Department of Computational Biology for Individualised Medicine([CIIM]BIIM)
head of the department: Prof. Li
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Sex-Specific Regulation of Inflammation and Metabolic Syndrome in Obesity.Metabolic dysregulation and inflammation are important consequences of obesity and impact susceptibility to cardiovascular disease. Anti-inflammatory therapy in cardiovascular disease is being developed under the assumption that inflammatory pathways are identical in women and men, but it is not known if this is indeed the case. In this study, we assessed the sex-specific relation between inflammation and metabolic dysregulation in obesity. Approach and Results: Three hundred two individuals were included, half with a BMI 27 to 30 kg/m2 and half with a BMI>30 kg/m2, 45% were women. The presence of metabolic syndrome was assessed according to the National Cholesterol Education Program-ATPIII criteria, and inflammation was studied using circulating markers of inflammation, cell counts, and ex vivo cytokine production capacity of isolated immune cells. Additionally, lipidomic and metabolomic data were gathered, and subcutaneous fat biopsies were histologically assessed. Metabolic syndrome is associated with an increased inflammatory profile that profoundly differs between women and men: women with metabolic syndrome show a lower concentration of the anti-inflammatory adiponectin, whereas men show increased levels of several pro-inflammatory markers such as IL (interleukin)-6 and leptin. Adipose tissue inflammation showed similar sex-specific associations with these markers. Peripheral blood mononuclear cells isolated from men, but not women, with metabolic syndrome display enhanced cytokine production capacity.
Performance of Roche qualitative HEV assay on the cobas 6800 platform for quantitative measurement of HEV RNA.Background: Hepatitis E virus (HEV) infection is an increasingly recognized cause of acute and chronic hepatitis in high-income countries and is the most frequent cause of acute viral hepatitis in many European countries. Appropriate tools to detect and quantify HEV RNA are needed. This study aimed to evaluate the performance of the Roche cobas® HEV assay and compare it with the Fast Track Diagnostics (FTD) Hepatitis E RNA assay. Methods: HEV viral load determination and lower limit of detection (LOD, defined as the lowest amount of viral copies that could be detected in 95 % of repeats) were assessed using a WHO standard dilution panel, testing 240 samples of various concentrations. Reproducibility was tested at three different concentration levels, for different genotypes, and with different sample types (serum, plasma) in 30 samples. Sample stability was analyzed after three freeze/thaw cycles in 25 samples. Results: Cobas HEV assay showed a strong linear relationship between log of HEV WHO dilution series and Ct values over the reportable range from 200-5000 IU/mL HEV RNA copies. The amplification efficiency was higher than 92 %. LOD was 22 IU/mL (95 % CI: 17.4-31.8) and reproducibility tests showed a 100 % nucleic acid test (NAT) reactivity of cobas HEV for WHO dilution series (range 200-5000 IU/mL, n = 90). Cobas HEV assay detected all different HEV genotypes from biobank samples irrespective of the sample type. NAT reactivity of cobas HEV was not affected by three freeze/thaw cycles. Conclusions: Roche cobas HEV assay is a powerful NAT tool in terms of robustness, reproducibility and linearity. It is a feasible alternative for high-volume testing.
BCG Vaccination in Humans Elicits Trained Immunity via the Hematopoietic Progenitor Compartment.Induction of trained immunity by Bacille-Calmette-Guérin (BCG) vaccination mediates beneficial heterologous effects, but the mechanisms underlying its persistence and magnitude remain elusive. In this study, we show that BCG vaccination in healthy human volunteers induces a persistent transcriptional program connected to myeloid cell development and function within the hematopoietic stem and progenitor cell (HSPC) compartment in the bone marrow. We identify hepatic nuclear factor (HNF) family members 1a and b as crucial regulators of this transcriptional shift. These findings are corroborated by higher granulocyte numbers in BCG-vaccinated infants, HNF1 SNP variants that correlate with trained immunity, and elevated serum concentrations of the HNF1 target alpha-1 antitrypsin. Additionally, transcriptomic HSPC remodeling was epigenetically conveyed to peripheral CD14+ monocytes, displaying an activated transcriptional signature three months after BCG vaccination. Taken together, transcriptomic, epigenomic, and functional reprogramming of HSPCs and peripheral monocytes is a hallmark of BCG-induced trained immunity in humans.
The Set7 Lysine Methyltransferase Regulates Plasticity in Oxidative Phosphorylation Necessary for Trained Immunity Induced by β-Glucan.Trained immunity confers a sustained augmented response of innate immune cells to a secondary challenge, via a process dependent on metabolic and transcriptional reprogramming. Because of its previous associations with metabolic and transcriptional memory, as well as the importance of H3 histone lysine 4 monomethylation (H3K4me1) to innate immune memory, we hypothesize that the Set7 methyltransferase has an important role in trained immunity induced by β-glucan. Using pharmacological studies of human primary monocytes, we identify trained immunity-specific immunometabolic pathways regulated by Set7, including a previously unreported H3K4me1-dependent plasticity in the induction of oxidative phosphorylation. Recapitulation of β-glucan training in vivo additionally identifies Set7-dependent changes in gene expression previously associated with the modulation of myelopoiesis progenitors in trained immunity. By revealing Set7 as a key regulator of trained immunity, these findings provide mechanistic insight into sustained metabolic changes and underscore the importance of characterizing regulatory circuits of innate immune memory.
Tissue alarmins and adaptive cytokine induce dynamic and distinct transcriptional responses in tissue-resident intraepithelial cytotoxic T lymphocytes.The respective effects of tissue alarmins interleukin (IL)-15 and interferon beta (IFNβ), and IL-21 produced by T cells on the reprogramming of cytotoxic T lymphocytes (CTLs) that cause tissue destruction in celiac disease is poorly understood. Transcriptomic and epigenetic profiling of primary intestinal CTLs showed massive and distinct temporal transcriptional changes in response to tissue alarmins, while the impact of IL-21 was limited. Only anti-viral pathways were induced in response to all the three stimuli, albeit with differences in dynamics and strength. Moreover, changes in gene expression were primarily independent of changes in H3K27ac, suggesting that other regulatory mechanisms drive the robust transcriptional response. Finally, we found that IL-15/IFNβ/IL-21 transcriptional signatures could be linked to transcriptional alterations in risk loci for complex immune diseases. Together these results provide new insights into molecular mechanisms that fuel the activation of CTLs under conditions that emulate the inflammatory environment in patients with autoimmune diseases.