A deep-learning framework reveals whole-body perturbations at cell level

A deep-learning framework reveals whole-body perturbations at cell level.

Doris Kaltenecker^1,2,3, Izabela Horvath^4,5, Rami Al-Maskari^4,5,6, Ying Chen^6,7, Zeynep Ilgin Kolabas^4,6, Luciano Hoeher⁴, Mihail Todorov^4,6, David-Paul Minde⁴, Saketh Kapoor⁴, Sena Gül Turhan⁴, Louis B Kuemmerle^4,8,9, Hanno Steinke¹⁰, Tim Wohlgemuth¹⁰, Mayar Ali⁴, Florian Kofler^11,12,13,14, Pauline Morigny^1,2,3, Julia Geppert^1,2,3, Denise Jeridi⁴, Bastian Wittmann¹², Jie Luo^4,15,16, Suprosanna Shit¹², Carolina Cigankova⁴, Victor Miro Kolenic⁴, Nilsu Gür⁴, Eren Aydeniz⁴, Alara Yücecan⁴, Melissa Ertürk⁴, Laurent H A Simons^4,8, Chenchen Pan^4,6,17, Marie Piraud¹¹, Daniel Rueckert^18,19, Maria Rohm^1,2,3, Farida Hellal^4,6, Markus Elsner⁴, Harsharan Singh Bhatia^4,6, Ingo Bechmann¹⁰, Bjoern H Menze¹², Stephan Herzig^1,2,3,20, Johannes Christian Paetzold^4,18,21,22, Mauricio Berriel Diaz^1,2,3, Ali Ertürk^{23,24,25,26,27}

¹Institute for Diabetes and Cancer (IDC), Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany.

²Joint Heidelberg-IDC Translational Diabetes Program, Heidelberg University Hospital, Heidelberg, Germany.

³German Center for Diabetes Research (DZD), Neuherberg, Germany.

⁴Institute for Intelligent Biotechnologies, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany.

⁵TUM School of Computation, Information and Technology (CIT), Technical University of Munich, Munich, Germany.

⁶Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians-Universität LMU, Munich, Germany.

⁷Munich Medical Research School (MMRS), Munich, Germany.

⁸Institute of Computational Biology, Helmholtz Munich, Neuherberg, Germany.

⁹School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.

¹⁰Institute of Anatomy, University of Leipzig, Leipzig, Germany.

¹¹Helmholtz AI, Helmholtz Munich, Neuherberg, Germany.

¹²Department for Quantitative Biomedicine, University of Zurich, Zurich, Switzerland.

¹³AI for Image-Guided Diagnosis and Therapy, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany.

¹⁴Hertie Institute for AI in Brain Health, University of Tübingen, Tübingen, Germany.

¹⁵Department of Industrial and Molecular Pharmaceutics, Purdue University, West Lafayette, IN, USA.

¹⁶Purdue University Institute for Cancer Research, West Lafayette, IN, USA.

¹⁷Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.

¹⁸Department of Computing, Imperial College London, London, United Kingdom.

¹⁹Chair for AI in Healthcare and Medicine, Technical University of Munich (TUM) and TUM University Hospital, Munich, Germany.

²⁰Chair Molecular Metabolic Control, TU, Munich, Germany.

²¹Department of Radiology, Weill Cornell Medicine, New York, NY, USA.

²²Cornell Tech, New York, NY, USA.

²³Institute for Intelligent Biotechnologies, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany. ali.erturk@helmholtz-munich.de.

²⁴Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians-Universität LMU, Munich, Germany. ali.erturk@helmholtz-munich.de.

²⁵School of Medicine, Koç University, Istanbul, Turkey. ali.erturk@helmholtz-munich.de.

²⁶Munich Cluster for Systems Neurology (SyNergy), Munich, Germany. ali.erturk@helmholtz-munich.de.

²⁷Deep Piction, Munich, Germany. ali.erturk@helmholtz-munich.de.

Abstract

Many diseases, including obesity, have systemic effects that perturb multiple organ systems throughout the body1,2. However, tools for comprehensive, high-resolution analysis of disease-associated changes at the whole-body scale have been lacking. Here we developed MouseMapper, a suite of foundation-model-based deep-learning algorithms enabling multi-system analysis of disease across the entire mo…

Abstract

Create a free account to keep reading