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  1. Article ; Online: Rapid adaptation of cellular metabolic rate to the MicroRNA complements of mammals and its relevance to the evolution of endothermy.

    Fromm, Bastian / Sorger, Thomas

    iScience

    2023  Volume 27, Issue 2, Page(s) 108740

    Abstract: The metabolic efficiency of mammalian cells depends on the attenuation of intrinsic translation noise by microRNAs. We devised a metric of cellular metabolic rate ( ...

    Abstract The metabolic efficiency of mammalian cells depends on the attenuation of intrinsic translation noise by microRNAs. We devised a metric of cellular metabolic rate (
    Language English
    Publishing date 2023-12-21
    Publishing country United States
    Document type Journal Article
    ISSN 2589-0042
    ISSN (online) 2589-0042
    DOI 10.1016/j.isci.2023.108740
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  2. Article ; Online: A Novel Circulating MicroRNA for the Detection of Acute Myocarditis.

    Fromm, Bastian / Patil, Arun H / Halushka, Marc K

    The New England journal of medicine

    2022  Volume 387, Issue 13, Page(s) 1240

    MeSH term(s) Circulating MicroRNA ; Humans ; Myocarditis/diagnosis ; Myocarditis/genetics ; Myocardium
    Chemical Substances Circulating MicroRNA
    Language English
    Publishing date 2022-09-28
    Publishing country United States
    Document type Letter ; Comment
    ZDB-ID 207154-x
    ISSN 1533-4406 ; 0028-4793
    ISSN (online) 1533-4406
    ISSN 0028-4793
    DOI 10.1056/NEJMc2115639
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  3. Article: Transcriptional Regulation of Liver-Type OATP1B3 (Lt-OATP1B3) and Cancer-Type OATP1B3 (Ct-OATP1B3) Studied in Hepatocyte-Derived and Colon Cancer-Derived Cell Lines.

    Haberkorn, Bastian / Löwen, Dennis / Meier, Lukas / Fromm, Martin F / König, Jörg

    Pharmaceutics

    2023  Volume 15, Issue 3

    Abstract: Due to alternative splicing, ... ...

    Abstract Due to alternative splicing, the
    Language English
    Publishing date 2023-02-23
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2527217-2
    ISSN 1999-4923
    ISSN 1999-4923
    DOI 10.3390/pharmaceutics15030738
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  4. Article: Transport of Drugs and Endogenous Compounds Mediated by Human OCT1: Studies in Single- and Double-Transfected Cell Models.

    Haberkorn, Bastian / Fromm, Martin F / König, Jörg

    Frontiers in pharmacology

    2021  Volume 12, Page(s) 662535

    Abstract: Organic Cation Transporter 1 (OCT1, gene symbol: ...

    Abstract Organic Cation Transporter 1 (OCT1, gene symbol:
    Language English
    Publishing date 2021-04-22
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2587355-6
    ISSN 1663-9812
    ISSN 1663-9812
    DOI 10.3389/fphar.2021.662535
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  5. Book ; Online ; Thesis: Cancer-type (Ct-) OATP1B3: Untersuchungen zur transkriptionellen Regulation, Lokalisation und Funktion in kolorektalen Karzinomzellen

    Haberkorn, Bastian [Verfasser] / Fromm, Martin F. [Akademischer Betreuer] / Mühlich, Susanne [Gutachter]

    2023  

    Author's details Bastian Haberkorn ; Gutachter: Susanne Mühlich ; Betreuer: Martin F. Fromm
    Keywords Medizin, Gesundheit ; Medicine, Health
    Subject code sg610
    Language German
    Publisher Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
    Publishing place Erlangen
    Document type Book ; Online ; Thesis
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  6. Article ; Online: Direct observation of the evolution of cell-type-specific microRNA expression signatures supports the hematopoietic origin model of endothelial cells.

    Jenike, Ana E / Jenike, Katharine M / Peterson, Kevin J / Fromm, Bastian / Halushka, Marc K

    Evolution & development

    2023  Volume 25, Issue 3, Page(s) 226–239

    Abstract: The evolution of specialized cell-types is a long-standing interest of biologists, but given the deep time-scales very difficult to reconstruct or observe. microRNAs have been linked to the evolution of cellular complexity and may inform on ... ...

    Abstract The evolution of specialized cell-types is a long-standing interest of biologists, but given the deep time-scales very difficult to reconstruct or observe. microRNAs have been linked to the evolution of cellular complexity and may inform on specialization. The endothelium is a vertebrate-specific specialization of the circulatory system that enabled a critical new level of vasoregulation. The evolutionary origin of these endothelial cells is unclear. We hypothesized that Mir-126, an endothelial cell-specific microRNA may be informative. We here reconstruct the evolutionary history of Mir-126. Mir-126 likely appeared in the last common ancestor of vertebrates and tunicates, which was a species without an endothelium, within an intron of the evolutionary much older EGF Like Domain Multiple (Egfl) locus. Mir-126 has a complex evolutionary history due to duplications and losses of both the host gene and the microRNA. Taking advantage of the strong evolutionary conservation of the microRNA among Olfactores, and using RNA in situ hybridization, we localized Mir-126 in the tunicate Ciona robusta. We found exclusive expression of the mature Mir-126 in granular amebocytes, supporting a long-proposed scenario that endothelial cells arose from hemoblasts, a type of proto-endothelial amoebocyte found throughout invertebrates. This observed change of expression of Mir-126 from proto-endothelial amoebocytes in the tunicate to endothelial cells in vertebrates is the first direct observation of the evolution of a cell-type in relation to microRNA expression indicating that microRNAs can be a prerequisite of cell-type evolution.
    MeSH term(s) Animals ; Endothelial Cells/metabolism ; Vertebrates/genetics ; Invertebrates/genetics ; MicroRNAs/genetics ; MicroRNAs/metabolism
    Chemical Substances MicroRNAs
    Language English
    Publishing date 2023-05-08
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2020288-X
    ISSN 1525-142X ; 1520-541X
    ISSN (online) 1525-142X
    ISSN 1520-541X
    DOI 10.1111/ede.12438
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  7. Article ; Online: In Silico Analysis of Micro-RNA Sequencing Data.

    Aparicio-Puerta, Ernesto / Fromm, Bastian / Hackenberg, Michael / Halushka, Marc K

    Methods in molecular biology (Clifton, N.J.)

    2021  Volume 2284, Page(s) 231–251

    Abstract: High-throughput sequencing for micro-RNAs (miRNAs) to obtain expression estimates is a central method of molecular biology. Surprisingly, there are a number of different approaches to converting sequencing output into micro-RNA counts. Each has their own ...

    Abstract High-throughput sequencing for micro-RNAs (miRNAs) to obtain expression estimates is a central method of molecular biology. Surprisingly, there are a number of different approaches to converting sequencing output into micro-RNA counts. Each has their own strengths and biases that impact on the final data that can be obtained from a sequencing run. This chapter serves to make the reader aware of the trade-offs one must consider in analyzing small RNA sequencing data. It then compares two methods, miRge2.0 and the sRNAbench and the steps utilized to output data from their tools.
    MeSH term(s) Animals ; Computational Biology/methods ; Computer Simulation ; Datasets as Topic ; Gene Expression Profiling ; High-Throughput Nucleotide Sequencing/methods ; Humans ; MicroRNAs/analysis ; MicroRNAs/genetics ; Polymorphism, Single Nucleotide ; RNA Isoforms/analysis ; RNA Isoforms/genetics ; Sequence Analysis, RNA/methods ; Software
    Chemical Substances MicroRNAs ; RNA Isoforms
    Language English
    Publishing date 2021-04-09
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-1307-8_13
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  8. Article ; Online: The limits of human microRNA annotation have been met.

    Fromm, Bastian / Zhong, Xiangfu / Tarbier, Marcel / Friedländer, Marc R / Hackenberg, Michael

    RNA (New York, N.Y.)

    2022  Volume 28, Issue 6, Page(s) 781–785

    Abstract: Over the last few years, the number of microRNAs in the human genome has become a controversially debated issue. Several publications reported thousands of putative novel microRNAs not included in the curated microRNA gene database MirGeneDB and the ... ...

    Abstract Over the last few years, the number of microRNAs in the human genome has become a controversially debated issue. Several publications reported thousands of putative novel microRNAs not included in the curated microRNA gene database MirGeneDB and the repository miRBase. Recently, by using sequencing of ∼300 human tissues and cell lines, the human RNA atlas, an expanded inventory of human RNA annotations, was published, reporting thousands of putative microRNAs. We, the developers of established microRNA prediction tools and hosts of MirGeneDB, raise concerns about the frequently applied prediction and functional validation strategies, briefly discussing the drawbacks of false positive detections. By means of quantifying well-established biogenesis-derived features, we show that the reported novel microRNAs essentially represent false-positives and argue that the human microRNA complement, at about 550 microRNA genes, is already near complete. Output of available tools must be curated as false predictions will misguide scientists looking for biomarkers or therapeutic targets.
    MeSH term(s) Computational Biology ; Databases, Nucleic Acid ; Humans ; MicroRNAs/genetics ; Molecular Sequence Annotation
    Chemical Substances MicroRNAs
    Language English
    Publishing date 2022-03-02
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1241540-6
    ISSN 1469-9001 ; 1355-8382
    ISSN (online) 1469-9001
    ISSN 1355-8382
    DOI 10.1261/rna.079098.122
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    Zs.A 4777: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (2.OG)
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  9. Article ; Online: Accurate microRNA annotation of animal genomes using trained covariance models of curated microRNA complements in MirMachine.

    Umu, Sinan Uğur / Paynter, Vanessa M / Trondsen, Håvard / Buschmann, Tilo / Rounge, Trine B / Peterson, Kevin J / Fromm, Bastian

    Cell genomics

    2023  Volume 3, Issue 8, Page(s) 100348

    Abstract: The annotation of microRNAs depends on the availability of transcriptomics data and expert knowledge. This has led to a gap between the availability of novel genomes and high-quality microRNA complements. Using >16,000 microRNAs from the manually curated ...

    Abstract The annotation of microRNAs depends on the availability of transcriptomics data and expert knowledge. This has led to a gap between the availability of novel genomes and high-quality microRNA complements. Using >16,000 microRNAs from the manually curated microRNA gene database MirGeneDB, we generated trained covariance models for all conserved microRNA families. These models are available in our tool MirMachine, which annotates conserved microRNAs within genomes. We successfully applied MirMachine to a range of animal species, including those with large genomes and genome duplications and extinct species, where small RNA sequencing is hard to achieve. We further describe a microRNA score of expected microRNAs that can be used to assess the completeness of genome assemblies. MirMachine closes a long-persisting gap in the microRNA field by facilitating automated genome annotation pipelines and deeper studies into the evolution of genome regulation, even in extinct organisms.
    Language English
    Publishing date 2023-06-23
    Publishing country United States
    Document type Journal Article
    ISSN 2666-979X
    ISSN (online) 2666-979X
    DOI 10.1016/j.xgen.2023.100348
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  10. Article ; Online: EV-transported microRNAs of Schistosoma mansoni and Fasciola hepatica: Potential targets in definitive hosts.

    Ovchinnikov, Vladimir Y / Kashina, Elena V / Mordvinov, Viatcheslav A / Fromm, Bastian

    Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases

    2020  Volume 85, Page(s) 104528

    Abstract: Trematodes are widespread parasitic flatworms that significantly affect mankind either directly as human parasites, or indirectly via the infection of livestock and the related economic damage. The two most important trematode taxa are the blood flukes ... ...

    Abstract Trematodes are widespread parasitic flatworms that significantly affect mankind either directly as human parasites, or indirectly via the infection of livestock and the related economic damage. The two most important trematode taxa are the blood flukes Schistosoma and the liver flukes Fasciola, but detection and differentiation of these parasites remains a challenge. Recently, microRNAs (miRNAs) were described from extracellular vesicles (EV) for both parasites secreted into respective hosts. These molecules have been proposed as mediators of parasite-host communication, and potential biomarkers for the detection of parasitic infections from host blood. Our aim here was to study similarities and differences in the miRNA complements of Schistosoma mansoni and Fasciola hepatica, EV-load in particular, to predict their targets and potential functions in the parasite-host interaction. We reanalyzed the known miRNA complements of S. mansoni and F. hepatica and found 16 and 4 previously overlooked, but deeply conserved miRNAs, respectively, further moving their complements closer together. We found distinct miRNA enrichment patterns in EVs both showing high levels of flatworm miRNAs with potential for the detection of an infection from blood. Two miRNAs of the protostome specific MIR-71 and MIR-277 families were highly expressed in EVs and could, therefore, have potential as biomarkers for trematode infection. Curiously, we identified nucleotide differences in the sequence of Mir-277-P2 between S. mansoni and F. hepatica that hold great promise for the distinction of both parasites. To test whether the EV-miRNAs of S. mansoni and F. hepatica could be modulating the expression of host genes, we predicted miRNA targets in 321 human and cattle messenger RNAs that overlapped between both hosts. Of several predicted targets, wnt signaling pathway genes stood out and their suppression likely leads to changes in the glucose concentration in host blood and the reduction of inflammatory and immune responses.
    MeSH term(s) Adult ; Animals ; Biomarkers/blood ; Cattle ; Extracellular Vesicles/genetics ; Fasciola hepatica/genetics ; Female ; Genetic Variation ; Genotype ; Host-Parasite Interactions/genetics ; Humans ; Male ; MicroRNAs/blood ; MicroRNAs/genetics ; Middle Aged ; Schistosoma mansoni/genetics ; Schistosomiasis mansoni/blood ; Schistosomiasis mansoni/genetics
    Chemical Substances Biomarkers ; MicroRNAs
    Language English
    Publishing date 2020-09-04
    Publishing country Netherlands
    Document type Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2037068-4
    ISSN 1567-7257 ; 1567-1348
    ISSN (online) 1567-7257
    ISSN 1567-1348
    DOI 10.1016/j.meegid.2020.104528
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