| Literature DB >> 36018414 |
Johanna Rueter1, Gerald Rimbach2, Patricia Huebbe1.
Abstract
Human apolipoprotein E (APOE), originally known for its role in lipid metabolism, is polymorphic with three major allele forms, namely, APOEε2, APOEε3, and APOEε4, leading to three different human APOE isoforms. The ε4 allele is a genetic risk factor for Alzheimer's disease (AD); therefore, the vast majority of APOE research focuses on its role in AD pathology. However, there is increasing evidence for other functions of APOE through the involvement in other biological processes such as transcriptional regulation, mitochondrial metabolism, immune response, and responsiveness to dietary factors. Therefore, the aim of this review is to provide an overview of the potential novel functions of APOE and their characterization. The detection of APOE in various cell organelles points to previously unrecognized roles in mitochondria and others, although it is actually considered a secretory protein. Furthermore, numerous interactions of APOE with other proteins have been detected, providing indications for new metabolic pathways involving APOE. The present review summarizes the current evidence on APOE beyond its original role in lipid metabolism, to change the perspective and encourage novel approaches to future research on APOE and its isoform-dependent role in the cellular metabolism.Entities:
Keywords: Interactome; Mitochondria-associated ER membranes; Protein–protein interactions; Proteolytic fragmentation
Mesh:
Substances:
Year: 2022 PMID: 36018414 PMCID: PMC9418098 DOI: 10.1007/s00018-022-04516-7
Source DB: PubMed Journal: Cell Mol Life Sci ISSN: 1420-682X Impact factor: 9.207
Fig. 1Predicted spatial protein structure of human APOE (AlphaFold) and intracellular localisation of APOE. a The APOE isoproteins differ at one and two amino acid (AA) positions, respectively (112 and 158). This affects the structure and thus the function of the protein, e.g., APOE2 shows a significantly reduced affinity for the low-density lipoprotein receptor (LDLR) and the lipid binding preference differs between the isoforms. The different colours of the protein structure indicate the model confidence of the structure prediction (dark blue, very high; light blue, confident; yellow, low; orange, very low). Protein structure image downloaded from https://alphafold.ebi.ac.uk/. HDL high-density lipoprotein, VLDL very low-density lipoprotein. b Schematic illustration of an eukaryotic cell and the individual cell organelles and compartments. APOE is known to be a secreted protein, but has been detected inside the cell in, e.g., mitochondria, peroxisomes, and the nucleus. MAMs mitochondria-associated ER membranes
Experimental evidence for the localization of APOE in mitochondria and mitochondria-associated ER membranes (MAMs)
| Cellular component | Tissue/cell type | Isolation/labelling | Detection | References |
|---|---|---|---|---|
| Rat liver | Immunogold labelling of APOE in cryosections | Electron microscopy | [ | |
| Rat liver | Radioactive leucine labelling and Percoll density gradient ultracentrifugation | Anti-VLDL immunoprecipitation, SDS gel electrophoresis, excision of protein bands and radioactivity counting | [ | |
| APOE4-transfected Neuro2a cells | Not described1 | Western blotting of mitochondrial fractions | [ | |
| APOE TR mouse hippocampus | Isolation using a commercially available kit 2 and differential centrifugation | Western blotting, LC–MS | [ | |
| APOE TR mouse primary astrocytes | Coimmunostaining of Mito-GFP and APOE Isolation using a commercially available kit 3 and differential centrifugation | Fluorescence microscopy Western blotting of mitochondrial fractions | [ | |
| Rat liver | Radioactive leucine labelling and Percoll density gradient ultracentrifugation | Anti-VLDL immunoprecipitation, SDS gel electrophoresis, excision of protein bands and radioactivity counting | [ | |
| Mouse liver and brain | Percoll density gradient ultracentrifugation | LC–MS | [ | |
| Huh7 cells | Percoll density gradient ultracentrifugation | LC–MS | [ | |
| Mouse liver | Percoll density gradient ultracentrifugation | LC–MS | [ | |
| Mouse brain | Percoll density gradient ultracentrifugation | LC–MS | [ | |
| Mouse liver | Sucrose gradient centrifugation4 | LC–MS | [ |
APOE has been repeatedly detected in mitochondria and MAMs in rat, mouse, and human cultured cells and tissue using various methodological approaches
TR targeted replacement, LC–MS liquid chromatography–mass spectrometry
1“Mitochondrion-rich fractions” were isolated, but the isolation method was not described
2Benchtop mitochondria isolation kit for rodent tissue (Mitosciences)
3ProteoExtract cytosol/mitochondria fractionation kit (EMD Millipore)
4Analysis of rough ER wrapped around mitochondria, which include MAMs as a subdomain
Overview of the APOE isoform-dependent effects on mitochondrial and MAM function with the tissue or cell line studied (brain or periphery) indicated
| Readout | Isoform effect | Tissue source | References | ||
|---|---|---|---|---|---|
| Total ATP level | E3 > E4 | Brain (APOE TR mice) | [ | ||
| Periphery (Huh7 cells1) | [ | ||||
| Brain (temporal lobes of APOE TR mice) | [ | ||||
| Brain (primary astrocytes of APOE TR mice) | [ | ||||
| Brain (primary neurons of APOE TR mice) | [ | ||||
| E3 < E4 | Brain (entorhinal cortex of APOE TR mice) | [ | |||
| Brain (primary astrocytes of APOE TR mice) | [ | ||||
Basal: E3 = E4 Stress: E3 > E4 | Brain (Neuro2a cells2) | [ | |||
| E3 = E4 | Brain (primary endothelial cells of APOE TR mice) | [ | |||
| OXPHOS | Protein | E3 > E4 | Brain (primary neurons of NSE-APOE mice) | [ | |
| Brain (cortical synaptosome of APOE TR mice) | [ | ||||
| Brain (Neuro2a cells2) | [ | ||||
| Brain (primary neurons of APOE TR mice) | [ | ||||
| E3 = E4 | Brain (primary astrocytes of GFAP–APOE mice) | [ | |||
| Periphery (Huh7 cells1, liver from APOE TR mice) | [ | ||||
| E3 < E4 | Brain (primary astrocytes of APOE TR mice) | [ | |||
| mRNA | E3/3 < E3/4 | Brain (entorhinal cortex of APOE TR mice) | [ | ||
| PGC1α pathway | Protein | E3 > E4 | Brain (temporal lobes of APOE TR mice | [ | |
| Brain (primary neurons of APOE TR mice) | [ | ||||
| non-E4 > E4 | Brain (human postmortem brain tissue) | [ | |||
| mRNA | E3 > E4 | Brain (cortex from APOE TR mice) | [ | ||
| E3 = E4 | Periphery (Huh7 cells1, liver from APOE TR mice) | [ | |||
| Mitochondrial respiration (Seahorse) | E3 > E4 | Brain (Neuro2a cells2) | [ | ||
| Brain (primary neurons of APOE TR mice) | [ | ||||
| E3 = E4 | Periphery (H2c9 cells, treated with recombinant APOE) | [ | |||
| Depends on age, brain area and complex | Brain (entorhinal cortex and hippocampus of APOE TR mice) | [ | |||
| Mitochondrial membrane potential | E3 = E4 | Periphery (Huh7 cells1) | [ | ||
| E3 > E4 | Brain (primary astrocytes of APOE TR mice) | [ | |||
| Brain (primary neurons of APOE TR mice) | [ | ||||
| Mitochondrial translocation/accumulation | E3 < E4 (stress-induced) | Brain (hippocampus of APOE TR mice) | [ | ||
| E3 < E4 | Brain (primary astrocytes of APOE TR mice) | [ | |||
| MFN1/2 | Protein | E3 < E4 | Brain (Neuro2a cells2) | [ | |
| Brain (hippocampus of APOE TR mice) | [ | ||||
| Brain (primary astrocytes of APOE TR mice) | [ | ||||
| non-E4 > E4 | Brain (human postmortem brain tissue) | [ | |||
| mRNA | E3 = E4 | Periphery (Huh7 cells1, liver from APOE TR mice) | [ | ||
| GRP75 | Protein | GRP75c: E3 < E4 GRP75d: E3 > E4 | Brain (hippocampus from APOE TR mice) | [ | |
| E3 = E4 | Brain (Neuro2a cells2) | [ | |||
| E3 > E4 | Brain (Neuro2a cells2) | [ | |||
| VDAC1 | Protein | E3 = E4 | Brain (Neuro2a cells2) | [ | |
| E3 < E4 | Brain (Neuro2a cells2) | [ | |||
| mRNA | E3 < E4 | Brain (Neuro2a cells2) | [ | ||
| E3 = E4 | Periphery (Huh7 cells1, liver from APOE TR mice) | [ | |||
| Phospholipid synthesis | E3 < E4 | Brain (mouse hippocampus cells treated with APOE-containing astrocyte-conditioned media) | [ | ||
| ER-mitochondria calcium flux | E3 < E4 | Brain (Neuro2a cells2) | [ | ||
| ER-mitochondria colocalization | E3 < E4 (in trend) | Brain (mouse hippocampus cells treated with APOE-containing astrocyte-conditioned media) | [ | ||
| VLDL assembly | - | Periphery (liver from CAV1 knockout mice) | [ | ||
| Periphery (mouse liver) | [ | ||||
1Transient APOE3- and APOE4-transfected cells
2Stable APOE3- and APOE4-expressing cell lines
Fig. 2Illustration of the assembly of mitochondria and mitochondria–ER contacts and the inherent biochemical pathways with suggested APOE involvement or regulation by the APOE isoform. a Mitochondria-associated ER membrane complex (MAM). b Mitochondrial and MAM pathways in which APOE may be involved. (I) The impact of APOE isoforms on mitochondrial function depends on the cell type and species, but consistently decreased neuronal OXPHOS protein and ATP levels were observed in APOE4. (II) Mitochondrial accumulation and stress-induced translocation are increased in APOE4. (III) The different steps in phospholipid synthesis take place through consecutive exchange of substrates from the ER membrane (synthesis of phosphatidylserine; PS) to the mitochondrion (conversion of PS to phosphatidylethanolamine (PE), which is increased in APOE4) and back. The final methylation step by PEMT is accomplished in the ER membrane, yielding phosphatidylcholine (PC). (IV) Calcium is released from the ER through the IP3R1–GRP75–VDAC1 complex and shuttled to the mitochondrion through the mitochondrial calcium uniporter protein (MCU) into the inner matrix. Increased calcium flux was found in APOE4 Neuro2a cells, and higher mitochondrial swelling was observed in APOE4-treated H9c2 cells, which was caused by the interaction of APOE (derived from the lysosomal degradation of L5-LDL) with VDAC1. The protein–protein interaction of APOE with MAM proteins such as VDAC1 and GRP75 is one explanation for the presence of APOE in MAMs. (V) MFN2 dimers connect the OMM with the ER membrane, acting as MAM tethering proteins. Depending on the tissue and species, APOE affects the expression of MFN1 and MFN2. (VI) MAMs are involved in cholesterol metabolism, and proteomic analyses provide evidence for a possible role of APOE in VLDL assembly in MAMs
Fig. 3Potential APOE protein–protein interactions in human cells and tissue. An in silico analysis performed with BioGRID 4.4 software revealed that there is evidence for 145 potential protein binding partners whose physical interaction with APOE has been demonstrated in at least one study in each case. The larger the blue circle of the corresponding protein is, the stronger the connectivity with APOE, and thicker binding lines represent stronger evidence supporting the association. Image downloaded from https://thebiogrid.org/
Overview of “low-throughput” studies in which targeted APOE protein–protein interactions were investigated and characterized for their biological function
| Interacting proteins | Methods | Tissue/cells | Biological relevance | References |
|---|---|---|---|---|
| A2M | Co-IP WB | Human plasma | Interaction E2 = E3 > E4 Interaction affected by lipoproteins | [ |
| APP | Co-IP WB Affinity chromatography WB | COS-1 cells Human plasma | APP is the precursor of Aβ, which plays an important role in AD pathology due to its neurotoxic properties and accumulation in plaques | [ [ |
| ABCA1 | Co-IP WB | Human skin fibroblasts, human plasma | Interaction E2 = E3 = E4 APOE might act as a protector for ABCA1 against proteases | [ [ |
| HPT | HPT-coupled beads, loaded with human plasma, pulldown, WB | Human plasma | Interaction of APOE and HPT via a specific amino acid sequence in APOE (amino acids 131–150) HPT potentially enhances the formation of the APOE–Aβ complex, may be related to AD pathology Inhibition of LCAT activity | [ |
| NOS1 | Co-IP WB Coimmunostaining | HEK293 cells Human hippocampus | Interaction E2 = E3 = E4 Interaction potentially leads to | [ |
CDC37 ECSIT PDCD4 ST13 | Co-IP WB | SH-SY5Y cells COS-7 cells | All investigated proteins are related to AD pathology Identification of these protein–protein interactions provides a contribution to the elucidation of possible AD-relevant mechanisms | [ |
| SNCA | Co-IP WB Co-IP ELISA | Human plasma Human CSF | SNCA accumulation is a maker for Parkinson’s disease pathology SNCA interacts with APOE and other apolipoproteins Increased APOE level in CSF from Parkinson’s disease patients | [ [ |
| ATP5A/B | Affinity chromatography WB | Human liver | Potential function in mitochondrial metabolism | [ |
UQCRC1/2 CYC1 | Co-IP WB | Neuro2a cells | Interaction E4 fragment > E4 full-length APOE3 was not investigated APOE4 fragment alters mitochondrial activity | [ |
| GRP75 | Co-IP WB | Astrocytes from APOE TR mice Human hippocampus | Interaction only in E4 cells, not in E3 and E2 Interaction in hippocampus E3 control < E3 AD < E4 AD Different GRP75 isoforms are regulated differently depending on the APOE isoform | [ [ |
| VDAC1 | Co-IP WB Coimmunostaining | H9c2 cells | Interaction E3 = E4 Interaction of APOE (derived from the lysosomal degradation of L5-LDL) with VDAC1 induced mitochondrial swelling (higher in APOE4) | [ |
Co-IP co-immunoprecipitation, WB Western blot, ELISA enzyme-linked immunosorbent assay, A2M α2-macroglobulin, APP amyloid precursor protein, ABCA1 ATP-binding cassette transporter, HPT haptoglobin, NOS1 nitric oxide synthase 1, CDC37 cell division cycle 37 HSP90 cochaperone, ECSIT evolutionarily conserved signalling intermediate in the toll pathway, PDCD4 programmed cell death 4, ST13 suppression of tumorigenicity 13 protein, SNCA synuclein α, ATP5A/B ATP synthase subunit α/β, UQCRC1/2 cytochrome b–c1 complex subunit 1/2, CYC1 cytochrome C1, GRP75 glucose-regulated protein 75, VDAC1 voltage-dependent anion-selective channel 1