Transcriptional elongation control of hypoxic response.

The release of paused RNA polymerase II (RNAPII) from promoter-proximal regions is tightly controlled to ensure proper regulation of gene expression. The elongation factor PTEF-b is known to release paused RNAPII via phosphorylation of the RNAPII C-terminal domain by its cyclin-dependent kinase component, CDK9. However, the signal and stress-specific roles of the various RNAPII-associated macromolecular complexes containing PTEF-b/CDK9 are not yet clear. Here, we identify and characterize the CDK9 complex required for transcriptional response to hypoxia. Contrary to previous reports, our data indicate that a CDK9 complex containing BRD4 but not AFF1/4 is essential for this hypoxic stress response. We demonstrate that BRD4 bromodomains (BET) are dispensable for the release of paused RNAPII at hypoxia-activated genes and that BET inhibition by JQ1 is insufficient to impair hypoxic gene response. Mechanistically, we demonstrate that the C-terminal region of BRD4 is required for Polymerase-Associated Factor-1 Complex (PAF1C) recruitment to establish an elongation-competent RNAPII complex at hypoxia-responsive genes. PAF1C disruption using a small-molecule inhibitor (iPAF1C) impairs hypoxia-induced, BRD4-mediated RNAPII release. Together, our results provide insight into potentially targetable mechanisms that control the hypoxia-responsive transcriptional elongation.

ELOA3: A primate-specific RNA polymerase II elongation factor encoded by a tandem repeat gene cluster.

The biological role of the repetitive DNA sequences in the human genome remains an outstanding question. Recent long-read human genome assemblies have allowed us to identify a function for one of these repetitive regions. We have uncovered a tandem array of conserved primate-specific retrogenes encoding the protein Elongin A3 (ELOA3), a homolog of the RNA polymerase II (RNAPII) elongation factor Elongin A (ELOA). Our genomic analysis shows that the ELOA3 gene cluster is conserved among primates and the number of ELOA3 gene repeats is variable in the human population and across primate species. Moreover, the gene cluster has undergone concerted evolution and homogenization within primates. Our biochemical studies show that ELOA3 functions as a promoter-associated RNAPII pause-release elongation factor with distinct biochemical and functional features from its ancestral homolog, ELOA. We propose that the ELOA3 gene cluster has evolved to fulfil a transcriptional regulatory function unique to the primate lineage that can be targeted to regulate cellular hyperproliferation.

Distinct layers of BRD4-PTEFb reveal bromodomain-independent function in transcriptional regulation.

The BET family protein BRD4, which forms the CDK9-containing BRD4-PTEFb complex, is considered to be a master regulator of RNA polymerase II (Pol II) pause release. Because its tandem bromodomains interact with acetylated histone lysine residues, it has long been thought that BRD4 requires these bromodomains for its recruitment to chromatin and transcriptional regulatory function. Here, using rapid depletion and genetic complementation with domain deletion mutants, we demonstrate that BRD4 bromodomains are dispensable for Pol II pause release. A minimal, bromodomain-less C-terminal BRD4 fragment containing the PTEFb-interacting C-terminal motif (CTM) is instead both necessary and sufficient to mediate Pol II pause release in the absence of full-length BRD4. Although BRD4-PTEFb can associate with chromatin through acetyl recognition, our results indicate that a distinct, active BRD4-PTEFb population functions to regulate transcription independently of bromodomain-mediated chromatin association. These findings may enable more effective pharmaceutical modulation of BRD4-PTEFb activity.

STARD Adherence in an Interventional Radiology Guideline for Diagnostic Arteriography.

Objective: To assess the quality of reporting in diagnostic accuracy studies (DAS) referenced by the Quality Improvement Guidelines for Diagnostic Arteriography and their adherence to the Standards for Reporting of Diagnostic Accuracy (STARD) statement.Materials and Methods: Citations specific to the Society of Interventional Radiology's Quality Improvement Guidelines for Diagnostic Arteriography were collected. Using the 34-item STARD checklist, two authors in a duplicate and blinded fashion documented the number of items reported per diagnostic accuracy study. Authors met, and any discrepancies were resolved in a resolution meeting.Results: Of the 26 diagnostic accuracy studies included, the mean number of STARD items reported was 17.8 (SD ± 3.1). The median adherence was 18 (IQR, 17-19) items. Ten articles were published prior to 2003, the original date of STARD publication, and 16 articles were published after 2003. The mean number of reported items for the articles published prior to STARD 2003, and after STARD 2003 was 17.4 (SD ± 2.4) and 18.1 (SD ± 3.5), respectively. There were 14 STARD items that demonstrated an adherence of < 25%, and 13 an adherence > 75%.Conclusion: The dichotomous distribution of adherence to the STARD statement by DAS investigated demonstrates that areas of deficient reporting may be present and require attention to ensure complete and transparent reporting in the future.

Adherence to the RIGHT statement in Society of Interventional Radiology guidelines.

CONTEXT: The Reporting Items for Practice Guidelines in Health Care (RIGHT) Statement was developed by a multidisciplinary team of experts to improve reporting quality and transparency in clinical practice guideline development. OBJECTIVE: To assess the quality of reporting in clinical practice guidelines put forth by the Society of Interventional Radiology (SIR) and their adherence to the RIGHT statement checklist. METHODS: In March 2018, using the 22 criteria listed in the RIGHT statement, two researchers independently documented adherence to each item for all eligible guidelines listed by the SIR by reading through each guideline and using the RIGHT statement elaboration and explanation document as a guide to determine if each item was appropriately addressed as listed in the checklist. To qualify for inclusion in this study, each guideline must have met the strict definition for a clinical practice guideline as set forth by the National Institute of Health and the Institute of Medicine, meaning they were informed by a systematic review of evidence and intended to direct patient care and physician decisions. Guidelines were excluded if they were identified as consensus statements, position statements, reporting standards, and training standards or guidelines. After exclusion criteria were applied, the two researchers scored each of the remaining clinical practice guidelines (CPGs) using a prespecified abstraction Google form that reflected the RIGHT statement checklist (22 criteria; 35 items inclusive of subset questions). Each item on the abstraction form consisted of a "yes/no" option; each item on the RIGHT checklist was recorded as "yes" if it was included in the guideline and "no" if it was not. Each checklist item was weighed equally. Partial adherence to checklist items was recorded as "no." Data were extracted into Microsoft Excel (Microsoft Corporation) for statistical analysis. RESULTS: The initial search results yielded 129 CPGs in the following areas: 13 of the guidelines were in the field of interventional oncology; 16 in neurovascular disorders; five in nonvascular interventions; four in pediatrics; 25 in peripheral, arterial, and aortic disease; one in cardiac; one in portal and mesenteric vascular disease; 37 in practice development and safety; three in spine and musculoskeletal disorders; 14 in venous disease; five in renal failure/hemodialysis; and five in women's health. Of the 46 guidelines deemed eligible for evaluation by the RIGHT checklist, 12 of the checklist items showed less than 25% adherence and 13 showed more than 75% adherence. Of 35 individual RIGHT statement checklist items, adherence was found for a mean (SD) of 22.9 items (16.3). The median number of items with adherence was 21 (interquartile range, 7.5-38). CONCLUSION: The quality of reporting in interventional radiology guidelines is lacking in several key areas, including whether patient preferences were considered, whether costs and resources were considered, the strength of the recommendations, and the certainty of the body of evidence. Poor adherence to the RIGHT statement checklist in these guidelines reveals many areas for improvement in guideline reporting.

Analysis of completeness of reporting utilizing the Reporting Items for practice Guidelines in Healthcare Statement in gastroenterology clinical practice guidelines.

AIM: Assessing reporting quality is important as it allows distinctions to be made between poor methodology and poor reporting practices. The Reporting Items for practice Guidelines in Healthcare (RIGHT) Statement checklist was published in 2017 to improve the thoroughness and reporting quality of clinical practice guidelines (CPGs). CPGs are evidence-based recommendations developed to assist clinician decision-making in the diagnosis and management of patients. The aim of this study is to assess the completeness of reporting in CPGs listed by the American College of Gastroenterology (ACG) and their frequency of reporting items listed in the RIGHT Statement. METHODS: Using the 22 criteria (35 items) of the RIGHT Statement checklist, two researchers independently documented the adherence to each item for all eligible guidelines listed by the ACG. This study was conducted from 01/10/18 to 05/12/18. Data were recorded onto a prespecified Google data abstraction form and extracted into MS Excel for statistical analysis. RESULTS: Out of 38 eligible guidelines, nine of the 35 RIGHT (25.7%) checklist items were met with less than 50% adherence. The mean adherence was 26.8 (SD ±â€Š9.5); median adherence was 30 (interquartile range 21.5-33.5). The publication dates ranged from 2007 to 2017 with seven of the guidelines (18.4%) published between 2007 and 2009, 11 (29%) published between 2010 and 2013, and 20 (52.6%) published between 2014 and 2017. CONCLUSION: The completeness of reporting in CPGs listed by the ACG remains inadequate in several key areas. Poor adherence to items of the RIGHT Statement checklist demonstrates that there is area for improvement in reporting quality.

Predictors of postinjury acute respiratory distress syndrome: Lung injury persists in the era of hemostatic resuscitation.

BACKGROUND: Acute respiratory distress syndrome (ARDS) following trauma is historically associated with crystalloid and blood product exposure. Advances in resuscitation have occurred over the last decade, but their impact on ARDS is unknown. We sought to investigate predictors of postinjury ARDS in the era of hemostatic resuscitation. METHODS: Data were prospectively collected from arrival to 28 days for 914 highest-level trauma activations who required intubation and survived more than 6 hours from 2005 to 2016 at a Level I trauma center. Patients with ratio of partial pressure of oxygen to fraction of inspired oxygen of 300 mmHg or less during the first 8 days were identified. Two blinded expert clinicians adjudicated all chest radiographs for bilateral infiltrates in the first 8 days. Those with left-sided heart failure detected were excluded. Multivariate logistic regression was used to define predictors of ARDS. RESULTS: Of the 914 intubated patients, 63% had a ratio of partial pressure of oxygen to fraction of inspired oxygen of 300 or less, and 22% developed ARDS; among the ARDS cases, 57% were diagnosed early (in the first 24 hours), and 43% later. Patients with ARDS diagnosed later were more severely injured (ISS 32 vs. 20, p = 0.001), with higher rates of blunt injury (84% vs. 72%, p = 0.008), chest injury (58% vs. 36%, p < 0.001), and traumatic brain injury (72% vs. 48%, p < 0.001) compared with the no ARDS group. In multivariate analysis, head/chest Abbreviated Injury Score scores, crystalloid from 0 to 6 hours, and platelet transfusion from 0 to 6 hours and 7 to 24 hours were independent predictors of ARDS developing after 24 hours. CONCLUSIONS: Blood and plasma transfusion were not independently associated with ARDS. However, platelet transfusion was a significant independent risk factor. The role of platelets warrants further investigation but may be mechanistically explained by lung injury models of pulmonary platelet sequestration with peripheral thrombocytopenia. LEVEL OF EVIDENCE: Prognostic study, level IV.

Lack of Current Recommendations for Resuming Sexual Activity Following Spinal Surgery.

Patients are faced with many questions surrounding the after effects of the various surgical procedures and their ability to return to preoperative activities. While patients often question whether surgery would provide alleviation of pain, weakness, and instability, they often have additional questions about sexual activity during their convalescence that are not always addressed. Although the literature shows postsurgical improvement in sexual activity in association with improved low back pain, reports vaguely address the variability in sexual activity recommendations based on anatomic location and type of spinal surgery. We conducted a PubMed search of the English language from 1990 to 2018 with the following keywords: sexual activity, postoperative, spinal fusion, spinal decompression, functional outcomes, laminectomy, rehabilitation, biomechanics, lumbar disc surgery, metabolic energy expenditure, coital position, and Oswestry Disability Index. Additional studies are needed that survey both patients and spine surgeons to examine current recommendations and to help formulate future guidelines.

Does the Cage Position in Transforaminal Lumbar Interbody Fusion Determine Unilateral versus Bilateral Screw Placement?: A Review of the Literature.

This literature review examines the relative placement of the interbody cage with respect to the unilateral screw construct to address the need for bilateral screw placement versus unilateral screw placement. Transforaminal lumbar interbody fusion (TLIF) has become a widely used technique for correcting lumbar intervertebral pathologies. This review addresses the necessity for further study on the effects of the relative position of intervertebral cage placement on the outcome of lumbar spine surgery after TLIF with unilateral pedicle screw fixation. Previous studies have addressed various factors, including posterior screw fixation, cage size, cage shape, and number of levels fused, that impact the biomechanics of the lumbar spine following TLIF. A simple survey of the literature was conducted. A search of the English literature was conducted using the keywords 'TLIF,' 'transforaminal lumbar interbody fusion,' 'graft placement,' 'graft position,' 'cage position,' 'cage placement,' 'unilateral pedicle screw,' 'unilateral TLIF cage placement,' 'lumbar biomechanics,' 'lumbar stability,' 'lumbar fusion,' and 'lumbar intervertebral cage' with various combinations of the operators 'AND' and 'OR' and no date restrictions. Seventeen articles in the English literature that were most relevant to this research question were identified. To the best of our knowledge, there are no published data addressing the effects of cage placement relative to the unilateral screw on lumbar stability in TLIF with unilateral pedicle screw fixation. Investigation of the effects of cage placement is, thus, warranted to achieve optimal clinical outcomes in patients undergoing TLIF with unilateral pedicle screw fixation.

Health care utilization and the cost of posttraumatic acute respiratory distress syndrome care.

BACKGROUND: Posttraumatic acute respiratory distress syndrome (ARDS) is associated with prolonged mechanical ventilation and longer hospitalizations. The relationship between posttraumatic ARDS severity and financial burden has not been previously studied. We hypothesized that increasing ARDS severity is associated with incrementally higher health care costs. METHODS: Adults arriving as the highest level of trauma activation were enrolled in an ongoing prospective cohort study. Patients who survived 6 hours or longer are included in the analysis. Blinded review of chest radiographs was performed by two independent physicians for any intubated patient with PaO2:FIO2 ratio of 300 mmHg or lower during the first 8 days of admission. The severity of ARDS was classified by the Berlin criteria. Hospital charge data were used to perform standard costing analysis. RESULTS: Acute respiratory distress syndrome occurred in 13% (203 of 1,586). The distribution of disease severity was 33% mild, 42% moderate, and 25% severe. Patients with ARDS were older (41 years vs. 35 years, p < 0.01), had higher median Injury Severity Score (30 vs. 10, p < 0.01), more chest injury (Abbreviated Injury Scale score, ≥ 3: 51% vs. 21%, p < 0.01), and blunt mechanisms (85% vs. 53%, p < 0.01). By ARDS severity, there was no significant difference in age, mechanism, or rate of traumatic brain injury. Increasing ARDS severity was associated with higher Injury Severity Score and higher mortality rates. Standardized total hospital charges were fourfold higher for patients who developed ARDS compared with those who did not develop ARDS (US $434,000 vs. US $96,000; p < 0.01). Furthermore, the daily hospital charges significantly increased across categories of worsening ARDS severity (mild, US $20,451; moderate, US $23,994; severe, US $33,316; p < 0.01). CONCLUSION: The development of posttraumatic ARDS is associated with higher health care costs. Among trauma patients who develop ARDS, total hospital charges per day increase with worsening severity of disease. Prevention, early recognition, and treatment of ARDS after trauma are potentially important objectives for efforts to control health care costs in this population. LEVEL OF EVIDENCE: Economic and value-based evaluations, level IV.

Exposing the bidirectional effects of alcohol on coagulation in trauma: Impaired clot formation and decreased fibrinolysis in rotational thromboelastometry.

BACKGROUND: Alcohol has been associated with altered viscoelastic testing in trauma, indicative of impaired coagulation. Such alterations, however, show no correlation to coagulopathy-related outcomes. Other data suggest that alcohol may inhibit fibrinolysis. We sought to clarify these mechanisms after traumatic injury using thromboelastometry (ROTEM), hypothesizing that alcohol-related clot formation impairment may be counter-balanced by inhibited fibrinolysis. METHODS: Laboratory, demographic, clinical, and outcome data were prospectively collected from 406 critically injured trauma patients at a Level I trauma center. ROTEM and standard coagulation measures were conducted in parallel. Univariate comparisons were performed by alcohol level (EtOH), with subsequent regression analysis. RESULTS: Among 274 (58%) patients with detectable EtOH, median EtOH was 229 mg/dL. These patients were primarily bluntly injured and had lower GCS (p < 0.05) than EtOH-negative patients, but had similar admission pH and injury severity (p = NS). EtOH-positive patients had prolonged ROTEM clotting time and rate of clot formation time (CFT/α); they also had decreased fibrinolysis (max lysis %; all p < 0.05). In linear regression, for every 100 mg/dL increase in EtOH, clotting time increased by 13 seconds and fibrinolysis decreased by 1.5% (both p < 0.05). However, EtOH was not an independent predictor of transfusion requirements or mortality. In high-EtOH patients with coagulopathic ROTEM tracings, transfusion rates were significantly lower than expected, relative to EtOH-negative patients with similar ROTEM findings. CONCLUSION: As assayed by ROTEM, alcohol appears to have a bidirectional effect on coagulation in trauma, both impairing initial clot formation and inhibiting fibrinolysis. This balancing of mechanisms may explain lack of correlation between altered ROTEM and coagulopathy-related outcomes. Viscoelastic testing should be used with caution in intoxicated trauma patients. LEVEL OF EVIDENCE: Epidemiological study, level III.

Inconsistent selection of outcomes and measurement devices found in shoulder arthroplasty research: An analysis of studies on ClinicalTrials.gov.

INTRODUCTION: Recent evidence suggests a lack of standardization of shoulder arthroplasty outcomes. This issue is a limiting factor in systematic reviews. Core outcome set (COS) methodology could address this problem by delineating a minimum set of outcomes for measurement in all shoulder arthroplasty trials. METHODS: A ClinicalTrials.gov search yielded 114 results. Eligible trials were coded on the following characteristics: study status, study type, arthroplasty type, sample size, measured outcomes, outcome measurement device, specific metric of measurement, method of aggregation, outcome classification, and adverse events. RESULTS: Sixty-six trials underwent data abstraction and data synthesis. Following abstraction, 383 shoulder arthroplasty outcomes were organized into 11 outcome domains. The most commonly reported outcomes were shoulder outcome score (n = 58), pain (n = 33), and quality of life (n = 15). The most common measurement devices were the Constant-Murley Shoulder Outcome Score (n = 38) and American Shoulder and Elbow Surgeons Shoulder Score (n = 33). Temporal patterns of outcome use was also found. CONCLUSION: Our study suggests the need for greater standardization of outcomes and instruments. The lack of consistency across trials indicates that developing a core outcome set for shoulder arthroplasty trials would be worthwhile. Such standardization would allow for more effective comparison across studies in systematic reviews, while at the same time consider important outcomes that may be underrepresented otherwise. This review of outcomes provides an evidence-based foundation for the development of a COS for shoulder arthroplasty.

Systematic review: Outcome reporting bias is a problem in high impact factor neurology journals.

BACKGROUND: Selective outcome reporting is a significant methodological concern. Comparisons between the outcomes reported in clinical trial registrations and those later published allow investigators to understand the extent of selection bias among trialists. We examined the possibility of selective outcome reporting in randomized controlled trials (RCTs) published in neurology journals. METHODS: We searched PubMed for randomized controlled trials from Jan 1, 2010 -Dec 31, 2015 published in the top 3 impact factor neurology journals. These articles were screened according to specific inclusion criteria. Each author individually extracted data from trials following a standardized protocol. A second author verified each extracted element and discrepancies were resolved. Consistency between registered and published outcomes was evaluated and correlations between discrepancies and funding, journal, and temporal trends were examined. RESULTS: 180 trials were included for analysis. 10 (6%) primary outcomes were demoted, 38 (21%) primary outcomes were omitted from the publication, and 61 (34%) unregistered primary outcomes were added to the published report. There were 18 (10%) cases of secondary outcomes being upgraded to primary outcomes in the publication, and there were 53 (29%) changes in timing of assessment. Of 82 (46%) major discrepancies with reported p-values, 54 (66.0%) favored publication of statistically significant results. CONCLUSION: Across trials, we found 180 major discrepancies. 66% of major discrepancies with a reported p-value (n = 82) favored statistically significant results. These results suggest a need within neurology to provide more consistent and timely registration of outcomes.

Variable methodological quality and use found in systematic reviews referenced in STEMI clinical practice guidelines.

BACKGROUND: The objective of this study was to assess the methodological quality and clarity of reporting of the systematic reviews (SRs) supporting clinical practice guideline (CPG) recommendations in the management of ST-elevation myocardial infarction (STEMI) across international CPGs. METHODS: We searched 13 guideline clearinghouses including the National Guideline Clearinghouse and Guidelines International Network (GIN). To meet inclusion criteria CPGs must be pertinent to the management of STEMI, endorsed by a governing body or national organization, and written in English. We retrieved SRs from the reference sections using a combination of keywords and hand searching. Two investigators scored eligible SRs using AMSTAR and PRISMA. RESULTS: We included four CPGs. We extracted 71 unique SRs. These SRs received AMSTAR scores ranging from 1 (low) to 9 (high) on an 11-point scale. All CPGs consistently underperformed in areas including disclosure of funding sources, risk of bias, and publication bias according to AMSTAR. PRISMA checklist completeness ranged from 44% to 96%. The PRISMA scores indicated that SRs did not provide a full search strategy, study protocol and registration, assessment of publication bias or report funding sources. Only one SR was referenced in all four CPGs. All CPGs omitted a large subset of available SRs cited by other guidelines. CONCLUSIONS: Our study demonstrates the variable quality of SRs used to establish recommendations within guidelines included in our sample. Although guideline developers have acknowledged this variability, it remains a significant finding that needs to be addressed further. FUNDING: This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

Characterization of distinct coagulopathic phenotypes in injury: Pathway-specific drivers and implications for individualized treatment.

BACKGROUND: International normalized ratio (INR) and partial thromboplastin time (PTT) are used interchangeably to diagnose acute traumatic coagulopathy but reflect disparate activation pathways. In this study, we identified injury/patient characteristics and coagulation factors that drive contact pathway, tissue factor pathway (TF), and common pathway dysfunction by examining injured patients with discordant coagulopathies. We hypothesized that patients with INR/PTT discordance reflect differing phenotypes representing contact versus tissue factor pathway perturbations and that characterization will provide targets to guide individualized resuscitation. METHODS: Plasma samples were prospectively collected from 1,262 critically injured patients at a single Level I trauma center. Standard coagulation measures and an extensive panel of procoagulant and anticoagulant factors were assayed and analyzed with demographic and outcome data. RESULTS: Fourteen percent of patients were coagulopathic on admission. Among these, 48% had abnormal INR and PTT (BOTH), 43% had isolated prolonged PTT (PTT-CONTACT), and 9% had isolated elevated INR (INR-TF). PTT-CONTACT and BOTH had lower Glasgow Coma Scale score than INR-TF (p < 0.001). INR-TF had decreased factor VII activity compared with PTT-CONTACT, whereas PTT-CONTACT had decreased factor VIII activity compared with INR-TF. All coagulopathic patients had factor V deficits, but activity was lowest in BOTH, suggesting an additive downstream effect of disordered activation pathways. Patients with PTT-CONTACT received half as much packed red blood cell and fresh frozen plasma as did the other groups (p < 0.001). Despite resuscitation, mortality was higher for coagulopathic patients; mortality was highest in BOTH and higher in PTT-CONTACT than in INR-TF (71%, 60%, 41%; p = 0.04). CONCLUSIONS: Discordant phenotypes demonstrate differential factor deficiencies consistent with dysfunction of contact versus tissue factor pathways with additive effects from common pathway dysfunction. Recognition and treatment of pathway-specific factor deficiencies driving different coagulopathic phenotypes in injured patients may individualize resuscitation and improve outcomes. LEVEL OF EVIDENCE: Prognostic/epidemiological study, level II.

Correlation between factor (F)XIa, FIXa and tissue factor and trauma severity.

BACKGROUND: It has been observed that trauma patients often display elevated procoagulant activity that could be caused, in part, by tissue factor (TF). We previously observed that trauma patients with thermal, blunt, and penetrating injuries have active FIXa and FXIa in their plasma. In the current study, we evaluated the effect of injury severity, with or without accompanying shock, on the frequency and concentration of TF, FIXa, and FXIa in plasma from trauma patients. METHODS: Eighty trauma patients were enrolled and divided equally into four groups based on their Injury Severity Score and base deficit:Blood was collected at a 0 time-point (first blood draw upon arrival at hospital) and citrate plasma was prepared, frozen, and stored at -80 °C. FXIa, FIXa, and TF activity assays were based on a response of thrombin generation to corresponding monoclonal inhibitory antibodies. RESULTS: The frequency and median concentrations of TF were relatively low in non-severe injury groups (17.5% and 0 pM, respectively) but were higher in those with severe injury (65% and 0.5 pM, respectively). Although FXIa was observed in 91% of samples and was high across all four groups, median concentrations were highest (by approximately fourfold) in groups with shock. FIXa was observed in 80% of plasma samples and concentrations varied in a relatively narrow range between all four groups. No endogenous activity was observed in plasma from healthy individuals. CONCLUSIONS: (1) Frequency and concentration of TF is higher in patients with a higher trauma severity. (2) Concentration of FXIa is higher in patients with shock. (3) For the first time reported, the vast majority of plasma samples from trauma patients contain active FIXa and FXIa. LEVEL OF EVIDENCE: Prognostic/epidemiological study, level II.

Characterizing the gut microbiome in trauma: significant changes in microbial diversity occur early after severe injury.

BACKGROUND: Recent studies have demonstrated the vital influence of commensal microbial communities on human health. The central role of the gut in the response to injury is well described; however, no prior studies have used culture-independent profiling techniques to characterize the gut microbiome after severe trauma. We hypothesized that in critically injured patients, the gut microbiome would undergo significant compositional changes in the first 72 hours after injury. METHODS: Trauma stool samples were prospectively collected via digital rectal examination at the time of presentation (0 hour). Patients admitted to the intensive care unit (n=12) had additional stool samples collected at 24 hours and/or 72 hours. Uninjured patients served as controls (n=10). DNA was extracted from stool samples and 16S rRNA-targeted PCR amplification was performed; amplicons were sequenced and binned into operational taxonomic units (OTUs; 97% sequence similarity). Diversity was analyzed using principle coordinates analyses, and negative binomial regression was used to determine significantly enriched OTUs. RESULTS: Critically injured patients had a median Injury Severity Score of 27 and suffered polytrauma. At baseline (0 hour), there were no detectable differences in gut microbial community diversity between injured and uninjured patients. Injured patients developed changes in gut microbiome composition within 72 hours, characterized by significant alterations in phylogenetic composition and taxon relative abundance. Members of the bacterial orders Bacteroidales, Fusobacteriales and Verrucomicrobiales were depleted during 72 hours, whereas Clostridiales and Enterococcus members enriched significantly. DISCUSSION: In this initial study of the gut microbiome after trauma, we demonstrate that significant changes in phylogenetic composition and relative abundance occur in the first 72 hours after injury. This rapid change in intestinal microbiota represents a critical phenomenon that may influence outcomes after severe trauma. A better understanding of the nature of these postinjury changes may lead to the ability to intervene in otherwise pathological clinical trajectories. LEVEL OF EVIDENCE: III. STUDY TYPE: Prognostic/epidemiological.

Individual clotting factor contributions to mortality following trauma.

BACKGROUND: Acute traumatic coagulopathy affects 20% to 30% of trauma patients, but the extensive collinearity of the coagulation cascade complicates attempts to clarify global clotting factor dysfunction. This study aimed to characterize phenotypes of clotting factor dysfunction and their contributions to mortality after major trauma. METHODS: This prospective cohort study examines all adult trauma patients of the highest activation level presenting to San Francisco General Hospital between February 2005 and February 2015. Factors II, V, VII, VIII, IX, and X and protein C activity on admission and mortality status at 28 days were assessed. Predictors of 28-day mortality in univariate analysis were included in multiple logistic regression controlling for traumatic brain injury (TBI), acidosis, age, and mechanism of injury. Principal component analysis was utilized to identify phenotypic coagulation. RESULTS: Complete coagulation factor data were available for 876 (61%) of 1,429 patients. In multiple logistic regression, factors V (odds ratio [OR], 0.86; 95% confidence interval [CI], 0.76-0.97), VIII (OR, 0.97; 95% CI, 0.95-0.99), and X (OR, 0.79; 95% CI, 0.68-0.92) and protein C (OR, 1.17; 95% CI, 1.05-1.30) significantly predicted 28-day mortality after controlling for age, base deficit, mechanism of injury, and TBI. Principal component analysis identified two significant principal components (Phenotypes 1 and 2) that accounted for 66.3% of the total variance. Phenotype 1 (factors II, VII, IX, and X and protein C abnormalities) explained 49.3% and was associated with increased injury, coagulopathy, TBI, and mortality. Phenotype 2 (factors V and VIII abnormalities) explained 17.0% and was associated with increased coagulopathy, blunt injury, and mortality. Only Phenotype 2 remained significantly associated with 28-day mortality in multiple logistic regression. CONCLUSIONS: Principal component analysis identified two distinct phenotypes within the entirety of global clotting factor abnormalities, and these findings substantiate the crucial association of factors V and VIII on mortality following trauma. This may be the first step toward identifying unique phenotypes after injury and personalizing hemostatic resuscitation. LEVEL OF EVIDENCE: Prognostic study, level III.

m(6)A-LAIC-seq reveals the census and complexity of the m(6)A epitranscriptome.

N(6)-Methyladenosine (m(6)A) is a widespread, reversible chemical modification of RNA molecules, implicated in many aspects of RNA metabolism. Little quantitative information exists as to either how many transcript copies of particular genes are m(6)A modified ('m(6)A levels') or the relationship of m(6)A modification(s) to alternative RNA isoforms. To deconvolute the m(6)A epitranscriptome, we developed m(6)A-level and isoform-characterization sequencing (m(6)A-LAIC-seq). We found that cells exhibit a broad range of nonstoichiometric m(6)A levels with cell-type specificity. At the level of isoform characterization, we discovered widespread differences in the use of tandem alternative polyadenylation (APA) sites by methylated and nonmethylated transcript isoforms of individual genes. Strikingly, there is a strong bias for methylated transcripts to be coupled with proximal APA sites, resulting in shortened 3' untranslated regions, while nonmethylated transcript isoforms tend to use distal APA sites. m(6)A-LAIC-seq yields a new perspective on transcriptome complexity and links APA usage to m(6)A modifications.