Deep learning based behavioral profiling of rodent stroke recovery

Weber, R.; Mulders, Geertje; Kaiser, Julia; Tackenberg, Christian; Rust, Ruslan

doi:10.1101/2021.08.11.455647

Cited by 8 publications

(13 citation statements)

References 48 publications

(62 reference statements)

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“…Data points that did not pass the likelihood of detection of 95% were excluded. We confirmed that previously identified key parameters [16] were altered in all groups of animals after stroke. For instance, an asymmetric stride pattern describing the non-simultaneous placement of opposed front and back toes, was observed acutely after stroke in all groups (3dpi: all p < 0.05) ( Fig.…”

Section: Resultssupporting

confidence: 89%

“…Next, we applied a recently established deep learning algorithm to videos of mice during a voluntary run to identify specific gait changes after stroke [16,17]. We confirmed that the body parts of interest including tail base, iliac crest, hip, back ankles, back toe, shoulder, wrist, elbow, front toe, and head could be reliably detected from three perspectives ( Fig 3C, D ).…”

Section: Resultsmentioning

confidence: 54%

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Molecular and anatomical roadmap of stroke pathology in immunodeficient mice

Weber

Mulders

Perron

et al. 2022

Preprint

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Background Stroke remains a leading cause of disability and death worldwide. It has become apparent that inflammation and immune mediators have a pre-dominant role in initial tissue damage and long-term recovery following the injury. Still, different immunosuppressed mouse models are necessary in stroke research e.g., to evaluate therapies using human cell grafts. Despite mounting evidence delineating the importance of inflammation in the stroke pathology, it is poorly described to what extent partial immune deficiency influences the overall stroke outcome. Methods Here, we assessed the stroke pathology of popular genetic immunodeficient mouse models, i.e., NOD scid gamma (NSG) and recombination activating gene 2 (Rag2-/-) mice as well as pharmacologically immunosuppressed mice and compared them to immune competent, wildtype (WT) C57BL/6J mice up to three weeks after injury. We performed histology, gene expression profiling, serum analysis and functional behavioural tests to identify the impact of immunosuppression on the stroke progression. Results We detected distinct changes in microglia infiltration, scar-forming and vascular repair in immune-suppressed mice three weeks after injury. Gene expression analysis of stroked tissue revealed the strongest deviation from immune competent mice was observed in NSG mice, for instance, affecting immunological and angiogenic pathways. Pharmacological immunosuppression resulted in the least variation in gene expression compared with the WT. Major differences have been further identified in the systemic inflammatory response following stroke acutely and three weeks following injury. These anatomical, genetic, and systemic changes did not affect functional deficits and recovery in a time course of three weeks. To determine whether the timing of immunosuppression after stroke is critical, we compared mice with acute and delayed pharmacological immunosuppression after stroke. Mice with a delayed immunosuppression (7d) after stroke showed increased inflammatory and scarring responses compared to animals acutely treated with tacrolimus, thus more closely resembling WT pathology. Transplantation of human cells in the brains of immunosuppressed mouse models led to prolonged cell survival in all immunosuppressed mouse models, which was most consistent in NSG and Rag2-/- mice. Conclusions In sum, we detected distinct anatomical and molecular changes in the stroke pathology between the individual immunosuppressed mouse models that should be carefully considered when selecting an appropriate mouse model for stroke research.

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Section: Resultssupporting

confidence: 89%

Section: Resultsmentioning

confidence: 54%

Molecular and anatomical roadmap of stroke pathology in immunodeficient mice

Weber

Mulders

Perron

et al. 2022

Preprint

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“…The induction of a photothrombotic stroke was carried out as previously described in wild-type (wt) mice [ 14 , 17 – 20 ] and in NSG and Rag2 −/− mice. In brief, mice were anesthetized using isoflurane (4% induction, 1.5% maintenance, Attane, Provet AG).…”

Section: Methodsmentioning

confidence: 99%

Xeno-free induced pluripotent stem cell-derived neural progenitor cells for in vivo applications

et al. 2022

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Background Currently, there is no regenerative therapy for patients with neurological and neurodegenerative disorders. Cell-therapies have emerged as a potential treatment for numerous brain diseases. Despite recent advances in stem cell technology, major concerns have been raised regarding the feasibility and safety of cell therapies for clinical applications. Methods We generated good manufacturing practice (GMP)-compatible neural progenitor cells (NPCs) from transgene- and xeno-free induced pluripotent stem cells (iPSCs) that can be smoothly adapted for clinical applications. NPCs were characterized in vitro for their differentiation potential and in vivo after transplantation into wild type as well as genetically immunosuppressed mice. Results Generated NPCs had a stable gene-expression over at least 15 passages and could be scaled for up to 10 18 cells per initially seeded 10 6 cells. After withdrawal of growth factors in vitro, cells adapted a neural fate and mainly differentiated into active neurons. To ensure a pure NPC population for in vivo applications, we reduced the risk of iPSC contamination by applying micro RNA-switch technology as a safety checkpoint. Using lentiviral transduction with a fluorescent and bioluminescent dual-reporter construct, combined with non-invasive in vivo bioluminescent imaging, we longitudinally tracked the grafted cells in healthy wild-type and genetically immunosuppressed mice as well as in a mouse model of ischemic stroke. Long term in-depth characterization revealed that transplanted NPCs have the capability to survive and spontaneously differentiate into functional and mature neurons throughout a time course of a month, while no residual pluripotent cells were detectable. Conclusion We describe the generation of transgene- and xeno-free NPCs. This simple differentiation protocol combined with the ability of in vivo cell tracking presents a valuable tool to develop safe and effective cell therapies for various brain injuries. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03610-5.

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“…Furthermore, detecting motor-functional deficits in rodents following stroke is difficult as they show impressive recovery and have subtle, if any, long-term motor deficits in common behavioral tests. 17 The main goal of this study was to identify and compare different predictors of functional outcome following brain ischemia in mice. We therefore aggregated imaging and behavioral data from 13 MCAO studies.…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Prediction of Stroke Outcome in Mice Based on Non-Invasive MRI and Behavioral Testing

Knab

Koch

Major

et al. 2022

Preprint

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Background: Prediction of post-stroke outcome using the degree of subacute deficit or magnetic resonance imaging is well studied in humans. While mice are the most commonly used animals in preclinical stroke research, systematic analysis of outcome predictors is lacking. Methods: Data from 13 studies that included 45 min of middle cerebral artery occlusion on 148 mice were pooled. Motor function was measured using a modified protocol for the staircase test of skilled reaching. Phases of subacute and residual deficit were defined. Magnetic resonance images of stroke lesions were co-registered on the Allen Mouse Brain Atlas to characterize stroke topology. Different random forest prediction models that either used motor-functional deficit or imaging parameters were generated for the subacute and residual deficits. Results: We detected both a subacute and residual motor-functional deficit after stroke in mice. Different functional severity grades and recovery trajectories could be observed. In mice with small cortical lesions, lesion volume was the best predictor of the subacute deficit. The residual deficit could be predicted most accurately by the degree of the subacute deficit. When using imaging parameters for the prediction of the residual deficit, including information about the lesion topology increased prediction accuracy. A subset of anatomical regions within the ischemic lesion had particular impact on the prediction of long-term outcome. Prediction accuracy depended on the degree of functional impairment. Conclusions: For the first time, we identified and characterized predictors of post-stroke outcome in a large cohort of mice and found strong concordance with clinical data. These results are discussed in light of study design and imaging limitations. In the future, using outcome prediction can improve the design of preclinical studies and guide intervention decisions.

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Deep learning based behavioral profiling of rodent stroke recovery

Cited by 8 publications

References 48 publications

Molecular and anatomical roadmap of stroke pathology in immunodeficient mice

Molecular and anatomical roadmap of stroke pathology in immunodeficient mice

Xeno-free induced pluripotent stem cell-derived neural progenitor cells for in vivo applications

Prediction of Stroke Outcome in Mice Based on Non-Invasive MRI and Behavioral Testing

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