ErturkLab – Acute Brain Injury
A fundamental challenge in modern science is to understand how the brain functions in health and what goes wrong in the disease state. We develop and implement 3D imaging technologies to be able to generate the highest resolution views of intact rodent organs and bodies. We developed DISCO line tissues transparency technologies, which have been a great utility for scientists from diverse bio-medical research fields. Overall, this approach provides a holistic view of inter connected biological systems to perceive biological mechanisms in an unbiased way.
Our laboratory is interested in understanding key mechanisms leading to neurodegeneration after acute brain injuries, mainly stroke and dementia. To this quest, we take a multidisciplinary approach by using advanced neuroscience imaging, genetic engineering, nanotechnology and artificial intelligence.
While many diseases affect the entire body, research is usually conducted on the tissue of interest ignoring 99% rest of the organism. My lab believes that we need to see organism as a whole to correctly assess all biological systems affecting each other. Therefore, we use a holistic approach in research to overcome potential bias and discover essential cellular and molecular mechanisms in toto. Towards this goal, we have developed cutting-edge tissue transparency methods allowing 3D histology on intact organisms. We can now collect information on whole organism at the sub-cellular levels without sectioning. Obtained imaged data for example can for the first-time present the complete neuronal connectivity at single neuronal level, and determine what goes wrong in a neurological disease. We use machine-learning based image analysis methods to analyze these large imaging data. Finally, we are focusing on developing nanotechnology (nano-robots) to treat neurological diseases in a novel and potent way.
Contact: Dr. Ali Erturk
Ertürk, Ali, Dr., PI
Rami Al-Maskari, Ph.D. Candidate
Dr. Harsharan S. Bhatia, Postdoc
Karen Biniossek, Team Assistant
Marin Bralo, Technical Assistant
Dr. Benjamin Förstera, Postdoc
Dr. Farida Hellal, Postdoc
Izabela Horvath, Ph.D. Candidate
Dr. Doris Kaltenecker, Postdoc
Ilgin Kolabas, Ph.D. Candidate
Louis Kümmerle, Ph.D. Candidate
Hongcheng Mai, Ph.D. Candidate
Muge Molbay Ph.D. Candidate
Dr. Tzu-Lun Ohn, Postdoc
Furkan Ozturk, Ph.D. Candidate
Johannes Paetzold, Ph.D. Candidate
Dr. Chenchen Pan, Postdoc
Zhouyi Rong, PhD Candidate
Oliver Schoppe, Group Leader: Artificial Intelligence
Dr. Karen Stanic, Postdoc
Mihail Todorov, Ph.D. Candidate
Ana Toman Fabjan, Team Assistant
Dr. Alison Wright, Postdoc
Shan Zhao, Ph.D. Candidate
Francesca Paola Quacquarelli
Marika Ruiyao Cai
Ali Erturk, Principal investigator
I studied genetic engineering and molecular biology. My research has mainly focused on mechanisms of neurodegenerative diseases and developing new imaging tools to decipher details of complex biological systems in the whole organism.
Science has advanced enormously in the recent decades, however, we still lack effective treatments for devastating diseases such as stroke and dementia, partly due to incremental progress, where the majority of scientific effort focuses on the next “predicted” mechanisms. I believe a multi-disciplinary approach combining the expertise of diverse fields such as advance imaging, genetic engineering, nanotechnology and artificial intelligence will be a key to obtain “unbiased” readouts on biological systems and come up with breakthrough solutions to cure all diseases including the aging in the next a few decades.
We are an organism of interconnected systems from head-to-toe, via for example wiring of neurons and vessels. Thus, it is natural that most of the biological events will impact the whole-body, not only a small region. However, there is hardly any effort to study biological systems as a whole in research, also due to lack of methods that can provide readouts in the whole body at the cellular and molecular level. Towards this goal, we develop and use whole mouse transparency technologies (e.g., Ertürk et al., 2012 Nature Medicine, Pan et al., 2016 Nature Methods), enabling us to have a holistic view on cellular and molecular mechanisms in health and disease. For example, we study the effects of acute brain injuries not only in the brain but also throughout the whole nervous system and the body. We are also focusing on artificial intelligence to analyze the large data sets and nanorobots to discover new ways of drug delivery into the brain.
Current academic positions
07/2014–now: Independent group leader, Institute for Stroke and Dementia (ISD), Ludwig Maximilians-University of Munich (LMU), Germany
01/2017–now: Adjunct Assistant Professor, Rochester University, New York, USA
Education and training
2009–2014: Postdoctoral fellow at Genentech Inc., South San Francisco, (Supervisor: Morgan Sheng, VP of Genentech Neuroscience).
2003–2009: Doctoral thesis at Max–Planck–Institute of Neurobiology, (Supervisor: Frank Bradke, DZNE Bonn)
2002: Intern, Harvard University. School of Medicine, Timothy Vartanian lab
2001: Intern, Yale University, School of Medicine, Hal Blumenfeld lab
1998–2003: Bachelor of Science, Bilkent University, Molecular Biology and Genetics, Ankara
2018-2023: R01, NIH, USA
2014-2019: Solorz-Żak’s Foundation (Institute for Stroke and Dementia)
2017-2019: Fritz Thyssen Stiftung, Germany
2016-2019: DFG Research Grant
2015-2019: Excellent cluster of Munich SyNergy
2016-2018: Helmholtz Alliance ICEMED
2015-2018: ERA-Net Neuron, European Research Council
2015-2017: LMU Excellent seeding funds and FöFoLe research grants
Honors & Awards
2017: Fritz Thyssen Stiftung investigator award
2016: Interviewed by New York Times and Wall Street Journal for our novel technologies
2014: Sofja Kovalevskaja Award from Humboldt Foundation (offered)
2009–2014: Genentech postdoctoral program
2004–2007: Marie Curie PhD fellowship from European Resreach Concil
1998–2003: Full education scholarship awarded by Bilkent University
1998–2003: Scholarship awarded by The Scientific and Technological Research Council of Turkey
A visit from Nano – 3sat Mediathek.
Today at the lab we were very lucky to have a team from the Bayerisches Fernsehen come to our lab space at the Institute for Stroke and Dementia Research (ISD) and take a look at some of the cleared tissues we’ve produced.
Our work on AI-based analysis of the entire brain vasculature is now in press. This is the 5th publication of erturklab in its 5 years of existence. Congratulations to all team members and the collaborators, including Bjoern Menze and his lab. (March 2020) .
Todorov M, Paetzold J, Schoppe O,…Ertürk A. Automated analysis of whole brain vasculature using machine learning. bioRxiv version
Our 4th Paper in Cell
Our 4th publication also appears in Cell. We developed the first to technology to make intact human organs transparent for cellular & molecular mapping using novel tissue chemistry, light-sheet microscopy, and machine learning. The image below shows the highest resolution of the intact human kidney ever obtained. https://www.cell.com/cell/fulltext/S0092-8674(20)30111-2
Cure Alzheimer’s Fund
We received a grant from Cure Alzheimer’s Fund in a consortium led by Jony Kipnis. We will investigate the role of skull-meninges connections in relation to the lymphatic/glymphatic system and blood-brain barrier.
Publications by Ali Ertürk
Pan C, Schoppe O, Parra-Damas A, Cai R, Todorov MI, Gondi G, von Neubeck B, Böğürcü-Seidel N, Seidel S, Sleiman K, Veltkamp C, Förstera B, Mai H, Rong Z, Trompak O, Ghasemigharagoz A, Reimer MA, Cuesta AM, Coronel J, Jeremias I, Saur D, Acker-Palmer A, Acker T, Garvalov BK, Menze B, Zeidler R, Ertürk A. Deep Learning Reveals Cancer Metastasis and Therapeutic Antibody Targeting in the Entire Body. Cell. 2019 Dec 12;179(7):1661-1676.e19.
Cai R, Pan C, Ghasemigharagoz A, Todorov MI, Förstera B, Zhao S, Bhatia HS, Parra-Damas A, Mrowka L, Theodorou D, Rempfler M, Xavier ALR, Kress BT, Benakis C, Steinke H, Liebscher S, Bechmann I, Liesz A, Menze B, Kerschensteiner M, Nedergaard M, Ertürk A. Panoptic imaging of transparent mice reveals whole-body neuronal projections and skull-meninges connections. Nat Neurosci. 2019 Feb;22(2):317-327.
Parhizkar S, Arzberger T, Brendel M, Kleinberger G, Deussing M, Focke C, Nuscher B, Xiong M, Ghasemigharagoz A, Katzmarski N, Krasemann S, Lichtenthaler SF, Müller SA, Colombo A, Monasor LS, Tahirovic S, Herms J, Willem M, Pettkus N, Butovsky O, Bartenstein P, Edbauer D, Rominger A, Ertürk A, Grathwohl SA, Neher JJ, Holtzman DM, Meyer-Luehmann M, Haass C. Loss of TREM2 function increases amyloid seeding but reduces plaque-associated ApoE. Nat Neurosci. 2019 Feb;22(2):191-204.
von Neubeck B, Gondi G, Riganti C, Pan C, Parra Damas A, Scherb H, Ertürk A, Zeidler R. An inhibitory antibody targeting carbonic anhydrase XII abrogates chemoresistance and significantly reduces lung metastases in an orthotopic breast cancer model in vivo. Int J Cancer. 2018 Oct 15;143(8):2065-2075.
Llovera G, Benakis C, Enzmann G, Cai R, Arzberger T, Ghasemigharagoz A, Mao X, Malik R, Lazarevic I, Liebscher S, Ertürk A, Meissner L, Vivien D, Haffner C, Plesnila N, Montaner J, Engelhardt B, Liesz A. The choroid plexus is a key cerebral invasion route for T cells after stroke. Acta Neuropathol. 2017 Dec;134(6):851-868.
Ertürk A, Mauch CP, Hellal F, Förstner F, Keck T, Becker K, Jährling N, Steffens H, Richter M, Hübener M, Kramer E, Kirchhoff F, Dodt HU, Bradke F. Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury. Nat Med. 2011 Dec 25;18(1):166-71.
Usher LC, Johnstone A, Ertürk A, Hu Y, Strikis D, Wanner IB, Moorman S, Lee JW, Min J, Ha HH, Duan Y, Hoffman S, Goldberg JL, Bradke F, Chang YT, Lemmon VP, Bixby JL. A chemical screen identifies novel compounds that overcome glial-mediated inhibition of neuronal regeneration. J Neurosci. 2010 Mar 31;30(13):4693-706.