cells. The in vitro derivation of macrophages from human pluripotent stem cells provides new opportunities to study macrophage biology, including the factors that impact human myeloid development and those that induce macrophage activation. While sharing many of the functional characteristics of monocyte-derived macrophages, stem cell-derived macrophages may offer new opportunities to understand the role of development or tissue context in innate immune cell function. Immune responsiveness to pathogenic challenge is known to be impacted by a macrophage's history of prior exposure, as well as ontogeny and tissue context. Therefore, we explore the factors of in vitro derivation likely to influence macrophage phenotype and function.
- Published
- 2018
38. Defining the Role of Nuclear Factor (NF)-κB p105 Subunit in Human Macrophage by Transcriptomic Analysis of
- Author
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Domenico, Somma, Fatma O, Kok, David, Kerrigan, Christine A, Wells, and Ruaidhrí J, Carmody
- Subjects
Inflammation ,Immunity, Cellular ,NFKB1 ,THP-1 Cells ,Gene Expression Profiling ,Macrophages ,Toll-Like Receptors ,Immunology ,NF-kappa B p50 Subunit ,macrophage ,Adaptive Immunity ,Macrophage Activation ,NF-κB ,THP1 cells ,Gene Knockout Techniques ,transcriptomics ,Phenotype ,toll-like receptors ,Cytokines ,Humans ,RNA-Seq ,CRISPR-Cas Systems ,Transcriptome ,Original Research - Abstract
Since its discovery over 30 years ago the NF-ĸB family of transcription factors has gained the status of master regulator of the immune response. Much of what we understand of the role of NF-ĸB in immune development, homeostasis and inflammation comes from studies of mice null for specific NF-ĸB subunit encoding genes. The role of inflammation in diseases that affect a majority of individuals with health problems globally further establishes NF-ĸB as an important pathogenic factor. More recently, genomic sequencing has revealed loss of function mutations in the NFKB1 gene as the most common monogenic cause of common variable immunodeficiencies in Europeans. NFKB1 encodes the p105 subunit of NF-ĸB which is processed to generate the NF-ĸB p50 subunit. NFKB1 is the most highly expressed transcription factor in macrophages, key cellular drivers of inflammation and immunity. Although a key role for NFKB1 in the control of the immune system is apparent from Nfkb1-/- mouse studies, we know relatively little of the role of NFKB1 in regulating human macrophage responses. In this study we use the THP1 monocyte cell line and CRISPR/Cas9 gene editing to generate a model of NFKB1-/- human macrophages. Transcriptomic analysis reveals that activated NFKB1-/- macrophages are more pro-inflammatory than wild type controls and express elevated levels of TNF, IL6, and IL1B, but also have reduced expression of co-stimulatory factors important for the activation of T cells and adaptive immune responses such as CD70, CD83 and CD209. NFKB1 -/- THP1 macrophages recapitulate key observations in individuals with NFKB1 haploinsufficiency including decreased IL10 expression. These data supporting their utility as an in vitro model for understanding the role of NFKB1 in human monocytes and macrophages and indicate that of loss of function NFKB1 mutations in these cells is an important component in the associated pathology.
- Published
- 2021
39. Challenges for Computational Stem Cell Biology: A Discussion for the Field
- Author
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Samantha A. Morris, John F. Ouyang, Nancy Mah, Owen J. L. Rackham, Christine A. Wells, Patrick Cahan, Yoshiaki Tanaka, Anne L. Plant, and Publica
- Subjects
0301 basic medicine ,Field (Bourdieu) ,Research ,Stem Cells ,Computational Biology ,Cell Biology ,Biology ,Meeting Report ,Biochemistry ,Regenerative medicine ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,Genetics ,Humans ,Stem cell ,Stem cell biology ,Neuroscience ,030217 neurology & neurosurgery ,health care economics and organizations ,Developmental Biology - Abstract
The first meetup for Computational Stem Cell Biologists was held at the 2020 annual meeting of the International Society for Stem Cell Research. The discussions highlighted opportunities and barriers to computational stem cell research that require coordinated action across the stem cell sector.
- Published
- 2021
40. Computational Stem Cell Biology: open questions and guiding principles
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Susana M. Chuva de Sousa Lopes, Davide Cacchiarelli, Martin Hemberg, Patrick Cahan, Samantha A. Morris, Sara-Jane Dunn, Owen J. L. Rackham, Christine A. Wells, Antonio del Sol, Cahan, P., Cacchiarelli, D., Dunn, S. -J., Hemberg, M., de Sousa Lopes, S. M. C., Morris, S. A., Rackham, O. J. L., del Sol, A., and Wells, C. A.
- Subjects
0303 health sciences ,Guiding Principles ,Stem Cells ,Gene regulatory network ,Inference ,Computational Biology ,Cell Biology ,Cell typing ,Biology ,Regenerative Medicine ,Data science ,Regenerative medicine ,Article ,3. Good health ,03 medical and health sciences ,0302 clinical medicine ,Lineage tracing ,Drug Discovery ,Genetics ,Molecular Medicine ,Stem cell ,Stem cell biology ,030217 neurology & neurosurgery ,030304 developmental biology - Abstract
Computational biology is enabling an explosive growth in our understanding of stem cells and our ability to use them for disease modeling, regenerative medicine, and drug discovery. We discuss four topics that exemplify applications of computation to stem cell biology: cell typing, lineage tracing, trajectory inference, and regulatory networks. We use these examples to articulate principles that have guided computational biology broadly and call for renewed attention to these principles as computation becomes increasingly important in stem cell biology. We also discuss important challenges for this field with the hope that it will inspire more to join this exciting area.
- Published
- 2021
41. Access and Visualise High Quality Gene Expression Data with Stemformatics
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Jarny Choi and Christine A. Wells
- Published
- 2021
42. DLL4 and PDGF-BB regulate migration of human iPSC-derived skeletal myogenic progenitors
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Giulia Ferrari, Francesco Tedesco, Louise A. Moyle, Kirsty Mackinlay, Naira Naouar, SungWoo Choi, Francesco Muntoni, and Christine A. Wells
- Subjects
0303 health sciences ,biology ,Cell growth ,Regeneration (biology) ,Cell ,Skeletal muscle ,Cell migration ,Cell biology ,03 medical and health sciences ,0302 clinical medicine ,medicine.anatomical_structure ,030220 oncology & carcinogenesis ,medicine ,biology.protein ,Progenitor cell ,Stem cell ,Platelet-derived growth factor receptor ,030304 developmental biology - Abstract
SUMMARYMuscle satellite stem cells (MuSCs) are responsible for skeletal muscle growth and regeneration. Despite their differentiation potential, human MuSCs have limitedin vitroexpansion andin vivomigration capacity, limiting their use in cell therapies for diseases affecting multiple skeletal muscle groups such as muscular dystrophies. Several protocols have been developed to derive progenitor cells similar to MuSCs from human induced pluripotent stem cells (hiPSCs), in order to establish a source of myogenic cells with controllable proliferation and differentiation capacity. However, currently available hiPSC myogenic derivatives also suffer from limitations of cell migration, ultimately delaying their clinical translation. Here we provide evidence that activation of NOTCH and PDGF pathways with DLL4 and PDGF-BB improves migration of hiPSC-derived myogenic progenitorsin vitro. Transcriptomic and functional analyses demonstrate that this property is conserved across species and multiple hiPSC lines, including genetically-corrected hiPSC derivatives from a patient with Duchenne muscular dystrophy. DLL4 and PDGF-BB treatment had no negative impact on cell proliferation; cells maintained their myogenic memory, with differentiation fully rescued by NOTCH inhibition. RNAseq analysis indicate that pathways involved in cell migration are modulated in treated myogenic progenitors, consistent with results from functional profiling of cell motility at single cell resolution. Notably, treated cells also showed enhanced trans-endothelial migration in transwell assays. Enhancing extravasation is a key translational milestone for intravascular delivery of hiPSC myogenic derivatives: our study establishes the foundations of a transgene-free, developmentally inspired strategy to achieve this goal, moving hiPSCs one step closer to future muscle gene and cell therapies.
- Published
- 2021
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43. constclust: Consistent Clusters for scRNA-seq
- Author
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Kim-Anh Lê Cao, Isaac Virshup, Christine A. Wells, and Jarny Choi
- Subjects
Data set ,Current (mathematics) ,Computer science ,Consensus clustering ,Identity (object-oriented programming) ,Data mining ,Cluster analysis ,computer.software_genre ,Partition (database) ,computer - Abstract
1AbstractUnsupervised clustering to identify distinct cell types is a crucial step in the analysis of scRNA-seq data. Current clustering methods are dependent on a number of parameters whose effect on the resulting solution’s accuracy and reproducibility are poorly understood. The adjustment of clustering parameters is therefore ad-hoc, with most users deviating minimally from default settings. constclust is a novel meta-clustering method based on the idea that if the data contains distinct populations which a clustering method can identify, meaningful clusters should be robust to small changes in the parameters used to derive them. By reconciling solutions from a clustering method over multiple parameters, we can identify locally robust clusters of cells and their corresponding regions of parameter space. Rather than assigning cells to a single partition of the data set, this approach allows for discovery of discrete groups of cells which can correspond to the multiple levels of cellular identity. Additionally constclust requires significantly fewer computational resources than current consensus clustering methods for scRNA-seq data. We demonstrate the utility, accuracy, and performance of constclust as part of the analysis workflow. constclust is available at https://github.com/ivirshup/constclust1.
- Published
- 2020
44. Pharmacological validation of targets regulating CD14 during macrophage differentiation
- Author
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Catriona Sharp, Gisela Jimenez-Duran, Nil Turan, Emma Koppe, Meghana N. Patel, Christine A. Wells, Davina Angell, Seth L. Masters, Natalie Buchan, Ceara Rea, Rosario Luque-Martin, Palwinder K. Mander, Rick Cousins, Menno P.J. de Winther, Sharon G. Bernard, Graduate School, Medical Biochemistry, ACS - Atherosclerosis & ischemic syndromes, ACS - Pulmonary hypertension & thrombosis, AII - Inflammatory diseases, AGEM - Amsterdam Gastroenterology Endocrinology Metabolism, and ARD - Amsterdam Reproduction and Development
- Subjects
0301 basic medicine ,Cellular differentiation ,medicine.medical_treatment ,CD14 ,lcsh:Medicine ,Biology ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,0302 clinical medicine ,Downregulation and upregulation ,medicine ,Macrophage ,Humans ,lcsh:R5-920 ,SARS-CoV-2 ,lcsh:R ,COVID-19 ,Translation (biology) ,General Medicine ,medicine.disease ,Immunity, Innate ,Cell biology ,030104 developmental biology ,Cytokine ,030220 oncology & carcinogenesis ,Cytokine storm ,lcsh:Medicine (General) ,Function (biology) ,Research Paper - Abstract
The signalling receptor for LPS, CD14, is a key marker of, and facilitator for, pro-inflammatory macrophage function. Pro-inflammatory macrophage differentiation remains a process facilitating a broad array of disease pathologies, and has recently emerged as a potential target against cytokine storm in COVID19. Here, we perform a whole-genome CRISPR screen to identify essential nodes regulating CD14 expression in myeloid cells, using the differentiation of THP-1 cells as a starting point. This strategy uncovers many known pathways required for CD14 expression and regulating macrophage differentiation while additionally providing a list of novel targets either promoting or limiting this process. To speed translation of these results, we have then taken the approach of independently validating hits from the screen using well-curated small molecules. In this manner, we identify pharmacologically tractable hits that can either increase CD14 expression on non-differentiated monocytes or prevent CD14 upregulation during macrophage differentiation. An inhibitor for one of these targets, MAP2K3, translates through to studies on primary human monocytes, where it prevents upregulation of CD14 following M-CSF induced differentiation, and pro-inflammatory cytokine production in response to LPS. Therefore, this screening cascade has rapidly identified pharmacologically tractable nodes regulating a critical disease-relevant process.
- Published
- 2020
45. A simple, scalable approach to building a cross-platform transcriptome atlas
- Author
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Chris M. Pacheco, Jarny Choi, Paul W. Angel, Yidi Deng, Nadia Rajab, Christine A. Wells, Tyrone Chen, and Kim-Anh Lê Cao
- Subjects
0301 basic medicine ,Physiology ,Microarrays ,Computer science ,Gene Expression ,computer.software_genre ,Monocytes ,Transcriptome ,White Blood Cells ,Mathematical and Statistical Techniques ,0302 clinical medicine ,Animal Cells ,Gene expression ,Cross-platform ,Medicine and Health Sciences ,Cluster Analysis ,Profiling (information science) ,Lymphocytes ,Biology (General) ,Data Curation ,Principal Component Analysis ,0303 health sciences ,Ecology ,Statistics ,Genomics ,Body Fluids ,Blood ,Bioassays and Physiological Analysis ,medicine.anatomical_structure ,Computational Theory and Mathematics ,Modeling and Simulation ,Physical Sciences ,Scalability ,Data mining ,Anatomy ,Cellular Types ,DNA microarray ,Transcriptome Analysis ,Research Article ,Data integration ,QH301-705.5 ,Immune Cells ,Immunology ,Research and Analysis Methods ,Cellular and Molecular Neuroscience ,03 medical and health sciences ,Annotation ,Atlas (anatomy) ,Genetics ,medicine ,Humans ,Statistical Methods ,Cluster analysis ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,Blood Cells ,Data curation ,Gene Expression Profiling ,Biology and Life Sciences ,Computational Biology ,Cell Biology ,Genome Analysis ,030104 developmental biology ,Workflow ,Multivariate Analysis ,computer ,Mathematics ,030217 neurology & neurosurgery - Abstract
Gene expression atlases have transformed our understanding of the development, composition and function of human tissues. New technologies promise improved cellular or molecular resolution, and have led to the identification of new cell types, or better defined cell states. But as new technologies emerge, information derived on old platforms becomes obsolete. We demonstrate that it is possible to combine a large number of different profiling experiments summarised from dozens of laboratories and representing hundreds of donors, to create an integrated molecular map of human tissue. As an example, we combine 850 samples from 38 platforms to build an integrated atlas of human blood cells. We achieve robust and unbiased cell type clustering using a variance partitioning method, selecting genes with low platform bias relative to biological variation. Other than an initial rescaling, no other transformation to the primary data is applied through batch correction or renormalisation. Additional data, including single-cell datasets, can be projected for comparison, classification and annotation. The resulting atlas provides a multi-scaled approach to visualise and analyse the relationships between sets of genes and blood cell lineages, including the maturation and activation of leukocytes in vivo and in vitro. In allowing for data integration across hundreds of studies, we address a key reproduciblity challenge which is faced by any new technology. This allows us to draw on the deep phenotypes and functional annotations that accompany traditional profiling methods, and provide important context to the high cellular resolution of single cell profiling. Here, we have implemented the blood atlas in the open access Stemformatics.org platform, drawing on its extensive collection of curated transcriptome data. The method is simple, scalable and amenable for rapid deployment in other biological systems or computational workflows., Author summary Combining data from many different studies is an attractive way of capturing new aspects of the biology being studied. Biological variance attributable to cell type, cellular niche, origin, disease status or environmental stimuli is the basis of most small-n transcriptome studies. In aggregation, these promise to capture emergent dimensions of a biology that is not possible to view from any individual study. However biological signal is easily swamped by technical artifact, especially when data is generated on platforms with profoundly different data structures. This is the case when comparing microarray data to RNAseq, or RNAseq to single cell profiling. Consequently, transcriptome atlases are generally comprised from a small number of donors/conditions surveyed using one technology platform. In this paper we present a simple and scalable data integration method that is platform agnostic. We provide a proof-of-principle by constructing an atlas of blood cells that combines many data sets measured on different platforms, and that in combination, recapitulates the known blood hierarchy. The atlas provides a reference to compare external samples to, allowing users to benchmark new derivation or isolation methods. It also provides a reference point for new data types, such as the classification of single cells. The approach allows for FAIR data reuse and robust identification of molecular signatures across multiple studies and experimental conditions.
- Published
- 2020
46. Reimagining Merit and Representation: Promoting Equity and Reducing Bias in GME Through Holistic Review
- Author
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Nicolás E, Barceló, Sonya, Shadravan, Christine R, Wells, Nichole, Goodsmith, Brittany, Tarrant, Trevor, Shaddox, Yvonne, Yang, Eraka, Bath, and Katrina, DeBonis
- Subjects
Bias ,Humans ,Internship and Residency ,Medicine ,Schools, Medical - Abstract
This study aims to evaluate the capacity of a holistic review process in comparison with non-holistic approaches to facilitate mission-driven recruitment in residency interview screening and selection, with particular attention to the promotion of race equity for applicants underrepresented in medicine (URM).Five hundred forty-seven applicants to a psychiatry residency program from US allopathic medical schools were evaluated for interview selection via three distinct screening rubrics-one holistic approach (Holistic Review; HR) and two non-holistic processes: Traditional (TR) and Traditional Modified (TM). Each applicant was assigned a composite score corresponding to each rubric, and the top 100 applicants in each rubric were identified as selected for interview. Odds ratios (OR) of selection for interview according to URM status and secondary outcomes, including clinical performance and lived experience, were measured by analysis of group composition via univariate logistic regression.Relative to Traditional, Holistic Review significantly increased the odds of URM applicant selection for interview (TR-OR: 0.35 vs HR-OR: 0.84, p 0.01). Assigning value to lived experience and de-emphasizing USMLE STEP1 scores contributed to the significant changes in odds ratio of interview selection for URM applicants.Traditional interview selection methods systematically exclude URM applicants from consideration without due attention to applicant strengths or potential contribution to clinical care. Conversely, holistic screening represents a structural intervention capable of critically examining measures of merit, reducing bias, and increasing URM representation in residency recruitment, screening, and selection.
- Published
- 2019
47. The Impact of APP on Alzheimer-like Pathogenesis and Gene Expression in Down Syndrome iPSC-Derived Neurons
- Author
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Dmitry A. Ovchinnikov, Isaac Virshup, Ernst J. Wolvetang, Othmar Korn, and Christine A. Wells
- Subjects
0301 basic medicine ,cortical neurogenesis ,Hsa21 trisomy ,Amyloid ,Cellular differentiation ,Down syndrome ,Induced Pluripotent Stem Cells ,Gene Dosage ,Gene Expression ,Biochemistry ,Gene dosage ,Protein Aggregation, Pathological ,03 medical and health sciences ,Amyloid beta-Protein Precursor ,Protein Aggregates ,Alzheimer Disease ,Report ,Gene expression ,mental disorders ,Genetics ,Amyloid precursor protein ,medicine ,Humans ,Induced pluripotent stem cell ,CRISPR/Cas9 ,lcsh:QH301-705.5 ,Cells, Cultured ,Neurons ,lcsh:R5-920 ,Amyloid beta-Peptides ,iPSC ,biology ,Gene Expression Profiling ,tau phosphorylation ,beta-amyloid ,Cell Differentiation ,Cell Biology ,medicine.disease ,Cell biology ,Gene expression profiling ,030104 developmental biology ,lcsh:Biology (General) ,biology.protein ,Disease Susceptibility ,Alzheimer's disease ,Transcriptome ,lcsh:Medicine (General) ,Developmental Biology - Abstract
Summary Early-onset Alzheimer disease (AD)-like pathology in Down syndrome is commonly attributed to an increased dosage of the amyloid precursor protein (APP) gene. To test this in an isogenic human model, we deleted the supernumerary copy of the APP gene in trisomic Down syndrome induced pluripotent stem cells or upregulated APP expression in euploid human pluripotent stem cells using CRISPRa. Cortical neuronal differentiation shows that an increased APP gene dosage is responsible for increased β-amyloid production, altered Aβ42/40 ratio, and deposition of the pyroglutamate (E3)-containing amyloid aggregates, but not for several tau-related AD phenotypes or increased apoptosis. Transcriptome comparisons demonstrate that APP has a widespread and temporally modulated impact on neuronal gene expression. Collectively, these data reveal an important role for APP in the amyloidogenic aspects of AD but challenge the idea that increased APP levels are solely responsible for increasing specific phosphorylated forms of tau or enhanced neuronal cell death in Down syndrome-associated AD pathogenesis., Graphical Abstract, Highlights • Normalization of APP copy number in Down syndrome (DS) iPSCs • APP controls neuronal amyloid levels and pyroglutamate (pE3) accumulation • APP in DS neurons does not affect levels of neurotoxic tau species or apoptosis • APP gene dosage has stage-specific and genome-wide effects on gene expression, Wolvetang and colleagues used CRISPR/Cas9 technologies to manipulate the copy number and expression of the amyloid precursor protein (APP) gene in Down syndrome and corresponding euploid pluripotent stem cells. They demonstrate that APP modulates the expression of a surprisingly large cohort of genes and dictates Aβ42/40 ratio and pyroglutamate-E3 foci but does not affect hyperphosphorylated forms of tau associated with Alzheimer disease or neuronal cell death of in vitro generated cortical neurons.
- Published
- 2018
48. Fungal-derived cues promote ocular autoimmunity through a Dectin-2/Card9-mediated mechanism
- Author
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Gordon D. Brown, Paige E. Snow, Holly L. Rosenzweig, Xin Lin, E. J. Lee, Emily E. Vance, Naohito Ohno, Christine A. Wells, Yoichiro Iwakura, Noriko Miura, Brieanna Brown, Rachel R. Caspi, and Justine R. Smith
- Subjects
0301 basic medicine ,T cell ,Immunology ,Saccharomyces cerevisiae ,Biology ,medicine.disease_cause ,Autoimmune Diseases ,Immune tolerance ,Autoimmunity ,Uveitis ,Mice ,03 medical and health sciences ,0302 clinical medicine ,Antigen ,Candida albicans ,medicine ,Animals ,Immunology and Allergy ,Lectins, C-Type ,Eye Proteins ,Receptor ,Innate immune system ,Effector ,Candidiasis ,Original Articles ,medicine.disease ,Mice, Mutant Strains ,eye diseases ,CARD Signaling Adaptor Proteins ,Retinol-Binding Proteins ,030104 developmental biology ,medicine.anatomical_structure ,Th17 Cells ,030215 immunology - Abstract
Summary Uveitis (intraocular inflammation) is a leading cause of loss of vision. Although its aetiology is largely speculative, it is thought to arise from complex genetic–environmental interactions that break immune tolerance to generate eye-specific autoreactive T cells. Experimental autoimmune uveitis (EAU), induced by immunization with the ocular antigen, interphotoreceptor retinoid binding protein (IRBP), in combination with mycobacteria-containing complete Freund's adjuvant (CFA), has many clinical and histopathological features of human posterior uveitis. Studies in EAU have focused on defining pathogenic CD4+ T cell effector responses, such as those of T helper type 17 (Th17) cells, but the innate receptor pathways precipitating development of autoreactive, eye-specific T cells remain poorly defined. In this study, we found that fungal-derived antigens possess autoimmune uveitis-promoting function akin to CFA in conventional EAU. The capacity of commensal fungi such as Candida albicans or Saccharomyces cerevisae to promote IRBP-triggered EAU was mediated by Card9. Because Card9 is an essential signalling molecule of a subgroup of C-type lectin receptors (CLRs) important in host defence, we evaluated further the proximal Card9-activating CLRs. Using single receptor-deficient mice we identified Dectin-2, but not Mincle or Dectin-1, as a predominant mediator of fungal-promoted uveitis. Conversely, Dectin-2 activation by α-mannan reproduced the uveitic phenotype of EAU sufficiently, in a process mediated by the Card9-coupled signalling axis and interleukin (IL)-17 production. Taken together, this report relates the potential of the Dectin-2/Card9-coupled pathway in ocular autoimmunity. Not only does it contribute to understanding of how innate immune receptors orchestrate T cell-mediated autoimmunity, it also reveals a previously unappreciated ability of fungal-derived signals to promote autoimmunity.
- Published
- 2017
49. Mural lymphatic endothelial cells regulate meningeal angiogenesis in the zebrafish
- Author
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Maria Rondon-Galeano, Cathy Pichol-Thievend, Benjamin W. Lindsey, Naoki Mochizuki, Jan Kaslin, Stephen J. Bent, Sungmin Baek, Cas Simons, Isaac Virshup, Neil I. Bower, Mathias Francois, Daniel G. Hurley, Christine A. Wells, Benjamin M. Hogan, Weili Wang, Katarzyna Koltowska, Anne K. Lagendijk, and Scott Paterson
- Subjects
Male ,0301 basic medicine ,Angiogenesis ,government.form_of_government ,Population ,Neovascularization, Physiologic ,Biology ,Mural cell ,Animals, Genetically Modified ,03 medical and health sciences ,Meninges ,Animals ,education ,Zebrafish ,education.field_of_study ,Vascular Endothelial Growth Factors ,General Neuroscience ,Brain ,Endothelial Cells ,Anatomy ,Zebrafish Proteins ,biology.organism_classification ,Neural stem cell ,Cell biology ,Lipoproteins, LDL ,Endothelial stem cell ,Lymphatic Endothelium ,030104 developmental biology ,Lymphatic system ,cardiovascular system ,government ,Female ,Neuroscience ,Signal Transduction - Abstract
Mural cells of the vertebrate brain maintain vascular integrity and function, play roles in stroke and are involved in maintenance of neural stem cells. However, the origins, diversity and roles of mural cells remain to be fully understood. Using transgenic zebrafish, we identified a population of isolated mural lymphatic endothelial cells surrounding meningeal blood vessels. These meningeal mural lymphatic endothelial cells (muLECs) express lymphatic endothelial cell markers and form by sprouting from blood vessels. In larvae, muLECs develop from a lymphatic endothelial loop in the midbrain into a dispersed, nonlumenized mural lineage. muLEC development requires normal signaling through the Vegfc-Vegfd-Ccbe1-Vegfr3 pathway. Mature muLECs produce vascular growth factors and accumulate low-density lipoproteins from the bloodstream. We find that muLECs are essential for normal meningeal vascularization. Together, these data identify an unexpected lymphatic lineage and developmental mechanism necessary for establishing normal meningeal blood vasculature.
- Published
- 2017
50. An integrated analysis of myeloid cells identifies gaps in in vitro models of in vivo biology
- Author
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Simon Milling, Mariola Kurowska-Stolarska, Paul W. Angel, Jarny Choi, Jennifer Gu, Chris M. Pacheco, Andrew L. Laslett, Christine A. Wells, Matt Rutar, Kim-Anh Lê Cao, Nadia Rajab, Vanta Jameson, and Yidi Deng
- Subjects
0303 health sciences ,Cell type ,Myeloid ,Microglia ,Cell ,Pattern recognition receptor ,Biology ,Phenotype ,Cell biology ,Transcriptome ,03 medical and health sciences ,0302 clinical medicine ,medicine.anatomical_structure ,medicine ,030217 neurology & neurosurgery ,Conventional Dendritic Cell ,030304 developmental biology - Abstract
SummaryThe Stemformatics myeloid atlas is an integrated transcriptome atlas of human macrophages and dendritic cells that systematically compares freshly isolated tissue-resident, cultured, and stem-cell derived myeloid cell types. We identified two broad classes of tissue-resident macrophages with lung, gut and tumour-associated macrophages most similar to monocytes. Microglia, Kupffer cells and synovial macrophages shared similar profiles with each other, and with cultured macrophages. Pluripotent stem cell-derived macrophages were not reminiscent of fetal-derived cells. Instead, they were characterized by atypical expression of collagen and a highly efferocytotic phenotype. Likewise, Flt3L-derived cord blood dendritic cells were distinct from conventional dendritic cell subsets isolated from primary tissues and lacked expression of key pattern recognition receptors. Myeloid subsets were reproducible across different experimental series, showing the resource is a robust reference for new data. External users can annotate and benchmark their own samples, including annotation of myeloid single cell data at www.stemformatics.org/atlas/myeloid/.
- Published
- 2019
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