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

Impact of potential biomarkers, SNRPE, COX7C, and RPS27, on idiopathic Parkinson's disease

BACKGROUND

Parkinson's disease (PD) is a progressive neuro-degenerative disorder most common in older adults which is associated with impairments in movement and other body functions. Most PD cases are classified as idiopathic PD (IPD), meaning that the etiology remains unidentified.

OBJECTIVE

To identify key genes and molecular mechanisms to identify biomarkers applicable to IPD.

METHODS

We applied a bioinformatics approach using a gene expression in whole blood dataset to pinpoint differentially expressed genes (DEGs) and pathways involved in IPD. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of DEGs were subsequently performed. A protein-protein interaction (PPI) network was then constructed to select hub genes that may influence IPD. We further investigated the levels of differentially methylated regions (DMRs) and differentially expressed microRNA (DEMs) of whole blood of patients with IPD to validate hub genes. Additionally, we examined the hub gene expression patterns in the substantia nigra (STN) using single-cell RNA sequencing datasets.

RESULTS

In total, we identified 124 DEGs in the blood samples of patients with IPD, with GO and KEGG analyses highlighting their significant enrichment. Analysis of PPI networks revealed three major clusters and hub genes: small nuclear ribonucleoprotein polypeptide E (SNRPE), cytochrome C oxidase subunit 7 C (COX7C), and ribosomal protein S27 (RPS27). DMRs and DEMs analyses revealed hub gene regulation via epigenetic and RNA interference. In particular, SNRPE and RPS27 showed identically regulated gene expression in the STN.

CONCLUSION

This study suggests that SNRPE, COX7C, and RPS27 in whole-blood samples derived from patients may be useful biomarkers for IPD.

Hydroxy Fatty Acid Synthesis-Related mRNA as the Biomarker for Detecting Mislabeling of Honey Entomological Origin

The authentication of the entomological origin of honey is a widespread concern, necessitating the prompt establishment of an effective approach for distinguishing between Apis cerana cerana honey (ACH) and Apis mellifera ligustica honey (AMH). Hydroxy fatty acids (HFAs) found in honey are bee-derived components synthesized by the mandibular glands of worker bees. We previously discovered significant variations in the hydroxy fatty acid composition between ACH and AMH, suggesting their potential as indicators for identifying the authenticity of the entomological origin of honey. Herein, we identified differentially expressed genes associated with HFA synthesis by conducting transcriptome sequencing of the mandibular glands of AC and AM honeybees. Subsequently, we proposed a method for the relative quantitative analysis of bee-derived RNA components using real-time fluorescence quantitative polymerase chain reaction, which was supplemented by multivariate statistical analysis to further discern differences in HFA synthesis-related mRNA between ACH and AMH. The results showed that the mRNAs of FAXDC2 (fatty acid hydroxylase domain-containing protein 2) and FAS (fatty acid synthase) may serve as indicators to discern the entomological origin of honey. This study presents two novel biomarkers for detecting mislabeling of the entomological origin in ACH and AMH based on variations in bee-derived components.

Transcriptomic imputation of genetic risk variants uncovers novel whole-blood biomarkers of Parkinson's disease

Blood-based gene expression signatures could potentially be used as biomarkers for PD. However, it is unclear whether genetically-regulated transcriptomic signatures can provide novel gene candidates for use as PD biomarkers. We leveraged on the Genotype-Tissue Expression (GTEx) database to impute whole-blood transcriptomic expression using summary statistics of three large-scale PD GWAS. A random forest classifier was used with the consensus whole-blood imputed gene signature (IGS) to discriminate between cases and controls. Outcome measures included Area under the Curve (AUC) of Receiver Operating Characteristic (ROC) Curve. We demonstrated that the IGS (n = 37 genes) is conserved across PD GWAS studies and brain tissues. IGS discriminated between cases and controls in an independent whole-blood RNA-sequencing study (1176 PD, 254 prodromal, and 860 healthy controls) with mean AUC and accuracy of 64.8% and 69.4% for PD cohort, and 78.8% and 74% for prodromal cohort. PATL2 was the top-performing imputed gene in both PD and prodromal PD cohorts, whose classifier performance varied with biological sex (higher performance for males and females in the PD and prodromal PD, respectively). Single-cell RNA-sequencing studies (scRNA-seq) of healthy humans and PD patients found PATL2 to be enriched in terminal effector CD8+ and cytotoxic CD4+ cells, whose proportions are both increased in PD patients. We demonstrated the utility of GWAS transcriptomic imputation in identifying novel whole-blood transcriptomic signatures which could be leveraged upon for PD biomarker derivation. We identified PATL2 as a potential biomarker in both clinical and prodromic PD.

Early-stage idiopathic Parkinson's disease is associated with reduced circular RNA expression

Neurodegeneration in Parkinson's disease (PD) precedes diagnosis by years. Early neurodegeneration may be reflected in RNA levels and measurable as a biomarker. Here, we present the largest quantification of whole blood linear and circular RNAs (circRNA) in early-stage idiopathic PD, using RNA sequencing data from two cohorts (PPMI = 259 PD, 161 Controls; ICICLE-PD = 48 PD, 48 Controls). We identified a replicable increase in TMEM252 and LMNB1 gene expression in PD. We identified novel differences in the expression of circRNAs from ESYT2, BMS1P1 and CCDC9, and replicated trends of previously reported circRNAs. Overall, using circRNA as a diagnostic biomarker in PD did not show any clear improvement over linear RNA, minimising its potential clinical utility. More interestingly, we observed a general reduction in circRNA expression in both PD cohorts, accompanied by an increase in RNASEL expression. This imbalance implicates the activation of an innate antiviral immune response and suggests a previously unknown aspect of circRNA regulation in PD.

Molecular Gene Expression Testing to Identify Alzheimer's Disease with High Accuracy from Fingerstick Blood

Background

There is no molecular test for Alzheimer's disease (AD) using self-collected samples, nor is there a definitive molecular test for AD. We demonstrate an accurate and potentially definitive TempO-Seq® gene expression test for AD using fingerstick blood spotted and dried on filter paper, a sample that can be collected in any doctor's office or can be self-collected.

Objective

Demonstrate the feasibility of developing an accurate test for the classification of persons with AD from a minimally invasive sample of fingerstick blood spotted on filter paper which can be obtained in any doctor's office or self-collected to address health disparities.

Methods

Fingerstick blood samples from patients clinically diagnosed with AD, Parkinson's disease (PD), or asymptomatic controls were spotted onto filter paper in the doctor's office, dried, and shipped to BioSpyder for testing. Three independent patient cohorts were used for training/retraining and testing/retesting AD and PD classification algorithms.

Results

After initially identifying a 770 gene classification signature, a minimum set of 68 genes was identified providing classification test areas under the ROC curve of 0.9 for classifying patients as having AD, and 0.94 for classifying patients as having PD.

Conclusions

These data demonstrate the potential to develop a screening and/or definitive, minimally invasive, molecular diagnostic test for AD and PD using dried fingerstick blood spot samples that are collected in a doctor's office or clinic, or self-collected, and thus, can address health disparities. Whether the test can classify patients with AD earlier then possible with cognitive testing remains to be determined.

Role of Non-Receptor-Type Tyrosine Phosphatases in Brain-Related Diseases

The non-receptor protein tyrosine phosphatase is a class of enzymes that catalyze the dephosphorylation of phosphotyrosines in protein molecules. They are involved in cellular signaling by regulating the phosphorylation status of a variety of receptors and signaling molecules within the cell, thereby influencing cellular physiological and pathological processes. In this article, we detail multiple non-receptor tyrosine phosphatase and non-receptor tyrosine phosphatase genes involved in the pathological process of brain disease. These include PTPN6, PTPN11, and PTPN13, which are involved in glioma signaling; PTPN1, PTPN5, and PTPN13, which are involved in the pathogenesis of Alzheimer's disease Tau protein lesions, PTPN23, which may be involved in the pathogenesis of Epilepsy and PTPN1, which is involved in the pathogenesis of Parkinson's disease. The role of mitochondrial tyrosine phosphatase in brain diseases was also discussed. Non-receptor tyrosine phosphatases have great potential for targeted therapies in brain diseases and are highly promising research areas.

Molecular Mechanisms for Changing Brain Connectivity in Mice and Humans

The goal of this study was to examine commonalities in the molecular basis of learning in mice and humans. In previous work we have demonstrated that the anterior cingulate cortex (ACC) and hippocampus (HC) are involved in learning a two-choice visuospatial discrimination task. Here, we began by looking for candidate genes upregulated in mouse ACC and HC with learning. We then determined which of these were also upregulated in mouse blood. Finally, we used RT-PCR to compare candidate gene expression in mouse blood with that from humans following one of two forms of learning: a working memory task (network training) or meditation (a generalized training shown to change many networks). Two genes were upregulated in mice following learning: caspase recruitment domain-containing protein 6 (Card6) and inosine monophosphate dehydrogenase 2 (Impdh2). The Impdh2 gene product catalyzes the first committed step of guanine nucleotide synthesis and is tightly linked to cell proliferation. The Card6 gene product positively modulates signal transduction. In humans, Card6 was significantly upregulated, and Impdh2 trended toward upregulation with training. These genes have been shown to regulate pathways that influence nuclear factor kappa B (NF-κB), a factor previously found to be related to enhanced synaptic function and learning.

Exploring the association of addiction-related genetic factors with non-suicidal self-injury in adolescents

Background

Non-suicidal self-injury (NSSI) is self-injurious behavior without suicidal intent commonly seen in the adolescent population and poses a serious threat to the life safety of adolescents. Related researches suggest a possible correlation between addiction and the occurrence of NSSI. This study aimed to explore the correlation between addiction and NSSI from a molecular biological perspective by analyzing the differential expression of addiction-related genes in NSSI patients.

Methods

(1) The association between addiction and non-suicidal self-injury in a Chinese adolescent population was verified with the help of questionnaires on substance and non-substance addictions and non-suicidal self-injury among 1,329 adolescents in China, (2) Screening for key genes associated with addiction by bioinformatics analysis, and (3) RT-qPCR experiment was performed to validate key genes and Receiver Operating Characteristic curves were plotted for target genes.

Results

(1) Substance and non-substance addictions were all significantly correlated with non-suicidal self-injury, (2) Four target genes: SERPINA3, SLC14A1, RPS6 and RPS3A were screened by bioinformatics technique, and (3) Relative quantitative analysis by RT-qPCR revealed that the expression levels of SLC14A1 (p < 0.01), RPS6 (p < 0.05) and RPS3A (p < 0.01) were significantly higher in NSSI patients than in healthy controls.

Conclusion

(1) The significant association between addiction and NSSI exists in the Chinese adolescent population and (2) Addiction-related genes SLC14A1, RPS6, and RPS3A are differentially expressed in adolescents with NSSI. The genes have the potential to become biological markers for the diagnosis of NSSI.

Joint Modeling Study Identifies Blood-Based Transcripts Link to Cognitive Decline in Parkinson's Disease

BACKGROUND

Cognitive decline in Parkinson's disease (PD) is prevalent, insidious, and burdensome during the progression of the disease.

OBJECTIVES

We aimed to find transcriptome-wide biomarkers in blood to predict cognitive decline and identify patients at high risk with cognitive impairment in PD.

METHODS

We carried out joint modeling analysis to characterize transcriptome-wide longitudinal gene expression and its association with the progression of mild cognitive impairment (MCI) in PD patients. The average time-dependent area under the curves (AUCs) were used for evaluating the accuracy of the significant joint models. A cognitive survival score (CogSs) derived from joint model was leveraged to predict the occurrence of MCI. All predicting models were built in a discovery cohort with 272 patients and replicated in an independent cohort with 177 patients.

RESULTS

We identified five longitudinal varied expression of transcripts that were significantly associated with MCI progression in patients with PD. The most significant transcript IGLC1 joint model accurately predicted the progression of MCI in PD patients in the discovery and replication cohorts (average time-dependent AUCs >0.82). The CogSs derived from the optimal IGLC1 joint model had a high accuracy at early study stage in both cohorts (AUC ≥0.91).

CONCLUSIONS

Our transcriptome-wide joint modeling analysis uncovered five blood-based transcripts related to cognitive decline in PD. The joint models will serve as a useful resource for clinicians and researchers to screen PD patients with high risk of development of cognitive impairment and pave the path for Parkinson's personalized medicine. © 2022 International Parkinson and Movement Disorder Society.

Systemic RNA Interference Defective (SID) genes modulate dopaminergic neurodegeneration in C. elegans

The fine-tuning of gene expression is critical for all cellular processes; aberrations in this activity can lead to pathology, and conversely, resilience. As their role in coordinating organismal responses to both internal and external factors have increasingly come into focus, small non-coding RNAs have emerged as an essential component to disease etiology. Using Systemic RNA interference Defective (SID) mutants of the nematode Caenorhabditis elegans, deficient in gene silencing, we examined the potential consequences of dysfunctional epigenomic regulation in the context of Parkinson's disease (PD). Specifically, the loss of either the sid-1 or sid-3 genes, which encode a dsRNA transporter and an endocytic regulatory non-receptor tyrosine kinase, respectively, conferred neuroprotection to dopaminergic (DA) neurons in an established transgenic C. elegans strain wherein overexpression of human α-synuclein (α-syn) from a chromosomally integrated multicopy transgene causes neurodegeneration. We further show that knockout of a specific microRNA, mir-2, attenuates α-syn neurotoxicity; suggesting that the native targets of mir-2-dependent gene silencing represent putative neuroprotective modulators. In support of this, we demonstrated that RNAi knockdown of multiple mir-2 targets enhanced α-syn-induced DA neurodegeneration. Moreover, we demonstrate that mir-2 overexpression originating in the intestine can induce neurodegeneration of DA neurons, an effect that was reversed by pharmacological inhibition of SID-3 activity. Interestingly, sid-1 mutants retained mir-2-induced enhancement of neurodegeneration. Transcriptomic analysis of α-syn animals with and without a sid-1 mutation revealed 27 differentially expressed genes with human orthologs related to a variety of diseases, including PD. Among these was pgp-8, encoding a P-glycoprotein-related ABC transporter. Notably, sid-1; pgp-8 double mutants abolished the neurodegeneration resulting from intestinal mir-2 overexpression. This research positions known regulators of small RNA-dependent gene silencing within a framework that facilitates mechanistic evaluation of epigenetic responses to exogenous and endogenous factors influencing DA neurodegeneration, revealing a path toward new targets for therapeutic intervention of PD.

Parkinson's Disease Subtyping Using Clinical Features and Biomarkers: Literature Review and Preliminary Study of Subtype Clustering

The second most common progressive neurodegenerative disorder, Parkinson’s disease (PD), is characterized by a broad spectrum of symptoms that are associated with its progression. Several studies have attempted to classify PD according to its clinical manifestations and establish objective biomarkers for early diagnosis and for predicting the prognosis of the disease. Recent comprehensive research on the classification of PD using clinical phenotypes has included factors such as dominance, severity, and prognosis of motor and non-motor symptoms and biomarkers. Additionally, neuroimaging studies have attempted to reveal the pathological substrate for motor symptoms. Genetic and transcriptomic studies have contributed to our understanding of the underlying molecular pathogenic mechanisms and provided a basis for classifying PD. Moreover, an understanding of the heterogeneity of clinical manifestations in PD is required for a personalized medicine approach. Herein, we discuss the possible subtypes of PD based on clinical features, neuroimaging, and biomarkers for developing personalized medicine for PD. In addition, we conduct a preliminary clustering using gait features for subtyping PD. We believe that subtyping may facilitate the development of therapeutic strategies for PD.

A review of migraine genetics: gathering genomic and transcriptomic factors

Migraine is a common and complex neurologic disorder that affects approximately 15-18% of the general population. Although the cause of migraine is unknown, some genetic studies have focused on unravelling rare and common variants underlying the pathophysiological mechanisms of this disorder. This review covers the advances in the last decade on migraine genetics, throughout the history of genetic methodologies used, including recent application of next-generation sequencing techniques. A thorough review of the literature interweaves the genomic and transcriptomic factors that will allow a better understanding of the mechanisms underlying migraine pathophysiology, concluding with the clinical utility landscape of genetic information and future consideration to creating a new frontier toward advancing the field of personalized medicine.

Parkinson's Disease: Available Clinical and Promising Omics Tests for Diagnostics, Disease Risk Assessment, and Pharmacotherapy Personalization

Parkinson's disease is the second most frequent neurodegenerative disease, representing a significant medical and socio-economic problem. Modern medicine still has no answer to the question of why Parkinson's disease develops and whether it is possible to develop an effective system of prevention. Therefore, active work is currently underway to find ways to assess the risks of the disease, as well as a means to extend the life of patients and improve its quality. Modern studies aim to create a method of assessing the risk of occurrence of Parkinson's disease (PD), to search for the specific ways of correction of biochemical disorders occurring in the prodromal stage of Parkinson's disease, and to personalize approaches to antiparkinsonian pharmacotherapy. In this review, we summarized all available clinically approved tests and techniques for PD diagnostics. Then, we reviewed major improvements and recent advancements in genomics, transcriptomics, and proteomics studies and application of metabolomics in PD research, and discussed the major metabolomics findings for diagnostics and therapy of the disease.

Osmotic regulation of UT-B urea transporters in the RT4 human urothelial cell line

Facilitative UT-B urea transporters play important physiological roles in numerous tissues, including the urino-genital tract. Previous studies have shown that urothelial UT-B transporters are crucial to bladder function in a variety of mammalian species. Using the RT4 bladder urothelial cell line, this study investigated the potential osmotic regulation of human UT-B transporters. Initial end-point PCR experiments confirmed expression of both UT-B1 and UT-B2 transcripts in RT4 cells. Western blotting analysis revealed glycosylated UT-B protein to be highly abundant and immunolocalization experiments showed it was predominantly located on the plasma membrane. Further PCR experiments suggested that a 48 hr, NaCl-induced raise in external osmolality increased expression of UT-B transcripts. Importantly, these NaCl-induced changes also significantly increased UT-B protein abundance (p < .01, n = 7, ANOVA), whereas mannitol-induced changes in external osmolality had no effect (NS, n = 4, ANOVA). Finally, similar increases in both UT-B RNA expression and protein abundance were observed with urea-induced changes to external osmolality (p < .05, n = 4, ANOVA). In conclusion, these findings strongly suggest that increases in external osmolality, via either NaCl or urea, can regulate human urothelial UT-B transporters.

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.

Biomarkers of Parkinson's disease: 20 years later

Despite intensive effort, biomarker research for the detection of prodromal stage, diagnosis and progression of Parkinson's disease (PD) falls short of expectations. This article reviews the attempts in the last 20 years to find a biomarker, addresses challenges along the biomarker search and suggests the steps that should be taken to overcome these challenges. Although several biomarkers are currently available, none of them is specific enough for diagnosis, prediction of future PD or disease progression. The main reason for the failure finding a strong biomarker seems to be drastic heterogeneity of PD, which exhibits itself in all domains; from the clinic to pathophysiology or genetics. The diversity in patient selection, assessment methods or outcomes in biomarker studies also limit the interpretation and generalizability of the data. In search of a reliable biomarker, consideration of novel approaches encompassing individual demographic, clinical, genetic, epigenetic and environmental differences, employment of strategies enabling marker combinations, designing multicenter studies with compatible assessment methods, integration of data from preclinical domains and utilization of novel technology-based assessments are necessary.