| 1. |
- Akerman, Ildem, et al.
(författare)
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Human Pancreatic β Cell lncRNAs Control Cell-Specific Regulatory Networks
- 2017
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Ingår i: Cell Metabolism. - : Elsevier BV. - 1550-4131. ; 25:2, s. 400-411
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Tidskriftsartikel (refereegranskat)abstract
- Recent studies have uncovered thousands of long non-coding RNAs (lncRNAs) in human pancreatic β cells. β cell lncRNAs are often cell type specific and exhibit dynamic regulation during differentiation or upon changing glucose concentrations. Although these features hint at a role of lncRNAs in β cell gene regulation and diabetes, the function of β cell lncRNAs remains largely unknown. In this study, we investigated the function of β cell-specific lncRNAs and transcription factors using transcript knockdowns and co-expression network analysis. This revealed lncRNAs that function in concert with transcription factors to regulate β cell-specific transcriptional networks. We further demonstrate that the lncRNA PLUTO affects local 3D chromatin structure and transcription of PDX1, encoding a key β cell transcription factor, and that both PLUTO and PDX1 are downregulated in islets from donors with type 2 diabetes or impaired glucose tolerance. These results implicate lncRNAs in the regulation of β cell-specific transcription factor networks.
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| 2. |
- Miguel-Escalada, Irene, et al.
(författare)
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Human pancreatic islet three-dimensional chromatin architecture provides insights into the genetics of type 2 diabetes
- 2019
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 51:7, s. 1137-1148
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Tidskriftsartikel (refereegranskat)abstract
- Genetic studies promise to provide insight into the molecular mechanisms underlying type 2 diabetes (T2D). Variants associated with T2D are often located in tissue-specific enhancer clusters or super-enhancers. So far, such domains have been defined through clustering of enhancers in linear genome maps rather than in three-dimensional (3D) space. Furthermore, their target genes are often unknown. We have created promoter capture Hi-C maps in human pancreatic islets. This linked diabetes-associated enhancers to their target genes, often located hundreds of kilobases away. It also revealed >1,300 groups of islet enhancers, super-enhancers and active promoters that form 3D hubs, some of which show coordinated glucose-dependent activity. We demonstrate that genetic variation in hubs impacts insulin secretion heritability, and show that hub annotations can be used for polygenic scores that predict T2D risk driven by islet regulatory variants. Human islet 3D chromatin architecture, therefore, provides a framework for interpretation of T2D genome-wide association study (GWAS) signals.
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| 3. |
- Das Mahapatra, Kunal, et al.
(författare)
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A comprehensive analysis of coding and non-coding transcriptomic changes in cutaneous squamous cell carcinoma
- 2020
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Cutaneous Squamous Cell Carcinoma (cSCC) is the most common and fastest-increasing cancer with metastatic potential. Long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are novel regulators of gene expression. To identify mRNAs, lncRNAs and circRNAs, which can be involved in cSCC, RNA-seq was performed on nine cSCCs and seven healthy skin samples. Representative transcripts were validated by NanoString nCounter assays using an extended cohort, which also included samples from pre-cancerous skin lesions (actinic keratosis). 5,352 protein-coding genes, 908 lncRNAs and 55 circular RNAs were identified to be differentially expressed in cSCC. Targets of 519 transcription factors were enriched among differentially expressed genes, 105 of which displayed altered level in cSCCs, including fundamental regulators of skin development (MYC, RELA, ETS1, TP63). Pathways related to cell cycle, apoptosis, inflammation and epidermal differentiation were enriched. In addition to known oncogenic lncRNAs (PVT1, LUCAT1, CASC9), a set of skin-specific lncRNAs were were identified to be dysregulated. A global downregulation of circRNAs was observed in cSCC, and novel skin-enriched circRNAs, circ_IFFO2 and circ_POF1B, were identified and validated. In conclusion, a reference set of coding and non-coding transcripts were identified in cSCC, which may become potential therapeutic targets or biomarkers.
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| 4. |
- Gaulton, Kyle J, et al.
(författare)
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Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci.
- 2015
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 47:12, s. 1415-1415
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Tidskriftsartikel (refereegranskat)abstract
- We performed fine mapping of 39 established type 2 diabetes (T2D) loci in 27,206 cases and 57,574 controls of European ancestry. We identified 49 distinct association signals at these loci, including five mapping in or near KCNQ1. 'Credible sets' of the variants most likely to drive each distinct signal mapped predominantly to noncoding sequence, implying that association with T2D is mediated through gene regulation. Credible set variants were enriched for overlap with FOXA2 chromatin immunoprecipitation binding sites in human islet and liver cells, including at MTNR1B, where fine mapping implicated rs10830963 as driving T2D association. We confirmed that the T2D risk allele for this SNP increases FOXA2-bound enhancer activity in islet- and liver-derived cells. We observed allele-specific differences in NEUROD1 binding in islet-derived cells, consistent with evidence that the T2D risk allele increases islet MTNR1B expression. Our study demonstrates how integration of genetic and genomic information can define molecular mechanisms through which variants underlying association signals exert their effects on disease.
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| 5. |
- Ling, Charlotte, et al.
(författare)
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Epigenetics in type 2 diabetes
- 2016
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Ingår i: The Genetics of Type 2 Diabetes and Related Traits: Biology, Physiology and Translation. - Cham : Springer International Publishing. - 9783319015743 - 9783319015736 ; , s. 241-258
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Bokkapitel (refereegranskat)abstract
- Combinations of genetic and environmental factors contribute to the pathogenesis of type 2 diabetes (T2D); however, our knowledge of the molecular mechanisms by which these factors trigger diabetes is still limited. While genome-wide association studies have identified and characterized more than 60 genomic loci associated with T2D, recent methylome charts and reference regulatory maps obtained from tissues central to T2D can help to pinpoint the causative genetic variants. Yet, the proportion of overall trait variance explained by these genetic variants is still modest. Aging, diet, obesity, and physical inactivity represent nongenetic risk factors that may be reflected in epigenetic processes promoting T2D. Recent studies have characterized epigenetic modifications in pancreatic islets, skeletal muscle, and adipose tissue from T2D patients suggesting a central role for epigenetic mechanisms in the pathogenesis of the disease. Altered epigenetic patterns have also been found in first-degree relatives of patients with T2D and in healthy subjects born with a low birth weight suggesting that epigenetic modifications may predispose to diabetes. Lifestyle interventions including exercise and diet have also been shown to alter the epigenome in target tissues for T2D. Overall, these data propose a model where combinations of genetic, epigenetic, and nongenetic factors contribute to the risk of T2D. In this book chapter, we will explore the potential role of epigenetic mechanisms in T2D and discuss how genetics, epigenetics, and environment may interact to define the risk of developing the disease.
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| 6. |
- Lohcharoenkal, Warangkana, et al.
(författare)
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Genome-Wide Screen for MicroRNAs Reveals a Role for miR-203 in Melanoma Metastasis.
- 2018
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Ingår i: Journal of Investigative Dermatology. - : Elsevier BV. - 0022-202X .- 1523-1747. ; 138:4, s. 882-892
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Tidskriftsartikel (refereegranskat)abstract
- Melanoma is one of the deadliest human cancers with limited therapeutic options. MicroRNAs are a class of short noncoding RNAs regulating gene expression at the post-transcriptional level. To identify important miRNAs in melanoma, we compared the miRNome of primary and metastatic melanomas in The Cancer Genome Atlas dataset and found lower miR-203 abundance in metastatic melanoma. Lower level of miR-203 was associated with poor overall survival in metastatic disease. We found that the methylation levels of several CpGs in the MIR203 promoter negatively correlated with miR-203 expression and that treatment with the demethylating agent 5-aza-2-deoxycytidine induced miR-203 expression, which was associated with demethylation of the promoter CpGs, in melanoma cell lines. In vitro, there was a decreased expression of miR-203 in melanoma cell lines in comparison with primary melanocytes. Ectopic overexpression of miR-203 suppressed cell motility, colony formation, and sphere formation as well as the angiogenesis-inducing capacity of melanoma cells. In vivo, miR-203 inhibited xenograft tumor growth and reduced lymph node and lung metastasis. SLUG was shown as a target of miR-203, and knockdown of SLUG recapitulated the effects of miR-203, whereas its restoration was able to reverse the miR-203-mediated suppression of cell motility. These results establish a role for miR-203 as a tumor suppressor in melanoma which suppresses both early and late steps of metastasis. Hence, restoration of miR-203 has therapeutic potential in melanoma.
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| 7. |
- Luo, Longlong, et al.
(författare)
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The Long Noncoding RNA LINC00958 Is Induced in Psoriasis Epidermis and Modulates Epidermal Proliferation
- 2023
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Ingår i: Journal of Investigative Dermatology. - : Elsevier. - 0022-202X .- 1523-1747. ; 143:6, s. 999-1010
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Tidskriftsartikel (refereegranskat)abstract
- Psoriasis is a common, immune-mediated skin disease characterized by epidermal hyperproliferation and chronic skin inflammation. Long noncoding RNAs are >200 nucleotide-long transcripts that possess important regulatory functions. To date, little is known about the contribution of long noncoding RNAs to psoriasis. In this study, we identify LINC00958 as a long noncoding RNA overexpressed in keratinocytes (KCs) from psoriasis skin lesions, in a transcriptomic screen performed on KCs sorted from psoriasis and healthy skin. Increased levels of LINC00958 in psoriasis KCs were confirmed by RT-qPCR and single-molecule in situ hybridization. Confocal microscopy and analysis of subcellular fractions showed that LINC00958 is mainly localized in the cytoplasm of KCs. IL-17A, a key psoriasis cytokine, induced LINC00958 in KCs through C/EBP-β and the p38 pathway. The inhibition of LINC00958 led to decreased proliferation as measured by Ki-67 expression, live cell analysis imaging, and 5-ethynyl-2-deoxyuridine assays. Transcriptomic analysis of LINC00958-depleted KCs revealed enrichment of proliferation- and cell cycle‒related genes among differentially expressed transcripts. Moreover, LINC00958 depletion led to decreased basal and IL-17A‒induced phosphorylation of p38. Furthermore, IL-17A‒induced KC proliferation was counteracted by the inhibition of LINC00958. In summary, our data support a role for the IL-17A‒induced long noncoding RNA, LINC00958, in the pathological circuits of psoriasis by reinforcing IL-17A‒induced epidermal hyperproliferation.
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| 8. |
- Pasquali, Lorenzo
(författare)
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Psoriasis : from transcriptome to miRNA function and biomarkers
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Psoriasis is a chronic inflammatory, immune-mediated skin condition that affects in average 2 to 3% of the world population, phenotypically characterized by red and scaly plaques on the skin of affected patients. It is a multifactorial disorder, in which both genetic predisposition and environment play key roles. Psoriasis lesional skin is characterized by abnormal keratinocyte differentiation and proliferation, as well as dermal immune cell infiltration. Psoriasis is associated with several comorbidities, e.g. arthritis, however, currently no biomarkers exist that could be used to predict or identify these at an early stage. Many studies aimed to characterize the psoriasis transcriptome, but few studies have been focusing on elucidating the gene alterations in keratinocytes in this disease. In this thesis, we explored the transcriptomic landscape of epidermal cells from lesional and non-lesional skin of patients with psoriasis, as well as from healthy volunteers’ skin and investigated the biomarker-potential of circulating microRNAs. In our first study, we investigated the alterations of the protein-coding transcriptome in the psoriasis epidermal compartment. The separation of the epidermis from the dermis and sorting for CD45-neg cells allowed us to exclude dermal signatures including those from fibroblasts, endothelial cells, dendritic cells and T cells, but also from immune cells infiltrating the epidermis, known to populate at increased ratio the psoriasis lesional skin. We have identified biological pathways related to immune responses, cell cycle and keratinization involved in the epidermal alterations, as well as the enrichment and dominance of psoriasis-associated cytokine signatures. Moreover, we established that genetic variations associated with psoriasis may contribute to the keratinocyte transcriptomic changes in the disease. In our second study, we investigated the alterations of the non-protein-coding transcriptome in psoriasis and identified a set of long non-coding RNAs differentially expressed in psoriasis epidermal cells. Several had genomic localization overlapping psoriasis-associated SNPs, suggesting their potential implication in the genetic susceptibility to psoriasis. We validated the over-expression of the lncRNA LINC00958 in CD45-neg cells from psoriasis lesions compared to non-lesional and healthy skin and determined its expression in different skin cell types and subcellular localization. In our third study, we focused on psoriatic arthritis, the major psoriasis comorbidity, affecting about 1/3 of the patients with cutaneous psoriasis. In particular, we investigated the potential of circulating microRNAs as biomarkers for early diagnosis of psoriatic arthritis symptoms in patients with cutaneous psoriasis. We have identified two circulating microRNAs, let-7b-5p and miR-30e-5p, with significantly reduced levels in plasma-derived extracellular vesicles of patients with confirmed psoriatic arthritis, compared to cutaneous-only psoriasis patients. Finally, in our fourth study, we investigated the role and functions of miR-378a, previously found overexpressed in psoriasis lesional keratinocytes compared to non-lesional and healthy skin. In vivo, in a mouse model of psoriasis-like skin inflammation, the injection of miR-378a resulted in increased clinical signs of inflammation, increased skin thickness and number of proliferating cells in the epidermis. In vitro, in cultured primary human keratinocytes, miR-378a overexpression enhanced the expression of pro-inflammatory chemokines CXCL8/IL8 and CCL20, as well as reduction of NFKBIA proteins levels.
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| 9. |
- Pasquali, Lorenzo, et al.
(författare)
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The Keratinocyte Transcriptome in Psoriasis : Pathways Related to Immune Responses, Cell Cycle and Keratinization.
- 2019
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Ingår i: Acta Dermato-Venereologica. - : Medical Journals Sweden AB. - 0001-5555 .- 1651-2057. ; 99:2, s. 196-205
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Tidskriftsartikel (refereegranskat)abstract
- Psoriasis is a common immune-mediated disease resulting from altered cross-talk between keratinocytes and immune cells. Previous transcriptomic studies have identified thousands of deregulated genes in psoriasis skin; however, the transcriptomic changes confined to the epidermal compartment remained poorly characterized. The aim of this study was to characterize the transcriptomic landscape of psoriatic keratinocytes, using sorted CD45neg epidermal cells. Genes with functions in innate immunity, type I interferon response, cell cycle and keratinization were enriched among deregulated genes in psoriatic keratinocytes. Gene set enrichment analysis indicated the dominance of interleukin (IL)-22/IL-17A signatures in the epidermal psoriasis-signature. A set of deregulated genes overlapped with psoriasis-associated genetic regions, suggesting that genetic variations affecting gene expression in keratinocytes contribute to susceptibility to psoriasis. Several psoriasis-susceptibility genes, which were previously believed to be expressed preferentially or exclusively in immune cells, were identified as having altered expression in psoriatic keratinocytes. These results highlight the role of keratinocytes in the pathogenesis of psoriasis, and indicate that both genetic factors and an inflammatory microenvironment contribute to epidermal alterations in psoriasis.
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| 10. |
- Srivastava, Ankit, et al.
(författare)
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Cross-talk between IFN-γ and TWEAK through miR-149 amplifies skin inflammation in psoriasis
- 2021
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Ingår i: Journal of Allergy and Clinical Immunology. - : Elsevier. - 0091-6749 .- 1097-6825. ; 147:6, s. 2225-2235
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Psoriasis is a chronic inflammatory skin disease with disturbed interplay between immune cells and keratinocytes. A strong IFN-γ signature is characteristic for psoriasis skin, but the role of IFN-γ has been elusive. MicroRNAs are short RNAs regulating gene expression.OBJECTIVE: Our aim was to investigate the role of miR-149 in psoriasis and in the inflammatory responses of keratinocytes.METHODS: miR-149 expression was measured by quantitative RT-PCR in keratinocytes isolated from healthy skin and lesional and nonlesional psoriasis skin. Synthetic miR-149 was injected intradermally into the back skin of mice, and imiquimod was applied to induce psoriasis-like skin inflammation, which was then evaluated at the morphologic, histologic, and molecular levels. miR-149 was transiently overexpressed or inhibited in keratinocytes in combination with IFN-γ- and/or TNF-related weak inducer of apoptosis (TWEAK)-treatment.RESULTS: Here we report a microRNA-mediated mechanism by which IFN-γ primes keratinocytes to inflammatory stimuli. Treatment with IFN-γ results in a rapid and long-lasting suppression of miR-149 in keratinocytes. Depletion of miR-149 in keratinocytes leads to widespread transcriptomic changes and induction of inflammatory mediators with enrichment of the TWEAK pathway. We show that IFN-γ-mediated suppression of miR-149 leads to amplified inflammatory responses to TWEAK. TWEAK receptor (TWEAKR/Fn14) is identified as a novel direct target of miR-149. The in vivo relevance of this pathway is supported by decreased miR-149 expression in psoriasis keratinocytes, as well as by the protective effect of synthetic miR-149 in the imiquimod-induced mouse model of psoriasis.CONCLUSION: Our data define a new mechanism, in which IFN-γ primes keratinocytes for TWEAK-induced inflammatory responses through suppression of miR-149, promoting skin inflammation.
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