Differential Expression
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2021 ◽  
Leire Iparraguirre ◽  
Ainhoa Alberro ◽  
Thomas Birkballe Hansen ◽  
Tamara Castillo-Triviño ◽  
Maider Muñoz-Culla ◽  

Abstract Background Extracellular vesicles (EVs) are released by almost all cell types and are implicated in a number of biological and pathological processes including autoimmune diseases such as multiple sclerosis (MS). Differences in the number and cargo of plasma derived EVs have been described in MS. In this work, we attempt to characterise the EV RNA cargo of MS patients with particular attention to a recently discovered non coding RNA type, circular RNAs (circRNAs), which have been shown to play important roles in physiology and disease and hold a great biomarker potential. Methods Plasma was collected from 20 MS patients and 8 healthy controls (HC) and total RNA was isolated from plasma-derived extracellular vesicles isolated by differential centrifugation. Samples were pooled in disease status, sex and age paired groups and RNA-Sequenced with Illumina HiSeq X Ten after rRNA depletion. CircRNAs were detected by both find_circ and CIRI2 and their quantification was based on BSJ-spanning reads. Linear transcripts were quantified by HTSEq. Differential expression analysis was performed using DESeq2. RNA type distribution was analyzed based on biomart classification. MiRNA binding site number and density for circRNAs was calculated based on the TargetScan prediction performed by Circinteractome. CircRNA secondary structure prediction was calculated by their length normalized Gibbs free energy. All the statistical analysis were performed in Rstudio. Results The EV linear and circular transcriptome of MS patients and controls is characterized and compared to the transcriptome previously described in leucocytes. Results reveal differences in the RNA type distribution, showing that circRNAs are enriched in EVs compared to leucocytes. Nevertheless, highly structured circRNAs are preferentially retained in leukocytes. Additionally, differential expression analysis reports significant differences in circRNA and linear RNA expression between MS patients and controls as well as between different MS types. Conclusions The plasma derived EV RNA cargo is not a representation of leukocytes’ cytoplasm but a message that must be studied. Moreover, our results reveal the interest of circRNAs as part of this message highlighting the importance to further understand the RNA regulation in MS.

2021 ◽  
Vol 11 (1) ◽  
Madhuri Amulya Koduri ◽  
Deeksha Prasad ◽  
Shriya Upadhyaya ◽  
Jilu Jaffet ◽  
Swapna S. Shanbhag ◽  

AbstractTo investigate the differential expression of tear cytokine levels among chronic Stevens–Johnson syndrome (SJS) patients to better understand the role of significantly altered cytokines in disease development. Tear samples were collected using Schirmer strips in 24 eyes of chronic SJS, 24 eyes of age and gender-matched controls, and 14 eyes of aqueous deficiency dry eye disease (DED) patients. The cytokine analysis was performed among 18 analytes which include pro-inflammatory, anti-inflammatory factors, and ELR-negative CXC chemokines. String analysis was performed for the significantly altered cytokines to understand their co-expression and role in the disease development. Additionally, a literature review was conducted to identify the signature cytokines present in chronic SJS tears. The differential expression of IL-6 (p ≤ 0.029), CXCL8/IL-8 (p ≤ 0.009), IL-1β (p ≤ 0.041), IL-2 (p ≤ 0.025), IL-10 (p ≤ 0.053), and CXCL-10 (p ≤ 0.044) were observed in chronic SJS patients and healthy controls. Whereas, IL-6 (p ≤ 0.029), CXCL8/IL-8 (p ≤ 0.058), CCL4 (p ≤ 0.056), GM-CSF (p ≤ 0.0001) IL-10 (p ≤ 0.025), and CXCL-10 (p ≤ 0.010), were differentially expressed in SJS as compared to severe DED patients. String analysis of the significantly altered cytokines revealed the involvement of several biological processes including the chronic inflammatory response, nitric oxide synthesis, angiogenesis, and cellular response to drugs. Among all the cytokines evaluated, the expression of CXCL8/IL-8 and CXCL10 levels were consistently reported in the literature. There was a differential expression of tear cytokines in SJS when compared to DED and healthy controls. The differential expression of CXCL8/IL-8 and CXCL10 was in line with existing literature and their role in chronic SJS pathogenesis merits further evaluation.

2021 ◽  
Wenbin Guo ◽  
Max Coulter ◽  
Robbie Waugh ◽  
Runxuan Zhang

High quality transcriptome assembly using short reads from RNA-seq data still heavily relies upon reference-based approaches, of which the primary step is to align RNA-seq reads to a single reference genome of haploid sequence. However, it is increasingly apparent that while different genotypes within a species share core genes, they also contain variable numbers of specific genes that are only present a subset of individuals. Using a common reference may thus lead to a loss of genotype-specific information in the assembled transcript dataset and the generation of erroneous, incomplete or misleading transcriptomics analysis results. With the recent development of pan-genome information in many species, it is important that we understand the limitations of single genotype references for transcriptomics analysis. In this study, we quantitively evaluated the advantages of using genotype-specific reference genomes for transcriptome assembly and analysis using cultivated barley as a model. We mapped barley cultivar Barke RNA-seq reads to the Barke genome and to the cultivar Morex genome (common barley genome reference) to construct a genotype specific Reference Transcript Dataset (sRTD) and a common Reference Transcript Datasets (cRTD), respectively. We compared the two RTDs according to their transcript diversity, transcript sequence and structure similarity and the accuracy they provided for transcript quantification and differential expression analysis. Our evaluation shows that the sRTD has a significantly higher diversity of transcripts and alternative splicing events. Despite using a high-quality reference genome for assembly of the cRTD, we miss ca. 40% transcripts present in the sRTD and cRTD only has ca. 70% true assemblies. We found that the sRTD is more accurate for transcript quantification as well as differential expression and differential alternative splicing analysis. However, gene level quantification and comparative expression analysis are less affected by the source RTD, which indicates that analysing transcriptomic data at the gene level may be a reasonable compromise when a high-quality genotype-specific reference is not available.

2021 ◽  
Ye Hong ◽  
Dani Flinkman ◽  
Tomi Suomi ◽  
Sami Pietilä ◽  
Peter James ◽  

ABSTRACTLarge-scale phospho-proteome profiling using mass spectrometry (MS) provides functional insight that is crucial for disease biology and drug discovery. However, extracting biological understanding from this data is an arduous task requiring multiple analysis platforms that are not adapted for automated high-dimensional data analysis. Here, we introduce an integrated pipeline that combines several R packages to extract high-level biological understanding from largescale phosphoproteomic data by seamless integration with existing databases and knowledge resources. In a single run, PhosPiR provides data clean-up, fast data overview, multiple statistical testing, differential expression analysis, phospho-site annotation and translation across species, multi-level enrichment analyses, proteome-wide kinase activity and substrate mapping and network hub analysis. Data output includes graphical formats such as heatmap, box-, volcano- and circos-plots. This resource is designed to assist proteome-wide data mining of pathophysiological mechanism without a need for programming knowledge.

Affif Zaccaria ◽  
Paola Antinori ◽  
Virginie Licker ◽  
Enikö Kövari ◽  
Johannes A. Lobrinus ◽  

AbstractDopaminergic neurons (DA) of the substantia nigra pars compacta (SNpc) selectively and progressively degenerate in Parkinson’s disease (PD). Until now, molecular analyses of DA in PD have been limited to genomic or transcriptomic approaches, whereas, to the best of our knowledge, no proteomic or combined multiomic study examining the protein profile of these neurons is currently available. In this exploratory study, we used laser capture microdissection to extract regions from DA in 10 human SNpc obtained at autopsy in PD patients and control subjects. Extracted RNA and proteins were identified by RNA sequencing and nanoliquid chromatography–mass spectrometry, respectively, and the differential expression between PD and control group was assessed. Qualitative analyses confirmed that the microdissection protocol preserves the integrity of our samples and offers access to specific molecular pathways. This multiomic analysis highlighted differential expression of 52 genes and 33 proteins, including molecules of interest already known to be dysregulated in PD, such as LRP2, PNMT, CXCR4, MAOA and CBLN1 genes, or the Aldehyde dehydrogenase 1 protein. On the other hand, despite the same samples were used for both analyses, correlation between RNA and protein expression was low, as exemplified by the CST3 gene encoding for the cystatin C protein. This is the first exploratory study analyzing both gene and protein expression of laser-dissected neuronal parts from SNpc in PD. Data are available via ProteomeXchange with identifier PXD024748 and via GEO with identifier GSE 169755.

2021 ◽  
Johanna Karlsson Sundbaum ◽  
Eva Baecklund ◽  
Niclas Eriksson ◽  
Hugo Kohnke ◽  
Matilda Wallenberg ◽  

Aim: To identify novel genetic variants predisposing to elevation of Alanine aminotransferase (ALT) in rheumatoid arthritis (RA) patients after initiation of methotrexate (MTX) treatment. Patients & methods: We performed genome-wide association studies in 198 RA patients starting MTX. Outcomes were maximum level of ALT and ALT >1.5-times the upper level of normal within the first 6 months of treatment. Results: RAVER2 (rs72675408) was significantly associated with maximum level of ALT (p = 4.36 × 10-8). This variant is in linkage disequilibrium with rs72675451, which is associated with differential expression of JAK1 and RAVER2. Conclusion: We found an association between ALT elevation and genetic variants that may regulate the expression of JAK1 and RAVER2. JAK1 encodes a janus kinase involved in the pathogenesis of RA.

2021 ◽  
Giselle C Wong ◽  
Yewon Jung ◽  
Kevin Lee ◽  
Chantelle Fourie ◽  
Kim M. Handley ◽  

Abstract Background: Shank genes are implicated in ~1% of people with autism and mice with Shank3 knock out mutations exhibit autism-like behaviours. Zinc deficiency and gastrointestinal problems can be common among people with autism, and zinc is a key element required for SHANK protein function and gut development. In Shank3B-/- mice, a supplementary zinc diet reverses autism behaviours. We hypothesise that dietary zinc may alter the gut microbiome, potentially affecting the gut-microbiota-brain axis, which may contribute to changes in autism-like behaviours. Methods: Four types of gastrointestinal samples (ileum, caecum, colon, faecal) were collected from wild-type and knock-out Shank3B-/- mice on either control or supplemented-zinc diets. Bacterial 16S rRNA gene and fungal ITS2 genomic region amplicons were sequenced on the Illumina MiSeq platform and RNA on the Illumina HiSeq platform.Results: Cage, genotype and zinc diet each contributed significantly to bacterial community variation (accounting for 12.8%, 3.9% and 2.3% of the variation, respectively). Fungal diversity differed significantly between wild-type and knock-out Shank3B-/- mice on the control zinc diet, and the fungal biota differed among gut locations. RNA-seq analysis of host (mouse) transcripts revealed differential expression of genes involved in host metabolism that may be regulated by the gut microbiota and genes involved in anti-microbial interactions. Limitations: This study used the Shank3B-/- mouse model of autism spectrum disorder. Heterozygous and homozygous Shank3 gene mutations are found in 1% of the ASD population, only homozygous Shank3 mice were utilised in this study. Any translational conclusions should consider these limitations.Conclusions: By utilising the Shank3B-/- knock-out mouse model we were able to examine the influence of – and interactions between – dietary zinc and ASD-linked host genotype. Differential expression of host antimicrobial interaction genes as well as gut microbiota-regulated host metabolism genes among the treatment groups, suggests that the interplay between gut microbes, the gastrointestinal tract and the brain may play a major role towards the observed amelioration of ASD behaviours seen previously with supplemented dietary zinc. These data broaden understanding of the gut microbiome in autism and pave the way towards potential microbial therapeutics for gastrointestinal problems in people with autism.

2021 ◽  
min yang ◽  
Kailu Sun ◽  
Jianmin Chang

Abstract Objective:The aim of this study was to investigate the expression profile of circRNA in Vulvar Lichen Sclerosus, and to identify the underlying core genes of Vulvar Lichen Sclerosus.Methods:rRNA removal was used for sequencing, and mRNA, lncRNA and circRNA differentially expressed between 20 groups of VLS tissues and 20 groups of healthy female vulva skin tissues were screened. Bioinformatics analysis was used to analyze its potential function.Results:A total of 1545 differentially expressed mRNAs were assessed in VLS patients, of which 1541 were upregulated and 1004 were down-regulated; A total of 1453 differentially expressed lncRNAs were assessed, of which 812 were up-regulated and 641 were down-regulated. A total of 79 differentially expressed circRNAs were assessed, of which 54 were upregulated and 25 were down-regulated. The differential expression of CircRNA is closely related to biological processes and molecular functions. The differences in circRNA were mainly related to the "human T-cell leukemia virus 1 infection" signaling pathway and the "axon guidance" signaling pathway.Conclusion:This study identified the profile of abnormal regulation of circRNA in VLS. Biological informatics analysis showed that the dysregulation of circRNAs could be related to the pathogenesis and pathological process of VLS.

2021 ◽  
Vol 12 ◽  
Pengjuan Ma ◽  
Ping Zhang ◽  
Shuxia Chen ◽  
Wen Shi ◽  
Jinguo Ye ◽  

Purpose: We performed single-cell RNA sequencing (scRNA-seq), an unbiased and high-throughput single cell technology, to determine phenotype and function of peripheral immune cells in patients with diabetic macular edema (DME).Methods: Peripheral blood mononuclear cells (PBMCs) were isolated from DME patients and healthy controls (HC). The single-cell samples were loaded on the Chromium platform (10x Genomics) for sequencing. R package Seurat v3 was used for data normalizing, clustering, dimensionality reduction, differential expression analysis, and visualization.Results: We constructed a single-cell RNA atlas comprising 57,650 PBMCs (24,919 HC, 32,731 DME). We divided all immune cells into five major immune cell lineages, including monocytes (MC), T cells (TC), NK cells (NK), B cells (BC), and dendritic cells (DC). Our differential expression gene (DEG) analysis showed that MC was enriched of genes participating in the cytokine pathway and inflammation activation. We further subdivided MC into five subsets: resting CD14++ MC, proinflammatory CD14++ MC, intermediate MC, resting CD16++ MC and pro-inflammatory CD16++ MC. Remarkably, we revealed that the proinflammatory CD14++ monocytes predominated in promoting inflammation, mainly by increasingly production of inflammatory cytokines (TNF, IL1B, and NFKBIA) and chemokines (CCL3, CCL3L1, CCL4L2, CXCL2, and CXCL8). Gene Ontology (GO) and pathway analysis of the DEGs demonstrated that the proinflammatory CD14++ monocytes, especially in DME patients, upregulated inflammatory pathways including tumor necrosis factor-mediated signaling pathway, I-kappaB kinase/NF-kappaB signaling, and toll-like receptor signaling pathway.Conclusion: In this study, we construct the first immune landscape of DME patients with T2D and confirmed innate immune dysregulation in peripheral blood based on an unbiased scRNA-seq approach. And these results demonstrate potential target cell population for anti-inflammation treatments.

2021 ◽  
Vol 12 ◽  
Jinhao Zeng ◽  
Xiao Ma ◽  
Ziyi Zhao ◽  
Yu Chen ◽  
Jundong Wang ◽  

Background: Seeking novel and effective therapies for gastric precancerous lesions (GPL) is crucial to reducing the incidence of gastric cancer. Ginsenoside Rb1 (GRb1) is a major ginsenoside in ginseng and has been proved to possess multiple bioactivities. However, whether GRb1 could protect against GPL and the underlying mechanisms have not been explored.Methods: We evaluated the effects of GRb1 on gastric precancerous lesions in rats on macroscopic, microscopic and ultramicroscopic levels. Then, an antibody array was employed to screen differential expression proteins (DEPs). Validation for the targeting DEP and investigation for the possible mechanism was conducted using immunohistochemistry, qRT-PCR, TUNEL apoptosis assay, immunoprecipitation and immunoblotting.Results: GRb1 was found to reverse intestinal metaplasia and a portion of dysplasia in the MNNG-induced GPL rats. The antibody array assay revealed seven DEPs in GPL rats as compared to control rats (5 DEPs were up-regulated, while two DEPs were down-regulated). Among the DEPs, β-catenin, beta-NGF and FSTL1 were significantly down-regulated after GRb1 administration. Our validation results revealed that enhanced protein expression and nuclear translocation of β-catenin were present in animal GPL samples. In addition, analysis of human gastric specimens demonstrated that β-catenin up-regulation and nuclear translocation were significantly associated with advanced GPL pathology. GRb1 intervention not only decreased protein expression and nuclear translocation of β-catenin, but interfered with β-catenin/TCF4 interaction. Along with this, declined transcriptional and protein expression levels of downstream target genes including c-myc, cyclin D1 and Birc5 were observed in GRb1-treated GPL rats.Conclusion: GRb1 is capable of preventing the occurrence and progression of GPL, which might be contributed by diminishing protein expression and nuclear translocation of β-catenin and interfering with β-catenin/TCF4 interaction.

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