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Jalkanen, S.

Publications and source records attributed to Jalkanen, S..

10 recordsLinked to original sources

Adenosine impairs T cell function via activation of purine salvage pathway and AMP-induced inhibition of pyrimidine nucleotide biosynthesis

Extracellular adenosine (ADO) is a well-established immune checkpoint mediator suppressing T cells via activation of A2A receptors, yet intracellular mechanisms of ADO action remain less understood. Here, we show that activated human T cells transport extracellular ADO through equilibrative nucleoside transporter 1 (ENT1) and metabolize it through ATP salvage pathway. The generated ADO metabolite AMP inhibits UMP synthase (UMPS), the rate-limiting enzyme of de novo pyrimidine biosynthesis, leading to diminished ATP production via conventional bioenergetic pathways, increased apoptosis, and impaired effector functions of T cells. Flow cytometric and single-cell transcriptomic analyses further revealed that ADO restrains the exit of naive T cells from quiescence. All effects of ADO were phenocopied by treating T cells with the inhibitors of UMPS and reversed after pharmacological blockage of ENT1 or uridine supplementation. Additional molecular docking, molecular dynamics simulations, and free-energy analyses indicate that AMP can occupy the orotidine 5'-monophosphate (OMP) decarboxylase catalytic site of UMPS with the same anchoring contacts as substrate OMP and product UMP, providing a structural rationale for direct AMP-mediated inhibition of pyrimidine biosynthesis. These findings demonstrate that immunosuppressive effects of ADO extend beyond canonical adenosinergic signaling and involve cellular ADO uptake and modulation of purine and pyrimidine metabolism.

immunology↗

CXCL12, SCF, and eotaxin are prognostic serum biomarkers in gastric cancer

Gastric cancer is the fifth most common cancer worldwide and the fifth leading cause of cancer-related death. Its poor prognosis is primarily due to a late diagnosis and a lack of effective treatments for advanced disease. We aimed to identify new prognostic serum biomarkers to aid clinical decision-making. Our patient cohort consisted of 240 individuals who underwent surgery for histologically verified gastric adenocarcinoma in the Department of Surgery, Helsinki University Hospital, between 2000 and 2009. To determine serum protein concentrations of cytokines and growth factors, we utilized Bio-Rads premixed Bio-Plex Pro Human Cytokine 27-plex and 21-plex assay kits. Among the 48 biomarkers analyzed, three emerged as statistically significant prognostic markers for disease-specific survival using the Cox proportional hazards univariate analysis: C-X-C motif chemokine ligand 12 (CXCL12) (hazard ratio [HR] 0.39, 95% confidence interval [CI] 0.23-0.63, p<0.001), stem cell factor (HR 0.38, 95%CI 0.19-0.77, p=0.007), and eotaxin (HR 0.57, 95%CI 0.37-0.89, p=0.013). Multivariate survival analysis revealed that, among the 48 biomarkers analyzed, CXCL12 and eotaxin served as independent prognostic markers among gastric cancer patients. The prognostic effect of inflammatory serum biomarkers in gastric cancer could provide new insights into the immunological microenvironment of disease.

pathology↗

CCL5, CLEC11A, IL-7, IL-8, and IL-13: Diagnostic serum biomarkers of gastric cancer identified in a 48-multiplex panel

BackgroundGastric cancer is the fifth most common cancer worldwide and the fifth leading cause of cancer-related death. Its poor prognosis is primarily due to a late diagnosis and a lack of effective treatments for advanced disease. MethodsWe examined a patient cohort comprising 239 individuals who underwent surgery for histologically verified gastric adenocarcinoma in the Department of Surgery at Helsinki University Hospital between 2000 and 2009, comparing them to 48 healthy controls. We measured the serum protein concentrations for 48 different cytokines and growth factors using two of Bio-Rads premixed Bio-Plex Pro Human Cytokine 27-plex and 21-plex assay kits. ResultsFive serum biomarkers were identified as indicative of gastric cancer. Cancer patients had higher serum levels of CLEC11A [odds ratio (OR) 1.16, 95% confidence interval (CI) 1.08- 1.26, p = 0.004], IL-7 (OR 2.73, 95% CI 1.48-5.04, p = 0.014), IL-8 (OR 6.30, 95% CI 2.23-20.0, p = 0.017), and IL-13 (OR 2.67, 95% CI 1.33-5.37, p = 0.041). The CCL5 levels were lower in cancer patients compared with controls (OR 0.30, 95% CI 0.14-0.60, p = 0.014). ConclusionsIn a large cohort of 239 patients, we identified five biomarkers for which serum levels associated with gastric cancer: CCL5, CLEC11A, IL-7, IL-8, and IL-13. High serum levels of CLEC11A have not previously been associated with gastric cancer. Our results provide new support to further explore the effect of these inflammatory molecules and the role they play in gastric cancer. This may help identify novel noninvasive diagnostic methods as well as potential new druggable targets.

pathology↗

Breast Cancer Remodels Lymphatics in Sentinel Lymph Nodes

Cancer metastasis to sentinel lymph nodes (LNs) is often the first marker of potential disease progression. Although it is recognized that tumor-induced lymphangiogenesis facilitates metastasis into LNs in murine models, tumor-induced alterations in human lymphatic vessels remain obscure. We used single-cell RNA sequencing to profile lymphatic endothelial cell (LEC) subsets in paired metastatic and non-metastatic LNs obtained from patients with treatment-naive breast cancer. Tumor metastasis decreases immunoregulatory LEC subsets, such as PD-L1+ subcapsular sinus LECs, while inducing an increase in capillary-like CD200+ HEY1+ LECs. Matrix Gla protein (MGP) was the most upregulated gene in metastatic LN LECs, and its expression on LECs was TGF-{beta} and VEGF dependent. Upregulated MGP promotes cancer cell adhesion to LN lymphatics. Thus, breast cancer cell metastasis to LNs remodels LEC subsets in human LNs and escalates MGP expression, potentially facilitating cancer cell dissemination through the lymphatic system.

immunology↗

BRAFV600E expression in thyrocytes causes recruitment of immunosuppressive STABILIN-1 macrophages

Papillary thyroid carcinoma (PTC) is the most frequent histological subtype of thyroid cancers (TC), and BRAFV600E genetic alteration is found in 60% of this endocrine cancer. This oncogene is associated with poor prognosis, resistance to radioiodine therapy and tumor progression. Histological follow-up by anatomo-pathologists reveals that 2/3 of surgically-removed thyroids do not present malignant lesions. Continued fundamental research into the molecular mechanisms of TC downstream of BRAFV600E remains thus central to better understand the clinical behavior of these tumors. To study PTC, we used a mouse model in which expression of BRAFV600E is specifically switched on in thyrocytes by doxycycline administration. Upon daily intraperitoneal doxycycline injection, thyroid tissue rapidly acquired histological features mimicking human PTC. Transcriptomic analysis revealed major changes in immune signaling pathways upon BRAFV600E induction. Multiplex immunofluorescence confirmed the abundant recruitment of macrophages, among which a population of LYVE-1+/CD206+/STABILIN-1+ was dramatically increased. By genetically inactivating the gene coding for the scavenger receptor STABILIN-1, we showed an increase of CD8+ T cells in this in situ BRAFV600E dependent TC. Finally, we demonstrated the presence of CD206+/STABILIN-1+ macrophages in human thyroid pathologies. Altogether, we revealed the recruitment of immunosuppressive STABILIN-1 macrophages a PTC mouse model and the relevance of these observations in human thyroid tissues.

cancer biology↗

Stabilin-1 plays a protective role against Listeria monocytogenes infection through the regulation of cytokine and chemokine production and immune cell recruitment

Scavenger receptors are part of a complex surveillance system expressed by host cells to efficiently orchestrate innate immune response against bacterial infections. Stabilin-1 (STAB-1) is a scavenger receptor involved in cell trafficking, inflammation and cancer, however its role in infection remains to be elucidated. Listeria monocytogenes (Lm) is a major intracellular human food-borne pathogen causing severe infections in susceptible hosts. Using a mouse model of infection, we demonstrate here that STAB-1 controls Lm-induced cytokine and chemokine production and immune cell accumulation in Lm-infected organs. We show that STAB-1 also regulates the recruitment of myeloid cells in response to Lm infection and contributes to clear circulating bacteria. In addition, whereas STAB-1 appears to promote bacterial uptake by macrophages, infection by pathogenic Listeria induces the down regulation of STAB-1 expression and its delocalization from the host cell membrane. We propose STAB-1 as a new SR involved in the control of Lm infection through the regulation of host defense mechanisms, a process that would be targeted by bacterial virulence factors to promote infection.

microbiology↗

A single-cell transcriptional roadmap of the mouse and human lymph node lymphatic vasculature

Single-cell transcriptomics promises to revolutionize our understanding of the vasculature. Emerging computational methods applied to high dimensional single cell data allow integration of results between samples and species, and illuminate the diversity and underlying developmental and architectural organization of cell populations. Here, we illustrate these methods in analysis of mouse lymph node (LN) lymphatic endothelial cells (LEC) at single cell resolution. Clustering identifies five well-delineated subsets, including two medullary sinus subsets not recognized previously as distinct. Nearest neighbor alignments in trajectory space position the major subsets in a sequence that recapitulates known and suggests novel features of LN lymphatic organization, providing a transcriptional map of the lymphatic endothelial niches and of the transitions between them. Differences in gene expression reveal specialized programs for (1) subcapsular ceiling endothelial interactions with the capsule connective tissue and cells, (2) subcapsular floor regulation of lymph borne cell entry into the LN parenchyma and antigen presentation, and (3) medullary subset specialization for pathogen interactions and LN remodeling. LEC of the subcapsular sinus floor and medulla, which represent major sites of cell entry and exit from the LN parenchyma respectively, respond robustly to oxazolone inflammation challenge with enriched signaling pathways that converge on both innate and adaptive immune responses. Integration of mouse and human single-cell profiles reveals a conserved cross-species pattern of lymphatic vascular niches and gene expression, as well as specialized human subsets and genes unique to each species. The examples provided demonstrate the power of single-cell analysis in elucidating endothelial cell heterogeneity, vascular organization and endothelial cell responses. We discuss the findings from the perspective of LEC functions in relation to niche formations in the unique stromal and highly immunological environment of the LN. Highlights Computational alignments ("trajectories") predict LN LEC organization in situ, revealing a continuum of phenotypes punctuated by specialized clusters Multiple intermediate phenotypes suggest LEC malleability Gene profiles define niche-specific functional specialization Medullary sinus LECs are comprised of Ptx3-LECs and Marco-LECs O_LIDistinct mechanisms for pathogen interactions and matrix modeling C_LIO_LIPtx3-LECs: paracortical and central medullary sinuses near hilus; enriched for genes driving lymphangiogenic responses and lymphocyte egress C_LIO_LIMarco-LECs: peri-follicular medullary sinuses; macrophage-associated genes, complement and coagulation cascade C_LI Niche-specific responses to inflammation O_LIIFN gene responses in SCS floor and medullary sinus LECs C_LIO_LISuppression of LEC identity genes in responding subsets C_LI Conserved and unique LEC subsets and gene programs across species O_LICore subsets common to mouse and human C_LIO_LIGreater diversity of subsets and intermediates in human LN LECs C_LI

systems biology↗

An expanded analysis framework for multivariate GWAS connects inflammatory biomarkers to functional variants and disease

Multivariate methods are known to increase the statistical power of association detection, but they have lacked essential follow-up analysis tools necessary for understanding the biology underlying these associations. We developed a novel computational workflow for multivariate GWAS follow-up analyses, including fine-mapping and identification of the subset of traits driving associations (driver traits). Many follow-up tools require univariate regression coefficients which are lacking from multivariate results. Our method overcomes this problem by using Canonical Correlation Analysis to turn each multivariate association into its optimal univariate Linear Combination Phenotype (LCP). This enables an LCP-GWAS, which in turn generates the statistics required for follow-up analyses. We implemented our method on 12 highly correlated inflammatory biomarkers in a Finnish population-based study. Altogether, we identified 11 associations, four of which (F5, ABO, C1orf140 and PDGFRB) were not detected by biomarker-specific analyses. Fine-mapping identified 19 signals within the 11 loci and driver trait analysis determined the traits contributing to the associations. A phenome-wide association study on the 19 putative causal variants from the signals in 176,899 individuals from the FinnGen study revealed 53 disease associations (p < 1x10-4). Several reported pQTLs in the 11 loci provided orthogonal evidence for the biologically relevant functions of the putative causal variants. Our novel multivariate analysis workflow provides a powerful addition to standard univariate GWAS analyses by enabling multivariate GWAS follow-up and thus promoting the advancement of powerful multivariate methods in genomics.

genetics↗

Multivariate genome-wide association analysis of a cytokine network reveals variants with widespread immune, haematological and cardiometabolic pleiotropy

Cytokines are essential regulatory components of the immune system and their aberrant levels have been linked to many disease states. Despite increasing evidence that cytokines operate in concert, many of the physiological interactions between cytokines, and the shared genetic architecture that underlie them, remain unknown. Here we aimed to identify and characterise genetic variants with pleiotropic effects on cytokines - to do this we performed a multivariate genome-wide association study on a correlation network of 11 circulating cytokines measured in 9,263 individuals. Meta-analysis identified a total of 8 loci significantly associated with the cytokine network, of which two (PDGFRB and ABO) had not been detected previously. Bayesian colocalisation analysis revealed shared causal variants between the eight cytokine loci and other traits; in particular, cytokine network variants at the ABO, SERPINE2, and ZFPM2 loci showed pleiotropic effects on the production of immune-related proteins; on metabolic traits such as lipoprotein and lipid levels; on blood-cell related traits such as platelet count; and on disease traits such as coronary artery disease and type 2 diabetes.

genomics↗

Genome-wide association study identifies seven novel loci associating with circulating cytokines and cell adhesion molecules in Finns

BackgroundInflammatory processes contribute to the pathophysiology of multiple chronic conditions. Genetic factors play a crucial role in modulating the inflammatory load, but the exact mechanisms are incompletely understood.\n\nMethodsTo add understanding to the molecular mechanisms in inflammation, we performed a genome-wide association study (GWAS) on 16 circulating cytokines and cell adhesion molecules (inflammatory phenotypes) in Northern Finland Birth Cohort 1966 (NFBC1966, N=5,284). A subsequent meta-analysis was completed for 10 phenotypes available in a GWAS of three other Finnish population cohorts adding up to 13,577 individuals in the study. Complementary association tests were performed to study the effect of the ABO blood types on soluble adhesion molecule levels.\n\nResultsWe identified seven novel and confirmed six previously reported loci associating with at least one of the studied inflammatory phenotypes (p<3.1x10-9). We observed three loci associating with the concentration of soluble vascular cell adhesion molecule-1 (sVCAM-1), one of which is the ABO locus that has been previously associated with soluble E-selectin (sE-selectin) and intercellular adhesion molecule-1 (sICAM-1) levels. Results from the complementary analyses suggest that the blood type B associates primarily with the concentration of sVCAM-1 while the A1 subtype shows a robust effect on sE-selectin and sICAM-1 levels. Furthermore, the genotypes in the ABO locus associating with higher soluble adhesion molecule levels tend to associate with lower low-density lipoprotein cholesterol level and lower cardiovascular disease risk.\n\nConclusionThe present results extend the knowledge about genetic factors contributing to the inflammatory load. Our findings suggest that two distinct mechanisms contribute to the soluble adhesion molecule levels at the ABO locus. The negative correlation between the genetic effects on soluble adhesion molecule levels and cardiovascular traits in this locus further suggests that increased soluble adhesion molecule levels per se may not be a risk factor for cardiovascular disease.

genetics↗