Analyses of sphingosine-1-phosphate in the context of transfusion: how much is in stored blood products and in patient blood?

BACKGROUND: Sphingosine-1-phosphate (S1P) is a bloodborne lipid that regulates vascular tone and endothelial permeability. S1P concentrations are reduced in critically ill patients. As hematopoietic cells produce S1P, this study intends to investigate S1P concentrations in blood products during storage and in patient plasma after blood transfusion. STUDY DESIGN AND METHODS: S1P concentrations were measured in 83 red blood cell (RBC) units and 73 platelet concentrates (PCs) before and after storage. In addition, 26 critically ill patients who received one or two RBC units were recruited to measure S1P plasma levels before and three times within 24 hours after transfusion. RESULTS: The highest S1P concentrations were found in fresh PCs. S1P concentrations in PCs are reduced by 60% when stored at room temperature for 4 days, whereas in RBCs S1P concentrations remained stable when stored at 4°C within 35 days. S1P concentrations in PCs and RBCc were 2.5 to 6 times higher compared to patient plasma. Plasma S1P levels in critically ill patients, however, transiently decreased after transfusion of RBCs and recover to pretransfusion values within the following 24 hours. CONCLUSION: S1P concentrations in blood products are significantly higher compared to human plasma S1P levels, even though plasma S1P levels decreased after RBC transfusion in critically ill patients and reached pretransfusion values within 24 hours.

Model-guided combinatorial optimization of complex synthetic gene networks.

Constructing gene circuits that satisfy quantitative performance criteria has been a long-standing challenge in synthetic biology. Here, we show a strategy for optimizing a complex three-gene circuit, a novel proportional miRNA biosensor, using predictive modeling to initiate a search in the phase space of sensor genetic composition. We generate a library of sensor circuits using diverse genetic building blocks in order to access favorable parameter combinations and uncover specific genetic compositions with greatly improved dynamic range. The combination of high-throughput screening data and the data obtained from detailed mechanistic interrogation of a small number of sensors was used to validate the model. The validated model facilitated further experimentation, including biosensor reprogramming and biosensor integration into larger networks, enabling in principle arbitrary logic with miRNA inputs using normal form circuits. The study reveals how model-guided generation of genetic diversity followed by screening and model validation can be successfully applied to optimize performance of complex gene networks without extensive prior knowledge.

Transplantation of prokaryotic two-component signaling pathways into mammalian cells.

Signaling pathway engineering is a promising route toward synthetic biological circuits. Histidine-aspartate phosphorelays are thought to have evolved in prokaryotes where they form the basis for two-component signaling. Tyrosine-serine-threonine phosphorelays, exemplified by MAP kinase cascades, are predominant in eukaryotes. Recently, a prokaryotic two-component pathway was implemented in a plant species to sense environmental trinitrotoluene. We reasoned that "transplantation" of two-component pathways into mammalian host could provide an orthogonal and diverse toolkit for a variety of signal processing tasks. Here we report that two-component pathways could be partially reconstituted in mammalian cell culture and used for programmable control of gene expression. To enable this reconstitution, coding sequences of histidine kinase (HK) and response regulator (RR) components were codon-optimized for human cells, whereas the RRs were fused with a transactivation domain. Responsive promoters were furnished by fusing DNA binding sites in front of a minimal promoter. We found that coexpression of HKs and their cognate RRs in cultured mammalian cells is necessary and sufficient to strongly induce gene expression even in the absence of pathways' chemical triggers in the medium. Both loss-of-function and constitutive mutants behaved as expected. We further used the two-component signaling pathways to implement two-input logical AND, NOR, and OR gene regulation. Thus, two-component systems can be applied in different capacities in mammalian cells and their components can be used for large-scale synthetic gene circuits.

Rescue bedside laparotomy in the intensive care unit in patients too unstable for transport to the operating room.

INTRODUCTION: The prognoses of critically ill patients with a requirement for emergency laparotomy and severe respiratory and/or hemodynamic instability precluding transport to the operating room (OR) are often fatal without surgery. Attempting emergency surgery at the bedside might equally result in an adverse outcome. However, risk factors and predictors that could support clinical decision making have not been identified so far. This study describes the clinical characteristics, indicative pathophysiology and outcomes in patients undergoing resuscitative laparotomy in the intensive care unit (ICU). METHODS: This was a retrospective observational study of all critically ill adult patients undergoing resuscitative laparotomy in the ICUs of a German university hospital from January 2005 to July 2013. Clinical characteristics, risk factors, and treatments were compared between survivors and non-survivors. The primary endpoint was 28-day survival. RESULTS: A total of 41 patients with a median age of 64 (21 to 83) were included. The most frequent reasons for ICU admission were sepsis, pneumonia, and pancreatic surgery. All patients were mechanically ventilated, receiving vasopressors, and were in multiple organ failure. Twenty-nine patients (70.7%) were on renal replacement therapy and two patients (4.9%) on extracorporeal membrane oxygenation. The main reasons for surgery were suspected intra-abdominal bleeding (39.0%), suspected intestinal ischemia (24.4%) or abdominal compartment syndrome (24.4%). Twenty-eight-day, ICU and hospital mortalities were 75.6%, 80.5%, and 82.9%, respectively. In six out of ten patients (60%) who survived surgery for more than 28 days, bedside laparotomy was rated as a life-saving procedure by an interdisciplinary group of the investigators. CONCLUSIONS: These findings suggest that in selected critically ill patients with a vital indication for emergency laparotomy and severe cardiopulmonary instability precluding transport to the OR, a bedside resuscitative laparotomy in the ICU can be considered as a rescue procedure, even though very high mortality is to be expected.

An AAV gene therapy computes over multiple cellular inputs to enable precise targeting of multifocal hepatocellular carcinoma in mice.

Clinical translation of multi-input biomolecular computing systems holds potential to lead to disease-tailored, data-driven rational design of next-generation therapeutic modalities. However, practical demonstrations of this potential are lacking. Here, we developed a clinically translatable approach for the design and implementation of therapeutic agents comprising biomolecular multi-input logic modules for precision cell targeting, compatible with adeno-associated virus (AAV) vectors. We used this approach to engineer an AAV-encoded gene therapy prototype that, when delivered systemically, successfully treated hepatocellular carcinoma in an orthotopic mouse tumor model. The therapy performed a molecular-scale computation over multiple transcriptional and microRNA inputs based on the differential molecular profiles of tumor and nontumor cells, to guide the activation of a herpes simplex virus thymidine kinase (HSV-TK) effector gene. Multi-input computation in individual cells was necessary and sufficient to drive in vivo and in situ tumor-specific expression of HSV-TK with minimal concomitant expression in nontumor liver and other organs. Intravenous vector injection in combination with ganciclovir resulted in marked reduction in tumor burden in treated mice compared with controls, without negative effects on general well-being or weight. The therapeutic approach has the capacity to perform logical integration of diseased and healthy cell­specific molecular inputs to precisely regulate therapeutic effector gene expression and is a promising avenue for the next generation of cancer therapies. Moreover, our systematic data-driven workflow illustrates how gene expression data can shape the molecular composition of future therapeutic candidates.

Preoperative autologous blood donation versus intraoperative blood salvage: intraindividual analyses and modeling of efficacy in 1103 patients.

BACKGROUND: Preoperative autologous blood donation (PABD) and intraoperative blood salvage (IBS) represent established blood conservation measures. However, data comparing PABD to IBS are very sparse. STUDY DESIGN AND METHODS: We analyzed data from 1103 patients undergoing PABD and subsequent major orthopedic surgery in one center. We then used a validated model to compare PABD to IBS. We calculated maximal allowable blood losses (MABLs) for both IBS and PABD. We also identified criteria for efficacious use of either PABD or IBS. Our calculations were based on exclusive application of either technique, complete exhaustion of predeposited or salvaged blood, and one round of IBS. RESULTS: The vast majority of patients would have tolerated greater MABLs if subjected to IBS rather than PABD (425 of 432 with 1 PABD unit, 580 of 664 patients with 2 PABD units, 3 of 7 patients with 3 PABD units). For a few patients, however, our model demonstrated greater MABL with PABD than with IBS. These patients were characterized by 1) lower initial hematocrit (Hct), 2) recovery from PABD with return to baseline Hct or above by the time of surgery, and 3) longer time between first PABD and surgery. CONCLUSION: IBS appears to be the superior blood conservation technique if PABD cannot be performed under optimal conditions. Tolerable predonation anemia and sufficient time for regeneration appear to be crucial for post-PABD erythropoiesis. If these goals cannot be accomplished, PABD should be abandoned and be replaced by IBS.

A Workflow for In Vivo Evaluation of Candidate Inputs and Outputs for Cell Classifier Gene Circuits.

Cell classifier gene circuits that integrate multiple molecular inputs to restrict the expression of therapeutic outputs to cancer cells have the potential to result in efficacious and safe cancer therapies. Preclinical translation of the hitherto developments requires creating the conditions where the animal model, the delivery platform, in vivo expression levels of the inputs, and the efficacy of the output, all come together to enable detailed evaluation of the fully assembled circuits. Here we show an integrated workflow that addresses these issues and builds the framework for preclinical classifier studies using the design framework of microRNA (miRNA, miR)-based classifier gene circuits. Specifically, we employ HCT-116 colorectal cancer cell xenograft in an experimental mouse metastatic liver tumor model together with Adeno-associated virus (AAV) vector delivery platform. Novel engineered AAV-based constructs are used to validate in vivo the candidate inputs miR-122 and miR-7 and, separately, the cytotoxic output HSV-TK/ganciclovir. We show that while the data are largely consistent with expectations, crucial insights are gained that could not have been obtained in vitro. The results highlight the importance of detailed stepwise interrogation of the experimental parameters as a necessary step toward clinical translation of synthetic gene circuits.

Ubiquitin ligase TRIM3 controls hippocampal plasticity and learning by regulating synaptic γ-actin levels.

Synaptic plasticity requires remodeling of the actin cytoskeleton. Although two actin isoforms, ß- and γ-actin, are expressed in dendritic spines, the specific contribution of γ-actin in the expression of synaptic plasticity is unknown. We show that synaptic γ-actin levels are regulated by the E3 ubiquitin ligase TRIM3. TRIM3 protein and Actg1 transcript are colocalized in messenger ribonucleoprotein granules responsible for the dendritic targeting of messenger RNAs. TRIM3 polyubiquitylates γ-actin, most likely cotranslationally at synaptic sites. Trim3(-/-) mice consequently have increased levels of γ-actin at hippocampal synapses, resulting in higher spine densities, increased long-term potentiation, and enhanced short-term contextual fear memory consolidation. Interestingly, hippocampal deletion of Actg1 caused an increase in long-term fear memory. Collectively, our findings suggest that temporal control of γ-actin levels by TRIM3 is required to regulate the timing of hippocampal plasticity. We propose a model in which TRIM3 regulates synaptic γ-actin turnover and actin filament stability and thus forms a transient inhibitory constraint on the expression of hippocampal synaptic plasticity.

Coordinated binding of NF-kappaB family members in the response of human cells to lipopolysaccharide.

The NF-kappaB family of transcription factors plays a critical role in numerous cellular processes, particularly the immune response. Our understanding of how the different NF-kappaB subunits act coordinately to regulate gene expression is based on a limited set of genes. We used genome-scale location analysis to identify targets of all five NF-kappaB proteins before and after stimulation of monocytic cells with bacterial lipopolysaccharide (LPS). In unstimulated cells, p50 and p52 bound to a large number of gene promoters that were also occupied by RNA polymerase II. After LPS stimulation, additional NF-kappaB subunits bound to these genes and to other genes. Genes that became bound by multiple NF-kappaB subunits were the most likely to show increases in RNA polymerase II occupancy and gene expression. This study identifies NF-kappaB target genes, reveals how the different NF-kappaB proteins coordinate their activity, and provides an initial map of the transcriptional regulatory network that underlies the host response to infection.

A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data.

MOTIVATION: Genome-wide chromatin-immunoprecipitation (ChIP-chip) detects binding of transcriptional regulators to DNA in vivo at low resolution. Motif discovery algorithms can be used to discover sequence patterns in the bound regions that may be recognized by the immunoprecipitated protein. However, the discovered motifs often do not agree with the binding specificity of the protein, when it is known. RESULTS: We present a powerful approach to analyzing ChIP-chip data, called THEME, that tests hypotheses concerning the sequence specificity of a protein. Hypotheses are refined using constrained local optimization. Cross-validation provides a principled standard for selecting the optimal weighting of the hypothesis and the ChIP-chip data and for choosing the best refined hypothesis. We demonstrate how to derive hypotheses for proteins from 36 domain families. Using THEME together with these hypotheses, we analyze ChIP-chip datasets for 14 human and mouse proteins. In all the cases the identified motifs are consistent with the published data with regard to the binding specificity of the proteins.