Use of IFNγ/IL10 Ratio for Stratification of Hydrocortisone Therapy in Patients With Septic Shock.

Large clinical trials testing hydrocortisone therapy in septic shock have produced conflicting results. Subgroups may benefit of hydrocortisone treatment depending on their individual immune response. We performed an exploratory analysis of the database from the international randomized controlled clinical trial Corticosteroid Therapy of Septic Shock (CORTICUS) employing machine learning to a panel of 137 variables collected from the Berlin subcohort comprising 83 patients including demographic and clinical measures, organ failure scores, leukocyte counts and levels of circulating cytokines. The identified theranostic marker was validated against data from a cohort of the Hellenic Sepsis Study Group (HSSG) (n = 246), patients enrolled in the clinical trial of Sodium Selenite and Procalcitonin Guided Antimicrobial Therapy in Severe Sepsis (SISPCT, n = 118), and another, smaller clinical trial (Crossover study, n = 20). In addition, in vitro blood culture experiments and in vivo experiments in mouse models were performed to assess biological plausibility. A low serum IFNγ/IL10 ratio predicted increased survival in the hydrocortisone group whereas a high ratio predicted better survival in the placebo group. Using this marker for a decision rule, we applied it to three validation sets and observed the same trend. Experimental studies in vitro revealed that IFNγ/IL10 was negatively associated with the load of (heat inactivated) pathogens in spiked human blood and in septic mouse models. Accordingly, an in silico analysis of published IFNγ and IL10 values in bacteremic and non-bacteremic patients with the Systemic Inflammatory Response Syndrome supported this association between the ratio and pathogen burden. We propose IFNγ/IL10 as a molecular marker supporting the decision to administer hydrocortisone to patients in septic shock. Prospective clinical studies are necessary and standard operating procedures need to be implemented, particularly to define a generic threshold. If confirmed, IFNγ/IL10 may become a suitable theranostic marker for an urging clinical need.

Reprogramming of macrophages employing gene regulatory and metabolic network models.

Upon exposure to different stimuli, resting macrophages undergo classical or alternative polarization into distinct phenotypes that can cause fatal dysfunction in a large range of diseases, such as systemic infection leading to sepsis or the generation of an immunosuppressive tumor microenvironment. Investigating gene regulatory and metabolic networks, we observed two metabolic switches during polarization. Most prominently, anaerobic glycolysis was utilized by M1-polarized macrophages, while the biosynthesis of inosine monophosphate was upregulated in M2-polarized macrophages. Moreover, we observed a switch in the urea cycle. Gene regulatory network models revealed E2F1, MYC, PPARγ and STAT6 to be the major players in the distinct signatures of these polarization events. Employing functional assays targeting these regulators, we observed the repolarization of M2-like cells into M1-like cells, as evidenced by their specific gene expression signatures and cytokine secretion profiles. The predicted regulators are essential to maintaining the M2-like phenotype and function and thus represent potential targets for the therapeutic reprogramming of immunosuppressive M2-like macrophages.

Molecular signature of an ancient organizer regulated by Wnt/ß-catenin signalling during primary body axis patterning in Hydra.

Wnt/ß-catenin signalling has been shown to play a critical role during head organizer formation in Hydra. Here, we characterized the Wnt signalling regulatory network involved in formation of the head organizer. We found that Wnt signalling regulates genes that are important in tissue morphogenesis. We identified that majority of transcription factors (TFs) regulated by Wnt/ß-catenin signalling belong to the homeodomain and forkhead families. Silencing of Margin, one of the Wnt regulated homeodomain TFs, results in loss of the ectopic tentacle phenotype typically seen upon activation of Wnt signalling. Furthermore, we show that the Margin promoter is directly bound and regulated by ß-catenin. Ectopic expression of Margin in zebrafish embryos results in body axis abnormalities suggesting that Margin plays a role in axis patterning. Our findings suggest that homeobox TFs came under the regulatory umbrella of Wnt/ß-catenin signalling presumably resulting in the evolution of primary body axis in animal phyla.

Temporal progression of gene regulation of peripheral white blood cells explains gender dimorphism of critically ill patients after trauma.

BACKGROUND: The immune response of the critically ill after severe trauma is sex-specific and may explain the different progression of the disease. This may be explained by a different gene regulatory program of their peripheral immune cells. We investigated the progression of the transcription profiles of peripheral immune cells of the patients to elucidate their distinct physiological response and clinical course. METHODS: We compared transcription profiles of whole blood of male and female patients from a larger longitudinal study of critically ill patients after trauma. We developed a statistical analysis pipeline that synchronized the time lapse of the profiles based on the temporal severity score of each patient. RESULTS: This enabled to categorize the temporal progression of the disease into two pre-acute, an acute and two post-acute phases. Comparing gene regulation of male and female patients at each phase, we identified distinctively regulated molecular processes mainly in the immune response, but also in the regulation of metabolism allowing to cluster these discriminative gene sets into sets of highly related cellular processes. Compared to male patients and healthy controls, female patients showed upregulation of gene sets of innate immunity in the early phase, upregulation of wound healing processes during the acute phase and upregulation of adaptive immunity in the late phase indicating early recovery. In turn, during the pre-acute and acute phase, male patients showed less suppression of gene sets coding for enzymes of energy metabolism and anabolism, most prominently the tricarboxylic acid cycle and ß-oxidation, and cellular maintenance, such as cell cycle, DNA replication and damage response, and RNA metabolism. CONCLUSIONS: A stronger innate immune response at the very early phase of the disease may support early clearance of the pathogen and its associated molecular patterns. Upregulation of wound healing processes may explain reduced multiple organ failure during the acute phase. Down regulated energy metabolism during the acute phase may make female patients less susceptible to oxidative stress, the upregulated adaptive immune system reflects an earlier recovery and rebuilding of the adaptive immune system that may protect them from secondary infections. Follow up studies need to be performed confirming these observations experimentally.

Modelling TERT regulation across 19 different cancer types based on the MIPRIP 2.0 gene regulatory network approach.

BACKGROUND: Reactivation of the telomerase reverse transcriptase gene TERT is a central feature for unlimited proliferation of the majority of cancers. However, the underlying regulatory processes are only partly understood. RESULTS: We assembled regulator binding information from serveral sources to construct a generic human and mouse gene regulatory network. Advancing our "Mixed Integer linear Programming based Regulatory Interaction Predictor" (MIPRIP) approach, we identified the most common and cancer-type specific regulators of TERT across 19 different human cancers. The results were validated by using the well-known TERT regulation by the ETS1 transcription factor in a subset of melanomas with mutations in the TERT promoter. Our improved MIPRIP2 R-package and the associated generic regulatory networks are freely available at https://github.com/KoenigLabNM/MIPRIP. CONCLUSION: MIPRIP 2.0 identified common as well as tumor type specific regulators of TERT. The software can be easily applied to transcriptome datasets to predict gene regulation for any gene and disease/condition under investigation.

MiR-192, miR-200c and miR-17 are fibroblast-mediated inhibitors of colorectal cancer invasion.

Colorectal cancer remains a leading cause of cancer-related death worldwide. A previous transcriptomics based study characterized molecular subgroups of which the stromal subgroup was associated with the worst clinical outcome. Micro-RNAs (miRNAs) are well-known regulators of gene expression and can follow a non-linear repression mechanism. We set up a model combining piecewise linear and linear regression and applied this combined regression model to a comprehensive colon adenocarcinoma dataset. We identified miRNAs involved in regulating characteristic gene sets, particularly extracellular matrix remodeling in the stromal subgroup. Comparison of expression data from separated (epithelial) cancer cells and stroma cells or fibroblasts associate these regulatory interactions with infiltrating stromal or tumor-associated fibroblasts. MiR-200c, miR-17 and miR-192 were identified as the most promising candidates regulating genes crucial for extracellular matrix remodeling. We validated our computational findings by in vitro assays. Enforced expression of either miR-200c, miR-17 or miR-192 in untransformed human colon fibroblasts down-regulated 85% of all predicted target genes. Expressing these miRNAs singly or in combination in human colon fibroblasts co-cultured with colon cancer cells considerably reduced cancer cell invasion validating these miRNAs as cancer cell infiltration suppressors in tumor associated fibroblasts.