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  1. Article ; Online: i2dash

    Arsenij Ustjanzew / Jens Preussner / Mette Bentsen / Carsten Kuenne / Mario Looso

    Genomics, Proteomics & Bioinformatics, Vol 20, Iss 3, Pp 568-

    Creation of Flexible, Interactive, and Web-based Dashboards for Visualization of Omics Data

    2022  Volume 577

    Abstract: Data visualization and interactive data exploration are important aspects of illustrating complex concepts and results from analyses of omics data. A suitable visualization has to be intuitive and accessible. Web-based dashboards have become popular ... ...

    Abstract Data visualization and interactive data exploration are important aspects of illustrating complex concepts and results from analyses of omics data. A suitable visualization has to be intuitive and accessible. Web-based dashboards have become popular tools for the arrangement, consolidation, and display of such visualizations. However, the combination of automated data processing pipelines handling omics data and dynamically generated, interactive dashboards is poorly solved. Here, we present i2dash, an R package intended to encapsulate functionality for the programmatic creation of customized dashboards. It supports interactive and responsive (linked) visualizations across a set of predefined graphical layouts. i2dash addresses the needs of data analysts/software developers for a tool that is compatible and attachable to any R-based analysis pipeline, thereby fostering the separation of data visualization on one hand and data analysis tasks on the other hand. In addition, the generic design of i2dash enables the development of modular extensions for specific needs. As a proof of principle, we provide an extension of i2dash optimized for single-cell RNA sequencing analysis, supporting the creation of dashboards for the visualization needs of such experiments. Equipped with these features, i2dash is suitable for extensive use in large-scale sequencing/bioinformatics facilities. Along this line, we provide i2dash as a containerized solution, enabling a straightforward large-scale deployment and sharing of dashboards using cloud services. i2dash is freely available via the R package archive CRAN (https://CRAN.R-project.org/package=i2dash).
    Keywords Data visualization ; Dashboard ; Cloud ; Data analysis ; Automation ; Biology (General) ; QH301-705.5
    Subject code 004
    Language English
    Publishing date 2022-06-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Proteomic and transcriptomic characterisation of FIA10, a novel murine leukemic cell line that metastasizes into the brain.

    Ursula Just / Helmut Burtscher / Sylvia Jeratsch / Meike Fischer / Carol Stocking / Jens Preussner / Mario Looso / Ralf Schwanbeck / Stefan Günther / Ralf Huss / Lynne Mullen / Thomas Braun

    PLoS ONE, Vol 19, Iss 1, p e

    2024  Volume 0295641

    Abstract: Brain metastasis leads to increased mortality and is a major site of relapse for several cancers, yet the molecular mechanisms of brain metastasis are not well understood. In this study, we established and characterized a new leukemic cell line, FIA10, ... ...

    Abstract Brain metastasis leads to increased mortality and is a major site of relapse for several cancers, yet the molecular mechanisms of brain metastasis are not well understood. In this study, we established and characterized a new leukemic cell line, FIA10, that metastasizes into the central nervous system (CNS) following injection into the tail vein of syngeneic mice. Mice injected with FIA10 cells developed neurological symptoms such as loss of balance, tremor, ataxic gait and seizures, leading to death within 3 months. Histopathology coupled with PCR analysis clearly showed infiltration of leukemic FIA10 cells into the brain parenchyma of diseased mice, with little involvement of bone marrow, peripheral blood and other organs. To define pathways that contribute to CNS metastasis, global transcriptome and proteome analysis was performed on FIA10 cells and compared with that of the parental stem cell line FDCP-Mix and the related FIA18 cells, which give rise to myeloid leukemia without CNS involvement. 188 expressed genes (RNA level) and 189 proteins were upregulated (log2 ratio FIA10/FIA18 ≥ 1) and 120 mRNAs and 177 proteins were downregulated (log2 ratio FIA10/FIA18 ≤ 1) in FIA10 cells compared with FIA18 cells. Major upregulated pathways in FIA10 cells revealed by biofunctional analyses involved immune response components, adhesion molecules and enzymes implicated in extracellular matrix remodeling, opening and crossing the blood-brain barrier (BBB), molecules supporting migration within the brain parenchyma, alterations in metabolism necessary for growth within the brain microenvironment, and regulators for these functions. Downregulated RNA and protein included several tumor suppressors and DNA repair enzymes. In line with the function of FIA10 cells to specifically infiltrate the brain, FIA10 cells have acquired a phenotype that permits crossing the BBB and adapting to the brain microenvironment thereby escaping immune surveillance. These data and our model system FIA10 will be valuable resources to study the ...
    Keywords Medicine ; R ; Science ; Q
    Subject code 572 ; 616
    Language English
    Publishing date 2024-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: UROPA

    Maria Kondili / Annika Fust / Jens Preussner / Carsten Kuenne / Thomas Braun / Mario Looso

    Scientific Reports, Vol 7, Iss 1, Pp 1-

    a tool for Universal RObust Peak Annotation

    2017  Volume 12

    Abstract: Abstract The annotation of genomic ranges of interest represents a recurring task for bioinformatics analyses. These ranges can originate from various sources, including peaks called for transcription factor binding sites (TFBS) or histone modification ... ...

    Abstract Abstract The annotation of genomic ranges of interest represents a recurring task for bioinformatics analyses. These ranges can originate from various sources, including peaks called for transcription factor binding sites (TFBS) or histone modification ChIP-seq experiments, chromatin structure and accessibility experiments (such as ATAC-seq), but also from other types of predictions that result in genomic ranges. While peak annotation primarily driven by ChiP-seq was extensively explored, many approaches remain simplistic (“most closely located TSS”), rely on fixed pre-built references, or require complex scripting tasks on behalf of the user. An adaptable, fast, and universal tool, capable to annotate genomic ranges in the respective biological context is critically missing. UROPA (Universal RObust Peak Annotator) is a command line based tool, intended for universal genomic range annotation. Based on a configuration file, different target features can be prioritized with multiple integrated queries. These can be sensitive for feature type, distance, strand specificity, feature attributes (e.g. protein_coding) or anchor position relative to the feature. UROPA can incorporate reference annotation files (GTF) from different sources (Gencode, Ensembl, RefSeq), as well as custom reference annotation files. Statistics and plots transparently summarize the annotation process. UROPA is implemented in Python and R.
    Keywords Medicine ; R ; Science ; Q
    Subject code 005 ; 004
    Language English
    Publishing date 2017-06-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation

    Mette Bentsen / Philipp Goymann / Hendrik Schultheis / Kathrin Klee / Anastasiia Petrova / René Wiegandt / Annika Fust / Jens Preussner / Carsten Kuenne / Thomas Braun / Johnny Kim / Mario Looso

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 11

    Abstract: Footprinting analysis allows genome-wide investigation of transcription factor (TF) binding on chromatin. Here the authors developed a framework termed TOBIAS aimed at identifying footprints of chromatin-associated proteins from ATAC-seq accessibility ... ...

    Abstract Footprinting analysis allows genome-wide investigation of transcription factor (TF) binding on chromatin. Here the authors developed a framework termed TOBIAS aimed at identifying footprints of chromatin-associated proteins from ATAC-seq accessibility profiles and apply it to zygotic development datasets.
    Keywords Science ; Q
    Language English
    Publishing date 2020-08-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation

    Mette Bentsen / Philipp Goymann / Hendrik Schultheis / Kathrin Klee / Anastasiia Petrova / René Wiegandt / Annika Fust / Jens Preussner / Carsten Kuenne / Thomas Braun / Johnny Kim / Mario Looso

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 11

    Abstract: Footprinting analysis allows genome-wide investigation of transcription factor (TF) binding on chromatin. Here the authors developed a framework termed TOBIAS aimed at identifying footprints of chromatin-associated proteins from ATAC-seq accessibility ... ...

    Abstract Footprinting analysis allows genome-wide investigation of transcription factor (TF) binding on chromatin. Here the authors developed a framework termed TOBIAS aimed at identifying footprints of chromatin-associated proteins from ATAC-seq accessibility profiles and apply it to zygotic development datasets.
    Keywords Science ; Q
    Language English
    Publishing date 2020-08-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Association of Clonal Hematopoiesis of Indeterminate Potential with Inflammatory Gene Expression in Patients with COPD

    Stefan Kuhnert / Siavash Mansouri / Michael A. Rieger / Rajkumar Savai / Edibe Avci / Gabriela Díaz-Piña / Manju Padmasekar / Mario Looso / Stefan Hadzic / Till Acker / Stephan Klatt / Jochen Wilhelm / Ingrid Fleming / Natascha Sommer / Norbert Weissmann / Claus Vogelmeier / Robert Bals / Andreas Zeiher / Stefanie Dimmeler /
    Werner Seeger / Soni S. Pullamsetti

    Cells, Vol 11, Iss 2121, p

    2022  Volume 2121

    Abstract: Chronic obstructive pulmonary disease (COPD) is a disease with an inflammatory phenotype with increasing prevalence in the elderly. Expanded population of mutant blood cells carrying somatic mutations is termed clonal hematopoiesis of indeterminate ... ...

    Abstract Chronic obstructive pulmonary disease (COPD) is a disease with an inflammatory phenotype with increasing prevalence in the elderly. Expanded population of mutant blood cells carrying somatic mutations is termed clonal hematopoiesis of indeterminate potential (CHIP). The association between CHIP and COPD and its relevant effects on DNA methylation in aging are mainly unknown. Analyzing the deep-targeted amplicon sequencing from 125 COPD patients, we found enhanced incidence of CHIP mutations (~20%) with a predominance of DNMT3A CHIP-mediated hypomethylation of Phospholipase D Family Member 5 ( PLD5 ), which in turn is positively correlated with increased levels of glycerol phosphocholine, pro-inflammatory cytokines, and deteriorating lung function.
    Keywords clonal hematopoiesis ; inflammation ; COPD ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2022-07-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Promoter hypermethylation as a mechanism for Lamin A/C silencing in a subset of neuroblastoma cells.

    Ines Rauschert / Fabian Aldunate / Jens Preussner / Miguel Arocena-Sutz / Vanina Peraza / Mario Looso / Juan C Benech / Ruben Agrelo

    PLoS ONE, Vol 12, Iss 4, p e

    2017  Volume 0175953

    Abstract: Nuclear lamins support the nuclear envelope and provide anchorage sites for chromatin. They are involved in DNA synthesis, transcription, and replication. It has previously been reported that the lack of Lamin A/C expression in lymphoma and leukaemia is ... ...

    Abstract Nuclear lamins support the nuclear envelope and provide anchorage sites for chromatin. They are involved in DNA synthesis, transcription, and replication. It has previously been reported that the lack of Lamin A/C expression in lymphoma and leukaemia is due to CpG island promoter hypermethylation. Here, we provide evidence that Lamin A/C is silenced via this mechanism in a subset of neuroblastoma cells. Moreover, Lamin A/C expression can be restored with a demethylating agent. Importantly, Lamin A/C reintroduction reduced cell growth kinetics and impaired migration, invasion, and anchorage-independent cell growth. Cytoskeletal restructuring was also induced. In addition, the introduction of lamin Δ50, known as Progerin, caused senescence in these neuroblastoma cells. These cells were stiffer and developed a cytoskeletal structure that differed from that observed upon Lamin A/C introduction. Of relevance, short hairpin RNA Lamin A/C depletion in unmethylated neuroblastoma cells enhanced the aforementioned tumour properties. A cytoskeletal structure similar to that observed in methylated cells was induced. Furthermore, atomic force microscopy revealed that Lamin A/C knockdown decreased cellular stiffness in the lamellar region. Finally, the bioinformatic analysis of a set of methylation arrays of neuroblastoma primary tumours showed that a group of patients (around 3%) gives a methylation signal in some of the CpG sites located within the Lamin A/C promoter region analysed by bisulphite sequencing PCR. These findings highlight the importance of Lamin A/C epigenetic inactivation for a subset of neuroblastomas, leading to enhanced tumour properties and cytoskeletal changes. Additionally, these findings may have treatment implications because tumour cells lacking Lamin A/C exhibit more aggressive behaviour.
    Keywords Medicine ; R ; Science ; Q
    Subject code 570
    Language English
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Promoter hypermethylation as a mechanism for Lamin A/C silencing in a subset of neuroblastoma cells.

    Ines Rauschert / Fabian Aldunate / Jens Preussner / Miguel Arocena-Sutz / Vanina Peraza / Mario Looso / Juan C Benech / Ruben Agrelo

    PLoS ONE, Vol 12, Iss 4, p e

    2017  Volume 0175953

    Abstract: Nuclear lamins support the nuclear envelope and provide anchorage sites for chromatin. They are involved in DNA synthesis, transcription, and replication. It has previously been reported that the lack of Lamin A/C expression in lymphoma and leukaemia is ... ...

    Abstract Nuclear lamins support the nuclear envelope and provide anchorage sites for chromatin. They are involved in DNA synthesis, transcription, and replication. It has previously been reported that the lack of Lamin A/C expression in lymphoma and leukaemia is due to CpG island promoter hypermethylation. Here, we provide evidence that Lamin A/C is silenced via this mechanism in a subset of neuroblastoma cells. Moreover, Lamin A/C expression can be restored with a demethylating agent. Importantly, Lamin A/C reintroduction reduced cell growth kinetics and impaired migration, invasion, and anchorage-independent cell growth. Cytoskeletal restructuring was also induced. In addition, the introduction of lamin Δ50, known as Progerin, caused senescence in these neuroblastoma cells. These cells were stiffer and developed a cytoskeletal structure that differed from that observed upon Lamin A/C introduction. Of relevance, short hairpin RNA Lamin A/C depletion in unmethylated neuroblastoma cells enhanced the aforementioned tumour properties. A cytoskeletal structure similar to that observed in methylated cells was induced. Furthermore, atomic force microscopy revealed that Lamin A/C knockdown decreased cellular stiffness in the lamellar region. Finally, the bioinformatic analysis of a set of methylation arrays of neuroblastoma primary tumours showed that a group of patients (around 3%) gives a methylation signal in some of the CpG sites located within the Lamin A/C promoter region analysed by bisulphite sequencing PCR. These findings highlight the importance of Lamin A/C epigenetic inactivation for a subset of neuroblastomas, leading to enhanced tumour properties and cytoskeletal changes. Additionally, these findings may have treatment implications because tumour cells lacking Lamin A/C exhibit more aggressive behaviour.
    Keywords Medicine ; R ; Science ; Q
    Subject code 570
    Language English
    Publishing date 2017-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Single cell sequencing reveals endothelial plasticity with transient mesenchymal activation after myocardial infarction

    Lukas S. Tombor / David John / Simone F. Glaser / Guillermo Luxán / Elvira Forte / Milena Furtado / Nadia Rosenthal / Nina Baumgarten / Marcel H. Schulz / Janina Wittig / Eva-Maria Rogg / Yosif Manavski / Ariane Fischer / Marion Muhly-Reinholz / Kathrin Klee / Mario Looso / Carmen Selignow / Till Acker / Sofia-Iris Bibli /
    Ingrid Fleming / Ralph Patrick / Richard P. Harvey / Wesley T. Abplanalp / Stefanie Dimmeler

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Volume 12

    Abstract: Endothelial cells play a critical role in the adaptation of tissues to injury and show a remarkable plasticity. Here the authors show, using single cell sequencing, that endothelial cells acquire a transient mesenchymal state associated with metabolic ... ...

    Abstract Endothelial cells play a critical role in the adaptation of tissues to injury and show a remarkable plasticity. Here the authors show, using single cell sequencing, that endothelial cells acquire a transient mesenchymal state associated with metabolic adaptation after myocardial infarction.
    Keywords Science ; Q
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Transcriptome analysis of newt lens regeneration reveals distinct gradients in gene expression patterns.

    Konstantinos Sousounis / Mario Looso / Nobuyasu Maki / Clifford J Ivester / Thomas Braun / Panagiotis A Tsonis

    PLoS ONE, Vol 8, Iss 4, p e

    2013  Volume 61445

    Abstract: Regeneration of the lens in newts is quite a unique process. The lens is removed in its entirety and regeneration ensues from the pigment epithelial cells of the dorsal iris via transdifferentiation. The same type of cells from the ventral iris are not ... ...

    Abstract Regeneration of the lens in newts is quite a unique process. The lens is removed in its entirety and regeneration ensues from the pigment epithelial cells of the dorsal iris via transdifferentiation. The same type of cells from the ventral iris are not capable of regenerating a lens. It is, thus, expected that differences between dorsal and ventral iris during the process of regeneration might provide important clues pertaining to the mechanism of regeneration. In this paper, we employed next generation RNA-seq to determine gene expression patterns during lens regeneration in Notophthalmus viridescens. The expression of more than 38,000 transcripts was compared between dorsal and ventral iris. Although very few genes were found to be dorsal- or ventral-specific, certain groups of genes were up-regulated specifically in the dorsal iris. These genes are involved in cell cycle, gene regulation, cytoskeleton and immune response. In addition, the expression of six highly regulated genes, TBX5, FGF10, UNC5B, VAX2, NR2F5, and NTN1, was verified using qRT-PCR. These graded gene expression patterns provide insight into the mechanism of lens regeneration, the markers that are specific to dorsal or ventral iris, and layout a map for future studies in the field.
    Keywords Medicine ; R ; Science ; Q
    Subject code 572
    Language English
    Publishing date 2013-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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