Elevated NEGR1 in brain induces anxiety or depression-like phenotypes and synaptic dysfunction

Abstract

Single nucleotide polymorphisms (SNPs) within 1p31.1 region have shown significant associations with depression, and our prior functional genomics pinpointed a regulatory variant rs3101339 among them. However, its precise role in depression pathogenesis remains elusive. In this study, we employed a series of analytical and functional approaches, including regulatory element annotation, brain expression quantitative trait loci (eQTL), reporter gene assay, electrophoretic mobility shift assay (EMSA), and precise genome editing. Our results confirmed that rs3101339 is a causal variant within 1p31.1 with its risk allele C upregulating NEGR1 expression. To further investigate the consequences of NEGR1 upregulation, we overexpressed NEGR1 in specific region of the mouse brain (including medial prefrontal cortex (mPFC) and ventral hippocampus (vHIP)) using stereotaxic injection. Behavioral assessments revealed that elevated NEGR1 levels in the brain, particularly in the vHIP, resulted in working memory impairment as well as anxiety- and depression-like behaviors in mice. Neuronal sparse labeling assay and transmission electron microscopy revealed that NEGR1 overexpressing in the vHIP leads to dendritic spine loss and synaptic ultrastructure abnormality. Immunoprecipitation-mass spectrometry (IP-MS) further identified 67 high-confidence proteins that interacted with NEGR1, many of which are involved in neurotransmitter exocytosis and synaptic vesicle endocytosis. Transcriptomic profiling revealed 94 differentially expressed genes in NEGR1-OE (vHIP) mice compared to control mice (P adj < 0.05), which were enriched in myelination-related signaling pathways (such as myelination, ensheathment of neurons, axon ensheathment in central nervous system, etc.). Together, our findings implicated that the overexpression of the NEGR1 gene in the mouse brain as a potential driver of anxiety- or depression-like phenotypes potentially through impairing synaptic function and myelination.

Fig. 1. Validation of functional variant rs3101339 in 1p31.1 with its risk allele C upregulating NEGR1 expression.

A The depression genetic risk SNP rs3101339 is located in the crucial active promoter region of NEGR1 gene across multiple brain tissues. The genetic association between rs3101339 and depression was shown in LocusZoom using our recent results of cross-ancestry GWAS meta-analysis on depression (416,437 cases and 1,308,758 controls). The active promoter is marked with DNase, H3K4me3, H3K27ac, and transcription factors (REST, POLR2A and RAD21). B, C Brain eQTL data from GTEx and ROSMAP showed that rs3101339 is significantly associated with NEGR1 gene expression in caudate, nucleus accumbens, putamen tissues, and aged DLPFC. The risk allele C of rs3101339 is correlated with higher NEGR1 expression. D EMSA showed that the binding capacity of rs3101339-C allele with nuclear proteins extracted from SH-SY5Y cells was stronger than that of rs3101339-A allele. E, F Reporter gene assay showed that the 501 bp DNA sequences containing rs3101339 exhibited stronger promoter activity compared with control vectors, and rs3101339-C allele significantly increased promoter activity compared with rs3101339-A allele in SH-SY5Y and HEK293T cells. G, H Single-base editing assays showed that NEGR1 mRNA expression in HEK293T cells with the rs3101339-AC genotype was significantly higher than that of rs3101339-AA genotype. G Representative Sanger sequencing results of single-cell clones at rs3101339. H The internal reference gene is GAPDH. I The internal reference gene is ACTB. Data represent mean ± SD, n = 5 for E and F, n = 3 for H and I. Statistical analysis was performed using one-way ANOVA test E and F and two-tailed student’s t-test E and F. A P value less than 0.05 was considered as significance. Anterior caudate AC, Dorsolateral prefrontal cortex DLPFC, Hippocampus HIP.

Fig. 2. Overexpressing NEGR1 in the mPFC of mice leads to anxiety-like behaviors.

A Timeline of test mice model construction and behavioral tests. B Schematic illustration and stereotaxic injection coordinates of control AAVs or NEGR1-OE AAVs in the mPFC of mice (left), representative image showing correct AAV injection site expressing red fluorescent protein (right). C Validation of NEGR1 protein overexpression in the mPFC using western-blot, one representative mouse per group. D Overview of Y maze test. E, F The total number of entering arm and spontaneous alternation (%) in NEGR1-OE (mPFC) mice exhibited no significant difference compared with control mice. G Overview of open field test. H–M The total distance, average speed, times of entering center, average speed in center, distance in corner or center (%) were evaluated during the open field test, showing no significant difference between NEGR1-OE (mPFC) mice and controls. N Overview of elevated plus maze test. O–T The total distance, distance in close arm or open arm (%), average speed in open arm, times of entering open arm, time in open arm were evaluated during the elevated plus maze test, with NEGR1-OE (mPFC) mice exhibiting anxiety-like behaviors indicated by less times of entering open arm compared with controls. U Overview of forced swimming test. V and W Immobility time (%) and struggling time (%) were evaluated during the forced swimming test, showing no difference between NEGR1-OE (mPFC) mice and controls. Data represent mean ± SD, (Control: n = 12 and NEGR1-OE (mPFC): n = 13) for E and F, H–M, O–T, V and W. Two-tailed student’s t-test E, F, H–M, O–T, V, W was used for statistical analysis, with a significance level set at P < 0.05. Anterior cingulate cortex ACC, Prelimbic cortex PL, Infralimbic cortex IL, Caudoputamen CP, Nucleus accumbens ACB.

Fig. 3. Overexpressing NEGR1 in the vHIP of mice leads to working memory impairment, anxiety- and depression-like behaviors.

A Timeline of the test mice models construction and behavioral tests. B Schematic illustration and stereotaxic injection coordinates of control AAVs or NEGR1-OE AAVs in the vHIP of mice (left), representative image for showing the correct AAV injection site which is expressed red fluorescent protein (right). C The validation of NEGR1 protein overexpression in the vHIP, one representative mouse per group. D Overview of Y maze test. E, F The spontaneous alternation (%) in NEGR1-OE (vHIP) mice was significantly decreased compared with control mice. G Overview of open field test. H–M The total distance, average speed, times of entering center, average speed in center, distance in corner or center (%) were evaluated during the open field test, and NEGR1-OE (vHIP) mice exhibited anxiety-like behaviors with a higher average speed in center and more distance in corner (%) and less distance in center (%) compared with controls. N Overview of elevated plus maze test. O–T The total distance, distance in close arm or open arm (%), average speed in open arm, times of entering open arm, time in open arm were evaluated during the elevated plus maze test, and the NEGR1-OE (vHIP) mice exhibited anxiety-like behaviors at the index of less time of entering open arm (s) compared with controls. U Overview of forced swimming test. V and W The immobility time (%) and struggling time (%) were evaluated during the forced swimming test, and found that the immobility time (%) in NEGR1-OE (vHIP) mice was significantly increased compared with controls, while the struggling time (%) was significantly decreased. Data represent mean ± SD, (Control: n = 12 and NEGR1-OE (vHIP): n = 12) for E and F, H–M, (Control: n = 11 and NEGR1-OE (vHIP): n = 11) for O–T, V and W. Two-tailed student’s t-test E and F, H–M, O–T, V and W was used to test for statistical analysis, P < 0.05 was set as significant level. Hippocampus HIP; Dentate gyrus DG, Cornu Ammonis 1 CA1, Cornu Ammonis 1 CA3, Thalamus TH, Cerebral cortex CTX.

Fig. 4. Overexpressing NEGR1 in the vHIP of mice induces to the density of spines decrease and synaptic ultrastructure abnormality.

A Timeline of the neuronal sparse labeling assay and transmission electron microscopy assay. B Representative images of pyramidal neurons dendritic spines in ventral hippocampus CA1 region from controls and NEGR1-OE (vHIP) mice. C, D Total 40 images (100×) (n (Control) = 20, n (NEGR1-OE (vHIP)) = 20) from 4 mice (Control: n = 2, NEGR1-OE (vHIP): n = 2) were selected in random for morphological analysis of dendritic spines, total spines, and subtype (stubby, thin and mushroom) spines density were evaluated during neuronal sparse labeling assay, and the total spines density was significantly decreased in NEGR1-OE (vHIP) mice compared to controls in C, and the thin spines and mushroom spines density were also significantly decreased in NEGR1-OE (vHIP) mice compared to controls in D. E Representative images of synaptic ultrastructure in ventral hippocampus CA1 region from controls and NEGR1-OE (vHIP) mice. F Total 68 images (20,000×) (n (Control) = 33, n (NEGR1-OE (vHIP)) = 35) from 4 mice (Control: n = 2, NEGR1-OE (vHIP): n = 2) were selected in random for analysis typical synapse number per 19 μm². G–K Total 52 images (50,000×) (n (Control) = 26, n (NEGR1-OE (vHIP)) = 26) from 4 mice (Control: n = 2, NEGR1-OE (vHIP): n = 2) were selected in random for analysis synaptic vesicle density in boutons, synaptic cleft length, PSD thickness, PSD length and PSD area during transmission electron microscopy assay. These results showed that NEGR1-OE (vHIP) mice were significantly decreased in typical synapse number per 19 μm² and synaptic vesicle density in boutons compared with controls. Data represent mean ± SD. Two-tailed student’s t-test for C and F–K and two-way ANOVA test followed by FSD for D were used to test for statistical analysis, P < 0.05 was set as significant level.

Fig. 5. NEGR1 interacting proteins may contribute to exocytosis of neurotransmitter and synaptic vesicle endocytosis.

A Flow chart of IP-MS for NEGR1 overexpression in the vHIP region of mice, and we identified 64 high confident NEGR1 interacting proteins which the iBAQ ratio of NEGR1_IP to IGG_IP is greater than 5 and unique peptides in NEGR1-IP is greater than 2. B, C Functional analysis was conducted using Cytoscape (3.10.2) with the ClueGo (2.5.10) plug-in, and the 64 high confident NEGR1 interacting proteins were significant enrichment in 14 GO_Biological Processes presented in B, including calcium-ion-regulated exocytosis, synaptic vesicle endocytosis, and calcium ion-regulated exocytosis of neurotransmitters, etc. D Visualization of the protein-protein interaction network for Clathrin-dependent synaptic vesicle endocytosis cluster, and Snap25 seemly play as a central hub in this network.

Fig. 6. Overexpressing NEGR1 in the vHIP of mice may regulate the myelination related signaling pathways.

A The timeline of transcriptomic analysis for NEGR1 overexpression in the vHIP region of mice, and vHIP tissues from test mice (NEGR1-OE (vHIP): n = 3) and control mice (n = 3) were dissected for RNA sequencing. B A heatmap illustrating the expression levels of ninety-four differentially expressed genes, comprising forty-five upregulated and forty-nine downregulated between NEGR1-OE (vHIP) mice and controls (P adj < 0.05). C The top 10 terms for each biological process, cellular component, and molecular function enriched by the differentially expressed genes. D Visualization of genes involved in five myelination-related biological processes.