Abstract
Background
Among the anthropoids, humans uniquely have apolipoprotein E (ApoE) isoforms that modulate Alzheimer's disease (AD) risk and accelerate aspects of brain aging. While chimpanzee and human ApoE4 share R112 and R158, the oldest chimps do not show symptoms of advanced AD. Another key structural difference is T61 in chimps instead of R61 found in humans predicted to be structurally similar to ApoE3.
Objective
Besides their impact on later life brain health, ApoE isoforms influence the development of brain regions relevant to AD. We explored the functional impact of ApoE isoforms produced by astrocytes on neuronal morphology and considered structural predictions for their differences.
Methods
Astrocyte conditioned media (ACM) was collected from primary astrocytes cultured from mice with targeted replacement of mouse ApoE with human ApoE3, ApoE4, or chimp. Neuron morphology was then examined in neonatal rat hippocampal neurons cultured in ACM. In vitro data was complemented by structural analysis of ApoE isoforms.
Results
ApoE-chimp ACM stimulated 30% more neurites per neuron than human ApoE ACM. In contrast, ACM from ApoE-chimp more closely resembled human ApoE4 than ApoE3, yielding 40% shorter neurites and spines. Structural modeling confirmed that chimpanzee ApoE differs from both ApoE4 than ApoE3, consistent with the predicted evolutionary trajectory.
Conclusions
Chimpanzee ApoE is structurally and functionally closer to ApoE4 than ApoE3 but still differs for neuronal development and protein folding. These findings provide insight into species-specific ApoE evolution, with implications for AD susceptibility and neuronal development.
Introduction
The human ApoE alleles are unique among primates and most other mammals that are monogenic. Three decades ago, ApoE4 was hypothesized to have evolved from chimpanzee ApoE at least 6 million years ago. Chimpanzee and human ApoE differ by 8 amino acids; both share arginine R112 and R158.1–5 Chimpanzee ApoE from samples of wild-caught and captive have not shown coding variants, unlike in humans. 4 ApoE3 is globally the most prevalent, with cysteine substituted for arginine at residue 112 of chimpanzee and spread in Homo sapiens within the last 200,000 years. 6 Aging humans are also unique among the anthropoids in developing advanced neurodegeneration of Alzheimer's disease (AD) and related disorders for which ApoE4 is a major genetic risk factor. Although chimpanzees exhibit accelerated aging relative to humans with a twenty-year shorter lifespan and develop diffuse amyloid with age, they do not progress to the neuritic plaques with dystrophic synapses characteristic of AD, highlighting the clinical relevance of their resistance to full AD pathology.5,7–9 This divergence may be due to an amino acid site that is critical for protein folding: human R61 versus chimpanzee T61.
The primary role of ApoE is through lipid transport, and the few amino acid changes between isoforms alters their preferred lipid substrates. ApoE3 is considered the more efficient lipid carrier with higher binding capacity than ApoE4; lipid binding capacity of chimpanzee ApoE is not reported.6,10 Structural modeling and site-directed mutagenesis suggested that chimpanzee ApoE, although more similar to ApoE4 in sequence, may structurally resemble human ApoE3. 4 This was thought because the ApoE4 isoform has a unique domain from R61 being exposed not found in ApoE3 or all other mammals which have T61. This ApoE4 domain increases preference for low density lipoproteins contrary to ApoE3's binding to high density lipoproteins. 11
In brain, astrocytes are the primary producers of ApoE. Astrocyte ApoE is lipidated predominantly with cholesterol and secreted for neuronal uptake particularly in the hippocampus, an AD relevant brain region.12,13 Astrocyte ApoE is involved in protecting neurons against fatty acid associated toxicity, supporting axonal growth, and synaptic density.14–16 ApoE impact on neuron maintenance is determined by the ApoE isoform where neurite outgrowth and spine formation are greater with ApoE3 than E4.12,17,18 The contribution of chimpanzee ApoE on neuron differentiation has not been studied and is relevant to brain development and age-related cognitive decline.19–21 Brain development also differs by ApoE allele in AD-relevant brain regions. 22 The entorhinal cortex was thinner in ApoE4 carriers by gene dosage in healthy children and young adults aged 8–20 years. 23 A subsequent study partially confirmed these large differences on cortical thickness. 24
The current study explored the neurotrophic effects of astrocyte-derived ApoE3, ApoE4, and chimpanzee ApoE on the differentiation of primary rat neurons. Astrocyte-conditioned media (ACM) from immortalized astrocytes expressing each isoform was used to assess the ApoE isoform impact on primary neuron differentiation for neurite length, soma size, dendritic branching, and spine density (Figure 1A). The astrocytes were cultured from mice with targeted replacement of murine ApoE with human or chimpanzee ApoE.

Study schematic. A) Astrocyte-conditioned media (ACM) was obtained from immortalized mixed glial culture from ApoE targeted-replacement mice. Day-18 embryonic hippocampal rat neurons were grown in ACM to study the effects of ApoE isoforms on neuron morphology. B) ApoE sequences were compared for structural differences by Colabfold.
We then generated structural folding predictions and extracted information of 3D space per residue of ApoE isoforms to determine if the amino acid substitutions altered critical regions such as those involved in lipid binding (Figure 1B). We hypothesized that neurons exposed to chimpanzee ACM would resemble those treated with ApoE3 ACM, consistent with its predicted structural similarity, but might diverge in function due to evolutionary adaptations. Neuronal characteristics that differed by ApoE isoform and species include neurite density and length, while structurally ApoE3 was more tightly packed in lipid binding domains. We also confirmed that chimpanzee ApoE is more structurally similar to ApoE4, supported by in vitro data on neuron morphology. These findings identify further differences and similarities of chimp and human ApoE isoforms for their developmental roles, for the evolutionary context of AD vulnerability, and for the cellular underpinnings of neuronal morphology shaped by astrocytic lipid signaling.
Methods
Chimpanzee ApoE targeted-replacement
Chimpanzee targeted-replacement mice (TR) were generated by replacing mouse ApoE with chimpanzee: Supplemental Figure 1 compares human TR mice for ApoE3 and ApoE4.25,26 The chimpanzee ApoE gene, encompassing exons II-IV and associated introns, was subcloned from a chimpanzee bacterial artificial chromosome and inserted into a targeting vector, flanked by homologous mouse genomic sequences to facilitate homologous recombination. A neomycin resistance cassette provided positive selection, and a diphtheria toxin A cassette was used for negative selection. The targeting vector was electroporated into embryonic stem (ES) cells from C57BL/6 mouse and transfected clones were selected using G418 (geneticin). Southern blot analysis screened for homologous recombination events. Genomic DNA was extracted from ES cell colonies and digested with EcoRI or HindIII, followed by hybridization with external and internal radioactively labeled probes. PCR-based screening confirmed the correctly targeted allele.
TR-ES cells were microinjected into blastocysts derived from C57BL/6 mice and implanted into pseudopregnant female mice. Chimeric offspring were identified by coat color mosaicism and then bred with C57BL/6 wild-type mice to obtain germline transmission of the targeted allele. Germline transmission was confirmed by PCR genotyping using primers specific for chimpanzee ApoE. RNA splicing analysis used RT-PCR to confirm appropriate expression and transcript integrity. After these studies were completed, the Chimp-TR line was lost; tissues from limited numbers of ages mice are available. Genomic DNA from the offspring was analyzed by Southern blotting to verify correct TR.
ApoE cell lines
Immortalized primary astrocytes generated astrocyte condition media (ACM). Primary astrocytes from the neonatal ApoE chimp mice or ApoE3 and ApoE4 TR mice prior to immortalization. 26 Cells were maintained in DMEM/F12 (Gibco #11330-032), 10% FBS, 1 mM sodium pyruvate, 200 µg/ml G418 and plated at 500 k cells per dish. Upon confluency, cells were replated in serum-free media for 24 h to obtain ACM. ApoE levels were measured by dot blot with an ApoE specific antibody (1:1000, goat, Millipore).
Primary neuronal culture
Primary hippocampal neuronal cultures were derived from male and female embryonic day 18 (E18) rats. Briefly, six hippocampi were dissociated in Hank's balanced salt medium containing trypsin and DNase at 37°C per biological replicate. 27 Dissociated cells were plated on poly-D-lysine and laminin coated glass coverslips (20 k cells/cm2), or on 96 well plates (70 k cells/cm2). Cells were maintained in media DMEM supplemented with B27 (Invitrogen, Grand Island, NY), with serum-free media that favors neuronal survival. 28 Neurons were maintained at 37°C with 5% CO2.
Neuronal morphology
E18 cultures of hippocampal neurons were treated with ACM for 72 h. After incubation, cultures were fixed in 4% paraformaldehyde in phosphate buffered saline, pH 7.4 and immunostained for neuron-specific βIII-tubulin (1∶500, rabbit; Sigma Aldrich) and F-actin in lamellipodia and growth cones (rhodamine phalloidin, 1∶40; Molecular Probes). Images were captured by immunofluorescent microscopy using a Nikon Eclipse TE300 microscope (Nikon Inc., Melville, NY). One hundred or more neurons per ApoE isoform were sampled per measurement. Neuron morphology was analyzed in ImageJ. Neuronal length was assessed using the NeuronJ plugin in ImageJ. All in vitro data was obtained from a minimum of six biological replicates.
ApoE structural analysis
Local folding of ApoE structures was done using Colabfold v1.5.5. 29 ApoE3 and chimpanzee sequences were obtained from the UniProt database. The ApoE3 sequence was modified to generate ApoE4. Folding predictions were done with model alphafold2_ptm with multiple sequence alignment for 12 recycles. Five models were generated and ranked based on highest predicted local distance difference test (pLDDT) score; pLDDT scores per residue, Supplemental Table 1. Forty-seven structures from NMR, x-ray crystallography, and cryo-EM were superimposed to assess prediction validity (Supplemental Table 2). Secondary structures were assigned by DSSP (Supplemental Table 3). 30 Predicted structures were then subjected to Atom3D to extract nodes per residue; the amino acids within spatial proximity (≤10 Å). 31 Node features included atomic coordinates, amino acid identity, and backbone dihedral angles, while edge features encoded inter-residue distances and orientation vectors. Structures were visualized, aligned, and annotated with ChimeraX (ver.1.9) and color coded by data obtained from predicted structures or node connectivity. 32 Structures were deposited to Zenodo (#16920665).
Statistics
Group differences means (± SEM) were analyzed by one-way ANOVA with Tukey's post-hoc test, Kruskal-Wallis with Dunn's test for nonparametric distributions, or Welch's ANOVA with Games-Howell test when variances were unequal across groups. Neuronal categorical outcomes (e.g., pyramidal versus non-pyramidal or mature versus immature neurons) were analyzed by Chi-square tests. Where applicable, significant contingency table results were followed by pairwise 2 × 2 comparisons with Bonferroni correction. Significance was defined as p < 0.05. Analyses used GraphPad Prism version 10 (GraphPad Software, San Diego, CA).
Results
ApoE3 is associated with longer neurites and perikaryal area
To assess if ApoE-chimp modifies neuron morphology differently than the two main human ApoE isoforms, embryonic rat day 18 neurons were grown in astrocyte-conditioned media (ACM). Levels of the chimp and human ApoE isoforms did not differ in ACM by dotblot (Supplemental Figure 2A). Axonal length did not differ between neurons grown with ACM from ApoE4 or ApoE-chimp. However, ApoE3 ACM increased neuronal length by 35% above ApoE4 and ApoE-Chimp (Figure 2A). ApoE4 and Chimp ACM treated neurons had fewer neurites longer than 200 μM than ApoE3 (Figure 2B). The opposite was observed for the number of neurites per neuron, with ApoE-chimp having 25% more neurites (Figure 2C). Perikaryal area was 40% greater in ApoE3 neurons than human E4 or Chimp (Figure 2D).

Neuronal morphology characterized by A) neurite length, B) frequency distribution of neurite length, C) neurites per neurons, and D) perikaryal area. Representative images of embryonic rat neurons grown 72 h in ACM from ApoE3, ApoE4, or ApoE chimp ACM; scale bar, 15 μm. Statistics by one-way ANOVA with Tukey's posthoc or Kruskal-Wallis. *p < 0.05, **p < 0.01, ***p < 0.001.
ApoE3 ACM is associated with greater neurite spine density and neuron maturity
Next, we examined the density of neuritic spines and levels of neuronal maturation. Neurons with ApoE3 ACM had 40% more spines than ApoE4 and 55% more than ApoE-Chimp. ApoE4 ACM treated neurons had 10% more spines than ApoE Chimp (Figure 3A,B). Neuron maturity was evaluated by the type of spine present by classification: mature (mushroom or stubby) or immature (filopodia-like or thin). 33 Neurons grown in ApoE3 ACM had 25% more mature neurons than ApoE4. Chimp ApoE did not differ from ApoE3 and ApoE4 for neuron maturity (Figure 3C). The type of neuron (pyramidal versus non-pyramidal) also did not differ by ApoE isoform (Supplemental Figure 2B).

ApoE3 promotes the higher spine density. A) Neurite spine density, B) Frequency distribution of spine density, and C) Neuronal maturity of primary neurons grown in astrocyte-conditioned media (ACM) from ApoE-chimp, human ApoE3 and E4. Images of spine density in embryonic rat neurons exposed to ApoE3, ApoE4, or ApoE chimp ACM, 72 h; scale bar 5 μm. A) Statistics by one-way ANOVA with Tukey's posthoc or Kruskal-Wallis. C) Statistics by Chi-square with Bonferroni. **p < 0.01, ***p < 0.001, ****p < 0.0001.
Chimpanzee ApoE is structurally more similar to ApoE4 than ApoE3
ApoE structure was modeled to quantify conformational differences associated with key isoform-defining residues (61, 112, and 158). Structures generated in Colabfold were compared to x-ray crystallography (Supplemental Figure 3A), nuclear magnetic resonance (NMR; Supplemental Table 2), and structures downloaded from AlphaFold's database for the pruned and the full root mean standard deviation (RMSD) to measure structural similarity between proteins. Protein databases such as AlphaFold and UniProt use the ApoE precursor (pre-ApoE; 317aa). We found that the average pruned RMSD for our predicted structures and AlphaFold's ApoE structure compared to the empirical structure data did not differ (Supplemental Figure 3B). However, comparison of the average full RMSD values with empirical data and the Colabfold precursor, mature, and AlphaFold showed our predicted pre-ApoE was 30% closer than our mature ApoE and 55% closer than AlphaFold's model (Supplemental Figure 3C).
After validating the predicted structures, we then analyzed pairwise structural superposition of the mature ApoE isoforms, which showed minimal geometric deviation between ApoE3 and ApoE4, with pruned RMSD of 0.273 Å and full RMSD of 4.764 Å. The pruned RMSD indicates strong conservation of the core fold, while the higher full RMSD suggests peripheral or loop region flexibility between isoforms. In contrast, alignment between ApoE3 and chimpanzee ApoE showed a larger pruned RMSD of 0.350 Å and an even more pronounced full RMSD of 12.228 Å, indicating greater global structural divergence (Figure 4, Table 1). The increased full RMSD reflects both localized atomic displacements and broader shifts in loop and domain positioning. Similarly, alignment between ApoE4 and chimpanzee ApoE revealed a pruned RMSD of 0.337 Å and a full RMSD of 10.625 Å (not shown).

Comparison of mature ApoE3, ApoE4, and ApoE chimpanzee structures. Key residues at positions 61, 112, and 158 are highlighted in yellow. RMSD values (pruned and full) are calculated relative to ApoE3. Structures are colored by full RMSD gradient relative to ApoE3 to indicate structural deviation; darker indicates higher shifts in atom positions.
Pruned and full RMSD values for pre-ApoE and mature ApoE.
Pre-ApoE was then examined which contains the 18 amino acid signal peptide. ApoE3 and ApoE4 had a pruned RMSD of 0.482 Å and a full-length RMSD of 3.740 Å. Pre-ApoE3 and chimpanzee ApoE again had larger pruned RMSD of 0.611 Å and full RMSD of 6.611 Å (Supplemental Figure 4). ApoE4 and chimpanzee ApoE had a pruned RMSD of 0.625 Å and a full RMSD of 5.506 Å (not shown). Thus, while Pre-ApoE4 and chimpanzee ApoE are structurally more similar than ApoE3 in terms of overall folding, there are significant deviations, particularly in regions outside the core helices. Collectively, the chimpanzee ApoE structure maintains a broadly similar core fold to human ApoE isoforms, but exhibits greater overall conformational divergence, particularly outside the core helix bundle.
ApoE node connectivity is increased at position 61 for mature and precursor ApoE3
To further interrogate the influence of the few residue differences between ApoE isoform on structure we extracted per residue atom information from the predicted structures. The node connectivity (Δnode) is represented as the number of amino acids within a radius of 10 Å from the reference amino acid. The total number of nodes per structure did not differ between the ApoE isoforms, mature or precursor, consistent with the few amino acid substitutions (Figure 5A, Supplemental Figure 5A). Nodes were plotted by amino acid to highlight regions that differed between the isoforms. For mature ApoE isoforms, position 112 had increased node connectivity (17 to 18) in ApoE3 compared to ApoE4 and Chimp. Position 158 had no node differences between isoforms, and positions 112 and 158 did not differ (Table 2). Position 61 node connectivity was also increased in mature ApoE3 than ApoE4 and ApoE Chimp. For pre-ApoE both ApoE3 and ApoE4 had an increase in node connectivity with 18 atoms compared to 17 for chimp (Figure 5B, Supplemental Figure 5B). These differences become more apparent when overlaying the Δnode degree on ApoE3 or ApoE4 backbones wherein blue indicates a loosening of the domain while red indicates a tighter structure. ApoE3 and ApoE4 are more similar for the mature forms with some differences in domain flexibility in the C-terminal side (Figure 5C). Pre-ApoE3 and ApoE4 show moderate differences which become greater when comparing ApoE3 and ApoE-chimp. Conversely, comparing connectivity between pre-ApoE4 and ApoE Chimp, the connectivity differences are much smaller, consistent with the evolutionary trajectory (Supplemental Figure 5C). Interestingly, these differences are predominant in the lipid binding region (225–299; Figure 5B,C). Thus, these few amino substitutions cause major conformational changes in domains essential to ApoE functions.

Amino acid connectivity per residue for precursor ApoE3, ApoE4, and chimpanzee ApoE. A) The average number of nodes per ApoE isoform within a 10 Å radius. B) The number of nodes at each amino acid for precursor ApoE. Annotations (61, 112, and 158) are based on the mature 299 amino acid sequence. C) Reference structures of ApoE3 or ApoE4 are colored green by the Δnode degree for ApoE4 or ApoE chimpanzee. Red indicates increased node connectivity while blue represents decreased node connectivity.
Node connectivity for pre-ApoE and mature ApoE at isoform defining residues.
Discussion
This first direct functional comparison of chimpanzee and human ApoE isoforms on neuronal development shows structural and morphological distinctions with implications for brain evolution and AD susceptibility. Using ACM derived from mice expressing human ApoE3, ApoE4, or chimpanzee ApoE, we assessed the effects on primary hippocampal neuron morphology with connections to high-resolution structural predictions. Contrary to former predictions that chimpanzee ApoE is functionally equivalent to ApoE3, we show that chimpanzee ApoE induces neuronal differentiation more similar to ApoE4, matching our structural predictions. 4
Neurons exposed to chimpanzee ApoE ACM developed shorter neurites and reduced spine density than ApoE3, confirming prior studies on the restrictive influence of ApoE4 on neurite outgrowth and synaptic maturation.34–36 Unique to chimpanzee ApoE was the increased number of neurites per neuron, suggesting a divergent influence on early neurogenesis that may reflect adaptive evolutionary traits unrelated to AD vulnerability. Thus, while chimpanzee ApoE shares closer structural and sequence homology with ApoE4, chimpanzee ApoE may enhance synapse formation.
The structural analysis supports these functional differences. Chimpanzee ApoE shares greater overall similarity with ApoE4 than with ApoE3. Pruned RMSD, which reflects the core fold conservation, was modest across isoforms. Full RMSD values revealed substantial divergence between chimpanzee ApoE and ApoE3, suggesting domain-level flexibility and long-range conformational changes. Node-based residue connectivity analysis further confirmed that little difference exists between pre- and mature forms of ApoE for defining residues (112, and 158). However, 61 was associated with more connectivity with ApoE3 than ApoE chimp where ApoE matched ApoE3 for the mature structure. Overall, this may imply that functional divergence likely stems from global shifts in tertiary structure or domain reorganization rather than local residue environment alone. Furthermore, our data suggests that T61 alone does not recreate the neurotrophic properties of ApoE3 in the chimpanzee isoform. Instead, we observed broader structural loosening in chimpanzee ApoE than ApoE3, particularly at position 61, further decoupling local amino acid substitution from functional outcome. The pre-ApoE structural comparisons reinforced these findings, as chimpanzee ApoE maintained greater similarity to ApoE4 than to ApoE3 even before signal peptide cleavage, suggesting conserved folding trajectories during processing and secretion.
These phenotypic differences may be rooted in broader evolutionary divergence beyond the currently discussed residue positions (61, 112, 158). Noncoding regulatory elements, additional nonsynonymous substitutions within the ApoE gene, or adjacent loci on chromosome 19q13.32 which includes APOC1, APOC2, and APOC4 may contribute to the unique developmental and aging trajectories of the human brain (Figure 6). In mice this cluster is found on 7qA1 consistent with the tracked translocation events from 90 million years ago. 37 Recent studies suggest that these neighboring genes may modulate aspects of neuronal structure and AD risk independently or synergistically with ApoE. 38 The present study did not consider contributions from other apolipoprotein family members within ACM which may also modulate neuron differentiation.

The ApoE gene cluster found on chromosome 19q13.32 for A) human and B) chimpanzee which lacks ApoC2. The C) mouse ApoE gene cluster is located on chromosome 7qA1 with inverted synteny.
Our findings add to a growing body of evidence that ApoE isoforms exert substantial developmental influence on neuronal architecture, well before the onset of neurodegeneration. The observation that chimpanzees, despite having a sequence similar to ApoE4, do not develop AD, may therefore be due not only to protective amino acid substitutions like T61 but also to species-specific differences in gene regulation, lipid metabolism, and astrocyte-neuron signaling. Importantly, the absence of AD-like pathology in aged chimpanzees despite structural similarity to human ApoE4 underscores the limitations of residue-based assumptions about isoform function. Future studies of the chimpanzee ApoE knock-in mouse line across developmental and aging timepoints could reveal when and how these differences emerge.
Our present study is limited in several ways: 1) the use of mouse astrocytes with rat neurons mixes species with differing physiology, 2) we accounted for ApoE in ACM only and other factors found in ACM may be influenced by ApoE and ultimately on neuronal morphology, 3) 72 h of ACM exposure is not enough for complete neuron maturation or degeneration and should be seen as early synaptic changes, 4) morphology alone cannot resolve the effects of ApoE isoforms on synaptic transmission, and 5) the ApoE models and the extracted information from them requires biochemical validation.
Supplemental Material
sj-docx-1-alz-10.1177_13872877251386812 - Supplemental material for Chimpanzee and human ApoE isoforms differ in the stimulation of neurite differentiation consistent with structural predictions with relevance to brain development and aging
Supplemental material, sj-docx-1-alz-10.1177_13872877251386812 for Chimpanzee and human ApoE isoforms differ in the stimulation of neurite differentiation consistent with structural predictions with relevance to brain development and aging by Max A Thorwald, Mafalda Cacciottolo, Xiaogang Hou, Todd E Morgan and Caleb E Finch in Journal of Alzheimer's Disease
Supplemental Material
sj-xlsx-2-alz-10.1177_13872877251386812 - Supplemental material for Chimpanzee and human ApoE isoforms differ in the stimulation of neurite differentiation consistent with structural predictions with relevance to brain development and aging
Supplemental material, sj-xlsx-2-alz-10.1177_13872877251386812 for Chimpanzee and human ApoE isoforms differ in the stimulation of neurite differentiation consistent with structural predictions with relevance to brain development and aging by Max A Thorwald, Mafalda Cacciottolo, Xiaogang Hou, Todd E Morgan and Caleb E Finch in Journal of Alzheimer's Disease
Footnotes
Acknowledgements
Author contribution(s)
Funding
The authors disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: Lab studies were supported by NIH grants to CEF (R01-AG051521, P50-AG05142, P01-AG055367) and Cure Alzheimer's Fund.
Declaration of conflicting interests
The authors declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.
Data availability statement
The authors declare that the data supporting the findings of this study are available within the paper and its Supplemental Material. Raw data files may be requested in other format from corresponding authors.
Supplemental material
Supplemental material for this article is available online.
References
Supplementary Material
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