Biomarkers in Alzheimer's disease progression: a longitudinal cohort study of NPTX2, GRIA1, and GRIA4

Abstract

Early diagnosis and intervention are vital for slowing Alzheimer's disease progression and improving patient quality of life. Mild cognitive impairment, an early stage of Alzheimer's disease, offers a key opportunity for research and intervention. However, current diagnostic methods are typically applied after significant symptoms appear, limiting the effectiveness of early intervention. The data of middle-aged and older individuals collected from the publicly available NCBI datasets GSE5281 and GSE1297 were included in this longitudinal cohort study. The cognitive status changes in participants over time were assessed using standard cognitive assessment tools, such as the Mini-Mental State Examination, along with mild cognitive impairment-specific tools. There was a significant negative correlation between Mini-Mental State Examination scores and the expression levels of neuronal pentraxin 2, glutamate receptor ionotropic AMPA 1 and 4. These results suggest that higher expression levels of these genes are associated with more severe cognitive impairment, highlighting their potential as biomarkers for the early detection of mild cognitive impairment. This study provides new insights into the molecular mechanisms underlying cognitive decline and suggests directions for future research.

INTRODUCTION

Alzheimer's disease (AD) is an escalating global health crisis, characterized by insidious cognitive decline and memory impairment. It represents the most prevalent form of dementia among older people, afflicting millions of people worldwide. As populations age, the prevalence of AD is poised to surge, presenting a formidable challenge to public health. Currently, there is no cure for AD, with available treatments offering only symptomatic relief, rather than halting or reversing disease progression.^[1] Thus, early detection and intervention have emerged as imperative strategies to improve outcomes for at-risk patients.

Mild cognitive impairment (MCI) represents a critical stage in the trajectory of AD, offering a crucial window for intervention before irreversible neurodegeneration ensues. Individuals with MCI manifest subtle cognitive deficits that surpass age-related norms but do not significantly impair daily functioning. Consequently, identifying MCI and elucidating its progression mechanisms are of paramount importance for devising targeted interventions.^[2-4]

Recent research has revealed the potential significance of neuronal pentraxin 2 (NPTX2) in the context of AD. NPTX2, a synaptic protein intricately involved in synaptic plasticity and maintenance, has emerged as a focal point. Predominantly expressed in the brain, NPTX2 plays a pivotal role in the formation and stabilization of excitatory synapses. Previous studies have demonstrated alterations in NPTX2 expression in the brains of individuals with AD, indicating its potential role in disease pathogenesis.^[5,6]

The involvement of NPTX2 in synaptic function and its observed dysregulation in AD underscore its promise as a candidate worthy of further investigation. Understanding the nuanced changes in NPTX2 expression and its correlation with cognitive decline holds immense potential for revealing the intricate cascade of events precipitating AD onset and progression. Moreover, NPTX2 may serve as a putative biomarker for the early diagnosis and monitoring of AD, providing a means to identify individuals at risk before the emergence of overt symptoms.^[7-9]

METHODS

Ethical statement

In this study, the GSE5281 and GSE1297 datasets from the NCBI Gene Expression Omnibus (GEO) were used. These datasets are publicly available and have already undergone the necessary ethical reviews and approvals at the time of their creation. According to GEO's policies and practices, the creation and sharing of these datasets comply with relevant ethical standards and privacy protection requirements. Therefore, no additional ethics committee approval is needed when using these publicly available datasets for research purposes.

Specifically, the institutions that generated the GSE5281 and GSE1297 datasets obtained ethics committee approval and ensured informed consent was obtained from the participants. Researchers using these datasets adhere strictly to data sharing agreements and privacy protection regulations, without involving any additional human subjects or collection of participant information.

Thus, no additional ethics committee approval is required for this study using these publicly available datasets. The original approval information for the datasets can be found in the relevant records within the GEO database.

Participants

Middle-aged and older AD and healthy control individuals whose date were collected from the publicly available NCBI datasets GSE5281 and GSE1297 were included in this longitudinal cohort study. The individuals without overt cognitive impairment, determined through comprehensive baseline health screenings and cognitive assessments were included. The individuals with cognitive deficits or neurological conditions were exluded.^[10,11]

Data sources

• GSE5281: Used for calculating MCI indices based on gene expression changes across different brain regions.
• GSE1297: Utilized to compute Mini-Mental State Examination (MMSE) scores based on gene expression variations across different stages of AD.

Cognitive assessments

Cognitive function was assessed at regular intervals using a battery of standardized neuropsychological tests, including the MMSE and other MCI-specific instruments. These assessments encompass domains, such as memory, executive function, attention, and cognitive flexibility. Trained personnel blinded to the participants' NPTX2, glutamate ionotropic receptor AMPA type subunit 1 (GRIA1), and GRIA4 status administered the assessments to ensure reliability and validity.^[12,13]

Statistical analysis

Statistical analyses were performed using R language in R Studio (version 4.1) and Python in PyCharm (version 3.10). R Studio was utilized for data analysis and statistical computations, while PyCharm served as the environment for data processing and analysis.

Correlation analysis evaluates the strength and direction of linear relationships between two or more variables. In this study, we employed Pearson correlation coefficients to quantify the relationship between MMSE scores and the expression levels of NPTX2, GRIA1, and GRIA4 genes collected from GSE5281 and GSE1297. Pearson correlation coefficients range from −1 to +1, where −1 indicates a perfect negative correlation, +1 indicates a perfect positive correlation, and 0 indicates no correlation.

We utilized statistical software (e.g., the cor.test function in R or the scipy.stats.pearsonr function in Python) to compute correlation coefficients and their associated statistical significance. A significance level of P < 0.05 was typically used to denote statistical significance, indicating that the calculated correlation coefficients were significant.

RESULTS

Downregulation of NPTX2, GRIA1, and GRIA4 expression levels in AD states

In our study, we thoroughly examined the expression levels of NPTX2, GRIA1, and GRIA4 in the context of AD, utilizing data from the GSE1297 dataset. Our analyses consistently revealed a statistically significant downregulation of the expression levels of these genes in individuals affected by AD compared with healthy controls, as depicted in Figure 1.

The observed downregulation of NPTX2, GRIA1, and GRIA4 expression levels underscores their potential involvement in the pathogenesis of AD. NPTX2 is known for its critical role in synaptic plasticity and excitatory synapse function, while GRIA1 and GRIA4 are key AMPA-type glutamate receptors that are essential for synaptic transmission and plasticity. The aberrant expression of these genes suggests a disruption in synaptic function, a hallmark of AD pathology.^[14]

This downregulation may reflect various pathological processes occurring in AD. For instance, decreased NPTX2 expression could contribute to synaptic loss and neuronal damage, as synaptic dysfunction is a prominent feature of AD progression. Similarly, a reduction in GRIA1 and GRIA4 expression may impair glutamate neurotransmission and synaptic stability, further exacerbating cognitive decline in AD patients.^[15]

Regional downregulation of NPTX2, GRIA1, and GRIA4 expression across various brain regions in AD

Our investigation comprehensively analyzed the expression levels of NPTX2, GRIA1, and GRIA4 across various brain regions in individuals with AD. Notably, we observed a consistent downregulation of the expression levels of these genes across multiple brain regions, particularly in regions associated with MCI.^[16] Our findings underscore the relationship between decreased gene expression in MCI brain regions and neurodegenerative diseases.

This revision integrates your specific findings from Figure 2, emphasizing the decline in gene expression levels in MCI brain regions and its implications for neurodegenerative disorders.^[17]

Notably, our data revealed a particularly pronounced decrease in NPTX2 expression levels in the middle temporal gyrus (MTG) region. This specific regional downregulation of NPTX2 may hold significant implications for AD pathogenesis. The MTG region is known to play a crucial role in memory encoding and retrieval processes, functions that are severely affected in AD. Therefore, the observed downregulation of NPTX2 in the MTG suggests a targeted disruption of synaptic function in a brain region critical for memory function.^[14-16]

Several factors may contribute to the heightened sensitivity of the MTG to alterations in NPTX2 expression. First, the MTG is densely populated with synapses and is highly susceptible to synaptic dysfunction in neurodegenerative diseases such as AD.^[18] Second, NPTX2 is known to modulate synaptic plasticity and neurotransmission, processes that are essential for memory formation and consolidation, highlighting the relevance of its dysregulation in a memory-associated brain region like the MTG.^[19]

Correlation between MMSE scores and disease progression: implications of NPTX2 and GRIA1 in AD pathogenesis

Our investigation delved into the relationship between MMSE scores and disease progression in AD patients, shedding light on the potential roles of NPTX2 and GRIA1 in AD pathogenesis.

We observed a significant negative correlation between MMSE scores and disease progression, highlighting the decline in cognitive function as AD progressed. Importantly, our analyses revealed that MMSE scores were correlated with the expression levels of NPTX2, GRIA1, and GRIA4. Specifically, lower MMSE scores were associated with decreased expression levels of these genes, as depicted in Figure 3. These findings suggest a potential link between cognitive decline and the dysregulation of synaptic function mediated by NPTX2 and GRIA1, emphasizing their role in AD pathogenesis.

Increased correlation between NPTX2, GRIA1, and GRIA4 expression levels and AD progression

Our investigation uncovered a notable phenomenon: the correlation among the expression levels of neuronal pentraxin 2 (NPTX2), GRIA1, and GRIA4 intensified as AD progressed. This finding suggests a potential synergistic interaction between these genes in the context of AD pathogenesis.^[20]

As AD progressed, we observed a pronounced increase in the correlation coefficient between the expression levels of NPTX2, GRIA1, and GRIA4. This heightened correlation implies a synchronized dysregulation of synaptic function mediated by these genes during AD progression, as depicted in Figure 4. Such synchronized dysregulation may exacerbate synaptic dysfunction, a hallmark of AD, contributing to the cognitive decline observed in the later stages of the disease.

Moreover, our analysis utilizing the STRING network revealed significant associations between NPTX2, GRIA1, and GRIA4 and genes involved in neurotransmitter transmission. This observation underscores the pivotal roles of these genes in synaptic function and highlights their potential involvement in the dysregulation of neurotransmitter pathways implicated in AD pathogenesis.^[21,22]

The heightened correlation among NPTX2, GRIA1, and GRIA4 expression levels underscores their interconnectedness and collective impact on synaptic function in AD progression. These findings offer valuable insights into the molecular mechanisms underlying disease progression and suggest potential targets for therapeutic interventions aimed at preserving synaptic function and ameliorating cognitive decline in patients with AD (Figure 5).

DISCUSSION

Our study offers novel insights into the relationships between NPTX2, GRIA1, and GRIA4 expression levels and AD progression, shedding light on potential mechanisms underlying AD pathogenesis.

The ramifications of this research transcend mere academic inquiry, holding profound implications for clinical practice and public health policy. By identifying early biomarkers such as NPTX2, clinicians can intervene preemptively, potentially forestalling disease progression and mitigating the burden of AD on individuals, families, and society at large.^[23,24]

The observed decrease in correlation among NPTX2, GRIA1, and GRIA4 expression levels as AD advances suggests a coordinated dysregulation of synaptic function mediated by these genes. Given the critical role of synaptic dysfunction in AD pathophysiology, these finding implicate NPTX2, GRIA1, and GRIA4 in the cascade of events leading to cognitive decline in AD.

Moreover, our analysis using the STRING network revealed significant associations between NPTX2, GRIA1, and GRIA4 and genes involved in neurotransmitter transmission. This finding underscores the importance of synaptic pathways in AD pathogenesis and suggests a potential mechanism through which these genes contribute to synaptic dysfunction in this disease.

The implications of these findings are profound for our understanding of AD pathogenesis. NPTX2 and GRIA1 are integral components of synaptic function and involved in synaptic plasticity and neurotransmission. The observed correlation between their expression levels and MMSE scores suggested that synaptic dysfunction, mediated by dysregulated expression of these genes, may contribute to the cognitive decline observed in AD patients.^[25,26]

Furthermore, these results underscore the potential utility of NPTX2 and GRIA1 as biomarkers for disease progression and cognitive decline in AD patients. Monitoring their expression levels alongside cognitive assessments such as the MMSE could provide valuable insights into disease progression and aid in the development of targeted therapeutic interventions aimed at preserving synaptic function and ameliorating cognitive decline in AD patients.

LIMITATIONS

Lack of clinical trials: One of the primary limitations of this study is the absence of clinical trials. The findings are solely based on publicly available datasets, specifically GSE5281 and GSE1297, from the NCBI website. Although these datasets provide valuable insights, they cannot replace the robustness and reliability of data obtained through controlled clinical trials. Clinical trials would allow for a more comprehensive understanding of the gene expression changes over time and in response to specific interventions or treatments in patients with AD.

Data source limitations: The data used in this study were derived from publicly available datasets, which may have inherent biases or limitations. The datasets were collected by different researchers, potentially leading to variability in sample collection, processing, and analysis methods. These differences could impact the comparability and generalizability of the results.

Population specificity: The datasets analyzed focused on middle-aged and elderly individuals without overt cognitive impairment but excluded those with cognitive deficits or neurological conditions. Although this approach helps isolate the gene expression changes associated with early AD, it may not fully capture the entire spectrum of the disease, particularly in more advanced stages or in diverse populations.

Cross-sectional nature: The datasets used are cross-sectional, providing a snapshot of gene expression at a single point in time. Longitudinal data would be more informative in understanding the progression of AD and the dynamic changes in NPTX2, GRIA1, and GRIA4 expression levels over time.

Confounding factors: There may be confounding factors that were not accounted for in the datasets, such as lifestyle, environmental exposures, or other health conditions. These factors could influence gene expression and potentially confound the associations observed in this study.

CONCLUSIONS

Our study unveiled significant findings regarding the role of NPTX2, GRIA1, and GRIA4 in AD progression. First, we observed a consistent downregulation of NPTX2, GRIA1, and GRIA4 expression levels in individuals with AD, indicating their potential as biomarkers for disease diagnosis and progression monitoring. Second, our investigation revealed a regional downregulation of these genes across various brain regions, with particularly notable decreases observed in the MTG region for NPTX2. This regional specificity may offer insights into the differential vulnerability of brain regions to AD pathology. Third, correlation analysis revealed a significant association between lower expression levels of NPTX2, GRIA1, and GRIA4 and more severe cognitive impairment, as measured by MMSE scores, highlighting their critical relevance to disease severity and cognitive decline. This inference was consistently supported by analyses conducted across two independent datasets, underscoring the robustness of these associations and reinforcing their significance in the context of AD.

In summary, the collective evidence suggests the significant involvement of NPTX2, GRIA1, and GRIA4 in AD pathogenesis, particularly in synaptic dysfunction and cognitive decline. These findings underscore the potential utility of these genes as diagnostic markers and therapeutic targets for AD. Further exploration of their underlying mechanisms and validation in larger cohorts are warranted to fully elucidate their roles in AD progression and to develop effective interventions for this devastating neurodegenerative disease. This study facilitated our understanding of the relationship between MMSE scores and the expression levels of NPTX2, GRIA1, and GRIA4 genes, revealing potential associations between cognitive decline and dysregulated synaptic function.

Author contributions

Methodology, data analysis, writing - original draft, writing - review & editing, and data curation: KJ. Data analysis: ZL. Investigation and resources: XP. Software, validation, and visualization: CZ. Formal analysis, supervision, and project administration: RL. Supervision, funding acquisition, and writing - review & editing: YW. Supervision, funding acquisition, and writing - review & editing: CP. All authors approved the final version of the paper.

Conflicts of interest

The authors declare that they have no conflicts of interest.

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