DHCR7 Expression Predicts Poor Outcomes and Mortality From Sepsis.

This is a study of lipid metabolic gene expression patterns to discover precision medicine for sepsis. OBJECTIVES: Sepsis patients experience poor outcomes including chronic critical illness (CCI) or early death (within 14 d). We investigated lipid metabolic gene expression differences by outcome to discover therapeutic targets. DESIGN SETTING AND PARTICITPANTS: Secondary analysis of samples from prospectively enrolled sepsis patients (first 24 hr) and a zebrafish endotoxemia model for drug discovery. Patients were enrolled from the emergency department or ICU at an urban teaching hospital. Enrollment samples from sepsis patients were analyzed. Clinical data and cholesterol levels were recorded. Leukocytes were processed for RNA sequencing and reverse transcriptase polymerase chain reaction. A lipopolysaccharide zebrafish endotoxemia model was used for confirmation of human transcriptomic findings and drug discovery. MAIN OUTCOMES AND MEASURES: The derivation cohort included 96 patients and controls (12 early death, 13 CCI, 51 rapid recovery, and 20 controls) and the validation cohort had 52 patients (6 early death, 8 CCI, and 38 rapid recovery). RESULTS: The cholesterol metabolism gene 7-dehydrocholesterol reductase (DHCR7) was significantly up-regulated in both derivation and validation cohorts in poor outcome sepsis compared with rapid recovery patients and in 90-day nonsurvivors (validation only) and validated using RT-qPCR analysis. Our zebrafish sepsis model showed up-regulation of dhcr7 and several of the same lipid genes up-regulated in poor outcome human sepsis (dhcr24, sqlea, cyp51, msmo1, and ldlra) compared with controls. We then tested six lipid-based drugs in the zebrafish endotoxemia model. Of these, only the Dhcr7 inhibitor AY9944 completely rescued zebrafish from lipopolysaccharide death in a model with 100% lethality. CONCLUSIONS: DHCR7, an important cholesterol metabolism gene, was up-regulated in poor outcome sepsis patients warranting external validation. This pathway may serve as a potential therapeutic target to improve sepsis outcomes.

DHCR7 Expression Predicts Poor Outcomes and Mortality from Sepsis.

Objective: Sepsis patients experience poor outcomes including chronic critical illness (CCI) or early death (within 14 days). We investigated lipid metabolic gene expression differences by outcome to discover therapeutic targets. Design: Secondary analysis of samples from prospectively enrolled sepsis patients and a zebrafish sepsis model for drug discovery. Setting: Emergency department or ICU at an urban teaching hospital. Patients: Sepsis patients presenting within 24 hours. Methods: Enrollment samples from sepsis patients were analyzed. Clinical data and cholesterol levels were recorded. Leukocytes were processed for RNA sequencing (RNA-seq) and reverse transcriptase polymerase chain reaction (RT-qPCR). A lipopolysaccharide (LPS) zebrafish sepsis model was used for confirmation of human transcriptomic findings and drug discovery. Measurements and Main Results: There were 96 samples in the derivation (76 sepsis, 20 controls) and 52 in the validation cohort (sepsis only). The cholesterol metabolism gene 7-Dehydrocholesterol Reductase ( DHCR7) was significantly upregulated in both derivation and validation cohorts in poor outcome sepsis compared to rapid recovery patients and in 90-day non-survivors (validation only) and validated using RT-qPCR analysis. Our zebrafish sepsis model showed upregulation of dhcr7 and several of the same lipid genes upregulated in poor outcome human sepsis (dhcr24, sqlea, cyp51, msmo1 , ldlra) compared to controls. We then tested six lipid-based drugs in the zebrafish sepsis model. Of these, only the Dhcr7 inhibitor AY9944 completely rescued zebrafish from LPS death in a model with 100% lethality. Conclusions: DHCR7, an important cholesterol metabolism gene, was upregulated in poor outcome sepsis patients warranting external validation. This pathway may serve as a potential therapeutic target to improve sepsis outcomes.

Establishment of SEP-1 national practice guidelines does not impact fluid administration for septic shock patients.

BACKGROUND: The Centers for Medicare and Medicaid Services introduced the Early Management Bundle, Severe Sepsis/Septic Shock (SEP-1) as a national quality measure in October 2015. The purpose of SEP-1 is to facilitate the efficient, effective, and timely delivery of high-quality care to patients presenting along the spectrum of sepsis severity. OBJECTIVES: The primary aim of this study was to investigate whether provider practice surrounding emergency department (ED) fluid management of suspected septic shock patients was impacted by SEP-1. METHODS: The study was a retrospective observational analysis of 470,558 patient encounters at an urban academic center over a five-year period. The sample of suspected septic shock patients was defined by the following: blood cultures collected, antibiotics administered, and vasopressors initiated. Participants were divided into two cohorts based on date of presentation (Pre-SEP-1: May 1, 2013, - August 30, 2015, and Post-SEP-1: November 1, 2015, - February 28, 2018). The primary outcome was classified as a dichotomous variable based on whether the total volume of fluids administered equaled or exceeded the calculated weight-based (≥30 cc/kg) goal. Segmented logistic regression analyses were used to assess the immediate impact of SEP-1 as well as to compare the long-term trend of fluid volume administered between Pre-SEP-1 and Post-SEP-1 cohorts. RESULTS: A total of 413 and 482 septic shock patients were included in the Pre-SEP-1 and Post-SEP-1 cohorts, respectively. There was no statistically significant change in weight-based fluid management between the cohorts. The odds of compliance with the weight-based goal decreased 22% immediately following dissemination of SEP-1, however, this was not statistically significant (log-odds = -0.25, p = 0.41). A positive trend in compliance was observed during both the Pre-SEP-1 and Post-SEP-1 periods with odds ratios increasing 0.005 and 0.018 each month, respectively, however, these findings were not statistically significant (log-odds = 0.005, p = 0.736, and log-odds = 0.018, p = 0.10, respectively). CONCLUSIONS: Overall, there were no clinically or statistically meaningful changes in fluid volume resuscitation strategies for suspected septic shock patients following SEP-1. Broad mandates may not be effective tools for promoting practice change in the ED setting. Further research investigating barrier to changes in practice patterns surrounding fluid administration and other SEP-1 bundle elements is warranted.

Sepsis Fluid Metric Compliance and its Impact on Outcomes of Patients with Congestive Heart Failure, End-Stage Renal Disease or Obesity.

BACKGROUND: Emergency physicians express concern administering a 30-cc/kg fluid bolus to septic shock patients with pre-existing congestive heart failure (CHF), end-stage renal disease (ESRD), or obesity, due to the perceived risk of precipitating a fluid overload state. OBJECTIVE: Our aim was to determine whether there is a difference in fluid administration to septic shock patients with these pre-existing conditions in the emergency department (ED). Secondary objectives focused on whether compliance impacts mortality, need for intubation, and length of stay. METHODS: We conducted a retrospective chart review of 470,558 ED patient encounters at a single urban academic center during a 5-year period. RESULTS: Of 847 patients with septic shock, 308 (36.36%) had no pre-existing condition and 199 (23.49%), 17 (2.01%), and 154 (18.18%) had the single pre-existing condition of CHF, ESRD, and obesity, respectively, and 169 (19.95%) had multiple pre-existing conditions. Weight-based fluid compliance was achieved in 460 patients (54.31%). There was a lower likelihood of compliance among patients with CHF (adjusted odds ratio [aOR] 0.35; 95% confidence interval [CI] 0.24-0.52; p < 0.001), ESRD (aOR 0.11, 95% CI 0.04-0.32; p < 0.001), and obesity (aOR 0.29, 95% CI 0.19-0.44; p < 0.001) compared with patients with no pre-existing conditions. Compliance decreased further in patients with multiple pre-existing conditions (aOR 0.49, 95% CI 0.33-0.72; p < 0.001). Compliance was not associated with mortality in patients with CHF and ESRD, but was protective in patients with obesity and those with no pre-existing conditions. CONCLUSIONS: Septic shock patients with pre-existing CHF, ESRD, or obesity are less likely to achieve compliance with a 30-cc/kg weight-based fluid goal compared with those without these pre-existing conditions.

A review of micronutrients in sepsis: the role of thiamine, l-carnitine, vitamin C, selenium and vitamin D.

Sepsis is defined as the dysregulated host response to an infection resulting in life-threatening organ dysfunction. The metabolic demand from inefficiencies in anaerobic metabolism, mitochondrial and cellular dysfunction, increased cellular turnover, and free-radical damage result in the increased focus of micronutrients in sepsis as they play a pivotal role in these processes. In the present review, we will evaluate the potential role of micronutrients in sepsis, specifically, thiamine, l-carnitine, vitamin C, Se and vitamin D. Each micronutrient will be reviewed in a similar fashion, discussing its major role in normal physiology, suspected role in sepsis, use as a biomarker, discussion of the major basic science and human studies, and conclusion statement. Based on the current available data, we conclude that thiamine may be considered in all septic patients at risk for thiamine deficiency and l-carnitine and vitamin C to those in septic shock. Clinical trials are currently underway which may provide greater insight into the role of micronutrients in sepsis and validate standard utilisation.

Loss of DNA methylation in zebrafish embryos activates retrotransposons to trigger antiviral signaling.

Complex cytoplasmic nucleotide-sensing mechanisms can recognize foreign DNA based on a lack of methylation and initiate an immune response to clear the infection. Zebrafish embryos with global DNA hypomethylation caused by mutations in the ubiquitin-like with PHD and ring finger domains 1 (uhrf1) or DNA methyltransferase 1 (dnmt1) genes exhibit a robust interferon induction characteristic of the first line of defense against viral infection. We found that this interferon induction occurred in non-immune cells and examined whether intracellular viral sensing pathways in these cells were the trigger. RNA-seq analysis of uhrf1 and dnmt1 mutants revealed widespread induction of Class I retrotransposons and activation of cytoplasmic DNA viral sensors. Attenuating Sting, phosphorylated Tbk1 and, importantly, blocking reverse transcriptase activity suppressed the expression of interferon genes in uhrf1 mutants. Thus, activation of transposons in cells with global DNA hypomethylation mimics a viral infection by activating cytoplasmic DNA sensors. This suggests that antiviral pathways serve as surveillance of cells that have derepressed intragenomic parasites due to DNA hypomethylation.

DNA hypomethylation induces a DNA replication-associated cell cycle arrest to block hepatic outgrowth in uhrf1 mutant zebrafish embryos.

UHRF1 (ubiquitin-like, containing PHD and RING finger domains, 1) recruits DNMT1 to hemimethylated DNA during replication and is essential for maintaining DNA methylation. uhrf1 mutant zebrafish have global DNA hypomethylation and display embryonic defects, including a small liver, and they die as larvae. We make the surprising finding that, despite their reduced organ size, uhrf1 mutants express high levels of genes controlling S-phase and have many more cells undergoing DNA replication, as measured by BrdU incorporation. In contrast to wild-type hepatocytes, which are continually dividing during hepatic outgrowth and thus dilute the BrdU label, uhrf1 mutant hepatocytes retain BrdU throughout outgrowth, reflecting cell cycle arrest. Pulse-chase-pulse experiments with BrdU and EdU, and DNA content analysis indicate that uhrf1 mutant cells undergo DNA re-replication and that apoptosis is the fate of many of the re-replicating and arrested hepatocytes. Importantly, the DNA re-replication phenotype and hepatic outgrowth failure are preceded by global loss of DNA methylation. Moreover, uhrf1 mutants are phenocopied by mutation of dnmt1, and Dnmt1 knockdown in uhrf1 mutants enhances their small liver phenotype. Together, these data indicate that unscheduled DNA replication and failed cell cycle progression leading to apoptosis are the mechanisms by which DNA hypomethylation prevents organ expansion in uhrf1 mutants. We propose that cell cycle arrest leading to apoptosis is a strategy that restricts propagation of epigenetically damaged cells during embryogenesis.

UHRF1 overexpression drives DNA hypomethylation and hepatocellular carcinoma.

Ubiquitin-like with PHD and RING finger domains 1 (UHRF1) is an essential regulator of DNA methylation that is highly expressed in many cancers. Here, we use transgenic zebrafish, cultured cells, and human tumors to demonstrate that UHRF1 is an oncogene. UHRF1 overexpression in zebrafish hepatocytes destabilizes and delocalizes Dnmt1 and causes DNA hypomethylation and Tp53-mediated senescence. Hepatocellular carcinoma (HCC) emerges when senescence is bypassed. tp53 mutation both alleviates senescence and accelerates tumor onset. Human HCCs recapitulate this paradigm, as UHRF1 overexpression defines a subclass of aggressive HCCs characterized by genomic instability, TP53 mutation, and abrogation of the TP53-mediated senescence program. We propose that UHRF1 overexpression is a mechanism underlying DNA hypomethylation in cancer cells and that senescence is a primary means of restricting tumorigenesis due to epigenetic disruption.

UHRF1 phosphorylation by cyclin A2/cyclin-dependent kinase 2 is required for zebrafish embryogenesis.

Ubiquitin-like, containing PHD and RING finger domains 1 (uhrf1) is regulated at the transcriptional level during the cell cycle and in developing zebrafish embryos. We identify phosphorylation as a novel means of regulating UHRF1 and demonstrate that Uhrf1 phosphorylation is required for gastrulation in zebrafish. Human UHRF1 contains a conserved cyclin-dependent kinase 2 (CDK2) phosphorylation site at Ser-661 that is phosphorylated in vitro by CDK2 partnered with cyclin A2 (CCNA2), but not cyclin E. An antibody specific for phospho-Ser-661 recognizes UHRF1 in both mammalian cancer cells and in nontransformed zebrafish cells, but not in zebrafish bearing a mutation in ccna2. Depleting Uhrf1 from zebrafish embryos by morpholino injection causes arrest before gastrulation and early embryonic death. This phenotype is rescued by wild-type UHRF1, but not by UHRF1 in which the phospho-acceptor site is mutated, demonstrating that UHRF1 phosphorylation is essential for embryogenesis. UHRF1 was detected in the nucleus and cytoplasm, whereas nonphosphorylatable UHRF1 is unable to localize to the cytoplasm, suggesting the importance of localization in UHRF1 function. Together, these data point to an essential role for UHRF1 phosphorylation by CDK/CCNA2 during early vertebrate development.

Magnetic resonance imaging of urea transporter knockout mice shows renal pelvic abnormalities.

Many transgenic and knockout mice with increased urine flow have structural abnormalities of the renal pelvis and inner medulla. Here, we used high resolution contrast enhanced T1-weighted magnetic resonance imaging of mice whose urea transporters UT-A1 and UT-A3 were deleted (UT-A1/3(-/-) mice) as a model for the in vivo study of such abnormalities. Three distinct variations in the appearance of the renal pelvis were found. These included normal kidneys with no accumulation of contrast agent in the renal pelvis; infrequent frank right-sided unilateral hydronephrosis with marked atrophy of the renal medulla; and a renal pelvic reflux pattern characterized by the presence of contrast agent in the renal pelvis surrounding the renal inner medulla but no substantial atrophy of the medulla. This last pattern was found in most of the advanced age UT-A1/3(-/-) mice and in aquaporin-1 knockout mice. The UT-A1/3(-/-) mice also had increased mean arterial blood pressures. Feeding the mice a low protein diet did not prevent development of their renal pelvic abnormalities. Our studies show that real time imaging of renal pelvic structure in genetically manipulated mice provides a tool for the non-destructive, temporal evaluation of kidney structure.

Akt and ERK1/2 pathways are components of the vasopressin signaling network in rat native IMCD.

Vasopressin regulates water excretion through effects on the renal collecting duct. Vasopressin signaling in the inner medullary collecting duct (IMCD) is mediated by V2 receptor occupation coupled to the generation of cyclic AMP. Here, we employ a "systems" approach to analysis of vasopressin signaling. The objective is to investigate roles of activation of the Akt and ERK1/2 MAP kinase pathways, as well as Ca2+ mobilization, in IMCD cells isolated from rat kidney. The V2 receptor-selective vasopressin analog dDAVP increased the state of Akt activation (increased phosphorylation at T308 and S473) and decreased the state of ERK1/2 activation (decreased phosphorylation at T202 and Y204). Akt activation was blocked by an inhibitor of PI3K, LY294002. In microdissected IMCD segments, nonperiodic spike-like increases in intracellular Ca2+ (FLUO-4) were accelerated by vasopressin. Chelation of Ca2+ or calmodulin inhibition markedly decreased Akt phosphorylation. Decreased ERK1/2 phosphorylation was associated with a decrease in MEK1/2 phosphorylation and an increase in c-Raf phosphorylation at S259 (an inhibitory site). Based on the current findings integrated with previous findings in the IMCD, we now report a 33-node vasopressin signaling network involved in vasopressin regulation of IMCD function.

Functional specificity of a Hox protein mediated by the recognition of minor groove structure.

The recognition of specific DNA-binding sites by transcription factors is a critical yet poorly understood step in the control of gene expression. Members of the Hox family of transcription factors bind DNA by making nearly identical major groove contacts via the recognition helices of their homeodomains. In vivo specificity, however, often depends on extended and unstructured regions that link Hox homeodomains to a DNA-bound cofactor, Extradenticle (Exd). Using a combination of structure determination, computational analysis, and in vitro and in vivo assays, we show that Hox proteins recognize specific Hox-Exd binding sites via residues located in these extended regions that insert into the minor groove but only when presented with the correct DNA sequence. Our results suggest that these residues, which are conserved in a paralog-specific manner, confer specificity by recognizing a sequence-dependent DNA structure instead of directly reading a specific DNA sequence.