Expression Atlas update-an integrated database of gene and protein expression in humans, animals and plants

Expression Atlas (http://www.ebi.ac.uk/gxa) provides information about gene and protein expression in animal and plant samples of different cell types, organism parts, developmental stages, diseases and other conditions. It consists of selected microarray and RNA-sequencing studies from ArrayExpress, which have been manually curated, annotated with ontology terms, checked for high quality and processed using standardised analysis methods. Since the last update, Atlas has grown seven-fold (1572 studies as of August 2015), and incorporates baseline expression profiles of tissues from Human Protein Atlas, GTEx and FANTOM5, and of cancer cell lines from ENCODE, CCLE and Genentech projects. Plant studies constitute a quarter of Atlas data. For genes of interest, the user can view baseline expression in tissues, and differential expression for biologically meaningful pairwise comparisons—estimated using consistent methodology across all of Atlas. Our first proteomics study in human tissues is now displayed alongside transcriptomics data in the same tissues. Novel analyses and visualisations include: ‘enrichment’ in each differential comparison of GO terms, Reactome, Plant Reactome pathways and InterPro domains; hierarchical clustering (by baseline expression) of most variable genes and experimental conditions; and, for a given gene-condition, distribution of baseline expression across biological replicates.© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. The published article is available at: http://nar.oxfordjournals.org/content/44/D1/D74

Initial in vitro and in vivo Characterization of the Membrane Trafficking Protein Fer1L6

A fundamental difference between prokaryotic and eukaryotic cells is the presence of membrane bound organelles in eukaryotes. The dynamics of membrane trafficking within the cell are responsible for everything from intercellular communication and cell homeostasis, to mitosis, cell migration, and differentiation. These processes require exocytosis and compensatory endocytosis, often working in concert to create vesicle cycling. While constitutive exo‐ and endocytosis occurs independently of extracellular stimulus, , regulated membrane trafficking events are quiescent until triggered by a messenger, such as calcium. Exocytosis is primarily carried out by SNARE proteins, while endocytosis is carried out by either clatherin‐related proteins or clatherin‐independent proteins, such as Eps 15 homology domain proteins (EHDs). However, none of these proteins are directly calcium sensitive. Thus, calcium regulated exocytosis requires an additional calcium‐regulated protein. In neuronal exocytosis the synaptotagmin family confers calcium sensitivity to the process, and members are typically composed of a membrane anchor and two C2 domains. Another family of proteins involved in calcium sensitive exocytosis is the ferlin family. Composed of 5 to 7 C2 domains, these membrane proteins have been implicated in various membrane trafficking diseases, ranging from muscular dystrophy to non‐syndromic deafness, and have been implicated in multiple cancer types. The goal of this dissertation is to characterize the sixth mammalian ferlin protein, Fer1L6, which has not been previously studied. Currently, Fer1L6 has no known disease state links. Nevertheless, characterization of both tissue specificity and functional roles of the Fer1L6 protein will be highly valuable to furthering our understanding of the ferlin protein family, and strengthen our understanding of membrane dynamics inside eukaryotic cells. To date little is known about the function or expression of Fer1L6, despite the fact that it is a predicted protein coding gene in a wide range of vertebrate genomes. Reverse genetic techniques were used to elucidate a possible functional role of Fer1L6 in the model organism D. rerio (zebrafish). A Fer1L6 morpholino knockdown resulted in abnormal skeletal muscle development, in which the sarcoplasmic reticulum and t‐tubules do not form properly. Additionally, the myofibrils and myosepta are disorganized and irregularly shaped. Heart rate quantitation and microscopy of cardiac muscle shows underdevelopment of the heart chambers with decreased heart rate. However, initial studies with a first generation Fer1L6 mutant zebrafish line do not exhibit any of the same gross phenotypes that were observed with the morpholino knockdown. Further investigation of the mutant line is required to fully characterize the effects of the mutation. The muscle related phenotypes seen in the morpholino studies initiated an investigation into Fer1L6 in the C2C12 myoblast cell line. Using both q‐PCR and western blots, no changes in Fer1L6 expression was detected during myoblast differentiation into myotubes. Immunostaining of undifferentiated myoblasts showed Fer1L6 localization to the perinuclear region with Fer1L6 puncta also emanating outwards towards the plasma membrane. Additionally, there were small levels of accumulation at the plasma membrane. These results are consistent with previously proposed models in which Fer1L6 is involved in trans‐Golgi to plasma membrane endocytic recycling events with Rab 11. The results of this dissertation begin the process of determining a functional role for Fer1L6, and demonstrate the feasibility for both zebrafish and C2C12 cells as a model for future studies on the endogenous protein. The results validate high‐throughput proteomic studies, and lend support to recently literature with over expression in cell culture. Overall, we find that Fer1L6 is a widely expressed protein that may be involved in both embryonic development and maintaining homeostasis of tissues through endosomal recycling pathways

Maml1 acts cooperatively with Gli proteins to regulate Sonic hedgheog signaling pathway

Sonic hedgehog (Shh) signaling is essential for proliferation of cerebellar granule cell progenitors (GCPs) and its misregulation is linked to various disorders, including cerebellar cancer medulloblastoma. The effects of Shh pathway are mediated by the Gli family of transcription factors, which controls the expression of a number of target genes, including Gli1. Here, we identify Mastermind-like 1 (Maml1) as a novel regulator of the Shh signaling since it interacts with Gli proteins, working as a potent transcriptional coactivator. Notably, Maml1 silencing results in a significant reduction of Gli target genes expression, with a negative impact on cell growth of NIH3T3 and Patched1−/− mouse embryonic fibroblasts (MEFs), bearing a constitutively active Shh signaling. Remarkably, Shh pathway activity results severely compromised both in MEFs and GCPs deriving from Maml1−/− mice with an impairment of GCPs proliferation and cerebellum development. Therefore Maml1−/− phenotype mimics aspects of Shh pathway deficiency, suggesting an intrinsic requirement for Maml1 in cerebellum development. The present study shows a new role for Maml1 as a component of Shh signaling, which plays a crucial role in both development and tumorigenesis

gganatogram: An R package for modular visualisation of anatograms and tissues based on ggplot2 [version 1; referees: 2 approved]

Displaying data onto anatomical structures is a convenient technique to quickly observe tissue related information. However, drawing tissues is a complex task that requires both expertise in anatomy and the arts. While web based applications exist for displaying gene expression on anatograms, other non-genetic disciplines lack similar tools. Moreover, web based tools often lack the modularity associated with packages in programming languages, such as R. Here I present gganatogram, an R package used to plot modular species anatograms based on a combination of the graphical grammar of ggplot2 and the publicly available anatograms from the Expression Atlas. This combination allows for quick and easy, modular, and reproducible generation of anatograms. Using only one command and a data frame with tissue name, group, colour, and value, this tool enables the user to visualise specific human and mouse tissues with desired colours, grouped by a variable, or displaying a desired value, such as gene-expression, pharmacokinetics, or bacterial load across selected tissues. I hope that this tool will be useful by the wider community in biological sciences. Community members are welcome to submit additional anatograms, which can be incorporated into the package. A stable version gganatogram has been deposited to neuroconductor, and a development version can be found on github/jespermaag/gganatogram

Navigating in vitro bioactivity data by investigating available resources using model compounds.

The number of chemical compounds and associated experimental data in public databases is growing, but presently there is no simple way to access these data in a quick and synoptic manner. Instead, data are fragmented across different resources and interested parties need to invest invaluable time and effort to navigate these systems

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program

Abstract: Transformative technologies are enabling the construction of three-dimensional maps of tissues with unprecedented spatial and molecular resolution. Over the next seven years, the NIH Common Fund Human Biomolecular Atlas Program (HuBMAP) intends to develop a widely accessible framework for comprehensively mapping the human body at single-cell resolution by supporting technology development, data acquisition, and detailed spatial mapping. HuBMAP will integrate its efforts with other funding agencies, programs, consortia, and the biomedical research community at large towards the shared vision of a comprehensive, accessible three-dimensional molecular and cellular atlas of the human body, in health and under various disease conditions

A systematic analysis of orphan cyclins reveals CNTD2 as a new oncogenic driver in lung cancer

As lung cancer has increased to the most common cause of cancer death worldwide, prognostic biomarkers and effective targeted treatments remain lacking despite advances based on patients' stratification. Multiple core cyclins, best known as drivers of cell proliferation, are commonly deregulated in lung cancer where they may serve as oncogenes. The recent expansion of the cyclin family raises the question whether new members might play oncogenic roles as well. Here, we investigated the protein levels of eight atypical cyclins in lung cancer cell lines and formalin-fixed and paraffin-embedded (FFPE) human tumors, as well as their functional role in lung cancer cells. Of the new cyclins evaluated, CNTD2 was significantly overexpressed in lung cancer compared to adjacent normal tissue, and exhibited a predominant nuclear location. CNTD2 overexpression increased lung cancer cell viability, Ki-67 intensity and clonogenicity and promoted lung cancer cell migration. Accordingly, CNTD2 enhanced tumor growth in vivo on A549 xenograft models. Finally, the analysis of gene expression data revealed a high correlation between elevated levels of CNTD2 and decreased overall survival in lung cancer patients. Our results reveal CNTD2 as a new oncogenic driver in lung cancer, suggesting value as a prognostic biomarker and therapeutic target in this disease

Intron and gene size expansion during nervous system evolution

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in McCoy, M. J., & Fire, A. Z. Intron and gene size expansion during nervous system evolution. BMC Genomics, 21(1), (2020): 360, doi:10.1186/s12864-020-6760-4.Background The evolutionary radiation of animals was accompanied by extensive expansion of gene and genome sizes, increased isoform diversity, and complexity of regulation. Results Here we show that the longest genes are enriched for expression in neuronal tissues of diverse vertebrates and of invertebrates. Additionally, we show that neuronal gene size expansion occurred predominantly through net gains in intron size, with a positional bias toward the 5′ end of each gene. Conclusions We find that intron and gene size expansion is a feature of many genes whose expression is enriched in nervous systems. We speculate that unique attributes of neurons may subject neuronal genes to evolutionary forces favoring net size expansion. This process could be associated with tissue-specific constraints on gene function and/or the evolution of increasingly complex gene regulation in nervous systems.This study was supported by the following programs, grants, and fellowships: 2018 Grass Fellowship in Neuroscience (Grass Foundation), 2019 Whitman Fellowship at the Marine Biological Laboratory, and the Stanford Genomics Training Program (5T32HG000044–22; PI: M. Snyder) to MJM, and R01GM37706/R35GM130366 to AZF. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

gganatogram: An R package for modular visualisation of anatograms and tissues based on ggplot2 [version 2; referees: 2 approved]

Displaying data onto anatomical structures is a convenient technique to quickly observe tissue related information. However, drawing tissues is a complex task that requires both expertise in anatomy and the arts. While web based applications exist for displaying gene expression on anatograms, other non-genetic disciplines lack similar tools. Moreover, web based tools often lack the modularity associated with packages in programming languages, such as R. Here I present gganatogram, an R package used to plot modular species anatograms based on a combination of the graphical grammar of ggplot2 and the publicly available anatograms from the Expression Atlas. This combination allows for quick and easy, modular, and reproducible generation of anatograms. Using only one command and a data frame with tissue name, group, colour, and  value, this tool enables the user to visualise specific human and mouse tissues with desired colours, grouped by a variable, or displaying a desired value, such as gene-expression, pharmacokinetics, or bacterial load across selected tissues. gganatogram consists of 5 highly annotated organisms, male/female human/mouse, and a cell anatogram. It further consists of 24 other less annotated organisms from the animal and plant kingdom. I hope that this tool will be useful by the wider community in biological sciences. Community members are welcome to submit additional anatograms, which can be incorporated into the package. A stable version gganatogram has been deposited to neuroconductor, and a development version can be found on github/jespermaag/gganatogram. An interactive shiny app of gganatogram can be found on https://jespermaag.shinyapps.io/gganatogram/, which allows for non-R users to create anatograms