A network approach to diagnostic biomarkers in progressive supranuclear palsy

Potential of Non-Coding RNA as Biomarkers for Progressive Supranuclear Palsy

Objective markers for the neurodegenerative disorder progressive supranuclear palsy (PSP) are needed to provide a timely diagnosis with greater certainty. Non-coding RNA (ncRNA), including microRNA, piwi-interacting RNA, and transfer RNA, are good candidate markers in other neurodegenerative diseases, but have not been investigated in PSP. Therefore, as proof of principle, we sought to identify whether they were dysregulated in matched serum and cerebrospinal fluid (CSF) samples of patients with PSP. Small RNA-seq was undertaken on serum and CSF samples from healthy controls (n = 20) and patients with PSP (n = 31) in two cohorts, with reverse transcription-quantitative PCR (RT-qPCR) to confirm their dysregulation. Using RT-qPCR, we found in serum significant down-regulation in hsa-miR-92a-3p, hsa-miR-626, hsa-piR-31068, and tRNA-ValCAC. In CSF, both hsa-let-7a-5p and hsa-piR-31068 showed significant up-regulation, consistent with their changes observed in the RNA-seq results. Interestingly, we saw no correlation in the expression of hsa-piR-31068 within our matched serum and CSF samples, suggesting there is no common dysregulatory mechanism between the two biofluids. While these changes were in a small cohort of samples, we have provided novel evidence that ncRNA in biofluids could be possible diagnostic biomarkers for PSP and further work will help to expand this potential.

Well-Water Consumption and Risk of Parkinson's Disease: A Meta-Analysis of 15 Observational Studies

INTRODUCTION

The relationship between the risk of Parkinson disease and well-water consumption has been extensively studied, but the results have been contradictory. Therefore, we conducted a meta-analysis of observational studies to systematically assess the relationship between well-water consumption and Parkinson disease risk.

METHODS

We followed the PRISMA checklist in completing the meta-analysis. We searched two electronic databases (PubMed, EBSCO, EMBASE and Cochrane) from establishment to October, 2021, to identify relevant studies linking well-water drinking to Parkinson risk. We used a random-effects model to calculate the overall odds ratio (OR) with 95% confidence interval (CI). To reduce intragroup heterogeneity, we conducted subgroup analyses according to the research design and geographic area.

RESULTS

After careful review, a total of 15 case-control-designed studies included data suitable for our meta-analysis. The total number of cases and total controls that contribute to the combined OR were 2182 and 2456. The combined OR for ever well-water drinkers versus non-drinkers was 1.16 (95% CI: 0.97-1.39, I² = 44.52%). In subgroup analysis by geographic area, a significant association was observed in studies conducted in Asia (OR 1.29, 95% CI: 1.05-1.58, I² = 0.0%, p for heterogeneity = 0.460) but not in studies conducted in America (OR 0.97, 95% CI: 0.76-1.24, I² = 41.2%, p for heterogeneity = 0.164). In subgroup analysis by study design, a borderline significant association emerged in hospital-based case-control studies (OR 1.31, 95% CI: 1.04-1.65, I² = 40.9%, p for heterogeneity = 0.118) but not in population-based case-control studies (OR 0.96, 95% CI: 0.73-1.26, I² = 41.1%, p for heterogeneity = 0.165).

DISCUSSION

Our results indicate that there is no significant correlation between well-water consumption and PD risk.

PTPRC Expression in Blood is Downregulated in Parkinson's and Progressive Supranuclear Palsy Disorders

BACKGROUND

Parkinson's disease (PD) shares pathological and clinical features with progressive supranuclear palsy (PSP) patients making the diagnosis challenging. Distinguishing PD from PSP is crucial given differences in disease course, treatment and clinical management.

OBJECTIVE

Although some progress has been made in the discovery of biomarkers for PD and PSP, there is an urgent need to identify additional biomarkers capable of distinguishing between these diseases.

METHODS

In this study, we tested the phosphatases DUSP8 and PTPRC for their diagnostic potential using quantitative PCR assays, in blood of 138 samples from participants nested in the Parkinson's Disease Biomarkers Program.

RESULTS

Relative abundance of PTPRC mRNA was downregulated in PSP patients compared to PD and healthy controls, whereas there was no significant difference in the expression of DUSP8. Interestingly, PTPRC mRNA correlated with the Movement Disorder Society Unified Parkinson's Disease Rating Scale (MDS-UPDRS) total score and MDS-UPDRS- part III, thus indicating it might be useful as part of a biosignature to stratify patients according to disease severity and progression.

CONCLUSIONS

Collectively, these results suggest that PTPRC expression may be useful for distinguishing PD from PSP patients as part of a biosignature. Evaluation of PTPRC along with additional biomarkers in a larger and well-characterized longitudinal study is warranted.

Increased prefrontal cortex interleukin-2 protein levels and shift in the peripheral T cell population in progressive supranuclear palsy patients

Accumulating evidence suggests neuroinflammation to be an integrated feature of neurodegeneration. Profiling inflammatory mediators across diseases may reveal common and disease-specific signatures. Here, we focused on progressive supranuclear palsy (PSP), a tauopathy presenting motor and cognitive dysfunction. We screened for 21 cytokines and growth factors in the dorsomedial prefrontal cortex of 16 PSP and 16 control brains using different quantitative techniques. We found and validated increased interleukin (IL)-2 protein levels in the PSP group expressed locally by neurons and glia cells. We further investigated central players in neuroinflammatory pathways and found increased mRNA expression of glycogen synthase kinase 3 beta (GSK3B). IL-2 and GSK3B proteins are T and natural killer (NK) cell regulators and have previously been associated with other neurodegenerative diseases such as Alzheimer’s disease, Parkinson’s disease and multiple system atrophy. In addition, we identified a shift in peripheral CD4⁺ and CD8⁺ T cell populations toward increased numbers of memory and reduced numbers of naive T cells. We also observed increased numbers of CD56⁺ NK cells, but not of CD56⁺CD57⁺ or CD57⁺ NK cells. Our findings suggest a role for IL-2 in PSP disease processes and point toward active and possibly dysfunctional peripheral immune responses in these patients.

Evaluation of RNA Blood Biomarkers in the Parkinson's Disease Biomarkers Program

There is a high misdiagnosis rate between Parkinson’s disease (PD) and atypical parkinsonian disorders (APD), such as progressive supranuclear palsy (PSP), the second most common parkinsonian syndrome. In our earlier studies, we identified and replicated RNA blood biomarkers in several independent cohorts, however, replication in a cohort that includes PSP patients has not yet been performed. To this end, we evaluated the diagnostic potential of nine previously identified RNA biomarkers using quantitative PCR assays in 138 blood samples at baseline from PD, PSP and healthy controls (HCs) nested in the PD Biomarkers Program. Linear discriminant analysis showed that COPZ1 and PTPN1 distinguished PD from PSP patients with 62.5% accuracy. Five biomarkers, PTPN1, COPZ1, FAXDC2, SLC14A1s and NAMPT were useful for distinguishing PSP from controls with 69% accuracy. Several biomarkers correlated with clinical features in PD patients. SLC14A1-s correlated with Unified Parkinson’s Disease Rating Scale total and part III scores. In addition, COPZ1, PTPN1 and MLST8, correlated with Montreal Cognitive Assessment (MoCA). Interestingly, COPZ1, EFTUD2 and PTPN1 were downregulated in cognitively impaired (CI) compared to normal subjects. Linear discriminant analysis showed that age, PTPN1, COPZ1, FAXDC2, EFTUD2 and MLST8 distinguished CI from normal subjects with 65.9% accuracy. These results suggest that COPZ1 and PTPN1 are useful for distinguishing PD from PSP patients. In addition, the combination of PTPN1, COPZ1, FAXDC2, EFTUD2 and MLST8 is a useful signature for cognitive impairment. Evaluation of these biomarkers in a larger study will be a key to advancing these biomarkers into the clinic.

Dissecting the Molecular Mechanisms of Neurodegenerative Diseases through Network Biology

Neurodegenerative diseases are rarely caused by a mutation in a single gene but rather influenced by a combination of genetic, epigenetic and environmental factors. Emerging high-throughput technologies such as RNA sequencing have been instrumental in deciphering the molecular landscape of neurodegenerative diseases, however, the interpretation of such large amounts of data remains a challenge. Network biology has become a powerful platform to integrate multiple omics data to comprehensively explore the molecular networks in the context of health and disease. In this review article, we highlight recent advances in network biology approaches with an emphasis in brain-networks that have provided insights into the molecular mechanisms leading to the most prevalent neurodegenerative diseases including Alzheimer’s (AD), Parkinson’s (PD) and Huntington’s diseases (HD). We discuss how integrative approaches using multi-omics data from different tissues have been valuable for identifying biomarkers and therapeutic targets. In addition, we discuss the challenges the field of network medicine faces toward the translation of network-based findings into clinically actionable tools for personalized medicine applications.

A data-driven approach links microglia to pathology and prognosis in amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease that lacks a predictive and broadly applicable biomarker. Continued focus on mutation-specific upstream mechanisms has yet to predict disease progression in the clinic. Utilising cellular pathology common to the majority of ALS patients, we implemented an objective transcriptome-driven approach to develop noninvasive prognostic biomarkers for disease progression. Genes expressed in laser captured motor neurons in direct correlation (Spearman rank correlation, p < 0.01) with counts of neuropathology were developed into co-expression network modules. Screening modules using three gene sets representing rate of disease progression and upstream genetic association with ALS led to the prioritisation of a single module enriched for immune response to motor neuron degeneration. Genes in the network module are important for microglial activation and predict disease progression in genetically heterogeneous ALS cohorts: Expression of three genes in peripheral lymphocytes - LILRA2, ITGB2 and CEBPD – differentiate patients with rapid and slowly progressive disease, suggesting promise as a blood-derived biomarker. TREM2 is a member of the network module and the level of soluble TREM2 protein in cerebrospinal fluid is shown to predict survival when measured in late stage disease (Spearman rank correlation, p = 0.01). Our data-driven systems approach has, for the first time, directly linked microglia to the development of motor neuron pathology. LILRA2, ITGB2 and CEBPD represent peripherally accessible candidate biomarkers and TREM2 provides a broadly applicable therapeutic target for ALS.

Evaluation of RNA Blood Biomarkers in Individuals at Risk of Parkinson's Disease

BACKGROUND

Substantial progress has been made in the discovery of blood biomarkers for Parkinson's disease (PD), a progressive neurodegenerative disease that affects more than 4 million worldwide. Olfactory dysfunction and dopamine deficits usually precede motor symptoms years before the onset of PD. A readily accessible biomarker useful for identifying patients at risk of PD is expected to accelerate clinical trials.

OBJECTIVE

To evaluate previously identified PD blood RNA biomarkers in a cohort of asymptomatic individuals at risk of PD.

METHODS

Here we tested 16 previously identified PD RNA biomarkers using quantitative PCR assays in a total of 269 blood samples at baseline from hyposmic and normosmic participants enrolled in the Parkinson's Associated Risk Syndrome study.

RESULTS

Expression levels of four biomarkers, SOD2, PKM2, ZNF134, and ZNF160 were negatively correlated with the total Unified Parkinson's Disease Rating Scale, thus suggesting these biomarkers may be useful to stratify patients prior to the onset of motor symptoms. Levels of SOD2 were upregulated in hyposmic males compared to females, whereas levels of PKM2 were upregulated in hyposmic males compared to normosmic males and hyposmic females. Further, levels of SOD2 were upregulated in males with abnormal dopamine transporter (DAT) scans compared to females with abnormal DAT scans.

CONCLUSIONS

These results suggest that some of these biomarkers may be useful for stratification of individuals at risk for PD and that there may be sex differences in the expression of some biomarkers. Future studies in larger longitudinal studies will be key to assessing the validity of these findings.

Integrative transcriptomic meta-analysis of Parkinson's disease and depression identifies NAMPT as a potential blood biomarker for de novo Parkinson's disease

Emerging research indicates that depression could be one of the earliest prodromal symptoms or risk factors associated with the pathogenesis of Parkinson’s disease (PD), the second most common neurodegenerative disorder worldwide, but the mechanisms underlying the association between both diseases remains unknown. Understanding the molecular networks linking these diseases could facilitate the discovery of novel diagnostic and therapeutics. Transcriptomic meta-analysis and network analysis of blood microarrays from untreated patients with PD and depression identified genes enriched in pathways related to the immune system, metabolism of lipids, glucose, fatty acids, nicotinamide, lysosome, insulin signaling and type 1 diabetes. Nicotinamide phosphoribosyltransferase (NAMPT), an adipokine that plays a role in lipid and glucose metabolism, was identified as the most significant dysregulated gene. Relative abundance of NAMPT was upregulated in blood of 99 early stage and drug-naïve PD patients compared to 101 healthy controls (HC) nested in the cross-sectional Parkinson’s Progression Markers Initiative (PPMI). Thus, here we demonstrate that shared molecular networks between PD and depression provide an additional source of biologically relevant biomarkers. Evaluation of NAMPT in a larger prospective longitudinal study including samples from other neurodegenerative diseases, and patients at risk of PD is warranted.

Microarray gene and miRNA expression studies: looking for new therapeutic targets for frontotemporal lobar degeneration

Frontotemporal lobar degeneration (FTLD) encompasses a spectrum of neurodegenerative disorders characterized by behavioral, executive and language impairment, with a common overlap with parkinsonism and motor-neuron disease. Despite an increased understanding of its genetic background and molecular pathophysiology, FTLD is still an orphan disorder and there are currently no effective therapies available. In this brief overview we report the results obtained by several high-throughput and bioinformatic studies aimed at discovering impairment in the transcriptional profiles in brain and peripheral tissues from FTLD patients and in animal models. Taken together, all these results provide an interesting but still fragmentary list of genes and miRNAs whose role in FTLD should be thoroughly investigated.

Network-based metaanalysis identifies HNF4A and PTBP1 as longitudinally dynamic biomarkers for Parkinson's disease

Environmental and genetic factors are likely to be involved in the pathogenesis of Parkinson's disease (PD), the second most prevalent neurodegenerative disease among the elderly. Network-based metaanalysis of four independent microarray studies identified the hepatocyte nuclear factor 4 alpha (HNF4A), a transcription factor associated with gluconeogenesis and diabetes, as a central regulatory hub gene up-regulated in blood of PD patients. In parallel, the polypyrimidine tract binding protein 1 (PTBP1), involved in the stabilization and mRNA translation of insulin, was identified as the most down-regulated gene. Quantitative PCR assays revealed that HNF4A and PTBP1 mRNAs were up- and down-regulated, respectively, in blood of 51 PD patients and 45 controls nested in the Diagnostic and Prognostic Biomarkers for Parkinson's Disease. These results were confirmed in blood of 50 PD patients compared with 46 healthy controls nested in the Harvard Biomarker Study. Relative abundance of HNF4A mRNA correlated with the Hoehn and Yahr stage at baseline, suggesting its clinical utility to monitor disease severity. Using both markers, PD patients were classified with 90% sensitivity and 80% specificity. Longitudinal performance analysis demonstrated that relative abundance of HNF4A and PTBP1 mRNAs significantly decreased and increased, respectively, in PD patients during the 3-y follow-up period. The inverse regulation of HNF4A and PTBP1 provides a molecular rationale for the altered insulin signaling observed in PD patients. The longitudinally dynamic biomarkers identified in this study may be useful for monitoring disease-modifying therapies for PD.

A network approach to clinical intervention in neurodegenerative diseases

Network biology has become a powerful tool to dissect the molecular mechanisms triggering neurodegeneration. Recent developments in network biology have led to the discovery of disease-causing genes, diagnostic biomarkers, and therapeutic targets for several neurodegenerative diseases including Alzheimer's, Parkinson's, and Huntington's diseases. Network-based approaches have provided the molecular rationale for the relationship among cancer, diabetes, and neurodegenerative diseases, and have uncovered unexpected links between apparently unrelated diseases. Here, we summarize the recent advances in network biology to untangle the molecular underpinnings giving rise to the most prevalent neurodegenerative diseases. We propose that network analysis provides a feasible and practical tool for identifying biologically meaningful biomarkers and potential therapeutic targets for clinical intervention in neurodegenerative diseases.

Current Challenges Towards the Development of a Blood Test for Parkinson's Disease

Parkinson’ disease (PD) is the second most prevalent neurodegenerative disease worldwide. To date, there is no disease-modifying agent, and current medical treatment only provides symptomatic benefits. Early diagnosis of PD would be useful in clinical practice to identify patients for clinical trials, test potential drugs and neuroprotective agents and track their therapeutic effect. Considerable progress has been made in the discovery and validation of diagnostic biomarkers for PD. In particular, blood-based biomarkers have shown promise in identifying PD patients in samples from independent clinical trials. Evaluation of these biomarkers in de novo patients and individuals at risk for PD remains a top priority. Here, we review the current advances and challenges toward the clinical translation of these biomarkers into a blood-based test for PD.

Network analysis identifies SOD2 mRNA as a potential biomarker for Parkinson's disease

Increasing evidence indicates that Parkinson's disease (PD) and type 2 diabetes (T2DM) share dysregulated molecular networks. We identified 84 genes shared between PD and T2DM from curated disease-gene databases. Nitric oxide biosynthesis, lipid and carbohydrate metabolism, insulin secretion and inflammation were identified as common dysregulated pathways. A network prioritization approach was implemented to rank genes according to their distance to seed genes and their involvement in common biological pathways. Quantitative polymerase chain reaction assays revealed that a highly ranked gene, superoxide dismutase 2 (SOD2), is upregulated in PD patients compared to healthy controls in 192 whole blood samples from two independent clinical trials, the Harvard Biomarker Study (HBS) and the Diagnostic and Prognostic Biomarkers in Parkinson's disease (PROBE). The results from this study reinforce the idea that shared molecular networks between PD and T2DM provides an additional source of biologically meaningful biomarkers. Evaluation of this biomarker in de novo PD patients and in a larger prospective longitudinal study is warranted.

System-based approaches to decode the molecular links in Parkinson's disease and diabetes

A growing body of evidence indicates an increased risk for developing Parkinson's disease (PD) among people with type 2 diabetes (T2DM). The relationship between the etiology and development of both chronic diseases is beginning to be uncovered and recent studies show that PD and T2DM share remarkably similar dysregulated pathways. It has been proposed that a cascade of events including mitochondrial dysfunction, impaired insulin signaling, and metabolic inflammation trigger neurodegeneration in T2DM models. Network-based approaches have elucidated a potential molecular framework linking both diseases. Further, transcriptional signatures that modulate the neurodegenerative phenotype in T2DM have been identified. Here we contextualize the current experimental approaches to dissect the mechanisms underlying the association between PD and T2DM and discuss the existing challenges toward the understanding of the coexistence of these devastating aging diseases.