Characterization of Mitochondrial DNA Methylation of Alzheimer's Disease in Plasma Cell-Free DNA

Methylated cell-free DNA as a novel biomarker in Alzheimer's disease

Due to an aging population, Alzheimer's disease (AD), a neurodegenerative disorder, has affected more than 40 million people worldwide, a figure predicted to significantly increase in the coming decades. Despite much effort to understand AD pathogenesis, effective diagnosis and treatment remain a challenge. However, the development of liquid biopsy including the analysis of cell-free DNA (cfDNA) and methylation thereof has provided an alternative source of investigation to further explore the pathophysiology of AD. Herein, we discuss the research progress to date and highlight clinical applications of methylated cfDNA in AD.

The enigma of mitochondrial epigenetic alterations in air pollution-induced neurodegenerative diseases

The incidence of neurodegenerative diseases is a growing concern worldwide, affecting individuals from diverse backgrounds. Although these pathologies are primarily associated with aging and genetic susceptibility, their severity varies among the affected population. Numerous studies have indicated air pollution as a significant contributor to the increasing prevalence of neurodegeneration. Cohort studies have provided compelling evidence of the association between prolonged exposure to different air toxicants and cognitive decline, behavioural deficits, memory impairment, and overall neuronal health deterioration. Furthermore, molecular research has revealed that air pollutants can disrupt the body's protective mechanisms, participate in neuroinflammatory pathways, and cause neuronal epigenetic modifications. The mitochondrial epigenome is particularly interesting to the scientific community due to its potential to significantly impact our understanding of neurodegenerative diseases' pathogenesis and their release in the peripheral circulation. While protein hallmarks have been extensively studied, the possibility of using circulating epigenetic signatures, such as methylated DNA fragments, miRNAs, and genome-associated factors, as diagnostic tools and therapeutic targets requires further groundwork. The utilization of circulating epigenetic signatures holds promise for developing novel prognostic strategies, creating paramount point-of-care devices for disease diagnosis, identifying therapeutic targets, and developing clinical data-based disease models utilizing multi-omics technologies and artificial intelligence, ultimately mitigating the threat and prevalence of neurodegeneration.

The interplay of metabolic and epigenetic players in disease development

Epigenetic modifications and their alterations can cause variation in gene expression patterns which can ultimately affect a healthy individual. Until a few years ago, it was thought that the epigenome affects the transcriptome which can regulate the proteome and the metabolome. Recent studies have shown that the metabolome independently also plays a major role in regulating the epigenome bypassing the need for transcriptomic control. Alternatively, an imbalanced metabolome, stemming from transcriptome abnormalities, can further impact the transcriptome, creating a self-perpetuating cycle of interconnected occurrences. As a result, external factors such as nutrient intake and diet can have a direct impact on the metabolic pools and its reprogramming can change the levels and activity of epigenetic modifiers. Thus, the epigenetic landscape steers toward a diseased condition. In this review, we have discussed how different metabolites and dietary patterns can bring about changes in different arms of the epigenetic machinery such as methylation, acetylation as well as RNA mediated epigenetic mechanisms. We checked for limiting metabolites such as αKG, acetyl-CoA, ATP, NAD+, and FAD, whose abundance levels can lead to common diseases such as cancer, neurodegeneration etc. This gives a clearer picture of how an integrated approach including both epigenetics and metabolomics can be used for therapeutic purposes.

Liquid Biopsy in Neuropsychiatric Disorders: A Step Closer to Precision Medicine

Psychiatric disorders are among the leading causes of disease burden worldwide. Despite their significant impact, their diagnosis remains challenging due to symptom heterogeneity, psychiatric comorbidity, and the lack of objective diagnostic tests and well-defined biomarkers. Leveraging genomic, epigenomic, and fragmentomic technologies, circulating cell-free DNA (ccfDNA)-based liquid biopsies have emerged as a potential non-invasive diagnosis and disease-monitoring tool. ccfDNA is a DNA species released into circulation from all types of cells through passive and active mechanisms and can serve as a biomarker for various diseases, namely, cancer. Despite their potential, the application of ccfDNA in neuropsychiatry remains underdeveloped. In this review, we provide an overview of liquid biopsies and their components, with a particular focus on ccfDNA. With a summary of pre-analytical practices and current ccfDNA technologies, we highlight the current state of research regarding the use of ccfDNA as a biomarker for neuropsychiatric disorders. Finally, we discuss future steps to unlock ccfDNA's potential in clinical practice.

Mitochondrial One-Carbon Metabolism and Alzheimer's Disease

Mitochondrial one-carbon metabolism provides carbon units to several pathways, including nucleic acid synthesis, mitochondrial metabolism, amino acid metabolism, and methylation reactions. Late-onset Alzheimer's disease is the most common age-related neurodegenerative disease, characterised by impaired energy metabolism, and is potentially linked to mitochondrial bioenergetics. Here, we discuss the intersection between the molecular pathways linked to both mitochondrial one-carbon metabolism and Alzheimer's disease. We propose that enhancing one-carbon metabolism could promote the metabolic processes that help brain cells cope with Alzheimer's disease-related injuries. We also highlight potential therapeutic avenues to leverage one-carbon metabolism to delay Alzheimer's disease pathology.

From powerhouse to regulator: The role of mitoepigenetics in mitochondrion-related cellular functions and human diseases

Beyond their crucial role in energy production, mitochondria harbor a distinct genome subject to epigenetic regulation akin to that of nuclear DNA. This paper delves into the nascent but rapidly evolving fields of mitoepigenetics and mitoepigenomics, exploring the sophisticated regulatory mechanisms governing mitochondrial DNA (mtDNA). These mechanisms encompass mtDNA methylation, the influence of non-coding RNAs (ncRNAs), and post-translational modifications of mitochondrial proteins. Together, these epigenetic modifications meticulously coordinate mitochondrial gene transcription, replication, and metabolism, thereby calibrating mitochondrial function in response to the dynamic interplay of intracellular needs and environmental stimuli. Notably, the dysregulation of mitoepigenetic pathways is increasingly implicated in mitochondrial dysfunction and a spectrum of human pathologies, including neurodegenerative diseases, cancer, metabolic disorders, and cardiovascular conditions. This comprehensive review synthesizes the current state of knowledge, emphasizing recent breakthroughs and innovations in the field. It discusses the potential of high-resolution mitochondrial epigenome mapping, the diagnostic and prognostic utility of blood or tissue mtDNA epigenetic markers, and the promising horizon of mitochondrial epigenetic drugs. Furthermore, it explores the transformative potential of mitoepigenetics and mitoepigenomics in precision medicine. Exploiting a theragnostic approach to maintaining mitochondrial allostasis, this paper underscores the pivotal role of mitochondrial epigenetics in charting new frontiers in medical science.

Mitochondria in Alzheimer's Disease Pathogenesis

Alzheimer's disease (AD) is a progressive and incurable neurodegenerative disorder that primarily affects persons aged 65 years and above. It causes dementia with memory loss and deterioration in thinking and language skills. AD is characterized by specific pathology resulting from the accumulation in the brain of extracellular plaques of amyloid-β and intracellular tangles of phosphorylated tau. The importance of mitochondrial dysfunction in AD pathogenesis, while previously underrecognized, is now more and more appreciated. Mitochondria are an essential organelle involved in cellular bioenergetics and signaling pathways. Mitochondrial processes crucial for synaptic activity such as mitophagy, mitochondrial trafficking, mitochondrial fission, and mitochondrial fusion are dysregulated in the AD brain. Excess fission and fragmentation yield mitochondria with low energy production. Reduced glucose metabolism is also observed in the AD brain with a hypometabolic state, particularly in the temporo-parietal brain regions. This review addresses the multiple ways in which abnormal mitochondrial structure and function contribute to AD. Disruption of the electron transport chain and ATP production are particularly neurotoxic because brain cells have disproportionately high energy demands. In addition, oxidative stress, which is extremely damaging to nerve cells, rises dramatically with mitochondrial dyshomeostasis. Restoring mitochondrial health may be a viable approach to AD treatment.

Platelet mitochondria, a potent immune mediator in neurological diseases

Dysfunction of the immune response is regarded as a prominent feature of neurological diseases, including neurodegenerative diseases, malignant tumors, acute neurotraumatic insult, and cerebral ischemic/hemorrhagic diseases. Platelets play a fundamental role in normal hemostasis and thrombosis. Beyond those normal functions, platelets are hyperactivated and contribute crucially to inflammation and immune responses in the central nervous system (CNS). Mitochondria are pivotal organelles in platelets and are responsible for generating most of the ATP that is used for platelet activation and aggregation (clumping). Notably, platelet mitochondria show marked morphological and functional alterations under heightened inflammatory/oxidative stimulation. Mitochondrial dysfunction not only leads to platelet damage and apoptosis but also further aggravates immune responses. Improving mitochondrial function is hopefully an effective strategy for treating neurological diseases. In this review, the authors discuss the immunomodulatory roles of platelet-derived mitochondria (PLT-mitos) in neurological diseases and summarize the neuroprotective effects of platelet mitochondria transplantation.

Validating blood tests as a possible routine diagnostic assay of Alzheimer's disease

INTRODUCTION

In recent years, exciting developments in disease modifying treatments for Alzheimer's disease (AD) have made accurate and timely diagnosis of this disease a priority. Blood biomarkers (BBMs) for amyloid pathology using improved immunoassay and mass spectrometry techniques have been an area of intense research for the last 10 years and are coming to the fore, as a real prospect to be used in the clinical diagnostics of the disease.

AREAS COVERED

The following review will update and discuss blood biomarkers that will be most useful in diagnosing AD and the context necessary for their implementation.

EXPERT OPINION

It is clear we now have BBMs, and technology to measure them, that are capable of detecting amyloid pathology in AD. The challenge is to validate them across platforms and populations to incorporate them into clinical practice. It is important that implementation comes with education, we need to give clinicians the tools for appropriate use and interpretation. It is feasible that BBMs will be used to screen populations, initially for clinical trial entry but also therapeutic intervention in the foreseeable future. We now need to focus BBM research on other pathologies to ensure we accelerate the development of therapeutics for all neurodegenerative diseases.