| 1. |
- Mold, Jeff E., et al.
(författare)
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Clonally heritable gene expression imparts a layer of diversity within cell types
- 2024
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Ingår i: Cell systems. - : Elsevier BV. - 2405-4720. ; 15:2, s. 149-
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Tidskriftsartikel (refereegranskat)abstract
- Cell types can be classified according to shared patterns of transcription. Non-genetic variability among individual cells of the same type has been ascribed to stochastic transcriptional bursting and transient cell states. Using high-coverage single-cell RNA profiling, we asked whether long-term, heritable differences in gene expression can impart diversity within cells of the same type. Studying clonal human lymphocytes and mouse brain cells, we uncovered a vast diversity of heritable gene expression patterns among different clones of cells of the same type in vivo. We combined chromatin accessibility and RNA profiling on different lymphocyte clones to reveal thousands of regulatory regions exhibiting interclonal variation, which could be directly linked to interclonal variation in gene expression. Our findings identify a source of cellular diversity, which may have important implications for how cellular populations are shaped by selective processes in development, aging, and disease. A record of this paper's transparent peer review process is included in the supplemental information.
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| 2. |
- Engblom, Camilla, et al.
(författare)
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Spatial transcriptomics of B cell and T cell receptors reveals lymphocyte clonal dynamics
- 2023
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 382:6675, s. 8486-
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Tidskriftsartikel (refereegranskat)abstract
- The spatial distribution of lymphocyte clones within tissues is critical to their development, selection, and expansion. We have developed spatial transcriptomics of variable, diversity, and joining (VDJ) sequences (Spatial VDJ), a method that maps B cell and T cell receptor sequences in human tissue sections. Spatial VDJ captures lymphocyte clones that match canonical B and T cell distributions and amplifies clonal sequences confirmed by orthogonal methods. We found spatial congruency between paired receptor chains, developed a computational framework to predict receptor pairs, and linked the expansion of distinct B cell clones to different tumor-associated gene expression programs. Spatial VDJ delineates B cell clonal diversity and lineage trajectories within their anatomical niche. Thus, Spatial VDJ captures lymphocyte spatial clonal architecture across tissues, providing a platform to harness clonal sequences for therapy.
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| 3. |
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| 4. |
- Eriksson Ström, Jonas, et al.
(författare)
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Chronic obstructive pulmonary disease is associated with epigenome-wide differential methylation in BAL lung cells
- 2022
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Ingår i: American Journal of Respiratory Cell and Molecular Biology. - : American Thoracic Society. - 1044-1549 .- 1535-4989. ; 66:6, s. 638-647
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Tidskriftsartikel (refereegranskat)abstract
- DNA methylation patterns in chronic pulmonary obstructive disease (COPD) might offer new insights into disease pathogenesis. To assess methylation profiles in the main COPD target organ, we performed an epigenome-wide association study on BAL cells. Bronchoscopies were performed in 18 subjects with COPD and 15 control subjects (ex- and current smokers). DNA methylation was measured using the Illumina MethylationEPIC BeadChip Kit, covering more than 850,000 CpGs. Differentially methylated positions (DMPs) were examined for 1) enrichment in pathways and functional gene relationships using the Kyoto Encyclopedia of Genes and Genomes and Gene Ontology, 2) accelerated aging using Horvath's epigenetic clock, 3) correlation with gene expression, and 4) colocalization with genetic variation. We found 1,155 Bonferroni-significant (P < 6.74 × 10-8) DMPs associated with COPD, many with large effect sizes. Functional analysis identified biologically plausible pathways and gene relationships, including enrichment for transcription factor activity. Strong correlation was found between DNA methylation and chronological age but not between COPD and accelerated aging. For 79 unique DMPs, DNA methylation correlated significantly with gene expression in BAL cells. Thirty-nine percent of DMPs were colocalized with COPD-associated SNPs. To the best of our knowledge, this is the first epigenome-wide association study of COPD on BAL cells, and our analyses revealed many differential methylation sites. Integration with mRNA data showed a strong functional readout for relevant genes, identifying sites where DNA methylation might directly affect expression. Almost half of DMPs were colocated with SNPs identified in previous genome-wide association studies of COPD, suggesting joint genetic and epigenetic pathways related to disease.
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| 5. |
- Hagemann-Jensen, Michael
(författare)
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Breathe (in the air) : pulmonary immunology in multiple sclerosis
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Multiple Sclerosis (MS) is a demyelinating disease of the central nervous system, with etiology still unknown. MS is thought to arise from a complex interplay between genetic and environmental factors. One of the most well established environmental risk factor is smoking, which confers a striking increase in risk of developing MS and especially in interaction with the risk allele HLA-DRB1*15 and absence of the protective allele HLA-A*02. The major part of this thesis is focused on investigating the involvement of the pulmonary immune system in MS, and further to uncover underlying smoking associated changes that could elucidate on the role of smoking as a risk factor in MS. To characterize the lung immune cells, bronchoalveolar lavage (BAL) cells were obtained by bronchoscopy, from healthy volunteers and MS-patients, smokers and non-smokers. In project I we provide an initial characterization of our study cohort. We could observe that smokers carrying the MS specific risk allele HLA-DRB1*15 did not show a smoking-associated increase in macrophages defined in non-carriers. Smokers showed higher frequency of proliferating T-cells, while non-smoking MS-patients had increased levels of preformed CD40L in CD4+ T-cells. We could further provide a more in-depth characterization of pulmonary T-cells in MS-patients and smokers, in Project III. The majority of CD4+T-cells in both healthy and MS patients showed a tissue resident memory phenotype, characterized by expression of CD69 and CD44, while also expressing both CXCR3 and CCR6. Cells from healthy smokers showed an increased proliferative capacity and we also observed a significantly higher frequency of regulatory T-cells in the lungs of both healthy smokers and MS-patients compared to healthy non-smokers. When investigating the migratory profile of lung T-cells based on integrins VLA-4 and LFA-1, both implicated in MS pathogenesis, we found no upregulation of these in MS patients compared to healthy. In recent years, it has been suggested that dysbiosis of the commensal microbiome in the gut is involved in the pathogenies of MS. The lungs also host a unique commensal microbiota, which recently was shown to be dysregulated in the autoimmune disease Rheumatoid Arthritis and pulmonary Sarcoidosis. In Project IV we investigated if the microbiota in the lungs of MS patients also show dysbiosis. We found that the microbial composition in the lungs of MS patients differed considerably compared to healthy controls, with increased richness and diversity. We could further report that MS patients also had altered expression and presence of the antimicrobial peptide human beta defensin-1 (hBD1) in the lungs. In Project II we developed a novel method, called Small-seq, to study small RNAs, such as microRNAs (miRNA) from a scarce source of starting material; a single cell. Previously methods required large quantities of sample material in order to investigate small RNAs, which often can be a limitation to obtain in clinical samples, as well as average out biological variability and heterogeneity within populations. With Small-seq we are were able to capture different types of small RNAs from single cells, such as miRNA, snoRNA and tsRNA. Captured miRNAs revealed cellular heterogeneity in primed hESC, as well as being able to cluster and separate different cell types. The method implemented a masking strategy to efficiently limit capture of the highly abundant 5.8S rRNA, and incorporation of a unique molecular identifier allowed for molecular quantification of the detected small RNAs. The work provided in this thesis concludes that the pulmonary immune milieu is altered in MS patients, thereby presenting the lungs as an organ of interest for further investigation into the pathology and potential therapeutic opportunities in MS. The described changes in immune cell composition between smokers carrying the MS risk allele HLA-DRB1*15 and noncarriers, could further shed light upon the mechanisms behind the impact of smoking as a risk factor for disease and in exacerbating MS. Herein we further provide the development of a novel technique to capture and investigate small RNA, such as miRNAs in single cells
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| 6. |
- Jun, Seong-Hwan, et al.
(författare)
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Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics
- 2023
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- Functional characterization of the cancer clones can shed light on the evolutionary mechanisms driving cancer's proliferation and relapse mechanisms. Single-cell RNA sequencing data provide grounds for understanding the functional state of cancer as a whole; however, much research remains to identify and reconstruct clonal relationships toward characterizing the changes in functions of individual clones. We present PhylEx that integrates bulk genomics data with co-occurrences of mutations from single-cell RNA sequencing data to reconstruct high-fidelity clonal trees. We evaluate PhylEx on synthetic and well-characterized high-grade serous ovarian cancer cell line datasets. PhylEx outperforms the state-of-the-art methods both when comparing capacity for clonal tree reconstruction and for identifying clones. We analyze high-grade serous ovarian cancer and breast cancer data to show that PhylEx exploits clonal expression profiles beyond what is possible with expression-based clustering methods and clear the way for accurate inference of clonal trees and robust phylo-phenotypic analysis of cancer. The functional changes of individual clones in single cell RNA sequencing (scRNA-seq) data remain elusive. Here, the authors develop PhylEx that integrates bulk genomics data with co-occurrences of mutations revealed by scRNA-seq data and apply it to high-grade serous ovarian cancer cell line and breast cancer datasets.
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| 7. |
- Needhamsen, Maria, et al.
(författare)
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Integration of small RNAs from plasma and cerebrospinal fluid for classification of multiple sclerosis
- 2022
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Ingår i: Frontiers in Genetics. - : Frontiers Media SA. - 1664-8021. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- Multiple Sclerosis (MS) is an autoimmune, neurological disease, commonly presenting with a relapsing-remitting form, that later converts to a secondary progressive stage, referred to as RRMS and SPMS, respectively. Early treatment slows disease progression, hence, accurate and early diagnosis is crucial. Recent advances in large-scale data processing and analysis have progressed molecular biomarker development. Here, we focus on small RNA data derived from cell-free cerebrospinal fluid (CSF), cerebrospinal fluid cells, plasma and peripheral blood mononuclear cells as well as CSF cell methylome data, from people with RRMS (n = 20), clinically/radiologically isolated syndrome (CIS/RIS, n = 2) and neurological disease controls (n = 14). We applied multiple co-inertia analysis (MCIA), an unsupervised and thereby unbiased, multivariate method for simultaneous data integration and found that the top latent variable classifies RRMS status with an Area Under the Receiver Operating Characteristics (AUROC) score of 0.82. Variable selection based on Lasso regression reduced features to 44, derived from the small RNAs from plasma (20), CSF cells (8) and cell-free CSF (16), with a marginal reduction in AUROC to 0.79. Samples from SPMS patients (n = 6) were subsequently projected on the latent space and differed significantly from RRMS and controls. On contrary, we found no differences between relapse and remission or between inflammatory and non-inflammatory disease controls, suggesting that the latent variable is not prone to inflammatory signals alone, but could be MS-specific. Hence, we here showcase that integration of small RNAs from plasma and CSF can be utilized to distinguish RRMS from SPMS and neurological disease controls.
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| 8. |
- Zhao, Cheng, et al.
(författare)
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Single-cell multi-omics of human preimplantation embryos shows susceptibility to glucocorticoids
- 2022
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Ingår i: Genome Research. - : Cold Spring Harbor Laboratory Press (CSHL). - 1088-9051 .- 1549-5469. ; 32:9, s. 1627-1641
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Tidskriftsartikel (refereegranskat)abstract
- The preconceptual, intrauterine, and early life environments can have a profound and long-lasting impact on the developmental trajectories and health outcomes of the offspring. Given the relatively low success rates of assisted reproductive technologies (ART; similar to 25%), additives and adjuvants, such as glucocorticoids, are used to improve the success rate. Considering the dynamic developmental events that occur during this window, these exposures may alter blastocyst formation at a molecular level, and as such, affect not only the viability of the embryo and the ability of the blastocyst to implant, but also the developmental trajectory of the first three cell lineages, ultimately influencing the physiology of the embryo. In this study, we present a comprehensive single-cell transcriptome, methylome, and small RNA atlas in the day 7 human embryo. We show that, despite no change in morphology and developmental features, preimplantation glucocorticoid exposure reprograms the molecular profile of the trophectoderm (TE) lineage, and these changes are associated with an altered metabolic and inflammatory response. Our data also suggest that glucocorticoids can precociously mature the TE sublineages, supported by the presence of extravillous trophoblast markers in the polar sublineage and presence of X Chromosome dosage compensation. Further, we have elucidated that epigenetic regulation-DNA methylation and microRNAs (miRNAs)-likely underlies the transcriptional changes observed. This study suggests that exposures to exogenous compounds during preimplantation may unintentionally reprogram the human embryo, possibly leading to suboptimal development and longer-term health outcomes.
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| 9. |
- Zheleznyakova, Galina Yurevna, et al.
(författare)
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Small noncoding RNA profiling across cellular and biofluid compartments and their implications for multiple sclerosis immunopathology
- 2021
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 118:17
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Tidskriftsartikel (refereegranskat)abstract
- Multiple sclerosis (MS) is a chronic inflammatory demyelinating disease affecting the central nervous system (CNS). Small non-coding RNAs (sncRNAs) and, in particular, microRNAs (miRNAs) have frequently been associated with MS. Here, we performed a comprehensive analysis of all classes of sncRNAs in matching samples of peripheral blood mononuclear cells (PBMCs), plasma, cerebrospinal fluid (CSF) cells, and cell-free CSF from relapsing-remitting (RRMS, n = 12 in relapse and n = 11 in remission) patients, secondary progressive (SPMS, n = 6) MS patients, and noninflammatory and inflammatory neurological disease controls (NINDC, n = 11; INDC, n = 5). We show widespread changes in miRNAs and sncRNA-derived fragments of small nuclear, nucleolar, and transfer RNAs. In CSF cells, 133 out of 133 and 115 out of 117 differentially expressed sncRNAs were increased in RRMS relapse compared to remission and RRMS compared to NINDC, respectively. In contrast, 65 out of 67 differentially expressed PBMC sncRNAs were decreased in RRMS compared to NINDC. The striking contrast between the periphery and CNS suggests that sncRNA-mediated mechanisms, including alternative splicing, RNA degradation, and mRNA translation, regulate the transcriptome of pathogenic cells primarily in the CNS target organ.
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