Dysregulation of Human Somatic piRNA Expression in Parkinson's Disease Subtypes and Stages

Piwi interacting RNAs (piRNAs) are small non-coding single-stranded RNA species 20–31 nucleotides in size generated from distinct loci. In germline tissues, piRNAs are amplified via a “ping-pong cycle” to produce secondary piRNAs, which act in transposon silencing. In contrast, the role of somatic-derived piRNAs remains obscure. Here, we investigated the identity and distribution of piRNAs in human somatic tissues to determine their function and potential role in Parkinson’s disease (PD). Human datasets were curated from the Gene Expression Omnibus (GEO) database and a workflow was developed to identify piRNAs, which revealed 902 somatic piRNAs of which 527 were expressed in the brain. These were mainly derived from chromosomes 1, 11, and 19 compared to the germline tissues, which were from 15 and 19. Approximately 20% of somatic piRNAs mapped to transposon 3′ untranslated regions (UTRs), but a large proportion were sensed to the transcript in contrast to germline piRNAs. Gene set enrichment analysis suggested that somatic piRNAs function in neurodegenerative disease. piRNAs undergo dysregulation in different PD subtypes (PD and Parkinson’s disease dementia (PDD)) and stages (premotor and motor). piR-has-92056, piR-hsa-150797, piR-hsa-347751, piR-hsa-1909905, piR-hsa-2476630, and piR-hsa-2834636 from blood small extracellular vesicles were identified as novel biomarkers for PD diagnosis using a sparse partial least square discriminant analysis (sPLS-DA) (accuracy: 92%, AUC = 0.89). This study highlights a role for piRNAs in PD and provides tools for novel biomarker development.

Differentiating Pu-erh raw tea from different geographical origins by 1 H-NMR and U-HPLC/Q-TOF-MS combined with chemometrics

Pu-erh tea is believed to be a beneficial beverage for health due to its many kinds of pharmacological effects. Nevertheless, detailed information related to differences in metabolites of Pu-erh raw tea from different geographical origins remains scarce. In this study, 43 elements were found in water-soluble components of Pu-erh raw tea by highly sensitive ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry (U-HPLC/Q-TOF-MS). The characteristic groups of 29 metabolites from nondestructive proton nuclear magnetic resonance (¹ H-NMR) spectroscopy were assigned. The variables contributed largely to the origin classification, mainly including valine, threonine, chlorogenic acid, quinic acid, epiafzelechin, and gallic acid ester, were screened out by sparse partial least squares discriminant analysis (sPLS-DA) method. This study provided a feasible and rapid technique for distinguishing Pu-erh tea from different areas by ¹ H-NMR combined with sPLS-DA.

Computational Analysis of Neonatal Mouse Ultrasonic Vocalization

Neonatal vocalization is structurally altered in mouse models of autism spectrum disorder (ASD). Our published data showed that pup vocalization, under conditions of maternal separation, contains sequences whose alterations in a genetic mouse model of ASD impair social communication between pups and mothers. We describe details of a method which reveals the statistical structure of call sequences that are functionally critical for optimal maternal care. Entropy analysis determines the degree of non-random call sequencing. A Markov model determines the actual call sequences used by pups. Sparse partial least squares discriminant analysis (sPLS-DA) identifies call sequences that differentiate groups and reveals the degrees of individual variability in call sequences between groups. These three sets of analyses can be used to identify the otherwise hidden call structure that is altered in mouse models of developmental neuropsychiatric disorders, including not only autism but also schizophrenia. © 2018 by John Wiley & Sons, Inc.

Multivariate models from RNA-Seq SNVs yield candidate molecular targets for biomarker discovery: SNV-DA

BACKGROUND

It has recently been shown that significant and accurate single nucleotide variants (SNVs) can be reliably called from RNA-Seq data. These may provide another source of features for multivariate predictive modeling of disease phenotype for the prioritization of candidate biomarkers. The continuous nature of SNV allele fraction features allows the concurrent investigation of several genomic phenomena, including allele specific expression, clonal expansion and/or deletion, and copy number variation.

RESULTS

The proposed software pipeline and package, SNV Discriminant Analysis (SNV-DA), was applied on two RNA-Seq datasets with varying sample sizes sequenced at different depths: a dataset containing primary tumors from twenty patients with different disease outcomes in lung adenocarcinoma and a larger dataset of primary tumors representing two major breast cancer subtypes, estrogen receptor positive and triple negative. Predictive models were generated using the machine learning algorithm, sparse projections to latent structures discriminant analysis. Training sets composed of RNA-Seq SNV features limited to genomic regions of origin (e.g. exonic or intronic) and/or RNA-editing sites were shown to produce models with accurate predictive performances, were discriminant towards true label groupings, and were able to produce SNV rankings significantly different from than univariate tests. Furthermore, the utility of the proposed methodology is supported by its comparable performance to traditional models as well as the enrichment of selected SNVs located in genes previously associated with cancer and genes showing allele-specific expression. As proof of concept, we highlight the discovery of a previously unannotated intergenic locus that is associated with epigenetic regulatory marks in cancer and whose significant allele-specific expression is correlated with ER+ status; hereafter named ER+ associated hotspot (ERPAHS).

CONCLUSION

The use of models from RNA-Seq SNVs to identify and prioritize candidate molecular targets for biomarker discovery is supported by the ability of the proposed method to produce significantly accurate predictive models that are discriminant towards true label groupings. Importantly, the proposed methodology allows investigation of mutations outside of exonic regions and identification of interesting expressed loci not included in traditional gene annotations. An implementation of the proposed methodology is provided that allows the user to specify SNV filtering criteria and cross-validation design during model creation and evaluation.

Multivariate Time Series Analysis of Temperatures in the Archaeological Museum of L'Almoina (Valencia, Spain)

An earlier study carried out in 2010 at the archaeological site of L’Almoina (Valencia, Spain) found marked daily fluctuations of temperature, especially in summer. Such pronounced gradient is due to the design of the museum, which includes a skylight as a ceiling, covering part of the remains in the museum. In this study, it was found that the thermal conditions are not homogeneous and vary at different points of the museum and along the year. According to the European Standard EN10829, it is necessary to define a plan for long-term monitoring, elaboration and study of the microclimatic data, in order to preserve the artifacts. With the aforementioned goal of extending the study and offering a tool to monitor the microclimate, a new statistical methodology is proposed. For this propose, during one year (October 2019–October 2020), a set of 27 data-loggers was installed, aimed at recording the temperature inside the museum. By applying principal component analysis and k-means, three different microclimates were established. In order to characterize the differences among the three zones, two statistical techniques were put forward. Firstly, Sparse Partial Least Squares Discriminant Analysis (sPLS-DA) was applied to a set of 671 variables extracted from the time series. The second approach consisted of using a random forest algorithm, based on the same functions and variables employed by the first methodology. Both approaches allowed the identification of the main variables that best explain the differences between zones. According to the results, it is possible to establish a representative subset of sensors recommended for the long-term monitoring of temperatures at the museum. The statistical approach proposed here is very effective for discriminant time series analysis and for explaining the differences in microclimate when a net of sensors is installed in historical buildings or museums.

Potential Oral Microbial Markers for Differential Diagnosis of Crohn's Disease and Ulcerative Colitis Using Machine Learning Models

Although gut microbiome dysbiosis has been associated with inflammatory bowel disease (IBD), the relationship between the oral microbiota and IBD remains poorly understood. This study aimed to identify unique microbiome patterns in saliva from IBD patients and explore potential oral microbial markers for differentiating Crohn's disease (CD) and ulcerative colitis (UC). A prospective cohort study recruited IBD patients (UC: n = 175, CD: n = 127) and healthy controls (HC: n = 100) to analyze their oral microbiota using 16S rRNA gene sequencing. Machine learning models (sparse partial least squares discriminant analysis (sPLS-DA)) were trained with the sequencing data to classify CD and UC. Taxonomic classification resulted in 4041 phylotypes using Kraken2 and the SILVA reference database. After quality filtering, 398 samples (UC: n = 175, CD: n = 124, HC: n = 99) and 2711 phylotypes were included. Alpha diversity analysis revealed significantly reduced richness in the microbiome of IBD patients compared to healthy controls. The sPLS-DA model achieved high accuracy (mean accuracy: 0.908, and AUC: 0.966) in distinguishing IBD vs. HC, as well as good accuracy (0.846) and AUC (0.923) in differentiating CD vs. UC. These findings highlight distinct oral microbiome patterns in IBD and provide insights into potential diagnostic markers.

SIMOA Diagnostics on Alzheimer's Disease and Frontotemporal Dementia

BACKGROUND

Accurate diagnosis of Alzheimer's disease (AD) and frontotemporal dementia (FTD) represents a health issue due to the absence of disease traits. We assessed the performance of a SIMOA panel in cerebrospinal fluid (CSF) from 43 AD and 33 FTD patients with 60 matching Control subjects in combination with demographic-clinical characteristics.

METHODS

136 subjects (AD: n = 43, FTD: n = 33, Controls: n = 60) participated. Single-molecule array (SIMOA), glial fibrillary acidic protein (GFAP), neurofilament light (NfL), TAU, and ubiquitin carboxy-terminal hydrolase L1 (UCH-L1) in CSF were analyzed with a multiplex neuro 4plex kit. Receiver operating characteristic (ROC) curve analysis compared area under the curve (AUC), while the principal of the sparse partial least squares discriminant analysis (sPLS-DA) was used with the intent to strengthen the identification of confident disease clusters.

RESULTS

CSF exhibited increased levels of all SIMOA biomarkers in AD compared to Controls (AUCs: 0.71, 0.86, 0.92, and 0.94, respectively). Similar patterns were observed in FTD with NfL, TAU, and UCH-L1 (AUCs: 0.85, 0.72, and 0.91). sPLS-DA revealed two components explaining 19% and 9% of dataset variation.

CONCLUSIONS

CSF data provide high diagnostic accuracy among AD, FTD, and Control discrimination. Subgroups of demographic-clinical characteristics and biomarker concentration highlighted the potential of combining different kinds of data for successful and more efficient cohort clustering.

Identifying distinctive brain regions related to consumer choice behaviors on branded foods using activation likelihood estimation and machine learning

Introduction

Brand equity plays a crucial role in a brand's commercial success; however, research on the brain regions associated with brand equity has had mixed results. This study aimed to investigate key brain regions associated with the decision-making of branded and unbranded foods using quantitative neuroimaging meta-analysis and machine learning.

Methods

Quantitative neuroimaging meta-analysis was performed using the activation likelihood method. Activation of the ventral medial prefrontal cortex (VMPFC) overlapped between branded and unbranded foods. The lingual and parahippocampal gyri (PHG) were activated in the case of branded foods, whereas no brain regions were characteristically activated in response to unbranded foods. We proposed a novel predictive method based on the reported foci data, referencing the multi-voxel pattern analysis (MVPA) results. This approach is referred to as the multi-coordinate pattern analysis (MCPA). We conducted the MCPA, adopting the sparse partial least squares discriminant analysis (sPLS-DA) to detect unique brain regions associated with branded and unbranded foods based on coordinate data. The sPLS-DA is an extended PLS method that enables the processing of categorical data as outcome variables.

Results

We found that the lingual gyrus is a distinct brain region in branded foods. Thus, the VMPFC might be a core brain region in food categories in consumer behavior, regardless of whether they are branded foods. Moreover, the connection between the PHG and lingual gyrus might be a unique neural mechanism in branded foods.

Discussion

As this mechanism engages in imaging the feature-self based on emotionally subjective contextual associative memories, brand managers should create future-oriented relevancies between brands and consumers to build valuable brands.

Shared and Unique Disease Pathways in Amyotrophic Lateral Sclerosis and Parkinson's Disease Unveiled in Peripheral Blood Mononuclear Cells

Recent evidence supports an association between amyotrophic lateral sclerosis (ALS) and Parkinson's disease (PD). Indeed, prospective population-based studies demonstrated that about one-third of ALS patients develop parkinsonian (PK) signs, even though different neuronal circuitries are involved. In this context, proteomics represents a valuable tool to identify unique and shared pathological pathways. Here, we used two-dimensional electrophoresis to obtain the proteomic profile of peripheral blood mononuclear cells (PBMCs) from PD and ALS patients including a small cohort of ALS patients with parkinsonian signs (ALS-PK). After the removal of protein spots correlating with confounding factors, we applied a sparse partial least square discriminant analysis followed by recursive feature elimination to obtain two protein classifiers able to discriminate (i) PD and ALS patients (30 spots) and (ii) ALS-PK patients among all ALS subjects (20 spots). Functionally, the glycolysis pathway was significantly overrepresented in the first signature, while extracellular interactions and intracellular signaling were enriched in the second signature. These results represent molecular evidence at the periphery for the classification of ALS-PK as ALS patients that manifest parkinsonian signs, rather than comorbid patients suffering from both ALS and PD. Moreover, we confirmed that low levels of fibrinogen in PBMCs is a characteristic feature of PD, also when compared with another movement disorder. Collectively, we provide evidence that peripheral protein signatures are a tool to differentially investigate neurodegenerative diseases and highlight altered biochemical pathways.