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
Förstera, Benjamin, Dr. / postdoc
Kaltenecker, Doris, Dr. / postdoc
Bhatia, Harsharan Singh, Dr. / postdoc
Toman, Ana Marija / team assistant
Pan, ChenChen / PhD student
Mai, Hongcheng / PhD student
Kolabas, Ilgin / Master student
Paetzold, Johannes / master student
Cai, (Marika) Ruiyao / PhD student
Todorov, Mihail / PhD student
Molbay, Muge / PhD student
Bralo, Marin / technician
Schopp, Oliver / PhD student
Zhao, Shan / PhD student
Rong, Zhouyi / PhD student
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
Bettina von Neubeck, Gabor Gondi, Chiara Riganti, Chenchen Pan, Arnaldo Parra Damas, Hagen Scherb, Ali Ertürk, Reinhard Zeidler (2018) An inhibitory antibody targeting Carbonic Anhydrase XII abrogates chemoresistance and significantly reduces lung metastases in an orthotopic breast cancer model in vivo. International journal of cancer May.
Gemma Llovera, Corinne Benakis, Gaby Enzmann, Ruiyao Cai, Thomas Arzberger, Alireza Ghasemigharagoz, Xiang Mao, Rainer Malik, Ivana Lazarevic, Sabine Liebscher, Ali Ertürk, Lilja Meissner, Denis Vivien, Christof Haffner, Nikolaus Plesnila, Joan Montaner, Britta Engelhardt, Arthur Liesz (2017) The choroid plexus is a key cerebral invasion route for T cells after stroke. Acta neuropathologica 134: 6. 851-868 Dec.
Chenchen Pan, Ruiyao Cai, Francesca Paola Quacquarelli, Alireza Ghasemigharagoz, Athanasios Lourbopoulos, Paweł Matryba, Nikolaus Plesnila, Martin Dichgans, Farida Hellal, Ali Ertürk (2016) Shrinkage-mediated imaging of entire organs and organisms using uDISCO. Nature methods Aug.
Ali Ertürk, Susanne Mentz, Erik E Stout, Maj Hedehus, Sara L Dominguez, Lisa Neumaier, Franziska Krammer, Gemma Llovera, Karpagam Srinivasan, David V Hansen, Arthur Liesz, Kimberly A Scearce-Levie, Morgan Sheng (2016) Interfering with the Chronic Immune Response Rescues Chronic Degeneration After Traumatic Brain Injury. The Journal of neuroscience : the official journal of the Society for Neuroscience 36: 38. 9962-9975 Sep.
Athanasios Lourbopoulos, Ali Ertürk, Farida Hellal (2015) Microglia in action: how aging and injury can change the brain's guardians. Frontiers in cellular neuroscience 9: 02.
Morgan Sheng, Ali Ertürk (2014) Long-term depression: a cell biological view. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 369: 1633. Jan.
Ali Ertürk, Yuanyuan Wang, Morgan Sheng (2014) Local pruning of dendrites and spines by caspase-3-dependent and proteasome-limited mechanisms. The Journal of neuroscience : the official journal of the Society for Neuroscience 34: 5. 1672-1688 Jan.
Yelin Chen, Yuanyuan Wang, Ali Ertürk, Dara Kallop, Zhiyu Jiang, Robby M Weimer, Joshua Kaminker, Morgan Sheng (2014) Activity-induced nr4a1 regulates spine density and distribution pattern of excitatory synapses in pyramidal neurons. Neuron 83: 2. 431-443 Jul.
Ali Ertürk, Daniel Lafkas, Cecile Chalouni (2014) Imaging cleared intact biological systems at a cellular level by 3DISCO. Journal of visualized experiments : JoVE 89. 07.
Ali Ertürk, Frank Bradke (2013) High-resolution imaging of entire organs by 3-dimensional imaging of solvent cleared organs (3DISCO). Experimental neurology 242: 57-64 Apr.
Ali Ertürk, Klaus Becker, Nina Jährling, Christoph P Mauch, Caroline D Hojer, Jackson G Egen, Farida Hellal, Frank Bradke, Morgan Sheng, Hans-Ulrich Dodt (2012) Three-dimensional imaging of solvent-cleared organs using 3DISCO. Nature protocols 7: 11. 1983-1995 Nov.
Ali Ertürk, Christoph P Mauch, Farida Hellal, Friedrich Förstner, Tara Keck, Klaus Becker, Nina Jährling, Heinz Steffens, Melanie Richter, Mark Hübener, Edgar Kramer, Frank Kirchhoff, Hans Ulrich Dodt, Frank Bradke (2012) Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury. Nature medicine 18: 1. 166-171 Jan.
Lynn C Usher, Andrea Johnstone, Ali Ertürk, Ying Hu, Dinara Strikis, Ina B Wanner, Sanne Moorman, Jae-Wook Lee, Jaeki Min, Hyung-Ho Ha, Yuanli Duan, Stanley Hoffman, Jeffrey L Goldberg, Frank Bradke, Young-Tae Chang, Vance P Lemmon, John L Bixby (2010) A chemical screen identifies novel compounds that overcome glial-mediated inhibition of neuronal regeneration. The Journal of neuroscience : the official journal of the Society for Neuroscience 30: 13. 4693-4706 Mar.
Bhavna Ylera, Ali Ertürk, Farida Hellal, Fabien Nadrigny, Andres Hurtado, Sabina Tahirovic, Martin Oudega, Frank Kirchhoff, Frank Bradke (2009) Chronically CNS-injured adult sensory neurons gain regenerative competence upon a lesion of their peripheral axon. Current biology : CB 19: 11. 930-936 Jun.
Ali Ertürk, Farida Hellal, Joana Enes, Frank Bradke (2007) Disorganized microtubules underlie the formation of retraction bulbs and the failure of axonal regeneration. The Journal of neuroscience : the official journal of the Society for Neuroscience 27: 34. 9169-9180 Aug.
Gulcan Akgul, Ali Erturk, Mustafa Turkoz, Tolga Turan, Akitoyo Ichinose, Tsuyoshi Nagatake, Kamruddin Ahmed (2005) Role of lipooligosaccharide in the attachment of Moraxella catarrhalis to human pharyngeal epithelial cells. Microbiology and immunology 49: 10. 931-935.
A Ertürk (2014) High-resolution 3D imaging of intact transparent organs by 3DISCO. Fluorescence Microscopy: Super-Resolution and other Novel Techniques Edited by:Cornea A. and Conn PM. Elsevier.
F Bradke, H Witte, A Ertürk Use of microtubule stabilizing compounds for the treatment of lesions of CNS axons (WO/2006/094811). [Patents] .
The videos of our manuscript
"Panoptic vDISCO imaging reveals neuronal connectivity, remote trauma effects and meningeal vessels in intact transparent mice”