The role of mitochondrial genome abundance in Alzheimer's disease

The neuroimmune nexus: unraveling the role of the mtDNA-cGAS-STING signal pathway in Alzheimer's disease

The relationship between Alzheimer's disease (AD) and neuroimmunity has gradually begun to be unveiled. Emerging evidence indicates that cyclic GMP-AMP synthase (cGAS) acts as a cytosolic DNA sensor, recognizing cytosolic damage-associated molecular patterns (DAMPs), and inducing the innate immune response by activating stimulator of interferon genes (STING). Dysregulation of this pathway culminates in AD-related neuroinflammation and neurodegeneration. A substantial body of evidence indicates that mitochondria are involved in the critical pathogenic mechanisms of AD, whose damage leads to the release of mitochondrial DNA (mtDNA) into the extramitochondrial space. This leaked mtDNA serves as a DAMP, activating various pattern recognition receptors and immune defense networks in the brain, including the cGAS-STING pathway, ultimately leading to an imbalance in immune homeostasis. Therefore, modulation of the mtDNA-cGAS-STING pathway to restore neuroimmune homeostasis may offer promising prospects for improving AD treatment outcomes. In this review, we focus on the mechanisms of mtDNA release during stress and the activation of the cGAS-STING pathway. Additionally, we delve into the research progress on this pathway in AD, and further discuss the primary directions and potential hurdles in developing targeted therapeutic drugs, to gain a deeper understanding of the pathogenesis of AD and provide new approaches for its therapy.

Bioinformatics insights into mitochondrial and immune gene regulation in Alzheimer's disease

BACKGROUND

There is growing evidence that the pathogenesis of Alzheimer's disease is closely linked to the resident innate immune cells of the central nervous system, including microglia and astrocytes. Mitochondrial dysfunction in microglia has also been reported to play an essential role in the pathogenesis of AD and other neurological diseases. Therefore, finding the mitochondrial and immune-related gene (MIRG) signatures in AD can be significant in diagnosing and treating AD.

METHODS

In this study, the intersection of the differentially expressed genes (DEGs) from the GSE109887 cohort, immune-related genes (IRGs) obtained from WGCNA analysis, and mitochondria-related genes (MRGs) was taken to identify mitochondria-immune-related genes (MIRGs). Then, using machine learning algorithms, biomarkers with good diagnostic value were selected, and a nomogram was constructed. Subsequently, we further analyzed the signaling pathways and potential biological mechanisms of the biomarkers through gene set enrichment analysis, prediction of transcription factors (TFs), miRNAs, and drug prediction.

RESULTS

Using machine learning algorithms, five biomarkers (TSPO, HIGD1A, NDUFAB1, NT5DC3, and MRPS30) were successfully identified, and a nomogram model with strong diagnostic ability and accuracy (AUC > 0.9) was constructed. In addition, single-gene enrichment analysis revealed that NDUFAB1 was significantly enriched in pathways associated with diseases, such as Alzheimer's and Parkinson's, providing valuable insights for future clinical research on Alzheimer's in the context of mitochondrial-immune interactions. Interestingly, brain tissue pathology showed neuronal atrophy and demyelination in AD mice, along with a reduction in Nissl bodies. Furthermore, the escape latency of AD mice was significantly longer than that of the control group. After platform removal, there was a notable increase in the path complexity and time required to reach the target quadrant, suggesting a reduction in spatial memory capacity in AD mice. Moreover, qRT-PCR validation confirmed that the mRNA expression of the five biomarkers was consistent with bioinformatics results. In AD mice, TSPO expression was increased, while HIGD1A, NDUFAB1, NT5DC3, and MRPS30 expressions were decreased. However, peripheral blood samples did not show expression of HIGD1A or MRPS30. These findings provide new insights for research on Alzheimer's disease in the context of mitochondrial-immune interactions, further exploring the pathogenesis of Alzheimer's disease and offering new perspectives for the clinical development of novel drugs.

CONCLUSIONS

Five mitochondrial and immune biomarkers, i.e., TSPO, HIGD1A, NDUFAB1, NT5DC3, and MRPS30, with diagnostic value in Alzheimer's disease, were screened by machine-learning algorithmic models, which will be a guide for future clinical research of Alzheimer's disease in the mitochondria-immunity-related direction.

Mitochondrial DNA copy number associated dementia risk by somatic mutations and frailty

Mitochondrial dysfunction is linked to physical impairment and dementia. Mitochondrial DNA copy number (mtDNAcn) from blood may predict cognitive decline and dementia risk, but the effect of somatic mutations or frailty is unknown. We estimated mtDNAcn using fastMitoCalc and microheteroplasmies using mitoCaller, from Whole Genome Sequencing (WGS) data. In 189,566 participants free of dementia at study entry (mean age = 56 ± 8), we examined the association between mtDNAcn and subsequent dementia diagnosis using Cox regression. Cognition was assessed in a subset on average 8.9 years later. We examined the associations between mtDNAcn and cognitive measures using multivariable linear regression, adjusted for demographic factors, mtDNAcn-related parameters, and apolipoprotein E ε4 status. We further stratified by frailty and microheteroplasmies. Over an average follow-up of 13.2 years, 3533 participants developed dementia. Each SD higher mtDNAcn (16) was associated with 4.2% lower all-cause dementia hazard (HR = 0.958, p = 0.030), 6% lower non-AD dementia hazard (HR = 0.933, p = 0.022), and not-AD dementia hazard. The associations between mtDNAcn and all-cause dementia and non-AD dementia were stronger among those who were pre-frail or frail or with higher microheteroplasmies. Higher mtDNAcn was associated with higher DSST scores (p = 0.036) and significant only among those with higher microheteroplasmies or frailty (p = 0.029 and 0.048, respectively). mtDNAcn was also associated with delta TMT and paired associate learning only in pre-frail/frail participants (p = 0.007 and 0.045, respectively). Higher WGS-based mtDNAcn in human blood is associated with lower dementia risk, specifically non-AD dementia, and specific cognitive function. The relationships appear stronger in high somatic mutations or frailty. Future studies are warranted to investigate biological underpinnings.

Inhibiting mtDNA transcript translation alters Alzheimer's disease-associated biology

INTRODUCTION

Alzheimer's disease (AD) features changes in mitochondrial structure and function. Investigators debate where to position mitochondrial pathology within the chronology and context of other AD features.

METHODS

To address whether mitochondrial dysfunction alters AD-implicated genes and proteins, we treated SH-SY5Y cells and induced pluripotent stem cell (iPSC)-derived neurons with chloramphenicol, an antibiotic that inhibits mtDNA-generated transcript translation. We characterized adaptive, AD-associated gene, and AD-associated protein responses.

RESULTS

SH-SY5Y cells and iPSC neurons responded to mtDNA transcript translation inhibition by increasing mtDNA copy number and transcription. Nuclear-expressed respiratory chain mRNA and protein levels also changed. There were AD-consistent concordant and model-specific changes in amyloid precursor protein, beta amyloid, apolipoprotein E, tau, and α-synuclein biology.

DISCUSSION

Primary mitochondrial dysfunction induces compensatory organelle responses, changes nuclear gene expression, and alters the biology of AD-associated genes and proteins in ways that may recapitulate brain aging and AD molecular phenomena.

HIGHLIGHTS

In AD, mitochondrial dysfunction could represent a disease cause or consequence. We inhibited mitochondrial translation in human neuronal cells and neurons. Mitochondrial and nuclear gene expression shifted in adaptive-consistent patterns. APP, Aβ, APOE, tau, and α-synuclein biology changed in AD-consistent patterns. Mitochondrial stress creates an environment that promotes AD pathology.

SIRT1 Regulates Mitochondrial Damage in N2a Cells Treated with the Prion Protein Fragment 106-126 via PGC-1α-TFAM-Mediated Mitochondrial Biogenesis

Mitochondrial damage is an early and key marker of neuronal damage in prion diseases. As a process involved in mitochondrial quality control, mitochondrial biogenesis regulates mitochondrial homeostasis in neurons and promotes neuron health by increasing the number of effective mitochondria in the cytoplasm. Sirtuin 1 (SIRT1) is a NAD+-dependent deacetylase that regulates neuronal mitochondrial biogenesis and quality control in neurodegenerative diseases via deacetylation of a variety of substrates. In a cellular model of prion diseases, we found that both SIRT1 protein levels and deacetylase activity decreased, and SIRT1 overexpression and activation significantly ameliorated mitochondrial morphological damage and dysfunction caused by the neurotoxic peptide PrP106-126. Moreover, we found that mitochondrial biogenesis was impaired, and SIRT1 overexpression and activation alleviated PrP106-126-induced impairment of mitochondrial biogenesis in N2a cells. Further studies in PrP106-126-treated N2a cells revealed that SIRT1 regulates mitochondrial biogenesis through the PGC-1α-TFAM pathway. Finally, we showed that resveratrol resolved PrP106-126-induced mitochondrial dysfunction and cell apoptosis by promoting mitochondrial biogenesis through activation of the SIRT1-dependent PGC-1α/TFAM signaling pathway in N2a cells. Taken together, our findings further describe SIRT1 regulation of mitochondrial biogenesis and improve our understanding of mitochondria-related pathogenesis in prion diseases. Our findings support further investigation of SIRT1 as a potential target for therapeutic intervention of prion diseases.

Modifying Alzheimer's disease pathophysiology with photobiomodulation: model, evidence, and future with EEG-guided intervention

This manuscript outlines a model of Alzheimer's Disease (AD) pathophysiology in progressive layers, from its genesis to the development of biomarkers and then to symptom expression. Genetic predispositions are the major factor that leads to mitochondrial dysfunction and subsequent amyloid and tau protein accumulation, which have been identified as hallmarks of AD. Extending beyond these accumulations, we explore a broader spectrum of pathophysiological aspects, including the blood-brain barrier, blood flow, vascular health, gut-brain microbiodata, glymphatic flow, metabolic syndrome, energy deficit, oxidative stress, calcium overload, inflammation, neuronal and synaptic loss, brain matter atrophy, and reduced growth factors. Photobiomodulation (PBM), which delivers near-infrared light to selected brain regions using portable devices, is introduced as a therapeutic approach. PBM has the potential to address each of these pathophysiological aspects, with data provided by various studies. They provide mechanistic support for largely small published clinical studies that demonstrate improvements in memory and cognition. They inform of PBM's potential to treat AD pending validation by large randomized controlled studies. The presentation of brain network and waveform changes on electroencephalography (EEG) provide the opportunity to use these data as a guide for the application of various PBM parameters to improve outcomes. These parameters include wavelength, power density, treatment duration, LED positioning, and pulse frequency. Pulsing at specific frequencies has been found to influence the expression of waveforms and modifications of brain networks. The expression stems from the modulation of cellular and protein structures as revealed in recent studies. These findings provide an EEG-based guide for the use of artificial intelligence to personalize AD treatment through EEG data feedback.

Site-specific phosphorylation of tau impacts mitochondrial function and response to stressors

Phosphorylation of tau at sites associated with Alzheimer's disease (AD) likely plays a role in the disease progression. Mitochondrial impairment, correlating with increased presence of phosphorylated tau, has been identified as a contributing factor to neurodegenerative processes in AD. However, how tau phosphorylated at specific sites impacts mitochondrial function has not been fully defined. We examined how AD-relevant phosphomimetics of tau impact selected aspects of mitochondrial biology. To mimic phosphorylation at AD-associated sites, the serine/threonine (Ser/Thr) sites in wild-type green fluorescent protein (GFP)-tagged tau (T4) were converted to glutamic acid (E) to make pseudo-phosphorylated GFP-tagged Ser-396/404 (2EC) and GFP-tagged Thr-231/Ser-235 (2EM) constructs. These constructs were expressed in immortalized mouse hippocampal neuronal cell lines, and their impact on specific mitochondrial functions and responses to stressors were measured. Phosphomimetic tau altered mitochondrial distribution. Specifically, mitochondria accumulated in the soma of cells expressing either 2EC or 2EM and neurite-like extensions in 2EC cells were shorter. Additionally, adenosine triphosphate levels were reduced in both 2EC- and 2EM-expressing cells, and reactive oxygen species (ROS) production increased in 2EC cells during oxidation of succinate when compared to T4-expressing cells. Thapsigargin reduced mitochondrial membrane potential and increased ROS production in both 2EC and 2EM cells relative to T4 cells, with no significant difference in the effects of rotenone. These results show that tau phosphorylation at specific AD-relevant epitopes negatively affects mitochondria, with the extent of dysfunction and stress response varying according to the sites of phosphorylation. Altogether, these findings show that phosphorylated tau increases mitochondrial susceptibility to stressors and extend our understanding of potential mechanisms whereby phosphorylated tau promotes mitochondria dysfunction in tauopathies, including AD.

Mitochondrial calcium signaling in non-neuronal cells: Implications for Alzheimer's disease pathogenesis

Mitochondrial dysregulation is pivotal in Alzheimer's disease (AD) pathogenesis. Calcium governs vital mitochondrial processes impacting energy conversion, oxidative stress, and cell death signaling. Disruptions in mitochondrial calcium (mCa2+) handling induce calcium overload and trigger the opening of mitochondrial permeability transition pore, ensuing energy deprivation and resulting in AD-related neuronal cell death. However, the role of mCa2+ in non-neuronal cells (microglia, astrocytes, oligodendrocytes, endothelial cells, and pericytes) remains elusive. This review provides a comprehensive exploration of mitochondrial heterogeneity and calcium signaling, offering insights into specific differences among various brain cell types in AD.

Mitochondrial DNA: Inherent Complexities Relevant to Genetic Analyses

Mitochondrial DNA (mtDNA) exhibits distinct characteristics distinguishing it from the nuclear genome, necessitating specific analytical methods in genetic studies. This comprehensive review explores the complex role of mtDNA in a variety of genetic studies, including genome-wide, epigenome-wide, and phenome-wide association studies, with a focus on its implications for human traits and diseases. Here, we discuss the structure and gene-encoding properties of mtDNA, along with the influence of environmental factors and epigenetic modifications on its function and variability. Particularly significant are the challenges posed by mtDNA's high mutation rate, heteroplasmy, and copy number variations, and their impact on disease susceptibility and population genetic analyses. The review also highlights recent advances in methodological approaches that enhance our understanding of mtDNA associations, advocating for refined genetic research techniques that accommodate its complexities. By providing a comprehensive overview of the intricacies of mtDNA, this paper underscores the need for an integrated approach to genetic studies that considers the unique properties of mitochondrial genetics. Our findings aim to inform future research and encourage the development of innovative methodologies to better interpret the broad implications of mtDNA in human health and disease.

Recent Advances of Mitochondrial Alterations in Alzheimer's Disease: A Perspective of Mitochondrial Basic Events

Alzheimer's disease (AD) is one of the most common neurodegenerative disorders and is characterized by a decrease in learning capacity, memory loss and behavioral changes. In addition to the well-recognized amyloid-β cascade hypothesis and hyperphosphorylated Tau hypothesis, accumulating evidence has led to the proposal of the mitochondrial dysfunction hypothesis as the primary etiology of AD. However, the predominant molecular mechanisms underlying the development and progression of AD have not been fully elucidated. Mitochondrial dysfunction is not only considered an early event in AD pathogenesis but is also involved in the whole course of the disease, with numerous pathophysiological processes, including disordered energy metabolism, Ca2+ homeostasis dysfunction and hyperactive oxidative stress. In the current review, we have integrated emerging evidence to summarize the main mitochondrial alterations- bioenergetic metabolism, mitochondrial inheritance, mitobiogenesis, fission- fusion dynamics, mitochondrial degradation, and mitochondrial movement- underlying AD pathogenesis; precisely identified the mitochondrial regulators; discussed the potential mechanisms and primary processes; highlighted the leading players; and noted additional incidental signaling pathway changes. This review may help to stimulate research exploring mitochondrial metabolically-oriented neuroprotection strategies in AD therapies, leading to a better understanding of the link between the mitochondrial dysfunction hypothesis and AD pathogenesis.

Transcriptomic Analysis in the Hippocampus and Retina of Tg2576 AD Mice Reveals Defective Mitochondrial Oxidative Phosphorylation and Recovery by Tau 12A12mAb Treatment

Increasing evidence implicates decreased energy metabolism and mitochondrial dysfunctions among the earliest pathogenic events of Alzheimer's disease (AD). However, the molecular mechanisms underlying bioenergetic dysfunctions in AD remain, to date, largely unknown. In this work, we analyzed transcriptomic changes occurring in the hippocampus and retina of a Tg2576 AD mouse model and wild-type controls, evaluating their functional implications by gene set enrichment analysis. The results revealed that oxidative phosphorylation and mitochondrial-related pathways are significantly down-regulated in both tissues of Tg2576 mice, supporting the role of these processes in the pathogenesis of AD. In addition, we also analyzed transcriptomic changes occurring in Tg2576 mice treated with the 12A12 monoclonal antibody that neutralizes an AD-relevant tau-derived neurotoxic peptide in vivo. Our analysis showed that the mitochondrial alterations observed in AD mice were significantly reverted by treatment with 12A12mAb, supporting bioenergetic pathways as key mediators of its in vivo neuroprotective and anti-amyloidogenic effects. This study provides, for the first time, a comprehensive characterization of molecular events underlying the disrupted mitochondrial bioenergetics in AD pathology, laying the foundation for the future development of diagnostic and therapeutic tools.

Site-specific phosphorylation of tau impacts mitochondrial biology and response to stressors

Phosphorylation of tau at sites associated with Alzheimer's disease (AD) likely plays a role in the disease progression. Mitochondrial impairment, correlating with increased presence of phosphorylated tau, has been identified as a contributing factor to neurodegenerative processes in AD. However, how tau phosphorylated at specific sites impacts mitochondrial function has not been fully defined. We examined how AD-relevant phosphomimetics of tau impact selected aspects of mitochondrial biology. To mimic phosphorylation at AD-associated sites, the Ser/Thr sites in wild-type GFP tagged-tau (T4) were converted to glutamic acid (E) to make pseudophosphorylated GFP tagged-Ser-396/404 (2EC) and GFP tagged-Thr-231/Ser-235 (2EM) constructs. These constructs were expressed in neuronal HT22 cells and their impact on specific mitochondrial functions and responses to stressors were measured. Phosphomimetic tau altered mitochondrial distribution. Specifically, mitochondria accumulated in the soma of cells expressing either 2EC or 2EM, and neurite-like extensions in 2EC cells were shorter. Additionally, ATP levels were reduced in both 2EC and 2EM expressing cells, and ROS production increased in 2EC cells during oxidation of succinate when compared to T4 expressing cells. Thapsigargin reduced mitochondrial membrane potential (Ψ m ) and increased ROS production in both 2EC and 2EM cells relative to T4 cells, with no significant difference in the effects of rotenone. These results show that tau phosphorylation at specific AD-relevant epitopes negatively affects mitochondria, with the extent of dysfunction and stress response varying according to the sites of phosphorylation. Altogether, these findings extend our understanding of potential mechanisms whereby phosphorylated tau promotes mitochondria dysfunction in tauopathies, including AD.

Funding information

R01 AG067617.

Mitochondria Profoundly Influence Apolipoprotein E Biology

BACKGROUND

Mitochondria can trigger Alzheimer's disease (AD)-associated molecular phenomena, but how mitochondria impact apolipoprotein E (APOE; apoE) is not well known.

OBJECTIVE

Consider whether and how mitochondrial biology influences APOE and apoE biology.

METHODS

We measured APOE expression in human SH-SY5Y neuronal cells with different forms of mitochondrial dysfunction including total, chronic mitochondrial DNA (mtDNA) depletion (ρ0 cells); acute, partial mtDNA depletion; and toxin-induced mitochondrial dysfunction. We further assessed intracellular and secreted apoE protein levels in the ρ0 cells and interrogated the impact of transcription factors and stress signaling pathways known to influence APOE expression.

RESULTS

SH-SY5Y ρ0 cells exhibited a 65-fold increase in APOE mRNA, an 8-fold increase in secreted apoE protein, and increased intracellular apoE protein. Other models of primary mitochondrial dysfunction including partial mtDNA-depletion, toxin-induced respiratory chain inhibition, and chemical-induced manipulations of the mitochondrial membrane potential similarly increased SH-SY5Y cell APOE mRNA. We explored potential mediators and found in the ρ0 cells knock-down of the C/EBPα and NFE2L2 (Nrf2) transcription factors reduced APOE mRNA. The activity of two mitogen-activated protein kinases, JNK and ERK, also strongly influenced ρ0 cell APOE mRNA levels.

CONCLUSION

Primary mitochondrial dysfunction either directly or indirectly activates APOE expression in a neuronal cell model by altering transcription factors and stress signaling pathways. These studies demonstrate mitochondrial biology can influence the biology of the APOE gene and apoE protein, which are implicated in AD.

Efficient Enrichment Method for N-Phosphorylation Peptides in Mouse Brain Tissue

In addition to O-phosphorylation, protein N-phosphorylation was proven to play important roles in multiple biological processes. Although affinity methods were developed for the enrichment of N-phosphorylation peptides in cells, it was still difficult to enrich N-phosphorylation peptides in tissue due to its complexity. In this study, we established a workflow for the identification of N-phosphorylation peptides in mouse brain tissue by direct enrichment in high concentration urea. In total, 989 N-phosphorylation sites were obtained using 0.5 M urea as enrichment buffer. Among all identified N-phosphorylation sites, the localization probability over 0.75 was as high as 80%, suggesting the reliability of the method. Furthermore, the sequence motif analysis and gene ontology analysis results showed a good match to previous studies. The method was successfully used for N-phosphorylation analysis of mouse hippocampus from Alzheimer's disease model, and 533 N-phosphorylation sites were identified in 5 × FAD mouse hippocampus tissue. Biological process analysis results showed that "brain development", "cellular response to reactive oxygen species", "microtubule cytoskeleton organization", and "peptidyl-serine phosphorylation" were especially enriched in 5 × FAD mouse. It is suggested that N-phosphorylation may be related to Alzheimer's disease in these aspects.