Introduction
Alzheimer’s disease (AD) is the most common neurodegenerative disease that causes dementia, neuropathologically characterized by the accumulation of amyloid β (Aβ), phosphorylated Tau, and neuronal dystrophy and loss [
33]. Neuroinflammation is defined as an inflammatory response within the central nervous system (CNS), and it is mediated by activation of the innate immune system of the brain in response to inflammatory challenges, including misfolded protein aggregates that often accumulate in lesions of neurodegenerative diseases [
22,
43]. Microglia are the resident innate immune cells of the CNS, and are key players to mediate neuroinflammation, playing critical roles in the recognition and clearance of Aβ in AD [
9,
15,
27]. The activation phenotype of microglia was previously classified by the expression pattern of cytokines in analogy of activated macrophages: the proinflammatory “classical” activation phenotype (M1) and the anti-inflammatory “alternative” activated phenotype (M2) [
44]. However, this simplistic view of microglial phenotypes does not adequately reflect the complex physiology of microglia [
35]. The progression of neurodegenerative disease induces the loss of microglial homeostatic molecules and functions [
16], leading to chronically progressive neuroinflammation [
31]. In addition, recent studies demonstrated that a common disease-associated microglia (DAM) or “neurodegenerative” phenotype, defined by a small set of upregulated genes, was observed in neurodegenerative diseases including AD, amyotrophic lateral sclerosis (ALS), and frontotemporal dementia, and aging [
10,
20,
24]. However, it remains unclear whether the loss of homeostatic function in microglia or the DAM phenotype is correlated with the degree of neuronal cell loss, and whether DAM is beneficial or detrimental to neurodegenerative diseases.
Several transcriptomic studies using single nucleus analysis examined the molecular aspects of neuroinflammation in the prefrontal or entorhinal cortex of AD [
11,
26,
49]; however, neuroinflammatory alteration in the precuneus, which is vulnerable to Aβ deposition in preclinical AD, has yet to be examined. The precuneus is medially located in the parietal lobe of the cerebral cortex, and it is a component of the default mode network, which is implicated in episodic memory retrieval, and displays high metabolic activity during the baseline resting state [
6]. Amyloid PET studies demonstrated that the precuneus is one of the brain regions where Aβ accumulation preferentially starts in preclinical AD [
30,
47]. Therefore, it is important to uncover the neuroinflammatory aspects of the precuneus at the early amyloid pathology stage to better understand microglial response in early AD.
In this study, we first performed comparative gene expression analysis of isolated microglia from the three mouse models of neurodegenerative diseases:
AppNL-G-F/NL-G-F mice that display an amyloid pathology [
37], rTg4510 mice with tauopathy [
38], and SOD1
G93A mice with motor neurodegeneration [
12]. Despite robust neuroinflammation with microglial responses in all mouse models,
AppNL-G-F/NL-G-F mice do not show neuronal death, whereas rTg4510 and SOD1
G93A mice show a substantial loss of neurons. We found that most homeostatic microglial genes were downregulated in rTg4510 and SOD1
G93A mice, and were correlated with the degree of neuronal cell loss. In contrast, DAM genes were uniformly upregulated in all disease models, and this alteration was not correlated with neurodegeneration. Moreover, precunei of individuals with early AD pathology show downregulation of some microglial genes linked to homeostatic functions and genes linked to oligodendrocyte function.
Materials and methods
Postmortem human brain tissues
The postmortem brains from 25 individuals (non-AD = 14 and AD = 11) were obtained by autopsy with informed consent and diagnosed by a neuropathologist in the Brain Bank for Aging Research, Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology. All subjects with early AD pathology did not have apparent family history of dementia, therefore, were recognized as sporadic cases. The subjects were neuropathologically grouped according to the neurofibrillary tangle staging of Braak and Braak [
2]. The tissues were dissected from precuneus. A variation in the ratio of gray and white matter of dissected precuneus tissues, which may cause a substantial effect on relative levels of oligodendrocyte-derived mRNAs, was negligible, since we confirmed there was no changes in the
OLIG1/2 mRNA levels in non-AD and AD brain as internal controls. The use of human postmortem brain tissue was approved by the Ethics Committee of Research Institute of Environmental Medicine, Nagoya University and Tokyo Metropolitan Institute. Brain tissues for RNA preparation were immediately frozen using liquid nitrogen and stored at − 80 °C before use.
Animals
Heterozygous
App+/NL-G-F mice (C57BL/6-App < tm3(NL-G-F)Tcs >), carrying
App gene with humanized Aβ sequence (G676R, F681Y, R684H), Swedish (KM670/671NL), Beyreuther/Iberian (I716F), and Arctic (E693G) mutations, were previously established by a knock-in strategy [
37]. Homozygous
AppNL-G-F/NL-G-F and wild-type mice were obtained by crossbreeding, and were maintained as inbred lines. Tg(Camk2a-tTA)1Mmay
Fgf14Tg(tetO-MAPT*P301L)4510Kha/J mice were previously established [
38]. A parental mutant tau responder line, conditionally expressing the 4R0N isoform of human P301L mutant tau, in the FVB/N strain (Clea Inc., Tokyo, Japan), and a tTA activator line, under the control of CaMKII promoter, in the 129 + ter/SV strain (Clea Inc.) were crossbred to generate rTg4510 mice [
18]. tTA activator line was used as control for rTg4510 mice. Transgenic mice expressing the inherited ALS-linked human SOD1
G93A gene (B6.Cg-Tg (SOD1*G93A)1Gur/J) on the C57BL/6 background were obtained from Jackson Laboratory (Bar Harbor, ME, USA) [
12]. Genotyping of mice was performed as previously described [
18,
23,
37].
All mice were maintained under a standard specific pathogen-free environment (12 h light–dark-cycle; 23 ± 1 °C; 50 ± 5% humidity) with free access to food and water throughout experiments. Animals were treated in compliance with the guidelines established by the Institutional Animal Care and Use Committee of Nagoya University and National Institutes for Quantum and Radiological Science and Technology.
Microglia isolation from brain and spinal cord
Magnetic-activated cell sorting (MACS) of microglia in brain or spinal cord is performed as described elsewhere [
23]. In brief, the cerebral cortex or spinal cord, dissected from mice transcardially perfused with phosphate-buffered saline (PBS), was dissociated at 37 °C for 15 min using the Neural Tissue Dissociation Kit-Postnatal Neurons (Miltenyi Biotec, Bergisch-Gladbach, Germany) by the gentle MACS Dissociator (Miltenyi Biotec). For isolation of microglia, myelin debris was removed by using Myelin Removal Beads II (Miltenyi Biotec). Purified cells were incubated with anti-CD16/CD32 antibodies (Thermo Fisher Scientific, Waltham, MA, USA) for blocking Fc receptors, and then incubated with anti-CD11b microBeads (Miltenyi Biotec) for isolating microglia. CD11b-positive microglia were isolated by magnetic cell sorting through an LS column (Miltenyi Biotec).
RNA-seq experiments
For the RNA-seq of the mouse samples, total RNA was extracted from MACS-isolated microglia of each models using an RNeasy Mini Kit (Qiagen, Hilden, Germany). The RNAs were sampled from cerebral cortices of 8-month-old AppNL-G-F/NL-G-F and 7-month-old rTg4510 mice and lumbar spinal cords of 5-month-old SODG93A mice together with the corresponding wild-type or control mice, respectively. For the RNA-seq of the human samples, total RNA was prepared from precuneus of frozen postmortem brain using mirVana™ miRNA Isolation Kit (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer instructions. The total RNA was qualified by using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Libraries were prepared by using TruSeq mRNA or TruSeq Stranded mRNA (Illumina, San Diego, CA, USA), and, from these libraries, 151-nt paired-end reads were sequenced on the HiSeq X Ten with the HiSeq X Reagent Kits (Illumina) and the NovaSeq 6000 with the NovaSeq Reagent Kits (Illumina).
In silico analysis of the RNA-seq data
Differential expression analysis was performed using the Gene Spring Ver. 14.9.1 software from Agilent Technologies (Santa Clara, CA, USA) according to the manufacture’s protocol. Relative similarities of gene expression profiles of the samples were represented by a plot of the principal component analysis (PCA). The PCA analysis was performed with the prcomp function in R by using CPM values of the individual genes.
Quantification of mRNA levels by real-time PCR
Total RNA was extracted from MACS-sorted microglia using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions. Complementary DNA (cDNA) from MACS sorted cells was generated and amplified from 2.5 or 5 ng of total RNA by using the PrimeScript™ RT reagent Kit (Perfect Real Time) (TaKaRa Bio, Kusatsu, Japan) and 1/50 of the yield was amplified with the SYBR Premix Ex Taq II (Tli RNaseH Plus) (TaKaRa Bio) using the Thermal Cycler Dice Real Time System II or III (TaKaRa Bio). The thermocycle protocol was as follows: 1 cycle at 95 °C for 30 s, 40 cycles at 95 °C for 5 s and 60 °C for 30 s, and a dissociation stage of 95 °C for 15 s, 60 °C for 30 s, and 95 °C for 15 s. Actin was used for normalization. The primers used for real-time RT-PCR were as follows: human ACTB primer, forward, 5′-CTGGAACGGTGAAGGTGACA-3′; reverse, 5′-CGGCCACATTGTGAACTTTG-3′; human HBEGF primer, forward, 5′-GGACCCATGTCTTCGGAAAT-3′; reverse, 5′-CCCATGACACCTCTCTCCAT-3′; mouse Actb primer, forward, 5′-CGGACTCATCGTACTCCTGCTT-3′; reverse, 5′-TTGGCCTCACTGTCCACCTT-3′; mouse P2ry12 primer, forward, 5′-CATTGACCGCTACCTGAAGACC-3′; reverse, 5′-GCCTCCTGTTGGTGAGAATCATG-3′; mouse Sall1 primer, forward, 5′-TGTCAAGTTCCCAGAAATGTTCCA-3′; reverse, 5′-ATGCCGCCGTTCTGAATGA-3′; mouse Apoe primer, forward, 5′-GAACCGCTTCTGGGATTACCTG-3′; reverse, 5′- GCCTTTACTTCCGTCATAGTGTC-3′; mouse Itgax (Cd11c) primer, forward, 5′-CTGGATAGCCTTTCTTCTGCTG-3′; reverse, 5′-GCACACTGTGTCCGAACTCA-3′; mouse Hbegf primer, forward, 5′-ACCAGTGGAGAATCCCCTATAC-3′; reverse, 5′-GCCAAGACTGTAGTGTGGTCA-3′.
Immunofluorescence study
Immunofluorescence analysis was performed as described previously [
41]. In brief, mice were deeply anesthetized and perfused intracardially with PBS and 4% paraformaldehyde in PBS. The brains or spinal cords were dissected, post-fixed with the same fixative, and cryoprotected with 30% sucrose containing PBS. Twenty-micrometer-thick coronal brain sections or spinal cord transverse sections were fixed with 4% paraformaldehyde in PBS for 5 min and then permeabilized with 0.1% Triton X−100/PBS for 10 min. After an incubation in blocking solution (5% goat or donkey serum/PBS) for 1 h, sections were incubated with a combination of following antibodies: rabbit anti-Iba-1 (#019–19741, 1:500; Wako, Osaka, Japan), goat anti-AIF-1/Iba1 (#NB100-1028, 1:250; Novus Biologicals, CO, USA), mouse anti-human SOD1 (#M062-3, 1:500; MBL, Nagoya, Japan), mouse anti-AT8 (#MN1020, 1:500, Invitrogen, CA, USA), rabbit anti-Tmem119 (#ab209064, 1:500; abcam, Cambridge, UK), or mouse anti-ApoE (#sc-390925, 1:100, Santa Cruz Biotechnology, Inc, CA, USA) at 4 °C overnight. After washing with PBS, sections were incubated with fluorescent-conjugated anti-rabbit, anti-mouse, or anti-goat IgGs (1:1000; Thermo Fisher Scientific) at room temperature for 1 h. For thioflavin-S staining, after immunostaining with primary and secondary antibodies, sections were incubated with 0.02% thioflavin-S (#T1892, Sigma) at room temperature for 8 min, followed by incubation with 50% ethanol at room temperature for 1 min twice. After washing in PBS, sections were mounted on slides and analyzed with a confocal microscope (LSM700, Carl Zeiss, Oberkochen, Germany).
Statistical analysis
For RNA sequencing data, differential expression analysis between two groups with replicates was performed with edgeR v3.24.3 [
36] implemented in R v3.5.1, and
q-value was calculated for multiple testing correction of the
p-values with the
q-value package v2.24.1 [
42] in R. TPM (Transcripts Per Million) and CPM (Counts Per Million) values were computed with the StringTie and edgeR, respectively. A statistical comparison of the fold change values of gene expression quantities between two mutant experiments were performed with Wilcoxon’s signed rank test, followed by a multiple testing correction with the Bonferroni–Holm method [
1]. The representative log fold change values of the experiments for this purpose were computed with the edgeR. For quantitative PCR, differences between two groups were analyzed by a two-tailed Student’s
t test with the Bonferroni method.
Discussion
Our gene expression analysis of isolated microglia from mice of three neurodegenerative disease models including AD revealed that downregulation of homeostatic microglial genes and robust upregulation of DAM genes. More importantly, the extent of downregulation of homeostatic microglial genes was correlated with the degree of neuronal cell loss. In addition, a gene expression profile of human precuneus of early AD pathology shows reduced expression of some microglial homeostatic genes without induction of DAM genes, suggesting that the microglial signature in human early AD has limited similarity to that found in AD mice.
Previous studies reported a loss of homeostatic microglial genes in neurodegenerative diseases such as AD, ALS, and multiple sclerosis [
20,
24,
50]. In contrast to their findings, we found that rTg4510 and SOD1
G93A mice exhibited more robust downregulation in homeostatic microglial genes than that of
AppNL-G-F/NL-G-F mice, which exhibit neuroinflammation without neuronal loss (Fig.
2). In addition, rTg4510 mice show brain atrophy because of neurodegeneration, and SOD1
G93A mice exhibit fatal motor neurodegeneration. Of particular interest, changes in homeostatic microglial genes include
P2ry12,
Sall1, and
Tmem119 (Fig.
2a–d). P2RY12 regulates microglial activation via extracellular nucleotides [
3,
14]. SALL1 inhibits a reactive microglia phenotype and promotes a physiological surveilling phenotype [
17], and TMEM119 is expressed in microglia-derived cells and is absent in macrophages [
3,
46]. Although a loss of Tmem119 was limited to Aβ plaque-associated microglia in
AppNL-G-F/NL-G-F mice, more robust decreases in Tmem119 were observed in rTg4510 and SOD1
G93A microglia. Although there is a possibility that a loss of homeostatic microglial genes might be attributed to overexpression of transgenes, our result indicates that a loss of unique microglial homeostatic genes correlates with severity of neurodegeneration, and that decreased homeostatic microglial markers may be one of the hallmarks of progressive neuronal loss.
Consistent with the previous studies [
3,
20,
24], we found that DAM genes were uniformly upregulated in all three neurodegenerative mouse models. However, we also found that upregulation of most DAM genes was not correlated with the degree of neuronal cell loss (Fig.
3a, c, d). As a rare exception,
Apoe was correlated with the degree of neuronal cell loss (Fig.
3b), and the change in
Apoe expression was negatively associated with altered expression of homeostatic microglial genes (Fig.
2). The ApoE4 triggers induction of DAM with impaired homeostatic functions and is responsible for driving neurodegeneration [
24,
39]. This finding indicates that ApoE signaling may be involved in the loss of homeostatic microglial function. Combined with previous studies, our findings suggest that most DAM genes do not directly accelerate progression of neurodegeneration, but a few DAM genes, such as
APOE may be involved in severity of neurodegeneration. Since the relationship between
APOE genotypes and expressions of DAM and homeostatic microglial genes cannot be determined due to the limitation of
APOE e4 carriers in our study, further studies are required to clarify the potential role of
APOE e4 in human microglial phenotypes.
Despite its importance as a vulnerable region of amyloid deposition in early AD, gene expression in the precuneus of patients with AD has not been well explored in the past. Our study provides the first comprehensive gene expression profile of precuneus at the early stage of AD pathology (Braak NFT stage III–IV). Although the slight elevation of astrocytic and microglia activation markers in early AD precuneus was not statistically significant, the upregulation of chemokine and proinflammatory genes (
CXCL10, STAT1, ISG15, and
ITIF3) indicates neuroinflammatory changes in early AD precuneus. We also found downregulation of several microglial markers and DAM genes in early AD precuneus (Figs.
4,
5). In particular, the unaltered state of most DAM genes in human AD precuneus was in striking contrast with the data from AD mouse models. One possible interpretation is that the expression of genes of human AD and mouse models of AD is discordant, as demonstrated by a study using 5XFAD mice [
49]. Another possibility is that microglial function may be suppressed at the early stage of amyloid pathology. A recent study pointed out the low sensitivity of single nucleus RNA-seq to detect DAM genes in human postmortem brains [
45]. This low sensitivity may be attributed to redistribution of DAM mRNAs to the cytosol or instability of DAM mRNAs. As our study is based on the RNA-seq of whole brain tissues, cytosolic mRNAs can be detected, therefore, the latter possibility namely, instability of DAM mRNAs in human postmortem brain, remains. Further comparative gene expression analyses using the brain samples with early and advanced neuropathology will enable a conclusion regarding the significance of homeostatic microglia and DAM in human AD.
Another striking finding was the robust downregulation of genes linked to oligodendrocytes (
MBP, MAG, CLDN11, MOG, and
CNP) in early AD precuneus. In recent years, increasing evidence suggests that white matter abnormalities are also an important component of AD [
28], and oligodendrocyte abnormalities in advanced AD brain were also reported by a recent transcriptomic study [
49]. Compared with the microglia-mediated neuroinflammation, the role of oligodendrocytes in AD has been underestimated. Our data of the deregulation of oligodendrocytes and microglia in early AD precuneus suggest that both microglia and oligodendrocyte dysfunction may play a role in development of early AD pathology.
Although many risk genes for AD have been linked to microglia functions [
13], we found downregulation of
HBEGF/Hbegf was the only common change among the AD risk genes in human precuneus of early AD and AD model mice. A previous study reported an association between the single nucleotide polymorphism rs77493189 in
HBEGF and late-onset AD [
25]. Moreover, forebrain-specific
Hbegf knockout mice exhibited neurotrophic and growth factor imbalances as well as impaired memory function and synaptic plasticity [
29]. In this study, we performed comparative analysis of the gene expression profiles of sporadic AD precuneus and microglia isolated from familial AD models. Therefore, a small number of risk genes commonly deregulated in human precuneus and mouse microglia may be attributed to the different etiology between sporadic and familial AD. Despite of the limitation in our study, our results suggest that supplementation of HBEGF may be a viable therapeutic target for AD.
Comparative analysis of the gene expression profiles of AD precuneus and microglia isolated from
AppNL-G-F/NL-G-F and rTg4510 mouse cortices revealed that the number of commonly altered genes with AD precuneus were greater in
AppNL-G-F/NL-G-F microglia (76 genes) compared with rTg4510 microglia (45 genes).
AppNL-G-F/NL-G-F mice specifically shared 44 deregulated genes with AD precuneus, and
TNFSF10, one of the upregulated genes, is implicated in neuroinflammation and Aβ accumulation [
4]. In contrast,
SLC6A8 is one of the 41 downregulated genes, and it mediates inflammation by regulating creatine uptake [
19]. We also found that
PTPRD was decreased in both AD precuneus and rTg4510 mice; an association was reported between the rs560380 polymorphism in
PTPRD and NFT burden [
7]. These results suggest that
AppNL-G-F/NL-G-F and rTg4510 cortical microglia represent different aspects of AD pathologies.
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