Presenilin mutations deregulate mitochondrial Ca2+ homeostasis and metabolic activity causing neurodegeneration in Caenorhabditis elegans

A Machine Learning Method for Identifying Critical Interactions Between Gene Pairs in Alzheimer's Disease Prediction

Background: Alzheimer's disease (AD) is the most common type of dementia. Scientists have discovered that the causes of AD may include a combination of genetic, lifestyle, and environmental factors, but the exact cause has not yet been elucidated. Effective strategies to prevent and treat AD therefore remain elusive. The identified genetic causes of AD mainly focus on individual genes, but growing evidence has shown that complex diseases are usually affected by the interaction of genes in a network. Few studies have focused on the interactions and correlations between genes and how they are gradually destroyed or disappear during AD progression. A differential network analysis has been recognized as an essential tool for identifying the underlying pathogenic mechanisms and significant genes for prediction analysis. We therefore aim to conduct a differential network analysis to reveal potential networks involved in the neuropathogenesis of AD and identify genes for AD prediction. Methods: In this paper, we selected 365 samples from the Religious Orders Study and the Rush Memory and Aging Project, including 193 clinically and neuropathologically confirmed AD subjects and 172 no cognitive impairment (NCI) controls. Then, we selected 158 genes belonging to the AD pathway (hsa05010) of the Kyoto Encyclopedia of Genes and Genomes. We employed a machine learning method, namely, joint density-based non-parametric differential interaction network analysis and classification (JDINAC), in the analysis of gene expression data (RNA-seq data). We searched for the differential networks in the RNA-seq data with a pathological diagnosis of AD. Finally, an optimal prediction model was built through cross-validation, which showed good discrimination and calibration for AD prediction. Results: We used JDINAC to derive a gene co-expression network and to explore the relationship between the interaction of gene pairs and AD, and the top 10 differential gene pairs were identified. We then compared the prediction performance between JDINAC and individual genes based on prediction methods. JDINAC provides better accuracy of classification than the latest methods, such as random forest and penalized logistic regression. Conclusions: The interaction between gene pairs is related to AD and can provide more insight than the individual genes in AD prediction.

Impaired mitochondrial calcium efflux contributes to disease progression in models of Alzheimer's disease

Impairments in neuronal intracellular calcium (_iCa²⁺) handling may contribute to Alzheimer’s disease (AD) development. Metabolic dysfunction and progressive neuronal loss are associated with AD progression, and mitochondrial calcium (_mCa²⁺) signaling is a key regulator of both of these processes. Here, we report remodeling of the _mCa²⁺ exchange machinery in the prefrontal cortex of individuals with AD. In the 3xTg-AD mouse model impaired _mCa²⁺ efflux capacity precedes neuropathology. Neuronal deletion of the mitochondrial Na⁺/Ca²⁺ exchanger (NCLX, Slc8b1 gene) accelerated memory decline and increased amyloidosis and tau pathology. Further, genetic rescue of neuronal NCLX in 3xTg-AD mice is sufficient to impede AD-associated pathology and memory loss. We show that _mCa²⁺ overload contributes to AD progression by promoting superoxide generation, metabolic dysfunction and neuronal cell death. These results provide a link between the calcium dysregulation and metabolic dysfunction hypotheses of AD and suggest _mCa²⁺ exchange as potential therapeutic target in AD.

Dysregulation of intracellular calcium is reported in Alzheimer’s disease. Here the authors show that loss of the mitochondrial Na⁺ /Ca²⁺ exchanger, NCLX – primary route of mitochondrial calcium efflux, precedes neuronal pathology in experimental models and contributes to Alzheimer’s disease progression.

Niacinamide Protects Skin Cells from Oxidative Stress Induced by Particulate Matter

Niacinamide (NIA) is a water-soluble vitamin that is widely used in the treatment of skin diseases. Moreover, NIA displays antioxidant effects and helps repair damaged DNA. Recent studies showed that particulate matter 2.5 (PM_2.5) induced reactive oxygen species (ROS), causing disruption of DNA, lipids, and protein, mitochondrial depolarization, and apoptosis of skin keratinocytes. Here, we investigated the protective effects of NIA on PM_2.5-induced oxidative stress in human HaCaT keratinocytes. We found that NIA could inhibit the ROS generation induced by PM_2.5, as well block the PM_2.5-induced oxidation of molecules, such as lipids, proteins, and DNA. Furthermore, NIA alleviated PM_2.5-induced accumulation of cellular Ca²⁺, which caused cell membrane depolarization and apoptosis, and reduced the number of apoptotic cells. Collectively, the findings show that NIA can protect keratinocytes from PM_2.5-induced oxidative stress and cell damage.

Air Pollution Alters Caenorhabditis elegans Development and Lifespan: Responses to Traffic-Related Nanoparticulate Matter

Air pollution is a heterogeneous environmental toxicant that impacts humans throughout their life. We introduce Caenorhabditis elegans as a valuable air pollution model with its short lifespan, medium-throughput capabilities, and highly conserved biological pathways that impact healthspan. We exposed developmental and adult life stages of C. elegans to airborne nano-sized particulate matter (nPM) produced by traffic emissions and measured biological and molecular endpoints that changed in response. Acute nPM did not cause lethality in C. elegans, but short-term exposure during larval stage 1 caused delayed development. Gene expression responses to nPM exposure overlapped with responses of mouse and cell culture models of nPM exposure in previous studies. We showed further that the skn-1/Nrf2 antioxidant response has a role in the development and hormetic effects of nPM. This study introduces the worm as a new resource and complementary model for mouse and cultured cell systems to study air pollution toxicity across the lifespan.

Mitochondrial Dysfunctions: A Thread Sewing Together Alzheimer's Disease, Diabetes, and Obesity

Metabolic disorders are severe and chronic impairments of the health of many people and represent a challenge for the society as a whole that has to deal with an ever-increasing number of affected individuals. Among common metabolic disorders are Alzheimer's disease, obesity, and type 2 diabetes. These disorders do not have a univocal genetic cause but rather can result from the interaction of multiple genes, lifestyle, and environmental factors. Mitochondrial alterations have emerged as a feature common to all these disorders, underlining perhaps an impaired coordination between cellular needs and mitochondrial responses that could contribute to their development and/or progression.

Measurement of Oxygen Consumption Rates in Intact Caenorhabditis elegans

Optimal mitochondrial function is critical for healthy cellular activity, particularly in cells that have high energy demands like those in the nervous system and muscle. Consistent with this, mitochondrial dysfunction has been associated with a myriad of neurodegenerative diseases and aging in general. Caenorhabditis elegans have been a powerful model system for elucidating the many intricacies of mitochondrial function. Mitochondrial respiration is a strong indicator of mitochondrial function and recently developed respirometers offer a state-of-the-art platform to measure respiration in cells. In this protocol, we provide a technique to analyze live, intact C. elegans. This protocol spans a period of ~7 days and includes steps for (1) growing and synchronization of C. elegans, (2) preparation of compounds to be injected and hydration of probes, (3) drug loading and cartridge equilibration, (4) preparation of worm assay plate and assay run, and (5) post-experiment data analysis.

Role of Presenilin in Mitochondrial Oxidative Stress and Neurodegeneration in Caenorhabditis elegans

Neurodegenerative diseases like Alzheimer’s disease (AD) are poised to become a global health crisis, and therefore understanding the mechanisms underlying the pathogenesis is critical for the development of therapeutic strategies. Mutations in genes encoding presenilin (PSEN) occur in most familial Alzheimer’s disease but the role of PSEN in AD is not fully understood. In this review, the potential modes of pathogenesis of AD are discussed, focusing on calcium homeostasis and mitochondrial function. Moreover, research using Caenorhabditis elegans to explore the effects of calcium dysregulation due to presenilin mutations on mitochondrial function, oxidative stress and neurodegeneration is explored.