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  1. Article ; Online: Trace amine associated receptor 1 (TAAR1) expression and modulation of inflammatory cytokine production in mouse bone marrow-derived macrophages: a novel mechanism for inflammation in ulcerative colitis.

    Bugda Gwilt, Katlynn / Olliffe, Neva / Hoffing, Rachel A / Miller, Gregory M

    Immunopharmacology and immunotoxicology

    2019  Volume 41, Issue 6, Page(s) 577–585

    Abstract: Context: ...

    Abstract Context:
    MeSH term(s) Animals ; Bone Marrow ; Colitis, Ulcerative/metabolism ; Colitis, Ulcerative/pathology ; Cytokines/biosynthesis ; Gene Expression Regulation ; Inflammation/metabolism ; Inflammation/pathology ; Lipopolysaccharides/toxicity ; Macrophages/metabolism ; Macrophages/pathology ; Mice ; Receptors, G-Protein-Coupled/biosynthesis
    Chemical Substances Cytokines ; Lipopolysaccharides ; Receptors, G-Protein-Coupled ; Trace amine-associated receptor 1 (XMC8VP6RI2)
    Language English
    Publishing date 2019-10-01
    Publishing country England
    Document type Journal Article
    ZDB-ID 807033-7
    ISSN 1532-2513 ; 0892-3973
    ISSN (online) 1532-2513
    ISSN 0892-3973
    DOI 10.1080/08923973.2019.1672178
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Transcript-aware analysis of rare predicted loss-of-function variants in the UK Biobank elucidate new isoform-trait associations.

    Hoffing, Rachel A / Deaton, Aimee M / Holleman, Aaron M / Krohn, Lynne / LoGerfo, Philip J / Plekan, Mollie E / Akle Serrano, Sebastian / Nioi, Paul / Ward, Lucas D

    Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing

    2023  Volume 29, Page(s) 247–260

    Abstract: A single gene can produce multiple transcripts with distinct molecular functions. Rare-variant association tests often aggregate all coding variants across individual genes, without accounting for the variants' presence or consequence in resulting ... ...

    Abstract A single gene can produce multiple transcripts with distinct molecular functions. Rare-variant association tests often aggregate all coding variants across individual genes, without accounting for the variants' presence or consequence in resulting transcript isoforms. To evaluate the utility of transcript-aware variant sets, rare predicted loss-of-function (pLOF) variants were aggregated for 17,035 protein-coding genes using 55,558 distinct transcript-specific variant sets. These sets were tested for their association with 728 circulating proteins and 188 quantitative phenotypes across 406,921 individuals in the UK Biobank. The transcript-specific approach resulted in larger estimated effects of pLOF variants decreasing serum cis-protein levels compared to the gene-based approach (pbinom ≤ 2x10-16). Additionally, 251 quantitative trait associations were identified as being significant using the transcript-specific approach but not the gene-based approach, including PCSK5 transcript ENST00000376752 and standing height (transcript-specific statistic, P = 1.3x10-16, effect = 0.7 SD decrease; gene-based statistic, P = 0.02, effect = 0.05 SD decrease) and LDLR transcript ENST00000252444 and apolipoprotein B (transcript-specific statistic, P = 5.7x10-20, effect = 1.0 SD increase; gene-based statistic, P = 3.0x10-4, effect = 0.2 SD increase). This approach demonstrates the importance of considering the effect of pLOFs on specific transcript isoforms when performing rare-variant association studies.
    MeSH term(s) Humans ; UK Biobank ; Biological Specimen Banks ; Computational Biology ; Phenotype ; Protein Isoforms/genetics
    Chemical Substances Protein Isoforms
    Language English
    Publishing date 2023-12-31
    Publishing country United States
    Document type Journal Article
    ISSN 2335-6936
    ISSN (online) 2335-6936
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Rare loss of function variants in the hepatokine gene INHBE protect from abdominal obesity.

    Deaton, Aimee M / Dubey, Aditi / Ward, Lucas D / Dornbos, Peter / Flannick, Jason / Yee, Elaine / Ticau, Simina / Noetzli, Leila / Parker, Margaret M / Hoffing, Rachel A / Willis, Carissa / Plekan, Mollie E / Holleman, Aaron M / Hinkle, Gregory / Fitzgerald, Kevin / Vaishnaw, Akshay K / Nioi, Paul

    Nature communications

    2022  Volume 13, Issue 1, Page(s) 4319

    Abstract: Identifying genetic variants associated with lower waist-to-hip ratio can reveal new therapeutic targets for abdominal obesity. We use exome sequences from 362,679 individuals to identify genes associated with waist-to-hip ratio adjusted for BMI ( ... ...

    Abstract Identifying genetic variants associated with lower waist-to-hip ratio can reveal new therapeutic targets for abdominal obesity. We use exome sequences from 362,679 individuals to identify genes associated with waist-to-hip ratio adjusted for BMI (WHRadjBMI), a surrogate for abdominal fat that is causally linked to type 2 diabetes and coronary heart disease. Predicted loss of function (pLOF) variants in INHBE associate with lower WHRadjBMI and this association replicates in data from AMP-T2D-GENES. INHBE encodes a secreted protein, the hepatokine activin E. In vitro characterization of the most common INHBE pLOF variant in our study, indicates an in-frame deletion resulting in a 90% reduction in secreted protein levels. We detect associations with lower WHRadjBMI for variants in ACVR1C, encoding an activin receptor, further highlighting the involvement of activins in regulating fat distribution. These findings highlight activin E as a potential therapeutic target for abdominal obesity, a phenotype linked to cardiometabolic disease.
    MeSH term(s) Activin Receptors, Type I/genetics ; Body Mass Index ; Diabetes Mellitus, Type 2/genetics ; Humans ; Inhibin-beta Subunits/genetics ; Obesity/genetics ; Obesity, Abdominal/genetics ; Waist-Hip Ratio
    Chemical Substances INHBE protein, human ; Inhibin-beta Subunits (93443-12-0) ; ACVR1C protein, human (EC 2.7.11.30) ; Activin Receptors, Type I (EC 2.7.11.30)
    Language English
    Publishing date 2022-07-27
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-022-31757-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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