2.1. DCV distribution is altered in cultured neurons of two βNrxn deletion mouse models
Endogenous βNrxn are highly mobile molecules mostly on axons and within synaptic terminals [
31] where they affect not only the release of classical synaptic vesicles [
27,
31] but also the amount of DCVs [
47]. Strikingly, neuromodulators such as brain-derived neurotrophic factor (BDNF) are secreted from presynaptic DCVs [
48,
49,
50] and play a major role in spine development and plasticity [
51,
52]. At a time when replicability of exactly comparable experimental conditions is a topic of great concern in science, we decided to study dendritic spine structure in two different βNrxn deletion models and compared their phenotype in neuronal cell culture as well as brain tissue. To ensure that results from conditional and constitutive knockout of βNrxn variants are comparable, we first tested our previous conclusion of reduced amounts of DCVs [
47] in both βNrxn knockouts.
We conditionally deleted floxed βNrxn-specific exons by Cre recombinase-expressing lentivirus to remove all βNrxn variants in primary hippocampal neurons from KI mice as described before [
31,
47]. Inactive Cre recombinase (Cre
mut)-expressing KI neurons served as controls and efficient reduction of βNrxn was validated by immunoblots as shown [
31]. Similarly, we cultured hippocampal neurons from a constitutive βNrxn TKO mouse line generated by germline deletion and controls [
31,
47]. To probe the distribution of DCVs in both types of deletion models, we immunolabeled the neuronal cultures at DIV19 with antibodies against chromogranin A (ChrgA), a common matrix protein of DCVs present in a subset of axons [
53,
54,
55]. We observed ChrgA-positive clusters in axons of control neurons, for example, traveling along a neighbored neuronal soma (
Figure 1A) and less abundantly on axons of βNrxn TKO neurons (
Figure 1B), thereby closely resembling the images of Cre
mut and Cre
-expressing βNrxn KI neurons from our earlier study of DCVs [
47]. Measurements of the intensity of ChrgA fluorescence within a defined axonal window revealed a 35% reduction of ChrgA fluorescence intensity in axons of βNrxn cKO neurons compared to control neurons in our current set of experiments (
Figure 1C; Cre
mut control: 7,846 ± 442 arbitrary units [A.U.], Cre cKO: 5,133 ± 531, p = 0.0003), an even stronger effect than reported before [
47], presumably due to a higher number of experiments in this study. In cultures of the constitutive βNrxn KO model, the ChrgA fluorescence intensity was less strongly but also significantly diminished by 17% (
Figure 1D; WT control: 7,132 ± 340 arbitrary units [A.U.], TKO: 5,949 ± 320, p = 0.023). Together, these results confirm our previous conclusion that βNrxn is required for normal levels of ChrgA-containing DCVs in hippocampal neurons [
47]. Importantly, they also indicate that phenotypic observations made upon conditional deletion can be reproduced in constitutive βNrxn TKO mutants, despite the caveats associated with potential compensatory effects in germline deletions [
21].
2.2. Dendritic spine alterations in cultured βNrxn-deficient neurons
During our analysis of neuromodulator-containing DCVs, we noticed a large number of longer dendritic protrusions in the absence of βNrxn in hippocampal neurons, despite a previous study using cultured neurons derived from the cerebral cortex that did not observe such defects [
27]. We therefore first tested if the overall spine density was changed in our primary neurons cultured from the hippocampi of constitutive and conditional βNrxn mutants. To visualize dendrites and spines, we expressed cytosolic t-dimer-RFP in control (
Figure 2A) and knockout (
Figure 2B,C) neurons and determined their spine density by normalizing absolute numbers of protrusions along randomly chosen dendritic segments to the length of these segments. In cultures of the constitutive βNrxn TKO model, the spine density was undistinguishable from WT control (
Figure 3A; WT control: 6.49 ± 0.19 protrusions/10 µm dendrite length, TKO: 6.96 ± 0.16, p = 0.053), consistent with the earlier results in cortical neurons [
27]. Attesting to the reliability of our approach, we observed very similar values in measurements from cultures of βNrxn KI neurons expressing Cre recombinase (cKO) or inactive Cre
mut for control (Cre
mut control: 6.62 ± 0.20 protrusions/10 µm, Cre cKO: 6.82 ± 0.21, p = 0.48). Thus, deletion of βNrxn in cultures from the hippocampus has no impact on overall spine density.
In our analysis of spine numbers in RFP-transfected neurons from hippocampal cultures, however, we realized that many spinous protrusions from βNrxn-deficient cells extended farther from their dendrite than in comparable controls (
Figure 2A,B). To quantify such an effect, we measured the length of all protrusions and classified them in spines either longer or shorter than 2 µm (
Figure 2C). Confirming the initial observation, we found that the number of spines >2 µm was increased by almost 40% at dendrites of constitutive βNrxn TKO neurons compared to controls (
Figure 3B; WT control: 2.99 ± 0.13 protrusions/10 µm, TKO: 4.13 ± 0.13, p < 0.0001), whereas in contrast, spines below 2 µm length were reduced by almost 20% (
Figure 3C; WT control: 3.50 ± 0.13 protrusions/10 µm, TKO: 2.83 ± 0.11, p = 0.0002). In addition, the βNrxn-deficient neurons not only had a higher number of longer spines but also revealed a higher number of branched protrusions which was increased by 45% in comparison to controls (
Figure 3D; WT control: 0.82 ± 0.06 protrusions/10 µm, TKO: 1.19 ± 0.07, p < 0.0001). While this difference appears considerable, the absolute number of branched spines amounts only to 13% in controls and 17% in TKO neurons. Together, these data show that dendritic spines in culture extend farther and branch more frequently in the absence of all βNrxn isoforms, while their overall number remains normal.
2.3. Dendritic spine alterations in hippocampal tissue of βNrxn-deficient mice
Our observation of shifts between subpopulations of spines, i.e., shorter vs. longer and branched vs. unbranched, indicate that ßNrxn may exert subtle but significant influence on spine morphology. It is important to note that even small changes, for example, in spine neck length or head width, may represent major functional differences [
56,
57]. To investigate such morphological alterations in more detail, we decided to focus our further analysis on hippocampal brain tissue from constitutive ßNrxn TKO mice. The rationale for this restriction was fourfold: First, analyses in culture by conventional fluorescence microscopy tend to underestimate distinct subtypes of spines [
56]; second, the geometry of the extracellular space in intact tissue affects spinous synapses [
58]; third, the physical contact with perisynaptic astrocytic processes of glia cells, absent in our sandwich cell culture [
59], is known to affect dendritic spine structure [
60,
61,
62]; and fourth, transmission electron microscopy of fixed tissue samples still represents the benchmark for exquisitely detailed and quantitative analyses of spine morphology [
11].
To compare putative changes in spine morphology in intact brain tissue with our results from cultured primary hippocampal neurons (
Figure 2 and
Figure 3), we prepared samples of the hippocampal CA1 region for electron microscopy and analyzed images from the stratum radiatum (
Figure 4A,B) because most excitatory inputs terminate on spines in this layer [
11].
We first quantified the overall number of presumptive excitatory synapses by determining the area density of asymmetric terminals based on the classical criteria for ultrastructurally defined type 1 synapses [
63], as also described in the Materials & Methods section. Consistent with the unchanged glutamatergic synapse density in cortical cultures [
27] and unchanged overall number of spinous protrusions shown above (
Figure 3A), we found that the area density of type 1 terminals was very similar in WT control and ßNrxn TKO mice (
Figure 4C; WT control: 25.3 ± 0.79 type 1 contacts/45 µm
2, TKO: 25.7 ± 0.93, p = 0.7741). To analyze the most mature and stable subtype of dendritic spines in the stratum radiatum of adult CA1 hippocampus [
6,
7,
8], we outlined mushroom spines on the electron microscopic images as defined in the Materials & Methods section (
Figure 4A,B; mushroom spines colored in red). Visual appearance, as well as quantification of the area density of mushroom spines, confirmed an increase of almost 50% in the absence of ßNrxn (
Figure 4D; WT control: 12.5 ± 0.92 type 1 contacts/345 µm
2, TKO: 18.5 ± 0.99, p < 0.0001), indicating that deletion of the synaptic cell adhesion molecules ßNrxn affects the number of a major subpopulation of spines.
To investigate whether ßNrxn also affects the ultrastructural morphology of mushroom spines, we next reconstructed in 3D about 60 samples from serial sections of control and TKO hippocampi. Suitable viewing angles were selected and 10 representative images of 2D renderings from each genotype are shown in
Figure 5. Although the spines displayed are from the same brain region and belong to the same subpopulation, all samples were variable in shape and revealed a unique morphology (
Figure 5A,B) as noted before in comparable studies using 3D reconstructions, in particular of hippocampal neurons [
11,
64,
65].
While most morphological features such as curved and straight necks or round and oval heads were detectable in both control and ßNrxn TKO samples, we noticed in ßNrxn-deficient reconstructions a possibly higher number of spines with a prominent perforated PSD. To test this hypothesis, we identified dendritic spine profiles with a perforated PSD (
Figure 6A,B) in higher resolution electron microscopic and quantified their area density in ßNrxn TKO samples which was slightly but significantly elevated by about 28% compared to controls (
Figure 6C; WT control: 4.6 ± 0.4 perforated PSDs/345 µm
2, TKO: 5.85 ± 0.44, p = 0.037). This increase in dendritic spines containing a perforated PSD (
Figure 6B) is consistent with the elevated number of mushroom-type protrusions in ßNrxn-deficient samples (
Figure 4D) because mushroom spines are generally more likely to contain perforated PSDs [
66]. In addition, we noticed dendritic spines with other characteristic ultrastructural features such as spine apparatus (
Figure 6D) or spinules (
Figure 5) but preliminary estimations did not suggest quantitative differences between the genotypes analyzed here (data not shown).
Alterations in the functional strength or responsiveness of spinous synapses are often reflected by changes in the ultrastructure of PSDs [
67] such as the increase of perforated PSDs shown here (
Figure 6). Additional ultrastructural modifications are known to reflect dendritic spine plasticity, for example, spine head size [
64,
68] or neck dimensions [
56,
69]. To finally investigate if these structures are affected by the deletion of the ßNrxn variants, we outlined the head and neck of mushroom spines in our high-resolution electron microscopic images (
Figure 7A). Quantitative analysis of the head area of mushroom spines revealed a small reduction of about 12% in ßNrxn-deficient mice compared to controls (WT control: 0.17 ± 0.008 µm
2, TKO: 0.15 ± 0.008 µm
2, p = 0.0254), whereas their neck length remained unchanged (WT control: 0.32 ± 0.012 µm, TKO: 0.33 ± 0.015 µm
2, p = 0.5926). Together, our morphological results demonstrate that deletion of ßNrxn did not change the overall number of excitatory (asymmetric) synaptic contacts but caused a shift towards more mushroom-type spinous synapses with slightly smaller head size and a higher proportion of perforated PSDs.