Single-cell RNA Sequencing in Immunology

Cao, Yirui; Qiu, Yue; Tu, Guo-Wei; Yang, Cheng

doi:10.2174/1389202921999201020203249

Cited by 17 publications

(10 citation statements)

References 75 publications

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“…In addition, lymphocyte can be further classified into b cell, CD4+ T helper cell, CD8+ cytotoxic T cell, regulatory T cell, natural killer cells, and so on. Recently, single-cell sequencing technology was invented to provide higher resolution into cell-type-specific patterns [ 59 ]. With the application of single-cell technology combined with bisulfite sequencing, we may enhance our understanding from total WBC level into leukocyte cell-specific level.…”

Section: Discussionmentioning

confidence: 99%

DNA Methylation in LIME1 and SPTBN2 Genes Is Associated with Attention Deficit in Children

Kuo

Huang

et al. 2021

Children

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DNA methylation levels are associated with neurodevelopment. Attention-deficit/hyperactivity disorder (ADHD), characterized by attention deficits, is a common neurodevelopmental disorder. We used methylation microarray and pyrosequencing to detect peripheral blood DNA methylation markers of ADHD. DNA methylation profiling data from the microarray assays identified potential differentially methylated CpG sites between 12 ADHD patients and 9 controls. Five candidate CpG sites (cg00446123, cg20513976, cg07922513, cg17096979, and cg02506324) in four genes (LIME1, KCNAB2, CAPN9, and SPTBN2) were further examined with pyrosequencing. The attention of patients were tested using the Conners’ Continuous Performance Test (CPT). In total, 126 ADHD patients with a mean age of 9.2 years (78.6% males) and 72 healthy control subjects with a mean age of 9.3 years (62.5% males) were recruited. When all participants were categorized by their CPT performance, the DNA methylation levels in LIME1 (cg00446123 and cg20513976) were found to be significantly higher and those in SPTBN2 (cg02506324) were significantly lower in children with worse CPT performance. Therefore, DNA methylation of two CpG sites in LIME1 and one CpG site in SPTBN2 is associated with attention deficits in children. DNA methylation biomarkers may assist in identifying attention deficits of children in clinical settings.

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Section: Discussionmentioning

confidence: 99%

DNA Methylation in LIME1 and SPTBN2 Genes Is Associated with Attention Deficit in Children

Kuo

Huang

et al. 2021

Children

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“…Gene expression will be assessed by single-cell RNA sequencing of PBMC as described previously. 55 T and B cell epitope specificity will be confirmed using virus-derived antigens (peptide/HLA or RBD dextramers, respectively). Plasma levels of inflammatory markers including interferon (IFN)-y, interleukin (IL)-1β, IL-2, IL-4 IL-6, IL-8, IL-10, IL-13, IL-17, transforming growth factor-β, IFN-y-induced protein-10 (IP-10), IL-12p70 and tumour necrosis factor-α will be measured using multiplex Luminex assays, D-dimer, C reactive protein and markers of microbial translocation lipopolysaccharide, beta-d-glucan (ßdG) and soluble CD14 will be evaluated by ELISA.…”

Section: Methods and Analysismentioning

confidence: 99%

CTN 328: immunogenicity outcomes in people living with HIV in Canada following vaccination for COVID-19 (HIV-COV): protocol for an observational cohort study

et al. 2021

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IntroductionMost existing vaccines require higher or additional doses or adjuvants to provide similar protection for people living with HIV (PLWH) compared with HIV-uninfected individuals. Additional research is necessary to inform COVID-19 vaccine use in PLWH.Methods and analysisThis multicentred observational Canadian cohort study will enrol 400 PLWH aged >16 years from Montreal, Ottawa, Toronto and Vancouver. Subpopulations of PLWH of interest will include individuals: (1) >55 years of age; (2) with CD4 counts <350 cells/mm3; (3) with multimorbidity (>2 comorbidities) and (4) ‘stable’ or ‘reference’ PLWH (CD4 T cells >350 cells/mm3, suppressed viral load for >6 months and <1 comorbidity). Data for 1000 HIV-negative controls will be obtained via a parallel cohort study (Stop the Spread Ottawa), using similar time points and methods. Participants receiving >1 COVID-19 vaccine will attend five visits: prevaccination; 1 month following the first vaccine dose; and at 3, 6 and 12 months following the second vaccine dose. The primary end point will be the percentage of PLWH with COVID-19-specific antibodies at 6 months following the second vaccine dose. Humoral and cell-mediated immune responses, and the interplay between T cell phenotypes and inflammatory markers, will be described. Regression techniques will be used to compare COVID-19-specific immune responses to determine whether there are differences between the ‘unstable’ PLWH group (CD4 <350 cells/mm3), the stable PLWH cohort and the HIV-negative controls, adjusting for factors believed to be associated with immune response. Unadjusted analyses will reveal whether there are differences in driving factors associated with group membership.Ethics and disseminationResearch ethics boards at all participating institutions have granted ethics approval for this study. Written informed consent will be obtained from all study participants prior to enrolment. The findings will inform the design of future COVID-19 clinical trials, dosing strategies aimed to improve immune responses and guideline development for PLWH.Trial registration numberNCT04894448.

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“…The typical workflow of scRNA-seq consists of the following major steps: isolation of single cells, messenger RNA (mRNA) capture, reverse transcription and cDNA amplification, library preparation, high throughput sequencing, and bioinformatic data analysis. Different scRNA-seq platforms utilize different technologies to capture and physically separate single cells into individual compartments (reaction units), as well as different chemistry to amplify and create libraries for sequencing ( 13 , 17 , 18 ).…”

Section: Overview Of Scrna-seq Technologymentioning

confidence: 99%

Single Cell RNA Sequencing in Autoimmune Inflammatory Rheumatic Diseases: Current Applications, Challenges and a Step Toward Precision Medicine

et al. 2022

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Single cell RNA sequencing (scRNA-seq) represents a new large scale and high throughput technique allowing analysis of the whole transcriptome at the resolution of an individual cell. It has emerged as an imperative method in life science research, uncovering complex cellular networks and providing indices that will eventually lead to the development of more targeted and personalized therapies. The importance of scRNA-seq has been particularly highlighted through the analysis of complex biological systems, in which cellular heterogeneity is a key aspect, such as the immune system. Autoimmune inflammatory rheumatic diseases represent a group of disorders, associated with a dysregulated immune system and high patient heterogeneity in both pathophysiological and clinical aspects. This complicates the complete understanding of underlying pathological mechanisms, associated with limited therapeutic options available and their long-term inefficiency and even toxicity. There is an unmet need to investigate, in depth, the cellular and molecular mechanisms driving the pathogenesis of rheumatic diseases and drug resistance, identify novel therapeutic targets, as well as make a step forward in using stratified and informed therapeutic decisions, which could now be achieved with the use of single cell approaches. This review summarizes the current use of scRNA-seq in studying different rheumatic diseases, based on recent findings from published in vitro, in vivo, and clinical studies, as well as discusses the potential implementation of scRNA-seq in the development of precision medicine in rheumatology.

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Single-cell RNA Sequencing in Immunology

Cited by 17 publications

References 75 publications

DNA Methylation in LIME1 and SPTBN2 Genes Is Associated with Attention Deficit in Children

DNA Methylation in LIME1 and SPTBN2 Genes Is Associated with Attention Deficit in Children

CTN 328: immunogenicity outcomes in people living with HIV in Canada following vaccination for COVID-19 (HIV-COV): protocol for an observational cohort study

Single Cell RNA Sequencing in Autoimmune Inflammatory Rheumatic Diseases: Current Applications, Challenges and a Step Toward Precision Medicine

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