Research Groups

Holtman group

During her master (Behavioral Cognitive Neurosciences; 2008-2010, University of Groningen), Inge R. Holtman travelled to the internationally renowned lab of Prof. Dr. Michael Meaney at McGill University in Montreal, Canada, where her interest in epigenetics of brain diseases emerged. After that she successfully obtained funding from BCN-graduate school that enabled her to pursue a PhD.

During her doctoral studies (2011 – 2016, University of Groningen), she specialized in bioinformatics and NGS-data analysis approaches to study the role of microglia in brain development, aging and disease, across different species at the lab of Dr. Erik Boddeke and Dr. Bart Eggen. Additionally, she participated in a large number of international collaborations that successfully resulted in publications in peer reviewed scientific journals. Her PhD was awarded cum laude.

As a postdoctoral researcher (2016 – 2019), she worked in the critically acclaimed lab of Dr. Chris Glass at the University of California, San Diego. This work was co-sponsored by the Gemmy & Mibeth Tichelaar awards from the Dutch MS Research Foundation. Here she specialized in the effects of natural genetic variation on expression and enhancer signatures of CNS cell types and tissue-macrophages; and the 3D-structure of the chromatin by applying a wide-range of computational tools. In 2018, she was awarded a Veni fellowship by the Science Domain from the Dutch NWO to focus on the role of transcriptional regulation of microglia in Alzheimer’s Disease.

In 2020, Dr. Holtman successfully pursued a Rosalind Franklin Fellowship that enabled her to become a junior group leader in the section of Molecular Neurobiology. Here she continues to study the effect of natural genetic variation on susceptibility to brain diseases. In collaboration with the Netherlands Brain Bank, she established the Netherlands Neurogenomics Database, which is supported by the ‘Stichting Vrienden van het Herseninstituut’. The aim of this project is to integrate the extensive clinical and neuropathological data of the NHB, with a multi-omics map in order to study the effects of genetic variation on brain disease using state-of-the-art computational and machine learning  approaches.

  • People
  • Publications
  • Inge R. Holtman PhD Visit

    Assistant Professor - Rosalind Franklin Junior Group Leader

    Research fields

    Computational Neurobiology, (epi) genetics, Neurogenomics, Transcriptional regulation of microglia

    PhD students
    Kate (Ekaterina) Dagkesamanskaia, MSc
    People Holtman group
    • Selected publications  
      1. Brain cell type-specific enhancer-promoter interactome maps and disease-risk association. Nott A, Holtman IR, Coufal NG, Schlachetzki JCM, Yu M, Hu R, Han CZ, Pena M, Xiao J, Wu Y, Keulen Z, Pasillas MP, O'Connor C, Nickl CK, Schafer ST, Shen Z, Rissman RA, Brewer JB, Gosselin D, Gonda DD, Levy ML, Rosenfeld MG, McVicker G, Gage FH, Ren B, Glass CK. Science. 2019 Nov 29;366(6469):1134-1139. doi: 10.1126/science.aay0793. Epub 2019 Nov 14. PMID: 31727856 Free PMC article.
      2. Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function. Link VM, Duttke SH, Chun HB, Holtman IR, Westin E, Hoeksema MA, Abe Y, Skola D, Romanoski CE, Tao J, Fonseca GJ, Troutman TD, Spann NJ, Strid T, Sakai M, Yu M, Hu R, Fang R, Metzler D, Ren B, Glass CK. Cell. 2018 Jun 14;173(7):1796-1809.e17. doi: 10.1016/j.cell.2018.04.018. Epub 2018 May 17. PMID: 29779944 Free PMC article.
      3. An environment-dependent transcriptional network specifies human microglia identity. Gosselin D, Skola D, Coufal NG, Holtman IR, Schlachetzki JCM, Sajti E, Jaeger BN, O'Connor C, Fitzpatrick C, Pasillas MP, Pena M, Adair A, Gonda DD, Levy ML, Ransohoff RM, Gage FH, Glass CK. Science. 2017 Jun 23;356(6344):eaal3222. doi: 10.1126/science.aal3222. Epub 2017 May 25. PMID: 28546318 Free PMC article.
      4. Transcriptomic analysis of purified human cortical microglia reveals age-associated changes. Galatro TF, Holtman IR, Lerario AM, Vainchtein ID, Brouwer N, Sola PR, Veras MM, Pereira TF, Leite REP, Möller T, Wes PD, Sogayar MC, Laman JD, den Dunnen W, Pasqualucci CA, Oba-Shinjo SM, Boddeke EWGM, Marie SKN, Eggen BJL. Nat Neurosci. 2017 Aug;20(8):1162-1171. doi: 10.1038/nn.4597. Epub 2017 Jul 3. PMID: 28671693
      5. Transcriptional control of microglia phenotypes in health and disease. Holtman IR, Skola D, Glass CK. J Clin Invest. 2017 Sep 1;127(9):3220-3229. doi: 10.1172/JCI90604. Epub 2017 Jul 31. PMID: 28758903 Free PMC article. Review.
      6. Induction of a common microglia gene expression signature by aging and neurodegenerative conditions: a co-expression meta-analysis. Holtman IR, Raj DD, Miller JA, Schaafsma W, Yin Z, Brouwer N, Wes PD, Möller T, Orre M, Kamphuis W, Hol EM, Boddeke EW, Eggen BJ. Acta Neuropathol Commun. 2015 May 23;3:31. doi: 10.1186/s40478-015-0203-5. PMID: 26001565 Free PMC article.
      7. Glia Open Access Database (GOAD): A comprehensive gene expression encyclopedia of glia cells in health and disease. Holtman IR, Noback M, Bijlsma M, Duong KN, van der Geest MA, Ketelaars PT, Brouwer N, Vainchtein ID, Eggen BJ, Boddeke HW. Glia. 2015 Sep;63(9):1495-506. doi: 10.1002/glia.22810. Epub 2015 Mar 25. PMID: 25808223 Review.
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