Whole genome sequencing of nearly isogenic WMI and WLI inbred rats identifies genes potentially involved in depression and stress reactivity

Sex Influences Genetic Susceptibility to Depression-Like Behaviors in Chronic Unpredictable Mild Stress-Exposed Wistar Rats

Depression is one of the most common mood disorders among psychiatric diseases. It affects about 10% of the adult population. However, its etiopathogenesis remains poorly understood. Exploring the dynamics of stress-susceptibility and resilience will help in understanding the molecular and biological mechanisms underlying the etiopathogenesis of depression. This study aimed to determine the differences and/or similarities in factors responsible for susceptibility to depression-like behaviors in male and female Wistar rats subjected to chronic unpredictable mild stress (CUMS). Sixty Wistar rats (30 male and 30 female) weighing between 120 and 150 g were used for this study. The rats were divided into two sub-groups: control (10) and test (20) groups. Rats in the test groups were subjected to CUMS. Depression-like behaviors were assessed using light-dark box, sucrose preference, and tail suspension tests. Rats that showed depression-like behaviors following the behavioral tests (CUMS-susceptible group) were sacrificed, and their hippocampi were excised. Genomic deoxyribonucleic acid (gDNA) was purified from the hippocampal samples. Purified gDNA was subjected to whole genome sequencing (WGS). Base-calling of sequence reads from raw sequencing signal (FAST5) files was carried out, and variants were called from alignment BAM files. The corresponding VCF files generated from the variant calling experiment were filtered. Genes were identified, their impacts estimated, and variants annotated. Functional enrichment analysis was then carried out. Approximately 41% of the male and 49% of the female rats subjected to CUMS showed significant (p < 0.05) depression-like behaviors following assessment on behavioral tests. WGS of the hippocampal DNA revealed 289,839 single nucleotide polymorphisms variant types, 7002 insertions, and 34,459 deletions in males, and 1,570,186 single nucleotide polymorphisms variant types, 109,860 insertions, and 597,241 deletions in female Wistar rats. Three genes with high-impact variants were identified in male and 22 in female Wistar rats, respectively. In conclusion, female Wistar rats are more susceptible to depression-like behaviors after exposure to CUMS than males. They also have more gene variants (especially high-impact variants) than male Wistar rats.

The WMI Rat of Premature Cognitive Aging Presents Intrinsic Vulnerability to Oxidative Stress in Primary Neurons and Astrocytes Compared to Its Nearly Isogenic WLI Control

The primary neuronal and astrocyte culture described here is from the stress-hyperreactive Wistar Kyoto (WKY) More Immobile (WMI) rat with premature aging-related memory deficit, and its nearly isogenic control, the Less Immobile (WLI) strain. Primary WMI hippocampal neurons and cortical astrocytes are significantly more sensitive to oxidative stress (OS) generated by administration of H2O2 compared to WLI cells as measured by the trypan blue cell viability assay. Intrinsic genetic vulnerability is also suggested by the decreased gene expression in WMI neurons of catalase (Cat), and in WMI cortical astrocytes of insulin-like growth factor 2 (Igf2), synuclein gamma (Sncg) and glutathione peroxidase 2 (Gpx2) compared to WLI. The expressions of several mitochondrial genes are dramatically increased in response to H2O2 treatment in WLI, but not in WMI cortical astrocytes. We propose that the vulnerability of WMI neurons to OS is due to the genetic differences between the WLI and WMI. Furthermore, the upregulation of mitochondrial genes may be a compensatory response to the generation of free radicals by OS in the WLIs, and this mechanism is disturbed in the WMIs. Thus, this pilot study suggests intrinsic vulnerabilities in the WMI hippocampal neurons and cortical astrocytes, and affirm the efficacy of this bimodal in vitro screening system for finding novel drug targets to prevent oxidative damage in illnesses.

A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats

The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared to its predecessor. Gene annotations are now more complete, significantly improving the mapping precision of genomic, transcriptomic, and proteomics data sets. We jointly analyzed 163 short-read whole genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined ~20.0 million sequence variations, of which 18.7 thousand are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.

The Wistar Kyoto Rat: A Model of Depression Traits

There is an ongoing debate about the value of animal research in psychiatry with valid lines of reasoning stating the limits of individual animal models compared to human psychiatric illnesses. Human depression is not a homogenous disorder; therefore, one cannot expect a single animal model to reflect depression heterogeneity. This limited review presents arguments that the Wistar Kyoto (WKY) rats show intrinsic depression traits. The phenotypes of WKY do not completely mirror those of human depression but clearly indicate characteristics that are common with it. WKYs present despair- like behavior, passive coping with stress, comorbid anxiety, and enhanced drug use compared to other routinely used inbred or outbred strains of rats. The commonly used tests identifying these phenotypes reflect exploratory, escape-oriented, and withdrawal-like behaviors. The WKYs consistently choose withdrawal or avoidance in novel environments and freezing behaviors in response to a challenge in these tests. The physiological response to a stressful environment is exaggerated in WKYs. Selective breeding generated two WKY substrains that are nearly isogenic but show clear behavioral differences, including that of depression-like behavior. WKY and its substrains may share characteristics of subgroups of depressed individuals with social withdrawal, low energy, weight loss, sleep disturbances, and specific cognitive dysfunction. The genomes of the WKY and WKY substrains contain variations that impact the function of many genes identified in recent human genetic studies of depression. Thus, these strains of rats share characteristics of human depression at both phenotypic and genetic levels, making them a model of depression traits.

The REEP family of proteins: molecular targets and role in pathophysiology

Receptor expression-enhancing proteins (REEPs) are an evolutionarily conserved protein family that is pivotal to the structure and function of the endoplasmic reticulum (ER). The REEP family can be classified into two major subfamilies in higher species, the REEP1-4 and REEP5-6 subfamilies. Within the REEP1-4 subfamily, REEP1 and REEP2 are closely related, and REEP3 and REEP4 are similarly related. The REEP family is widely distributed in various tissues. Recent studies indicate that the REEP family is involved in many pathological and physiological processes, such as ER morphogenesis and remodeling, microtubule cytoskeleton regulation, and the trafficking and expression of G protein-coupled receptors (GPCRs). Moreover, the REEP family plays crucial roles in the occurrence and development of many diseases, including neurological diseases, diabetes, retinal diseases, cardiac diseases, infertility, obesity, oligoarticular juvenile idiopathic arthritis (OJIA), COVID-19, and cancer. In the present review, we describe the distribution and structure of the REEP family. Furthermore, we summarize the functions and the associated diseases of this family. Based on the pleiotropic actions of the REEP family, the study of its family members is crucial to understanding the relevant pathophysiological processes and developing strategies to modulate and control these related diseases. AVAILABILITY OF DATA AND MATERIAL: The datasets used or analyzed during the current study are available from the corresponding author on reasonable request.

MicroRNAs as novel peripheral markers for suicidality in patients with major depressive disorder

OBJECTIVE

Major depressive disorder (MDD) constitutes a main risk factor for suicide. Suicide risk in psychiatric patients is primarily determined by often unreliable, self-reported information. We assessed serum levels of three microRNAs (miRNAs), previously demonstrated to be dysregulated in post-mortem brain samples of suicide victims, as potential peripheral biomarkers for suicidality.

METHODS

All study participants were diagnosed with MDD according to Diagnostic and Statistical Manual of Mental Disorders, 5th edition criteria. Suicidality, defined as acute suicide risk or suicide attempt within one week prior to study entry, was assessed by clinical interview. Relative serum levels of miR-30a, miR-30e, and miR-200a, normalized to U6, were measured by quantitative real-time PCR in MDD inpatients with (MDD/SI, N = 19) and without (MDD, N = 31) acute suicide risk. Median age and gender distribution were comparable in both groups.

RESULTS

Levels of miR-30a, miR-30e, and miR-200a were significantly elevated in MDD/SI compared to MDD. Subgroup analysis of the MDD/SI group showed that levels of miR-30e and miR-200a were significantly higher and miR-30a was increased by trend in patients admitted following a suicide attempt (N = 7) compared to patients with acute suicide risk but without recent suicide attempt (N = 12). Additionally, use of two databases for in silico transcription factor-miRNA interaction prediction indicated early growth response protein (EGR) 1 as potential transcriptional regulator for all three miRNAs.

CONCLUSION

This study demonstrates suicide risk in MDD patients to be associated with increased levels of miR-30a, miR-30e, and miR-200a. Thus, these miRNAs might constitute potential biomarkers to predict suicidal behavior in MDD patients.

Immediate stress alters social and object interaction and recognition memory in nearly isogenic rat strains with differing stress reactivity

Stress prior to learning and recall is known to affect both processes depending on the learning paradigm, the sex of the animal, and their reactivity to stress. Male and female animals of the inbred Wistar-Kyoto More Immobile (WMI) and Less Immobile (WLI) strains were tested in the modified novel object and spatial recognition paradigm and in the social interaction-recognition paradigm immediately after a 30 min restraint stress. The WMI strain shows enhanced stress reactivity compared to its near isogenic WLI control and thus, represents a genetically stress-susceptible rodent model. Without stress, there were no strain differences in social or object recognition, but there were sex differences in both types of investigation. Immediate stress generally increased object investigation, but decreased social interaction in all groups, except the WMI males, who exhibited increased aggression toward the juveniles. While stress increased plasma corticosterone and decreased testosterone levels in WLI males as expected, it increased testosterone in the aggressive WMI males, despite elevated levels of corticosterone. Stress generally decreased recognition, except the spatial recognition of WMI females, which paradoxically improved after stress. The strain-specific effects of immediate stress indicate that stress unlocks the vulnerability encoded by the stable genetic differences between WLIs and WMIs to result in the observed phenotypes.

Genetic stress-reactivity, sex, and conditioning intensity affect stress-enhanced fear learning

The Stress-Enhanced Fear Learning (SEFL) model of posttraumatic stress disorder (PTSD) reveals increased fear memory in animals exposed to stress prior to contextual fear conditioning (CFC), similar to the increased likelihood of developing PTSD in humans after prior stress. The present study utilized the SEFL model by exposing animals to restraint stress as the first stressor, followed by CFC using foot-shocks with 0.6 mA or 0.8 mA intensity. Adult males and females from the two nearly isogenic rat strains, the genetically more stress-reactive Wistar Kyoto (WKY) More Immobile (WMI), and the less stress-reactive WKY Less Immobile (WLI) were employed. Percent time spent freezing at acquisition and at recall differed between these strains in both prior stress and no stress conditions. The significant correlations between percent freezing at acquisition and at recall suggest that fear memory differences represent a true phenotype related to the stress-reactivity differences between the strains. This assumption is further substantiated by the lack of effect of either conditioning intensity on percent freezing in WLI males, while WMI males were affected by both intensities albeit with opposite directional changes after prior stress. Differences between the sexes in sensitivity to the two conditioning intensities became apparent by the opposite directional and inverse relationship between fear memory and the intensity of conditioning in WMI males and females. The present data also illustrate that although corticosterone (CORT) responses to prior stress are known to be necessary for SEFL, plasma CORT and percent freezing were positively correlated only in the stress less-reactive WLI strain. These differences in baseline fear acquisition, fear memory, and the percent freezing responses to the SEFL paradigm in the two genetically close inbred WMI and WLI strains provide a unique opportunity to study the genetic contribution to the variation in these phenotypes.