scholarly journals The landscape of SNCA transcripts across synucleinopathies: New insights from long reads sequencing analysis

2019 ◽  
Author(s):  
Elizabeth Tseng ◽  
William J Rowell ◽  
Omolara-Chinue Glenn ◽  
Ting Hon ◽  
Julio Barrera ◽  
...  
Keyword(s):  
Disease Risk ◽  
Lewy Bodies ◽  
Alpha Synuclein ◽  
Sequencing Analysis ◽  
Snca Gene ◽  
Long Reads ◽  
Long Read ◽  
Alternatively Spliced ◽  
Gene Transcripts ◽  
And Control

AbstractDysregulation of alpha-synuclein expression has been implicated in the pathogenesis of synucleinopathies, in particular Parkinson’s Disease (PD) and Dementia with Lewy bodies (DLB). Previous studies have shown that the alternatively spliced isoforms of the SNCA gene are differentially expressed in different parts of the brain for PD and DLB patients. Similarly, SNCA isoforms with skipped exons can have a functional impact on the protein domains. The large intronic region of the SNCA gene was also shown to harbor structural variants that affect transcriptional levels. Here we apply the first study of using long read sequencing with targeted capture of both the gDNA and cDNA of the SNCA gene in brain tissues of PD, DLB, and control samples using the PacBio Sequel system. The targeted full-length cDNA (Iso-Seq) data confirmed complex usage of known alternative start sites and variable 3’ UTR lengths, as well as novel 5’ starts and 3’ ends not previously described. The targeted gDNA data allowed phasing of up to 81% of the ~114kb SNCA region, with the longest phased block excedding 54 kb. We demonstrate that long gDNA and cDNA reads have the potential to reveal long-range information not previously accessible using traditional sequencing methods. This approach has a potential impact in studying disease risk genes such as SNCA, providing new insights into the genetic etiologies, including perturbations to the landscape the gene transcripts, of human complex diseases such as synucleinopathies.

Epigenetic regulation of SNCA gene expression in Parkinson’s disease

2020 ◽  
pp. 96-98
Author(s):  
А.К. Емельянов ◽  
А.О. Лавринова ◽  
Н.В. Мельникова ◽  
А.А. Дмитриев ◽  
И.В. Милюхина ◽  
...  
Keyword(s):  
Gene Expression ◽  
Peripheral Blood ◽  
Blood Cells ◽  
Cpg Island ◽  
Alpha Synuclein ◽  
Peripheral Blood Cells ◽  
Snca Gene ◽  
Intron 1 ◽  
And Control ◽  
First Time

В настоящем исследовании проведена оценка уровня мРНК и белка генов SNCA, DNMT1, а также степени метилирования интрона 1 гена SNCA в CD45+ клетках периферической крови пациентов со спорадической болезнью Паркинсона (БП) и индивидуумов контрольной группы. Впервые было выявлено снижение концентрации белка DNMT1 в CD45+ клетках периферической крови пациентов с БП по сравнению с группой контроля. Обнаружено увеличение уровня мРНК гена DNMT1 у пациентов с БП по сравнению с контролем. Не выявлено статистически значимых различий при сравнении степени метилирования интрона 1 гена SNCA в CD45+ клетках периферической крови пациентов с БП и контроля. В группе контроля выявлена обратная корреляция степени метилирования отдельных CpG островков с концентрацией белка альфа-синуклеина и уровнем мРНК гена SNCA. Проведенное исследование позволяет предположить участие гена DNMT1 в патогенезе БП и отсутствие ассоциации степени метилирования интрона 1 гена SNCA с БП. The aim of this study was to assess the level of mRNA and protein of the SNCA, DNMT1 genes, as well as intron 1 methylation of the SNCA gene in CD45 + peripheral blood cells of patients with sporadic PD and control individuals. For the first time, a decrease in the concentration of DNMT1 protein in CD45 + peripheral blood cells from PD patients compare to controls was revealed. An increase in DNMT1 gene expression in PD patients compare to controls was found. No differences in intron 1 methylation of the SNCA gene in CD45 + peripheral blood cells was found between PD patients and controls. An inverse correlations between methylation level of 21, 22 CpG island in intron1 of SNCA gene and mRNA SNCA gene and alpha-synuclein protein level were found. The study suggests the involvement of DNMT1 in the pathogenesis of PD and the lack of association of PD with intron 1 methylation of the SNCA gene.

scholarly journals Similar neuronal imprint and absence of cross–seeded partner fibrils in α–synuclein aggregates from MSA and Parkinson′s disease brains

2021 ◽  
Author(s):  
Florent Laferriere ◽  
Stéphane Claverol ◽  
Erwan Bezard ◽  
Francesca De Giorgi ◽  
François Ichas
Keyword(s):  
Lewy Bodies ◽  
Building Blocks ◽  
Alpha Synuclein ◽  
Synaptic Proteins ◽  
Cytoplasmic Inclusions ◽  
Cellular Origin ◽  
Post Mortem Brain ◽  
Pathophysiological Role ◽  
And Control ◽  
Partner Proteins

Aggregated alpha–synuclein (α–syn) is a principal constituent of Lewy bodies (LBs) and glial cytoplasmic inclusions (GCIs) observed respectively inside neurons in Parkinson′s disease (PD) and oligodendrocytes in multiple system atrophy (MSA). Yet, the cellular origin, the pathophysiological role, and the mechanism of formation of these inclusions bodies (IBs) remain to be elucidated. It has recently been proposed that α–syn IBs eventually cause the demise of the host cell by virtue of the cumulative sequestration of partner proteins and organelles. In particular, the hypothesis of a local cross–seeding of other fibrillization–prone proteins like tau or TDP–43 has also been put forward. We submitted sarkosyl–insoluble extracts of post–mortem brain tissue from PD, MSA and control subjects to a comparative proteomic analysis to address these points. Our studies indicate that: i) α–syn is by far the most enriched protein in PD and MSA extracts compared to controls; ii) PD and MSA extracts share a striking overlap of their sarkosyl–insoluble proteomes, consisting of a vast majority of mitochondrial and neuronal synaptic proteins, and (iii) other fibrillization–prone protein candidates possibly cross–seeded by α–syn are neither found in PD nor MSA extracts. Thus, our results (i) support the idea that pre–assembled building blocks originating in neurons serve to the formation of GCIs in MSA, (ii) show no sign of amyloid cross-seeding in either synucleinopathy, and (iii) point to the sequestration of mitochondria and of neuronal synaptic components in both LBs and GCIs.

scholarly journals The Caribbean-Hispanic Alzheimer’s Brain Transcriptome Reveals Ancestry-Specific Disease Mechanisms

2020 ◽  
Author(s):  
Daniel Felsky ◽  
Sanjeev Sariya ◽  
Ismael Santa-Maria ◽  
Leon French ◽  
Julie A. Schneider ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Disease Risk ◽  
Expression Patterns ◽  
Sequencing Analysis ◽  
Specific Expression ◽  
Total N ◽  
Brain Transcriptome ◽  
The Caribbean ◽  
And Control

AbstractEthnicity impacts Alzheimer’s disease risk, especially among Caribbean-Hispanics. We report the first RNA-sequencing analysis of brain tissue from 45 Alzheimer’s disease and control Caribbean-Hispanics. Data were compared with two independent samples of non-Hispanic Caucasians (total n=729). By identifying and characterizing those genes with ancestry- and region-specific expression patterns in Alzheimer’s disease, we reveal molecular insights that may help explain epidemiological disparities in this understudied aging population.

scholarly journals Expression Levels of an Alpha-Synuclein Transcript in Blood May Distinguish between Early Dementia with Lewy Bodies and Parkinson’s Disease

2021 ◽  
Vol 22 (2) ◽  
pp. 725
Author(s):  
Laura Marsal-García ◽  
Aintzane Urbizu ◽  
Laura Arnaldo ◽  
Jaume Campdelacreu ◽  
Dolores Vilas ◽  
...  
Keyword(s):  
Dementia With Lewy Bodies ◽  
Disease Onset ◽  
Temporal Cortex ◽  
Lewy Bodies ◽  
Alpha Synuclein ◽  
Early Dementia ◽  
Specific Increase ◽  
Alpha Synuclein Aggregation ◽  
And Control ◽  
The Brain

Lewy body diseases (LBD) including dementia with Lewy bodies (DLB) and Parkinson disease (PD) are characterized by alpha-synuclein pathology. DLB is difficult to diagnose and peripheral biomarkers are urgently needed. Therefore, we analyzed the expression of five alpha-synuclein gene (SNCA) transcripts, SNCAtv1, SNCAtv2, SNCAtv3, SNCA126, and SNCA112, in 45 LBD and control temporal cortex samples and in the blood of 72 DLB, 59 PD, and 54 control subjects. The results revealed overexpression of SNCAtv1 and SNCA112 in DLB, and SNCAtv2 in PD temporal cortices. In DLB blood, diminution of all SNCA transcripts was observed. SNCAtv1 and SNCAtv2 were diminished in PD with disease onset before 70 years. SNCAtv3, driven by its own promoter, showed opposite expression in early DLB and PD, suggesting that its amount may be an early, DLB specific biomarker. Correlation between blood transcript levels and disease duration was positive in DLB and negative in PD, possibly reflecting differences in brain alpha-synuclein aggregation rates associated with differences in disease courses. In conclusion, SNCA transcripts showed a disease-specific increase in the brain and were diminished in blood of LBD patients. SNCAtv3 expression was decreased in early DLB and increased in early PD and could be a biomarker for early DLB diagnosis.

scholarly journals Metagenomic Analysis of the Fecal Archaeome in Suckling Piglets Following Perinatal Tulathromycin Metaphylaxis

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1825
Author(s):  
Mohamed Zeineldin ◽  
Ameer Megahed ◽  
Benjamin Blair ◽  
Brian Aldridge ◽  
James Lowe
Keyword(s):  
Sequencing Analysis ◽  
Metagenomic Sequencing ◽  
Post Intervention ◽  
Gastrointestinal Microbiome ◽  
Health And Wellbeing ◽  
Suckling Piglets ◽  
And Function ◽  
Changes Over Time ◽  
And Control ◽  
The Impact

The gastrointestinal microbiome plays an important role in swine health and wellbeing, but the gut archaeome structure and function in swine remain largely unexplored. To date, no metagenomics-based analysis has been done to assess the impact of an early life antimicrobials intervention on the gut archaeome. The aim of this study was to investigate the effects of perinatal tulathromycin (TUL) administration on the fecal archaeome composition and diversity in suckling piglets using metagenomic sequencing analysis. Sixteen litters were administered one of two treatments (TUL; 2.5 mg/kg IM and control (CONT); saline 1cc IM) soon after birth. Deep fecal swabs were collected from all piglets on days 0 (prior to treatment), 5, and 20 post intervention. Each piglet’s fecal archaeome was composed of rich and diverse communities that showed significant changes over time during the suckling period. At the phylum level, 98.24% of the fecal archaeome across all samples belonged to Euryarchaeota. At the genus level, the predominant archaeal genera across all samples were Methanobrevibacter (43.31%), Methanosarcina (10.84%), Methanococcus (6.51%), and Methanocorpusculum (6.01%). The composition and diversity of the fecal archaeome between the TUL and CONT groups at the same time points were statistically insignificant. Our findings indicate that perinatal TUL metaphylaxis seems to have a minimal effect on the gut archaeome composition and diversity in sucking piglets. This study improves our current understanding of the fecal archaeome structure in sucking piglets and provides a rationale for future studies to decipher its role in and impact on host robustness during this critical phase of production.

scholarly journals Ultra-accurate microbial amplicon sequencing with synthetic long reads

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Benjamin J. Callahan ◽  
Dmitry Grinevich ◽  
Siddhartha Thakur ◽  
Michael A. Balamotis ◽  
Tuval Ben Yehezkel
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Amplicon Sequencing ◽  
Species Level ◽  
Full Length ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Strain Identification ◽  
Long Reads ◽  
Long Read

Abstract Background Out of the many pathogenic bacterial species that are known, only a fraction are readily identifiable directly from a complex microbial community using standard next generation DNA sequencing. Long-read sequencing offers the potential to identify a wider range of species and to differentiate between strains within a species, but attaining sufficient accuracy in complex metagenomes remains a challenge. Methods Here, we describe and analytically validate LoopSeq, a commercially available synthetic long-read (SLR) sequencing technology that generates highly accurate long reads from standard short reads. Results LoopSeq reads are sufficiently long and accurate to identify microbial genes and species directly from complex samples. LoopSeq perfectly recovered the full diversity of 16S rRNA genes from known strains in a synthetic microbial community. Full-length LoopSeq reads had a per-base error rate of 0.005%, which exceeds the accuracy reported for other long-read sequencing technologies. 18S-ITS and genomic sequencing of fungal and bacterial isolates confirmed that LoopSeq sequencing maintains that accuracy for reads up to 6 kb in length. LoopSeq full-length 16S rRNA reads could accurately classify organisms down to the species level in rinsate from retail meat samples, and could differentiate strains within species identified by the CDC as potential foodborne pathogens. Conclusions The order-of-magnitude improvement in length and accuracy over standard Illumina amplicon sequencing achieved with LoopSeq enables accurate species-level and strain identification from complex- to low-biomass microbiome samples. The ability to generate accurate and long microbiome sequencing reads using standard short read sequencers will accelerate the building of quality microbial sequence databases and removes a significant hurdle on the path to precision microbial genomics.

scholarly journals The Catecholaldehyde Hypothesis for the Pathogenesis of Catecholaminergic Neurodegeneration: What We Know and What We Do Not Know

2021 ◽  
Vol 22 (11) ◽  
pp. 5999
Author(s):  
David S. Goldstein
Keyword(s):  
Lewy Bodies ◽  
Alpha Synuclein ◽  
Future Research ◽  
Catecholamine Metabolism ◽  
Secondary Effects ◽  
Drug Induced ◽  
Neuronal Homeostasis ◽  
Mitochondrial Functions ◽  
Environmental Agents ◽  
Spontaneous Oxidation

3,4-Dihydroxyphenylacetaldehyde (DOPAL) is the focus of the catecholaldehyde hypothesis for the pathogenesis of Parkinson’s disease and other Lewy body diseases. The catecholaldehyde is produced via oxidative deamination catalyzed by monoamine oxidase (MAO) acting on cytoplasmic dopamine. DOPAL is autotoxic, in that it can harm the same cells in which it is produced. Normally, DOPAL is detoxified by aldehyde dehydrogenase (ALDH)-mediated conversion to 3,4-dihydroxyphenylacetic acid (DOPAC), which rapidly exits the neurons. Genetic, environmental, or drug-induced manipulations of ALDH that build up DOPAL promote catecholaminergic neurodegeneration. A concept derived from the catecholaldehyde hypothesis imputes deleterious interactions between DOPAL and the protein alpha-synuclein (αS), a major component of Lewy bodies. DOPAL potently oligomerizes αS, and αS oligomers impede vesicular and mitochondrial functions, shifting the fate of cytoplasmic dopamine toward the MAO-catalyzed formation of DOPAL—destabilizing vicious cycles. Direct and indirect effects of DOPAL and of DOPAL-induced misfolded proteins could “freeze” intraneuronal reactions, plasticity of which is required for neuronal homeostasis. The extent to which DOPAL toxicity is mediated by interactions with αS, and vice versa, is poorly understood. Because of numerous secondary effects such as augmented spontaneous oxidation of dopamine by MAO inhibition, there has been insufficient testing of the catecholaldehyde hypothesis in animal models. The clinical pathophysiological significance of genetics, emotional stress, environmental agents, and interactions with numerous proteins relevant to the catecholaldehyde hypothesis are matters for future research. The imposing complexity of intraneuronal catecholamine metabolism seems to require a computational modeling approach to elucidate clinical pathogenetic mechanisms and devise pathophysiology-based, individualized treatments.

scholarly journals Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Seth Commichaux ◽  
Kiran Javkar ◽  
Padmini Ramachandran ◽  
Niranjan Nagarajan ◽  
Denis Bertrand ◽  
...  
Keyword(s):  
Public Health ◽  
Public Health Response ◽  
High Quality ◽  
Short Read ◽  
Short Reads ◽  
The Core ◽  
Long Reads ◽  
Health Response ◽  
Long Read ◽  
Core Genes

Abstract Background Whole genome sequencing of cultured pathogens is the state of the art public health response for the bioinformatic source tracking of illness outbreaks. Quasimetagenomics can substantially reduce the amount of culturing needed before a high quality genome can be recovered. Highly accurate short read data is analyzed for single nucleotide polymorphisms and multi-locus sequence types to differentiate strains but cannot span many genomic repeats, resulting in highly fragmented assemblies. Long reads can span repeats, resulting in much more contiguous assemblies, but have lower accuracy than short reads. Results We evaluated the accuracy of Listeria monocytogenes assemblies from enrichments (quasimetagenomes) of naturally-contaminated ice cream using long read (Oxford Nanopore) and short read (Illumina) sequencing data. Accuracy of ten assembly approaches, over a range of sequencing depths, was evaluated by comparing sequence similarity of genes in assemblies to a complete reference genome. Long read assemblies reconstructed a circularized genome as well as a 71 kbp plasmid after 24 h of enrichment; however, high error rates prevented high fidelity gene assembly, even at 150X depth of coverage. Short read assemblies accurately reconstructed the core genes after 28 h of enrichment but produced highly fragmented genomes. Hybrid approaches demonstrated promising results but had biases based upon the initial assembly strategy. Short read assemblies scaffolded with long reads accurately assembled the core genes after just 24 h of enrichment, but were highly fragmented. Long read assemblies polished with short reads reconstructed a circularized genome and plasmid and assembled all the genes after 24 h enrichment but with less fidelity for the core genes than the short read assemblies. Conclusion The integration of long and short read sequencing of quasimetagenomes expedited the reconstruction of a high quality pathogen genome compared to either platform alone. A new and more complete level of information about genome structure, gene order and mobile elements can be added to the public health response by incorporating long read analyses with the standard short read WGS outbreak response.

scholarly journals Investigation of TAGAP gene polymorphism (rs1738074) in Turkish pediatric celiac patients

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Melek Pehlivan ◽  
Tülay K. Ayna ◽  
Maşallah Baran ◽  
Mustafa Soyöz ◽  
Aslı Ö. Koçyiğit ◽  
...  
Keyword(s):  
Pediatric Patients ◽  
Disease Risk ◽  
Polymerase Chain Reaction Method ◽  
Control Group ◽  
Healthy Children ◽  
Single Nucleotide ◽  
Significant Difference ◽  
Allele Specific ◽  
And Control

Abstract Objectives There are several hypotheses on the effects of the rs1738074 T/C single nucleotide polymorphism in the TAGAP gene; however, there has been no study on Turkish pediatric patients. We aimed to investigate the association of celiac disease (CD) and type 1 diabetes mellitus (T1DM) comorbidity with the polymorphism in the TAGAP gene of Turkish pediatric patients. Methods Totally, 127 pediatric CD patients and 100 healthy children were included. We determined the polymorphism by the allele-specific polymerase chain reaction method. We used IBM SPSS Statistics version 25.0 and Arlequin 3.5.2 for the statistical analyses. The authors have no conflict of interest. Results It was determined that 72% (n=154) of only CD patients had C allele, whereas 28% (n=60) had T allele. Of the patients with celiac and T1DM, 42.5% (n=17) and 57.5% (n=23) had T and C alleles, respectively. Of the individuals in control group, 67% (n=134) had C allele, whereas 33% (n=66) had T allele. Conclusions There was no significant difference in the genotype and allele frequencies between the patient and control groups (p>0.05). There was no significant association between the disease risk and the polymorphism in our study group.

scholarly journals The TOMM40 ‘523’ polymorphism in disease risk and age of symptom onset in two independent cohorts of Parkinson’s disease

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Megan C. Bakeberg ◽  
Madison E. Hoes ◽  
Anastazja M. Gorecki ◽  
Frances Theunissen ◽  
Abigail L. Pfaff ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Symptom Onset ◽  
Disease Risk ◽  
Age Of Onset ◽  
Sequencing Analysis ◽  
Age Related ◽  
Australian Cohort ◽  
Progression Markers ◽  
Age Related Cognitive Decline

AbstractAbnormal mitochondrial function is a key process in the pathogenesis of Parkinson’s disease (PD). The central pore-forming protein TOM40 of the mitochondria is encoded by the translocase of outer mitochondrial membrane 40 homologue gene (TOMM40). The highly variant ‘523’ poly-T repeat is associated with age-related cognitive decline and age of onset in Alzheimer’s disease, but whether it plays a role in modifying the risk or clinical course of PD it yet to be elucidated. The TOMM40 ‘523’ allele length was determined in 634 people with PD and 422 healthy controls from an Australian cohort and the Parkinson’s Progression Markers Initiative (PPMI) cohort, using polymerase chain reaction or whole genome sequencing analysis. Genotype and allele frequencies of TOMM40 ‘523’ and APOE ε did not differ significantly between the cohorts. Analyses revealed TOMM40 ‘523’ allele groups were not associated with disease risk, while considering APOE ε genotype. Regression analyses revealed the TOMM40 S/S genotype was associated with a significantly later age of symptom onset in the PPMI PD cohort, but not after correction for covariates, or in the Australian cohort. Whilst variation in the TOMM40 ‘523’ polymorphism was not associated with PD risk, the possibility that it may be a modifying factor for age of symptom onset warrants further investigation in other PD populations.

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