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Comprehensive ethological analysis of fear expression in rats using DeepLabCut and SimBA machine learning model
Linköping University, Department of Biomedical and Clinical Sciences, Center for Social and Affective Neuroscience. Linköping University, Faculty of Medicine and Health Sciences. Mahidol Univ, Thailand.
Linköping University, Department of Biomedical and Clinical Sciences, Center for Social and Affective Neuroscience. Linköping University, Faculty of Medicine and Health Sciences.
Linköping University, Department of Biomedical and Clinical Sciences, Center for Social and Affective Neuroscience. Linköping University, Faculty of Medicine and Health Sciences.
Linköping University, Department of Biomedical and Clinical Sciences, Center for Social and Affective Neuroscience. Linköping University, Faculty of Medicine and Health Sciences. Univ Bordeaux, France.
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2024 (English)In: Frontiers in Behavioral Neuroscience, E-ISSN 1662-5153, Vol. 18, article id 1440601Article in journal (Refereed) Published
Abstract [en]

Introduction: Defensive responses to threat-associated cues are commonly evaluated using conditioned freezing or suppression of operant responding. However, rats display a broad range of behaviors and shift their defensive behaviors based on immediacy of threats and context. This study aimed to systematically quantify the defensive behaviors that are triggered in response to threat-associated cues and assess whether they can accurately be identified using DeepLabCut in conjunction with SimBA. Methods: We evaluated behavioral responses to fear using the auditory fear conditioning paradigm. Observable behaviors triggered by threat-associated cues were manually scored using Ethovision XT. Subsequently, we investigated the effects of diazepam (0, 0.3, or 1 mg/kg), administered intraperitoneally before fear memory testing, to assess its anxiolytic impact on these behaviors. We then developed a DeepLabCut + SimBA workflow for ethological analysis employing a series of machine learning models. The accuracy of behavior classifications generated by this pipeline was evaluated by comparing its output scores to the manually annotated scores. Results: Our findings show that, besides conditioned suppression and freezing, rats exhibit heightened risk assessment behaviors, including sniffing, rearing, free-air whisking, and head scanning. We observed that diazepam dose-dependently mitigates these risk-assessment behaviors in both sexes, suggesting a good predictive validity of our readouts. With adequate amount of training data (approximately > 30,000 frames containing such behavior), DeepLabCut + SimBA workflow yields high accuracy with a reasonable transferability to classify well-represented behaviors in a different experimental condition. We also found that maintaining the same condition between training and evaluation data sets is recommended while developing DeepLabCut + SimBA workflow to achieve the highest accuracy. Discussion: Our findings suggest that an ethological analysis can be used to assess fear learning. With the application of DeepLabCut and SimBA, this approach provides an alternative method to decode ongoing defensive behaviors in both male and female rats for further investigation of fear-related neurobiological underpinnings.

Place, publisher, year, edition, pages
FRONTIERS MEDIA SA , 2024. Vol. 18, article id 1440601
Keywords [en]
fear conditioning; ethological analysis; risk-assessment; DeepLabCut; SimBA
National Category
Neurosciences
Identifiers
URN: urn:nbn:se:liu:diva-207206DOI: 10.3389/fnbeh.2024.1440601ISI: 001291617500001PubMedID: 39148895OAI: oai:DiVA.org:liu-207206DiVA, id: diva2:1895079
Note

Funding Agencies|Swedish Research Council [2013-07434]; Stiftelsen Psykiatriska Forskningsfonden; Wallenberg Foundation; Knut och Alice Wallenberg Stiftelse Grant

Available from: 2024-09-04 Created: 2024-09-04 Last updated: 2024-11-28
In thesis
1. Epigenetic Mechanisms underlying Alcohol Dependence and Fear Memories
Open this publication in new window or tab >>Epigenetic Mechanisms underlying Alcohol Dependence and Fear Memories
2025 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Stress is a critical factor in the onset and progression of alcohol dependence, a chronic condition characterized by loss of control over alcohol drinking. Stress is also a major risk factor for other psychiatric disorders, such as anxiety disorders. Alcohol dependence and anxiety disorders share overlapping neuroadaptations, in part mediated by epigenetic mechanisms. We have previously demonstrated that chronic alcohol exposure induces DNA hypermethylation in the dorsomedial prefrontal cortex (dmPFC) in rats. In a follow-up study, our group reported that alcohol-induced hypermethylation reduces the expression of the histone methyltransferase PRDM2, which in turn promotes stress-induced reinstatement of alcohol. These findings point to undiscovered contributions of PRDM2 to stress responses.

This thesis aimed to further understand the role of PRDM2 in stress-induced maladaptive behaviors. Study 1 showed that decreased Prdm2 expression in the dmPFC-basolateral amygdala (BLA) projection resulted in an over-consolidation of fear memory through upregulated glutamatergic signaling. Study 2 showed that decreased PRDM2 activity promotes footshock-induced relapse-like behavior in both male and female rats. Together, these findings suggest that PRDM2 may be a shared molecular substrate between alcohol dependence and anxiety disorder. Downregulation of Prdm2 in the dmPFC-BLA projection did not impact stress-induced reinstatement, while decreased Prdm2 in the dmPFC-nucleus accumbens core projection promoted reinstatement. Consistent with our preclinical findings, Study 2 also found that people with alcohol dependence exhibited reduced PRDM2 expression and increased methylation at its promoter in the prefrontal cortex. This suggests that PRDM2 and its regulatory mechanisms have a mechanistic role in stress responses, and serve as epigenetic markers for alcohol dependence across species.

In both Study 1 and Study 2, we observed a broad range of defensive behaviors in rats. Therefore, in Study 3, an ethological analysis was performed to identify multiple behaviors in response to threat-associated cues. We also assessed the utility of a machine learning pipeline to perform ethological analysis. The approach from Study 3 was implemented in Study 4, in which patterns of behaviors were characterized among rats observing a conspecific undergoing fear conditioning. Heightened fear in the observer rats associated with increased neural activation in several areas, including the dmPFC. However, the increased dmPFC activity and the heightened vicarious fear were not mediated by decreased Prdm2 expression. This suggests that direct and observational fear learning in part rely on distinct molecular mechanisms. Collectively, this thesis highlights the importance of PRDM2 and its behavioral- and circuit-specific effect in mediating fear- and alcohol-associated behaviors.  

Place, publisher, year, edition, pages
Linköping: Linköping University Electronic Press, 2025. p. 138
Series
Linköping University Medical Dissertations, ISSN 0345-0082 ; 1941
Keywords
PRDM2, Epigenetic modifications, Alcohol dependence, Fear conditioning, Stress-induced reinstatement
National Category
Neurosciences
Identifiers
urn:nbn:se:liu:diva-210093 (URN)10.3384/9789180758208 (DOI)9789180758192 (ISBN)9789180758208 (ISBN)
Public defence
2025-01-16, Berzeliussalen, Building 463, Campus US, Linköping, 09:00 (English)
Opponent
Supervisors
Available from: 2024-11-28 Created: 2024-11-28 Last updated: 2024-11-28Bibliographically approved

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