Informing disease modelling with brain-relevant functional genomic annotations

The past decade has seen a surge in the number of disease/trait-associated variants, largely because of the union of studies to share genetic data and the availability of electronic health records from large cohorts for research use. Variant discovery for neurological and neuropsychiatric genome-wide association studies, including schizophrenia, Parkinson's disease and Alzheimer's disease, has greatly benefitted; however, the translation of these genetic association results to interpretable biological mechanisms and models is lagging. Interpreting disease-associated variants requires knowledge of gene regulatory mechanisms and computational tools that permit integration of this knowledge with genome-wide association study results. Here, we summarize key conceptual advances in the generation of brain-relevant functional genomic annotations and amongst tools that allow integration of these annotations with association summary statistics, which together provide a new and exciting opportunity to identify disease-relevant genes, pathways and cell types in silico. We discuss the opportunities and challenges associated with these developments and conclude with our perspective on future advances in annotation generation, tool development and the union of the two

A human colonic crypt culture system to study regulation of stem cell-driven tissue renewal and physiological function

The intestinal epithelium is one of the most rapidly renewing tissues in the human body and fulfils vital physiological roles such as barrier function and transport of nutrients and fluid. Investigation of gut epithelial physiology in health and disease has been hampered by the lack of ex vivo models of the native human intestinal epithelium. Recently, remarkable progress has been made in defining intestinal stem cells and in generating intestinal organoid cultures. In parallel, we have developed a 3D culture system of the native human colonic epithelium that recapitulates the topological hierarchy of stem cell-driven tissue renewal and permits the physiological study of native polarized epithelial cells. Here we describe methods to establish 3D cultures of intact human colonic crypts and conduct real-time imaging of intestinal tissue renewal, cellular signalling, and physiological function, in conjunction with manipulation of gene expression by lentiviral or adenoviral transduction. Visualization of mRNA- and protein-expression patterns in cultured human colonic crypts, and cross-validation with crypts derived from fixed mucosal biopsies, is also described. Alongside studies using intestinal organoids, the near-native human colonic crypt culture model will help to bridge the gap that exists between investigation of colon cancer cell lines and/or animal (tissue) studies, and progression to clinical trials. To this end, the near native human colonic crypt model provides a platform to aid the development of novel strategies for the prevention of inflammatory bowel disease and cancer

Mitochondrial-nuclear cross-talk in the human brain is modulated by cell type and perturbed in neurodegenerative disease

Mitochondrial dysfunction contributes to the pathogenesis of many neurodegenerative diseases. The mitochondrial genome encodes core respiratory chain proteins, but the vast majority of mitochondrial proteins are nuclear-encoded, making interactions between the two genomes vital for cell function. Here, we examine these relationships by comparing mitochondrial and nuclear gene expression across different regions of the human brain in healthy and disease cohorts. We find strong regional patterns that are modulated by cell-type and reflect functional specialisation. Nuclear genes causally implicated in sporadic Parkinson's and Alzheimer's disease (AD) show much stronger relationships with the mitochondrial genome than expected by chance, and mitochondrial-nuclear relationships are highly perturbed in AD cases, particularly through synaptic and lysosomal pathways, potentially implicating the regulation of energy balance and removal of dysfunction mitochondria in the etiology or progression of the disease. Finally, we present MitoNuclearCOEXPlorer, a tool to interrogate key mitochondria-nuclear relationships in multi-dimensional brain data

On the Thermoelectric Effect of Interface Imperfections

Ordinary thermocouples use the well-known Seebeck effect to measure the temperature at the junction of two different conductors. The electromotive force generated by the heat depends on the difference between the respective thermoelectric powers of the contacting metals and the junction temperature. Figure 1 shows the schematic diagram of the thermoelectric measurement as most often used in nondestructive materials characterization. One of the reference electrodes is heated by electrical means to a preset temperature of 100 – 300 °C, pretty much like the tip of a temperature-stabilized soldering iron, and connected to the inverting (−) input of the differential amplifier driving the indicator. The other electrode is left cold at essentially room temperature and connected to the non-inverting (+) input. The measurement is done quickly in a few seconds to assure (i) that the hot reference electrode is not cooled down perceivably by the specimen and (ii) that the rest of the specimen beyond the close vicinity of the contact point is not warmed up perceivably. Ideally, regardless of the temperature difference between the junctions, only thermocouples made of different materials, i.e., materials of different thermoelectric power, will generate thermoelectric signal. This unique feature makes the simple thermoelectric tester one of the most sensitive material discriminators used in nondestructive inspection

Heritability enrichment implicates microglia in Parkinson's disease pathogenesis

OBJECTIVE: Understanding how different parts of the immune system contribute to pathogenesis in Parkinson's disease is a burning challenge with important therapeutic implications. We studied enrichment of common variant heritability for Parkinson's disease stratified by immune and brain cell types. METHODS: We used summary statistics from the most recent meta-analysis of genome-wide association studies in Parkinson's disease and partitioned heritability using linkage disequilibrium score regression, stratified for specific cell types as defined by open chromatin regions. We also validated enrichment results using a polygenic risk score approach and intersected disease-associated variants with epigenetic data and expression quantitative loci to nominate and explore a putative microglial locus. RESULTS: We found significant enrichment of Parkinson's disease risk heritability in open chromatin regions of microglia and monocytes. Genomic annotations overlapped substantially between these two cell types, and only the enrichment signal for microglia remained significant in a joint model. We present evidence suggesting P2RY12, a key microglial gene and target for the anti-thrombotic agent clopidogrel, as the likely driver of a significant Parkinson's disease association signal on chromosome 3. INTERPRETATION: Our results provide further support for the importance of immune mechanisms in PD pathogenesis, highlight microglial dysregulation as a contributing etiological factor and nominate a targetable microglial gene candidate as a pathogenic player. Immune processes can be modulated by therapy, with potentially important clinical implications for future treatment in Parkinson's disease

CoExp: A Web Tool for the Exploitation of Co-expression Networks

Gene co-expression networks are a powerful type of analysis to construct gene groupings based on transcriptomic profiling. Co-expression networks make it possible to discover modules of genes whose mRNA levels are highly correlated across samples. Subsequent annotation of modules often reveals biological functions and/or evidence of cellular specificity for cell types implicated in the tissue being studied. There are multiple ways to perform such analyses with weighted gene co-expression network analysis (WGCNA) amongst one of the most widely used R packages. While managing a few network models can be done manually, it is often more advantageous to study a wider set of models derived from multiple independently generated transcriptomic data sets (e.g., multiple networks built from many transcriptomic sources). However, there is no software tool available that allows this to be easily achieved. Furthermore, the visual nature of co-expression networks in combination with the coding skills required to explore networks, makes the construction of a web-based platform for their management highly desirable. Here, we present the CoExp Web application, a user-friendly online tool that allows the exploitation of the full collection of 109 co-expression networks provided by the CoExpNets suite of R packages. We describe the usage of CoExp, including its contents and the functionality available through the family of CoExpNets packages. All the tools presented, including the web front- and back-ends are available for the research community so any research group can build its own suite of networks and make them accessible through their own CoExp Web application. Therefore, this paper is of interest to both researchers wishing to annotate their genes of interest across different brain network models and specialists interested in the creation of GCNs looking for a tool to appropriately manage, use, publish, and share their networks in a consistent and productive manner

Macroscopic effects of the spectral structure in turbulent flows

Two aspects of turbulent flows have been the subject of extensive, split research efforts: macroscopic properties, such as the frictional drag experienced by a flow past a wall, and the turbulent spectrum. The turbulent spectrum may be said to represent the fabric of a turbulent state; in practice it is a power law of exponent \alpha (the "spectral exponent") that gives the revolving velocity of a turbulent fluctuation (or "eddy") of size s as a function of s. The link, if any, between macroscopic properties and the turbulent spectrum remains missing. Might it be found by contrasting the frictional drag in flows with differing types of spectra? Here we perform unprecedented measurements of the frictional drag in soap-film flows, where the spectral exponent \alpha = 3 and compare the results with the frictional drag in pipe flows, where the spectral exponent \alpha = 5/3. For moderate values of the Reynolds number Re (a measure of the strength of the turbulence), we find that in soap-film flows the frictional drag scales as Re^{-1/2}, whereas in pipe flows the frictional drag scales as Re^{-1/4} . Each of these scalings may be predicted from the attendant value of \alpha by using a new theory, in which the frictional drag is explicitly linked to the turbulent spectrum. Our work indicates that in turbulence, as in continuous phase transitions, macroscopic properties are governed by the spectral structure of the fluctuations.Comment: 6 pages, 3 figure

Incomplete annotation has a disproportionate impact on our understanding of Mendelian and complex neurogenetic disorders

Growing evidence suggests that human gene annotation remains incomplete; however, it is unclear how this affects different tissues and our understanding of different disorders. Here, we detect previously unannotated transcription from Genotype-Tissue Expression RNA sequencing data across 41 human tissues. We connect this unannotated transcription to known genes, confirming that human gene annotation remains incomplete, even among well-studied genes including 63% of the Online Mendelian Inheritance in Man–morbid catalog and 317 neurodegeneration-associated genes. We find the greatest abundance of unannotated transcription in brain and genes highly expressed in brain are more likely to be reannotated. We explore examples of reannotated disease genes, such as SNCA, for which we experimentally validate a previously unidentified, brain-specific, potentially protein-coding exon. We release all tissue-specific transcriptomes through vizER: http://rytenlab.com/browser/app/vizER. We anticipate that this resource will facilitate more accurate genetic analysis, with the greatest impact on our understanding of Mendelian and complex neurogenetic disorders

Immunohistochemical detection and regulation of α5 nicotinic acetylcholine receptor (nAChR) subunits by FoxA2 during mouse lung organogenesis

<p>Abstract</p> <p>Background</p> <p>α₅nicotinic acetylcholine receptor (nAChR) subunits structurally stabilize functional nAChRs in many non-neuronal tissue types. The expression of α₅nAChR subunits and cell-specific markers were assessed during lung morphogenesis by co-localizing immunohistochemistry from embryonic day (E) 13.5 to post natal day (PN) 20. Transcriptional control of α₅nAChR expression by FoxA2 and GATA-6 was determined by reporter gene assays.</p> <p>Results</p> <p>Steady expression of α₅nAChR subunits was observed in distal lung epithelial cells during development while proximal lung expression significantly alternates between abundant prenatal expression, absence at PN4 and PN10, and a return to intense expression at PN20. α₅expression was most abundant on luminal edges of alveolar type (AT) I and ATII cells, non-ciliated Clara cells, and ciliated cells in the proximal lung at various periods of lung formation. Expression of α₅nAChR subunits correlated with cell differentiation and reporter gene assays suggest expression of α₅is regulated in part by FoxA2, with possible cooperation by GATA-6.</p> <p>Conclusions</p> <p>Our data reveal a highly regulated temporal-spatial pattern of α₅nAChR subunit expression during important periods of lung morphogenesis. Due to specific regulation by FoxA2 and distinct identification of α₅in alveolar epithelium and Clara cells, future studies may identify possible mechanisms of cell differentiation and lung homeostasis mediated at least in part by α₅-containing nAChRs.</p

Isotope effect on the transition temperature TcT_c in Fe-based superconductors: the current status

The results of the Fe isotope effect (Fe-IE) on the transition temperature $T_c$ obtained up to date in various Fe-based high temperature superconductors are summarized and reanalyzed by following the approach developed in [Phys. Rev. B 82, 212505 (2010)]. It is demonstrated that the very controversial results for Fe-IE on $T_c$ are caused by small structural changes occurring simultaneously with the Fe isotope exchange. The Fe-IE exponent on $T_c$ [$\alpha_{\rm Fe}=-(\Delta T_c/T_c)/(\Delta M/M)$, $M$ is the isotope mass] needs to be decomposed into two components with the one related to the structural changes ($\alpha_{\rm Fe}^{\rm str}$) and the genuine (intrinsic) one ($\alpha_{\rm Fe}^{\rm int}$). The validity of such decomposition is further confirmed by the fact that $\alpha_{\rm Fe}^{\rm int}$ coincides with the Fe-IE exponent on the characteristic phonon frequencies $\alpha_{\rm Fe}^{\rm ph}$ as is reported in recent EXAFS and Raman experiments.Comment: 7 pages, 4 figures. The paper is partially based on the results published in [New J. Phys. 12, 073024 (2010) = arXiv:1002.2510] and [Phys. Rev. B 82, 212505 (2010) = arXiv:1008.4540