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  1. Article ; Online: Dual-Specificity Protein Phosphatase 4 (DUSP4) Overexpression Improves Learning Behavior Selectively in Female 5xFAD Mice, and Reduces β-Amyloid Load in Males and Females

    Allen L. Pan / Mickael Audrain / Emmy Sakakibara / Rajeev Joshi / Xiaodong Zhu / Qian Wang / Minghui Wang / Noam D. Beckmann / Eric E. Schadt / Sam Gandy / Bin Zhang / Michelle E. Ehrlich / Stephen R. Salton

    Cells, Vol 11, Iss 3880, p

    2022  Volume 3880

    Abstract: Recent multiscale network analyses of banked brains from subjects who died of late-onset sporadic Alzheimer’s disease converged on VGF (non-acronymic) as a key hub or driver. Within this computational VGF network, we identified the dual-specificity ... ...

    Abstract Recent multiscale network analyses of banked brains from subjects who died of late-onset sporadic Alzheimer’s disease converged on VGF (non-acronymic) as a key hub or driver. Within this computational VGF network, we identified the dual-specificity protein phosphatase 4 ( DUSP4 ) [also known as mitogen-activated protein kinase (MAPK) phosphatase 2] as an important node. Importantly, DUSP4 gene expression, like that of VGF , is downregulated in postmortem Alzheimer’s disease (AD) brains. We investigated the roles that this VGF / DUSP4 network plays in the development of learning behavior impairment and neuropathology in the 5xFAD amyloidopathy mouse model. We found reductions in DUSP4 expression in the hippocampi of male AD subjects, correlating with increased CDR scores, and in 4-month-old female and 12–18-month-old male 5xFAD hippocampi. Adeno-associated virus (AAV5)-mediated overexpression of DUSP4 in 5xFAD mouse dorsal hippocampi (dHc) rescued impaired Barnes maze performance in females but not in males, while amyloid loads were reduced in both females and males. Bulk RNA sequencing of the dHc from 5-month-old mice overexpressing DUSP4, and Ingenuity Pathway and Enrichr analyses of differentially expressed genes (DEGs), revealed that DUSP4 reduced gene expression in female 5xFAD mice in neuroinflammatory, interferon-gamma (IFNγ), programmed cell death protein-ligand 1/programmed cell death protein 1 (PD-L1/PD-1), and extracellular signal-regulated kinase (ERK)/MAPK pathways, via which DUSP4 may modulate AD phenotype with gender-specificity.
    Keywords Alzheimer’s disease ; dual-specificity protein phosphatase 4 ; disease-associated microglia ; mitogen-activated protein kinase ; neuroinflammation ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2022-12-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Predictive network modeling in human induced pluripotent stem cells identifies key driver genes for insulin responsiveness.

    Ivan Carcamo-Orive / Marc Y R Henrion / Kuixi Zhu / Noam D Beckmann / Paige Cundiff / Sara Moein / Zenan Zhang / Melissa Alamprese / Sunita L D'Souza / Martin Wabitsch / Eric E Schadt / Thomas Quertermous / Joshua W Knowles / Rui Chang

    PLoS Computational Biology, Vol 16, Iss 12, p e

    2020  Volume 1008491

    Abstract: Insulin resistance (IR) precedes the development of type 2 diabetes (T2D) and increases cardiovascular disease risk. Although genome wide association studies (GWAS) have uncovered new loci associated with T2D, their contribution to explain the mechanisms ...

    Abstract Insulin resistance (IR) precedes the development of type 2 diabetes (T2D) and increases cardiovascular disease risk. Although genome wide association studies (GWAS) have uncovered new loci associated with T2D, their contribution to explain the mechanisms leading to decreased insulin sensitivity has been very limited. Thus, new approaches are necessary to explore the genetic architecture of insulin resistance. To that end, we generated an iPSC library across the spectrum of insulin sensitivity in humans. RNA-seq based analysis of 310 induced pluripotent stem cell (iPSC) clones derived from 100 individuals allowed us to identify differentially expressed genes between insulin resistant and sensitive iPSC lines. Analysis of the co-expression architecture uncovered several insulin sensitivity-relevant gene sub-networks, and predictive network modeling identified a set of key driver genes that regulate these co-expression modules. Functional validation in human adipocytes and skeletal muscle cells (SKMCs) confirmed the relevance of the key driver candidate genes for insulin responsiveness.
    Keywords Biology (General) ; QH301-705.5
    Subject code 571
    Language English
    Publishing date 2020-12-01T00:00:00Z
    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: An integrative multiomic network model links lipid metabolism to glucose regulation in coronary artery disease

    Ariella T. Cohain / William T. Barrington / Daniel M. Jordan / Noam D. Beckmann / Carmen A. Argmann / Sander M. Houten / Alexander W. Charney / Raili Ermel / Katyayani Sukhavasi / Oscar Franzen / Simon Koplev / Carl Whatling / Gillian M. Belbin / Jialiang Yang / Ke Hao / Eimear E. Kenny / Zhidong Tu / Jun Zhu / Li-Ming Gan /
    Ron Do / Chiara Giannarelli / Jason C. Kovacic / Arno Ruusalepp / Aldons J. Lusis / Johan L. M. Bjorkegren / Eric E. Schadt

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

    2021  Volume 13

    Abstract: Some cholesterol-lowering drugs can increase the risk of type 2 diabetes, but the mechanism behind this is not fully understood. Here the authors show that there is a single genetic regulatory module that influences both cholesterol levels and glucose ... ...

    Abstract Some cholesterol-lowering drugs can increase the risk of type 2 diabetes, but the mechanism behind this is not fully understood. Here the authors show that there is a single genetic regulatory module that influences both cholesterol levels and glucose levels, providing a link between cholesterol levels and diabetes.
    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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  4. Article ; Online: Downregulation of exhausted cytotoxic T cells in gene expression networks of multisystem inflammatory syndrome in children

    Noam D. Beckmann / Phillip H. Comella / Esther Cheng / Lauren Lepow / Aviva G. Beckmann / Scott R. Tyler / Konstantinos Mouskas / Nicole W. Simons / Gabriel E. Hoffman / Nancy J. Francoeur / Diane Marie Del Valle / Gurpawan Kang / Anh Do / Emily Moya / Lillian Wilkins / Jessica Le Berichel / Christie Chang / Robert Marvin / Sharlene Calorossi /
    Alona Lansky / Laura Walker / Nancy Yi / Alex Yu / Jonathan Chung / Matthew Hartnett / Melody Eaton / Sandra Hatem / Hajra Jamal / Alara Akyatan / Alexandra Tabachnikova / Lora E. Liharska / Liam Cotter / Brian Fennessy / Akhil Vaid / Guillermo Barturen / Hardik Shah / Ying-chih Wang / Shwetha Hara Sridhar / Juan Soto / Swaroop Bose / Kent Madrid / Ethan Ellis / Elyze Merzier / Konstantinos Vlachos / Nataly Fishman / Manying Tin / Melissa Smith / Hui Xie / Manishkumar Patel / Kai Nie

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

    2021  Volume 15

    Abstract: Multisystem inflammatory syndrome in children (MIS-C) onsets in COVID-19 patients with manifestations similar to Kawasaki disease (KD). Here the author probe the peripheral blood transcriptome of MIS-C patients to find signatures related to natural ... ...

    Abstract Multisystem inflammatory syndrome in children (MIS-C) onsets in COVID-19 patients with manifestations similar to Kawasaki disease (KD). Here the author probe the peripheral blood transcriptome of MIS-C patients to find signatures related to natural killer (NK) cell activation and CD8+ T cell exhaustion that are shared with KD patients.
    Keywords Science ; Q
    Language English
    Publishing date 2021-08-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Multiscale causal networks identify VGF as a key regulator of Alzheimer’s disease

    Noam D. Beckmann / Wei-Jye Lin / Minghui Wang / Ariella T. Cohain / Alexander W. Charney / Pei Wang / Weiping Ma / Ying-Chih Wang / Cheng Jiang / Mickael Audrain / Phillip H. Comella / Amanda K. Fakira / Siddharth P. Hariharan / Gillian M. Belbin / Kiran Girdhar / Allan I. Levey / Nicholas T. Seyfried / Eric B. Dammer / Duc Duong /
    James J. Lah / Jean-Vianney Haure-Mirande / Ben Shackleton / Tomas Fanutza / Robert Blitzer / Eimear Kenny / Jun Zhu / Vahram Haroutunian / Pavel Katsel / Sam Gandy / Zhidong Tu / Michelle E. Ehrlich / Bin Zhang / Stephen R. Salton / Eric E. Schadt

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

    2020  Volume 19

    Abstract: To investigate the molecular foundation of sporadic Alzheimer’s disease (AD), Beckmann et al. constructed multiscale causal networks on a large human AD multi-omics dataset, detecting AD-associated networks and their top predicted regulator, VGF, with ... ...

    Abstract To investigate the molecular foundation of sporadic Alzheimer’s disease (AD), Beckmann et al. constructed multiscale causal networks on a large human AD multi-omics dataset, detecting AD-associated networks and their top predicted regulator, VGF, with extensive validation in the 5xFAD mouse model.
    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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  6. Article ; Online: Multiscale causal networks identify VGF as a key regulator of Alzheimer’s disease

    Noam D. Beckmann / Wei-Jye Lin / Minghui Wang / Ariella T. Cohain / Alexander W. Charney / Pei Wang / Weiping Ma / Ying-Chih Wang / Cheng Jiang / Mickael Audrain / Phillip H. Comella / Amanda K. Fakira / Siddharth P. Hariharan / Gillian M. Belbin / Kiran Girdhar / Allan I. Levey / Nicholas T. Seyfried / Eric B. Dammer / Duc Duong /
    James J. Lah / Jean-Vianney Haure-Mirande / Ben Shackleton / Tomas Fanutza / Robert Blitzer / Eimear Kenny / Jun Zhu / Vahram Haroutunian / Pavel Katsel / Sam Gandy / Zhidong Tu / Michelle E. Ehrlich / Bin Zhang / Stephen R. Salton / Eric E. Schadt

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

    2020  Volume 19

    Abstract: To investigate the molecular foundation of sporadic Alzheimer’s disease (AD), Beckmann et al. constructed multiscale causal networks on a large human AD multi-omics dataset, detecting AD-associated networks and their top predicted regulator, VGF, with ... ...

    Abstract To investigate the molecular foundation of sporadic Alzheimer’s disease (AD), Beckmann et al. constructed multiscale causal networks on a large human AD multi-omics dataset, detecting AD-associated networks and their top predicted regulator, VGF, with extensive validation in the 5xFAD mouse model.
    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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