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Dahl, E.

Publications and source records attributed to Dahl, E..

6 recordsLinked to original sources

Shift in cellular crosstalk reveals the immunosuppressive environment in cholangiocarcinoma patients.

Background and aimsCholangiocarcinoma (CCA) is a deadly disease, and this cancer entity is characterized by an abundant stroma. The tumor microenvironment (TME) plays an important role in aggressive behavior and poor response to therapeutics; however, underlying pathways are unknown. MethodsTo fill this gap, we used multiplexed immunohistochemistry, high-dimensional phenotyping, and transcriptomics to analyze human CCA samples and identify cell cluster crosstalk in patients with a poor prognosis. ResultsOur findings confirmed the presence of Tregs and the lack of effector memory cells in the tumor. New findings are the spatiality of the effector memory cells being more present in the peripheral tissue, for some reason these immune cells fail to reach the tumor niche. We revealed cancer crosstalk with macrophages and stromal cells and identified responsible genes in the poor prognosis group. Amongst the responsible ligand pairs are GAS6-AXL belonging to the TAM family. We then identified VCAN-TLR2 to be present and influencing the ECM in a way to supports immune exhaustion. Last, EGFR-TGF-{beta} is expressed in macrophages and this finding is important in Tregs induction and blocking cytotoxic T cell function. ConclusionsThe multiple mechanisms leading to the exclusion of relevant immune cells needed for an anti-cancer response and mechanisms leading to active immune suppression are part of complex cell-cell crosstalk. This study provides a deeper insight into the immune exhausted phenotype in CCA.

cancer biology↗

TIGIT drives the immunosuppressive environment by downregulation of metalloproteinases MMP2 and MMP14 in perihilar cholangiocarcinoma.

BackgroundCheckpoint blockade in cholangiocarcinoma (CCA) is promising; however, little is known about the response to treatment in CCA subtypes. In this study, we investigated the spatial immune environment in combination with checkpoint expression in perihilar CCA (pCCA). Materials & MethodsThe levels of checkpoint molecules (PD-1, PD-L1, PD-L2, LAG-3, ICOS, TIGIT, TIM-3, and CTLA-4), macrophages (CD68), and T cells (CD4 and CD8) were assessed by multiplex immunofluorescence (mIF) in 50 patients. We investigated the transcriptomic profile using the NanoString Cancer Progression Panel, and validation was performed by mIF on tissue sections from 24 patients. ResultsThe expression of checkpoint molecules TIGIT, CTLA-4, and LAG-3 alone and in combination with other checkpoint molecules was more abundant in the Central Tumor (CT) and Invasive Margin (IM) than in peritumoral tissue (PT) (CD4 and CD8 TIGIT p<0.0001 for both CD4 and CD8 CTLA-4, p<0.0001 and p < 0.001, respectively, and CD8 LAG-3 p < 0.05). MMP2 and MMP14 were differentially expressed in patients with high TIGIT expression. ConclusionThe immune environment in pCCA is characterized by the expression of multiple checkpoints, demonstrating the complexity of ICI treatment. High TIGIT expression drives an immunosuppressive environment by modulating the extracellular matrix. Future clinical trials in pCCA could consider TIGIT as a therapeutically relevant target for (combination) treatment.

cancer biology↗

The global distribution of paired eddy covariance towers

The eddy covariance technique has revolutionized our understanding of ecosystem-atmosphere interactions. Eddy covariance studies often use a "paired" tower design in which observations from nearby towers are used to understand how different vegetation, soils, hydrology, or experimental treatment shape ecosystem function and surface-atmosphere exchange. Paired towers have never been formally defined and their global distribution has not been quantified. We compiled eddy covariance tower information to find towers that could be considered paired. Of 1233 global eddy covariance towers, 692 (56%) were identified as paired by our criteria. Paired towers had cooler mean annual temperature (mean = 9.9 {degrees}C) than the entire eddy covariance network (10.5 {degrees}C) but warmer than the terrestrial surface (8.9 {degrees}C) from WorldClim 2.1, on average. The paired and entire tower networks had greater average soil nitrogen (0.57-0.58 g/kg) and more silt (36.0-36.4%) than terrestrial ecosystems (0.38 g/kg and 30.5%), suggesting that eddy covariance towers sample richer soils than the terrestrial surface as a whole. Paired towers existed in a climatic space that was more different from the global climate distribution sampled by the entire eddy covariance network, as revealed by an analysis of the Kullback-Leibler divergence, but the edaphic space sampled by the entire network and paired towers was similar. The lack of paired towers with available data across much of Africa, northern, central, southern, and western Asia, and Latin America with few towers in savannas, shrublands, and evergreen broadleaf forests point to key regions, ecosystems, and ecosystem transitions in need of additional research. Few if any paired towers study the flux of ozone and other atmospherically active trace gases at the present. By studying what paired towers measure - and what they do not - we can make infrastructural investments to further enhance the value of FLUXNET as it moves toward its fourth decade.

ecology↗

SPAG6 promotes cell migration and induces epithelial-to-mesenchymal transition in luminal breast cancer cells

Understanding the involvement of promoter DNA methylation changes in the development of breast cancer may be highly informative for designing more effective therapeutic treatments. We recently characterized the Sperm Associated Antigen 6 (SPAG6) gene, encoding a flagellar motility protein, as a potential DNA methylation biomarker for blood-based early breast cancer detection. Here we present the first study to evaluate the functional role of SPAG6 in human breast cancer. In silico analysis of the HumanMethylation450 BeadChip and Illumina HiSeq data of The Cancer Genome Atlas (TCGA) was performed in both normal (n=114) and breast cancer patient tissues (n=1104) to determine SPAG6 DNA methylation and expression. Stable SPAG6 overexpressing cancer models for in vitro analysis were obtained by lentivirus-mediated gene delivery in T-47D, MCF-7, MDA-MB-231 and BT-549 breast cancer cells. Subsequently stable mock and SPAG6 cell lines were compared in cellular assays. In addition, involvement of SPAG6 in EMT was analysed by qPCR and immunolabeling experiments. All major molecular subtypes of breast cancer (luminal A, luminal B, basal-type, HER2-enriched) revealed a tumor-specific increased SPAG6 promoter hypermethylation that correlated with strong reduction in SPAG6 mRNA expression. Interestingly, a small group of luminal breast tumors exhibited SPAG6 mRNA overexpression compared to normal breast tissue. SPAG6 overexpression caused a significant reduction (p<0.05) in colony formation in basal MDA-MB-231 and BT-549 cells. In turn, luminal T-47D cells overexpressing SPAG6 showed a significant increase in colony formation (p=0.0004) and both T-47D-and MCF-7 cells overexpressing SPAG6 exhibited a robust increase in migration speed (p<0.0001). In SPAG6-positive T-47D cells SNAIL, TWIST1 and Vimentin expression was found to be significantly upregulated, while E-Cadherin expression was supressed. SPAG6 overexpressing T47D cells showed a typical epithelial-mesenchymal transition (EMT). This was accompanied by a nearly complete displacement of both actin and E-cadherin from cell-cell junctions. Our in vitro analyses give functional evidence that SPAG6 has a profound effect on colony formation, migration and intercellular junction composition in breast cancer cells. Our study is the first to show opposing SPAG6 effects in a single tumour entity depending on the molecular subtype. We propose that SPAG6 might be a key player for inducing the EMT program in luminal-type breast cancers, driving tumour progression and metastasis.

cell biology↗

Deconvolution of cellular subsets in human tissue based on targeted DNA methylation analysis at individual CpG sites

BackgroundThe complex composition of different cell types within a tissue can be estimated by deconvolution of omics datasets. For example, DNA methylation (DNAm) profiles have been used to establish an atlas for multiple human tissues and cell types. In this study, we investigated if deconvolution is also feasible with individual cell-type-specific CG dinucleotides (CpG sites), which can be addressed by targeted analysis, such as pyrosequencing. ResultsWe compiled and curated a dataset of 579 samples from Illumina 450k BeadChip technology that comprised 14 different purified and characterized human cell types. A training and validation strategy was applied to identify and test cell-type-specific CpGs. Initially, the amount of fibroblasts was estimated using two CpGs that were either hypermethylated or hypomethylated in fibroblasts. This FibroScore correlated with the state of fibrosis and was associated with overall survival in various types of cancer. Furthermore, we identified hypomethylated CpGs for leukocytes, endothelial cells, epithelial cells, hepatocytes, glia, neurons, fibroblasts and induced pluripotent stem cells. Using previously published BeadChip datasets with cell mixtures the accuracy of this eight CpG signature was comparable to previously published signatures based on several thousand CpGs. Finally, we established and validated pyrosequencing assays for the relevant CpGs that can be utilized for classification and deconvolution of cell types. ConclusionThis proof of concept study demonstrates that DNAm analysis at individual CpGs reflects the cellular composition of cellular mixtures and different tissues. Targeted analysis of these genomic regions facilitates robust methods for application in basic research and clinical settings.

genomics↗

Mutation analysis of multiple pilomatricomas in a patient with myotonic dystrophy type 1 suggests a DM1-associated hypermutation phenotype

Myotonic dystrophy type 1 (DM1) is an inherited neuromuscular disease which results from an expansion of repetitive DNA elements within the 3 untranslated region of the DMPK gene. Some patients develop multiple pilomatricomas as well as malignant tumors in other tissues. Mutations of the catenin-{beta} gene (CTNNB1) could be demonstrated in most non-syndromic pilomatricomas. In order to gain insight into the molecular mechanisms which might be responsible for the occurrence of multiple pilomatricomas and cancers in patients with DM1, we have sequenced the CTNNB1 gene of four pilomatricomas and of one pilomatrical carcinoma which developed in one patient with molecularly proven DM1 within 4 years. We further analyzed the pilomatrical tumors for microsatellite instability as well as by NGS for mutations in 161 cancer-associated genes. Somatic and independent point-mutations were detected at typical hotspot regions of CTNNB1 (S33C, S33F, G34V, T41I) while one mutation within CTNNB1 represented a duplication mutation (G34dup.). Pilomatricoma samples were analyzed for microsatellite instability and expression of mismatch repair proteins but no mutated microsatellites could be detected and expression of mismatch repair proteins MLH1, MSH2, MSH6, PMS2 was not perturbed. NGS analysis only revealed one heterozygous germline mutation c.8494C>T; p.(Arg2832Cys) within the ataxia telangiectasia mutated gene (ATM) which remained heterozygous in the pilomatrical tumors. The detection of different somatic mutations in different pilomatricomas and in the pilomatrical carcinoma as well as the observation that the patient developed multiple pilomatricomas and one pilomatrical carcinoma over a short time period strongly suggest that the patient displays a hypermutation phenotype. This hypermutability seems to be tissue and gene restricted. Co-translation of the mutated DMPK gene and the CTNNB1 gene in cycling hair follicles might constitute an explanation for the observed tissue and gene specificity of hypermutability observed in DM1 patients. Elucidation of putative mechanisms responsible for hypermutability in DM1 patients requires further research. Author summaryLess than 10% of patients with myotonic dystrophy type 1 (DM1), an inherited and the most common neuromuscular disorder, develop pilomatricomas, often as multiple tumors. Pilomatricomas are benign skin tumors deriving from hair matrix cells, and they are very rare in the general population. Recently it could be demonstrated that DM1 patients also harbour and enhanced risk for benign and malignant tumors in various other tissues. DM1 is characterized genetically by an expansion of trinucleotide repeats within the 3 untranslated region of the DMPK gene (DM1 protein kinase). It could be demonstrated that these expanded CTG-repeats are transcribed into RNA and that this non-translated repetitive RNA forms aggregates with various splicing regulators, which in turn impair transcription of multiple genes in various tissues. Following the gain-of-function-RNA hypothesis, Mueller and colleagues suggested in 2009 that the untranslated repetitive RNA directly enhances expression of {beta}-catenin resulting in pilomatricomas as well as in various cancers which rely on activation of the WNT/APC/{beta}-catenin pathway. In order to prove or to reject this hypothesis we have sequenced the CTNNB1 gene of four pilomatricomas and of one pilomatrical carcinoma which developed in one patient with molecularly proven DM1 within 4 years. Somatic and independent point-mutations were detected at typical hotspot regions of CTNNB1 (S33C, S33F, G34V, T41I) while one mutation within CTNNB1 represented a duplication mutation (G34dup.). We further analyzed the pilomatrical tumors for microsatellite instability but no mutated microsatellites could be detected and expression of mismatch repair proteins MLH1, MSH2, MSH6, PMS2 was not perturbed. NGS analysis in 161 cancer-associated genes only revealed one heterozygous germline mutation c.8494C>T; p.(Arg2832Cys) within the ataxia telangiectasia mutated gene (ATM) which remained heterozygous in the pilomatrical tumors. The detection of different somatic mutations in different pilomatricomas and in the pilomatrical carcinoma does not support the hypothesis that untranslated repetitive RNA directly enhances expression of {beta}-catenin resulting in pilomatricomas. In contrast, our results strongly suggest that the patient displays a tissue and gene restricted hypermutation phenotype. One putative mechanism for the assumed gene and tissue restriction could be co-translation of the mutated DMPK gene and the CTNNB1 gene in cycling hair follicles.

cancer biology↗