Discharge Time of Day and 30-day Hospital Reutilization at an Academic Children's Hospital

BACKGROUND

Pediatric hospital discharge is a complex process. Although morning discharges are operationally preferred, little is known about the association between discharge time of day and discharge outcomes. We assessed whether children discharged from the hospital in the evening have a higher 30-day hospital reutilization rate than those discharged in the morning or afternoon.

METHODS

We conducted a retrospective cohort study on discharges from a children's hospital between July 2016 and December 2019. The cohort was divided into morning, afternoon, and evening discharges. Multivariable modified least-squares regression was used to compare 30-day all-cause hospital reutilization rates between morning, afternoon, and evening discharges while adjusting for demographic and clinical characteristics.

RESULTS

Among 24 994 hospital discharges, 6103 (24.4%) were in the morning, 13 786 (55.2%) were in the afternoon, and 5105 (20.4%) were in the evening. The unadjusted 30-day hospital reutilization rates were 14.1% in children discharged in the morning, 18.2% in children discharged in the afternoon, and 19.3% in children discharged in the evening. The adjusted 30-day hospital reutilization rate was lowest in the morning (6.1%, 95% confidence interval [CI] 4.1%-8.2%), followed by afternoon (9.0%, 95% CI 7.0%-11.0%) and evening discharges (10.1%, 95% CI 8.0%-12.3%). Morning discharge had a significantly lower adjusted 30-day all-cause hospital reutilization rate compared with evening discharge (P < .001), whereas afternoon and evening discharges were not significantly different (P = .06).

CONCLUSIONS

The adjusted 30-day all-cause hospital reutilization rate was higher for evening discharges compared with morning discharges, whereas the rate was not significantly different between afternoon and evening discharges.

Association of HIV and viral suppression status with hospital acute kidney injury in the era of antiretroviral therapy

In the modern era, it is unknown if people that are virally suppressed with HIV (PWH) are at increased risk for acute kidney injury (AKI) compared to people without HIV and no studies have compared the risk of AKI by viral suppression status. Here, we determined the associations of HIV status and AKI among PWH with and without viral suppression compared to people without HIV. An observational cohort study of PWH and people without HIV hospitalized in a large New York City health system between 2010-2019 was conducted. Multivariable Cox proportional hazards models were used to determine associations between HIV status and risk of AKI, severe AKI and development of chronic kidney disease (CKD). Among 173,884 hospitalized patients, 4,718 had HIV; 2,532 (53.7%) were virally suppressed and 2,186 (46.3%) were not suppressed. Compared to people without HIV, PWH with and without viral suppression were at increased risk of AKI (adjusted hazard ratio 1.27, 95% confidence interval 1.15, 1.40 and 1.73, 1.58, 1.90, respectively) and AKI requiring kidney replacement therapy (1.89, 1.27, 2.84 and 1.87, 1.23, 2.84, respectively). Incremental, graded associations were observed between HIV status and Stage 2 or 3 AKI, and among AKI survivors, and incident CKD. The elevated risk of AKI across ages of PWH was similar in magnitude to older people without HIV. Thus, regardless of virologic control, HIV is an independent risk factor for AKI among hospitalized patients. Future studies should determine the mechanisms by which HIV increases susceptibility to AKI and identify strategies to prevent AKI in PWH.

Development of an automated, general-purpose prediction tool for postoperative respiratory failure using machine learning: A retrospective cohort study

STUDY OBJECTIVE

Postoperative respiratory failure is a major surgical complication and key quality metric. Existing prediction tools underperform, are limited to specific populations, and necessitate manual calculation. This limits their implementation. We aimed to create an improved, machine learning powered prediction tool with ideal characteristics for automated calculation.

DESIGN, SETTING, AND PATIENTS

We retrospectively reviewed 101,455 anesthetic procedures from 1/2018 to 6/2021. The primary outcome was the Standardized Endpoints in Perioperative Medicine consensus definition for postoperative respiratory failure. Secondary outcomes were respiratory quality metrics from the National Surgery Quality Improvement Sample, Society of Thoracic Surgeons, and CMS. We abstracted from the electronic health record 26 procedural and physiologic variables previously identified as respiratory failure risk factors. We randomly split the cohort and used the Random Forest method to predict the composite outcome in the training cohort. We coined this the RESPIRE model and measured its accuracy in the validation cohort using area under the receiver operating curve (AUROC) analysis, among other measures, and compared this with ARISCAT and SPORC-1, two leading prediction tools. We compared performance in a validation cohort using score cut-offs determined in a separate test cohort.

MAIN RESULTS

The RESPIRE model exhibited superior accuracy with an AUROC of 0.93 (95% CI, 0.92-0.95) compared to 0.82 for both ARISCAT and SPORC-1 (P-for-difference < 0.0001 for both). At comparable 80-90% sensitivities, RESPIRE had higher positive predictive value (11%, 95% CI: 10-12%) and lower false positive rate (12%, 95% CI: 12-13%) compared to 4% and 37% for both ARISCAT and SPORC-1. The RESPIRE model also better predicted the established quality metrics for postoperative respiratory failure.

CONCLUSIONS

We developed a general-purpose, machine learning powered prediction tool with superior performance for research and quality-based definitions of postoperative respiratory failure.

Improving quality of life and self-care for patients on hemodialysis using cognitive behavioral strategies: A randomized controlled pilot trial

INTRODUCTION

Behavioral-education interventions have the potential to improve quality of life and self-care for patients on hemodialysis (HD) but have not been incorporated into routine clinical practice. The purpose of this pilot study was to determine the feasibility of delivering a simple behavioral-education intervention using cognitive behavioral strategies in patients receiving HD with poor quality of life.

METHODS

In this mixed methods study, HD patients were randomly assigned to the study intervention (8 behavioral-education sessions delivered over 12 weeks) or a control group of dialysis education alone. Kidney disease quality of life (KDQOL)-36 scores, depressive symptoms and self-care behaviors were measured at weeks 0, 8, and 16. Following study completion, participants, social workers, and physicians provided their perspectives about the intervention via qualitative interviews.

FINDINGS

Forty-five participants were randomized. Due, in part, to social worker attrition from the intervention arm, 34 participants (76%) completed at least 1 study session and were included in the analysis. The intervention led to modest, but non-significant, increase in KDQOL-physical component summary scores (+3.1±1.2 points) from week 0 to week 16. There were small, non-significant decreases in interdialytic weight gain and pre-dialysis phosphorus levels in the intervention group. Participants felt that chair-side delivery was practical and efficient, and that content related to the impact of dialysis on daily life was unique and important. Suggestions for adapting the intervention included narrowing its content and its delivery by additional providers that are not necessarily therapy trained.

DISCUSSION

In this pilot study, we were able to deliver a simple behavioral-education intervention to improve both quality of life and self-care. Participants had a positive impression of the intervention, but we did not find significant improvements in quality of life or self-care. We will now adapt our intervention by narrowing its content and by using other providers that are focused solely on delivering the intervention.

Adverse pregnancy outcomes in women with systemic lupus erythematosus: can we improve predictions with machine learning?

OBJECTIVES

Nearly 20% of pregnancies in patients with SLE result in an adverse pregnancy outcome (APO). We previously developed an APO prediction model using logistic regression and data from Predictors of pRegnancy Outcome: bioMarkers In Antiphospholipid Antibody Syndrome and Systemic Lupus Erythematosus (PROMISSE), a large multicentre study of pregnant women with mild/moderate SLE and/or antiphospholipid antibodies. Our goal was to determine whether machine learning (ML) approaches improve APO prediction and identify other risk factors.

METHODS

The PROMISSE data included 41 predictors from 385 subjects; 18.4% had APO (preterm delivery due to placental insufficiency/pre-eclampsia, fetal/neonatal death, fetal growth restriction). Logistic regression with stepwise selection (LR-S), least absolute shrinkage and selection operator (LASSO), random forest (RF), neural network (NN), support vector machines (SVM-RBF), gradient boosting (GB) and SuperLearner (SL) were compared by cross-validated area under the ROC curve (AUC) and calibration.

RESULTS

Previously identified APO risk factors, antihypertensive medication use, low platelets, SLE disease activity and lupus anticoagulant (LAC), were confirmed as important with each algorithm. LASSO additionally revealed potential interactions between LAC and anticardiolipin IgG, among others. SL performed the best (AUC=0.78), but was statistically indistinguishable from LASSO, SVM-RBF and RF (AUC=0.77 for all). LR-S, NN and GB had worse AUC (0.71-0.74) and calibration scores.

CONCLUSIONS

We predicted APO with reasonable accuracy using variables routinely assessed prior to the 12th week of pregnancy. LASSO and some ML methods performed better than a standard logistic regression approach. Substantial improvement in APO prediction will likely be realised, not with increasingly complex algorithms but by the discovery of new biomarkers and APO risk factors.

Long-Term Follow up of Renal and Other Acute Organ Failure in Survivors of Critical Illness Due to Covid-19

BACKGROUND

Little is known about the long-term health sequelae and outcomes of various organ failures in ICU survivors of Covid-19. The aim of our research was to study the characteristics of 120-day ICU survivors of the initial pandemic surge and report their long term (>6 months) outcomes.

METHODS

We conducted a telephone questionnaire-based follow up study of 120- day survivors of Covid-19 admitted to ICUs at Montefiore Medical Center, Bronx, NY from 3/10/2020 to 4/11/2020. The study period was 2 months (11/1/2020-12/31/2020).

RESULTS

126 out of 300 (42%) survived to 120-days post-hospital discharge. The median age of survivors was 54 (47-61) years. Seventy-eight (62%) patients developed acute kidney injury (AKI); thirty-five (44.9%) of them required renal replacement therapy (RRT). One hundred-five (83.3%) required invasive mechanical ventilation; ten of them required tracheotomy. 103 (81.7%) completed the telephone questionnaire-based study, at a median (IQR) of 216.5 (200-234.5) days after hospital discharge. 29 (28.2%) patients reported persistent shortness of breath, 24, (23.3%) complained of persistent cough, and persistent anosmia in 9 (8.8%). AKI resolved completely in 58 (74.4%) patients. Of 35 AKI patients who required initiation of RRT during hospitalization, 27 (77%) were liberated from RRT and 20 (57%) had resolution of AKI. Of 20 patients without AKI resolution, 12 developed chronic kidney disease, whereas 8 still require RRT. Thirty-three (32.4%) patients developed post-traumatic stress disorder (PTSD) and 10 (11.8%) reported major depression. Many of the patients (68%) regained baseline functional status. Readmissions occurred in 22.3% patients within first 6 months after discharge.

CONCLUSION

Persistent symptoms of long Covid have been reported in ICU survivors of Covid-19 for extended durations. Outcomes of Covid-19 associated acute kidney injury are excellent. There is a high incidence of PTSD and depression in COVID-19 ICU survivors. Functional outcomes are good, but these patients remain at increased risk of hospital readmission.

Stress cardiomyopathy in critical care: A case series of 109 patients

BACKGROUND

Critically ill patients are at risk of developing stress cardiomyopathy (SC) but can be under-recognized.

AIM

To describe a case series of patients with SC admitted to critical care units.

METHODS

We conducted a retrospective observational study at a tertiary care teaching hospital. All adult (≥ 18 years old) patients admitted to the critical care units with stress cardiomyopathy over 5 years were included.

RESULTS

Of 24279 admissions to the critical care units [19139 to medical-surgical intensive care units (MSICUs) and 5140 in coronary care units (CCUs)], 109 patients with SC were identified. Sixty (55%) were admitted to the coronary care units (CCUs) and forty-nine (45%) to the medical-surgical units (MSICUs). The overall incidence of SC was 0.44%, incidence in CCU and MSICU was 1.16% and 0.25% respectively. Sixty-two (57%) had confirmed SC and underwent cardiac catheterization whereas 47 (43%) had clinical SC, and did not undergo cardiac catheterization. Forty-three (72%) patients in the CCUs were diagnosed with primary SC, whereas all (100%) patients in MSICUs developed secondary SC. Acute respiratory failure that required invasive mechanical ventilation and shock developed in twenty-nine (59%) MSICU patients. There were no statistically significant differences in intensive care unit (ICU) mortality, in-hospital mortality, use of inotropic or mechanical circulatory support based on type of unit or anatomical variant.

CONCLUSION

Stress cardiomyopathy can be under-recognized in the critical care setting. Intensivists should have a high index of suspicion for SC in patients who develop sudden or worsening unexplained hemodynamic instability, arrhythmias or respiratory failure in ICU.

Social support and dental caries experience: Findings from the Hispanic Community Health Study/Study of Latinos Sociocultural Ancillary Study

OBJECTIVE

To examine the association of social support with dental caries experience in Hispanics/Latinos living in the United States (US) and to assess whether the relationship is modified by nativity status.

METHODS

This cross-sectional study analysed data for 4459 dentate men and women aged 18-74 years in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL) Sociocultural Ancillary Study. At baseline (2008-2011), dentists quantified dental caries experience as the number of decayed, missing, and filled permanent tooth surfaces (DMFS) for all teeth excluding third molars. Social support was assessed according to measures of structural support (Social Network Index) and functional support (Interpersonal Support Evaluation List). Covariate-adjusted multiple linear regression estimated the relationship between social support and dental caries experience and tested whether the association was modified by nativity status (born within the 50 US states, foreign-born <10 years in the United States, foreign-born >10 years or more in the United States).

RESULTS

In covariate-adjusted models, each additional role in the social network was associated with 1.39 fewer DMF tooth surfaces (95% CI: -2.21, -0.58) among foreign-born Hispanics/Latinos with fewer than 10 years lived in the US. For foreign-born Hispanics/Latinos with 10 years or more in the United States, each additional social network role was associated with 0.57 fewer DMF tooth surfaces (95% CI: -1.19, 0.04). No association was observed between functional social support and dental caries experience regardless of nativity status.

CONCLUSIONS

Our findings suggest that structural social support is protective against dental caries experience among recent immigrants of Hispanic/Latino background. This association may reflect the importance of social support to integration into the medical and dental infrastructure and thus receipt of dental care. Future research that examines the behavioural and cultural factors that moderate the relationship between social support and dental caries experience will inform development of culturally sensitive dental caries prevention programs for Hispanics/Latinos in the United States.

Brief Report: Acute Kidney Injury in People Living With HIV Hospitalized With Coronavirus Disease 2019: Clinical Characteristics and Outcomes

BACKGROUND

Data on clinical characteristics and outcomes of people living with HIV (PLWH) hospitalized with coronavirus disease 2019 (COVID-19) who develop acute kidney injury (AKI) are limited.

SETTING

Large tertiary health care system in the Bronx, NY.

METHODS

We performed a retrospective cohort study of 83 PLWH and 4151 patients without HIV hospitalized with COVID-19 from March 10, 2020, to May 11, 2020. We compared the clinical characteristics and outcomes associated with AKI by HIV serostatus and evaluated HIV-related factors for AKI among PLWH. AKI was defined and staged using Kidney Disease Improving Global Outcomes criteria.

RESULTS

The incidence of AKI in hospitalized patients with COVID-19 did not differ significantly by HIV serostatus (54.2% in PLWH vs 49.5% in patients without HIV, P = 0.6). Despite a higher incidence of stage 3 AKI (28.9% vs 17.1% P = 0.05) in PLWH compared with those without HIV, there was no significant difference in the need for renal replacement therapy (22.2% vs 13.4% P = 0.12), renal recovery (76.9% vs 82.5% P = 0.61), or dependence on renal replacement therapy (7.7% vs 3.8% P = 0.27). CD4 T-cell count, HIV-1 RNA viral suppression, and antiretroviral therapy use were not associated with AKI. AKI was associated with increased need for invasive ventilation and in-hospital death, but HIV was not an independent risk factor of in-hospital death after AKI [adjusted hazard ratio 1.01 (95% CI: 0.59 to 1.72), P = 0.98].

CONCLUSIONS

HIV-related factors were not associated with increased risk of AKI in PLWH hospitalized with COVID-19. PLWH hospitalized with COVID-19 had more stage 3 AKI, but outcomes after AKI were similar to those without HIV.

Subgroup discovery in non-inferiority trials

Approaches and guidelines for performing subgroup analysis to assess heterogeneity of treatment effect in clinical trials have been the topic of numerous papers in the statistical and clinical literature, but have been discussed predominantly in the context of conventional superiority trials. Concerns about treatment heterogeneity are the same if not greater in non-inferiority (NI) trials, especially since overall similarity between two treatment arms in a successful NI trial could be due to the existence of qualitative interactions that are more likely when comparing two active therapies. Even in unsuccessful NI trials, subgroup analyses can yield important insights about the potential reasons for failure to demonstrate non-inferiority of the experimental therapy. Recent NI trials have performed a priori subgroup analyses using standard statistical tests for interaction, but there is increasing interest in more flexible machine learning approaches for post-hoc subgroup discovery. The performance and practical application of such methods in NI trials have not been systematically explored, however. We considered the Virtual Twin method for the NI setting, an algorithm for subgroup identification that combines random forest with classification and regression trees, and conducted extensive simulation studies to examine its performance under different NI trial conditions and to devise decision rules for selecting the final subgroups. We illustrate the utility of the method with data from a NI trial that was conducted to compare two acupuncture treatments for chronic musculoskeletal pain.

Clinical Outcomes and Inflammatory Markers by HIV Serostatus and Viral Suppression in a Large Cohort of Patients Hospitalized With COVID-19

BACKGROUND

Limited data exist about clinical outcomes and levels of inflammatory and immune markers among people hospitalized with COVID-19 by HIV serostatus and by HIV viral suppression.

SETTING

Large tertiary care health system in the Bronx, NY, USA.

METHODS

We conducted a retrospective cohort study of 4613 SARS-CoV-2 PCR-positive patients admitted between March 10, 2020, and May 11, 2020. We examined in-hospital intubation, acute kidney injury (AKI), hospitalization length, and in-hospital mortality by HIV serostatus, and by HIV-viral suppression and CD4 counts among people living with HIV (PLWH) using adjusted competing risks regression. We also compared immune and inflammatory marker levels by HIV serostatus and viral suppression.

RESULTS

Most patients were either non-Hispanic Black (36%) or Hispanic (37%); 100/4613 (2.2%) were PLWH, among whom 15 had detectable HIV viral load. PLWH compared to patients without HIV had increased intubation rates (adjusted hazard ratio 1.73 [95% CI: 1.12 to 2.67], P = 0.01). Both groups had similar rates of AKI, length of hospitalization, and death. No (0%) virally unsuppressed PLWH were intubated or died, versus 21/81 (26%, P = 0.04) and 22/81 (27%, P = 0.02) of virally suppressed PLWH, respectively. Among PLWH, higher CD4 T-cell counts were associated with increased intubation rates. C-reactive protein, IL-6, neutrophil counts, and ferritin levels were similar between virally suppressed PLWH and patients without HIV, but significantly lower for unsuppressed PLWH (all P < 0.05).

CONCLUSIONS

PLWH had increased risk of intubation but similarly frequent rates of AKI and in-hospital death as those without HIV. Findings of no intubations or deaths among PLWH with unsuppressed HIV viral load warrant further investigation.

COVID-19-Associated Critical Illness-Report of the First 300 Patients Admitted to Intensive Care Units at a New York City Medical Center

BACKGROUND

The first confirmed case of novel coronavirus (2019-nCoV) infection in the United States was reported from the state of Washington in January, 2020. By March, 2020, New York City had become the epicenter of the outbreak in the United States.

METHODS

We tracked all patients with confirmed coronavirus-19 (COVID-19) infection admitted to intensive care units (ICU) at Montefiore Medical Center (Bronx, NY). Data were obtained through manual review of electronic medical records. Patients had at least 30 days of follow-up.

RESULTS

Our first 300 ICU patients were admitted March 10 through April 11, 2020. The majority (60.7%) of patients were men. Acute respiratory distress syndrome (ARDS) was documented in 91.7% of patients; 91.3% required mechanical ventilation. Prone positioning was employed in 58% of patients and neuromuscular blockade in 47.8% of mechanically-ventilated patients. Neither intervention was associated with decreased mortality. Vasopressors were required in 77.7% of patients. Acute kidney injury (AKI) was present on admission in 40.7% of patients, and developed subsequently in 36.0%; 50.9% of patients with AKI received renal replacement therapy (RRT). Overall 30-day mortality rate was 52.3%, and 55.8% among patients receiving mechanical ventilation. In univariate analysis, higher mortality rate was associated with increasing age, male sex, hypertension, obesity, smoking, number of comorbidities, AKI on presentation, and need for vasopressor support. A representative multivariable model for 30-day mortality is also presented, containing patient age, gender, body mass index, and AKI at admission. As of May 11, 2020, 2 patients (0.7%) remained hospitalized.

CONCLUSIONS

Mortality in critical illness associated with COVID-19 is high. The majority of patients develop ARDS requiring mechanical ventilation, vasopressor-dependent shock, and AKI. The variation in mortality rates reported to date likely reflects differences in the severity of illness of the evaluated populations.

Early prediction of placenta accreta spectrum in women with prior cesarean delivery using transvaginal ultrasound at 11 to 14 weeks

BACKGROUND

There is a growing body of evidence that sonographic signs of placenta accreta spectrum can be observed in the first trimester of pregnancy. The most significant marker is placental location next to or in the scar niche in women with a prior cesarean delivery.

OBJECTIVE

This study aimed to assess the performance of transvaginal ultrasound in the early prediction of placenta accreta spectrum in women with a prior cesarean delivery.

STUDY DESIGN

This was a retrospective cohort of women with a history of cesarean delivery who had transvaginal ultrasound at 11 to 14 weeks' gestation between September 2016 and May 2018. Ultrasound reports were reviewed and graded for suspicion of placenta accreta spectrum as follows: Grade 0 (no suspicion) if the placenta is not next to the scar; Grade 1 (intermediate suspicion) if the placenta is next or on the scar; Grade 2 (high suspicion) if the placenta was inside the scar niche. In addition, all images were reviewed and graded by trained specialists blinded to the outcome. The primary outcome was a histologic diagnosis of placenta accreta spectrum. Sensitivity, specificity, positive predictive value, and negative predictive value of first-trimester transvaginal ultrasound to detect placenta accreta spectrum were assessed.

RESULTS

In this study, 467 patients were included, and 8 (1.7%) had placenta accreta spectrum at delivery. Using the original report, 442 patients (94.6%) were Grade 0, 20 (4.3%) Grade 1, and 5 (1.1%) Grade 2. The revised grading had 456 patients (97.6%) with Grade 0, 5 (1.1%) with Grade 1, and 6 (1.3%) with Grade 2. Patients with Grade 2 yielded a sensitivity of 62.5% (95% confidence interval, 24.5-91.5), specificity of 100% (95% confidence interval, 99.2-100.0), positive predictive value of 100% (95% confidence interval, 97.0-100.0), and negative predictive value of 99.4% (95% confidence interval, 98.4-99.7). Any sonographic suspicion of placenta accreta spectrum (Grade 1 or Grade 2) had a sensitivity of 75% (95% confidence interval, 34.9-96.8), specificity of 95.9% (95% confidence interval, 93.6-97.5), positive predictive value of 24% (95% confidence interval, 14.8-36.4), and negative predictive value of 99.6% (95% confidence interval, 98.5-99.9). The blinded image review yielded a better specificity (99.1% vs 95.9%; P=.001) and a positive predictive value (63.6% vs 24%; P=.02) with similar sensitivity (87.5% vs 75%; P=.52) and negative predictive value (99.8% vs 99.6%; P=.55).

CONCLUSION

Transvaginal ultrasound between 11 and 14 weeks' gestation in women a with prior cesarean delivery can identify at least 3 of 4 cases of placenta accreta spectrum. A finding of placental implantation within the scar niche has high positive predictive value for placenta accreta spectrum. Prospective studies are needed to assess routine screening for placenta accreta spectrum at 11 to 14 weeks' gestation in women with a prior cesarean delivery.

Maternal Dairy Consumption and Hematochezia in Exclusively Breastfed Infants

BACKGROUND

When an exclusively breastfed infant develops hematochezia, the pediatrician may recommend elimination of dairy and soy products from a mother's diet, but there is limited scientific evidence to indicate that altering the maternal diet will lead to resolution of the problem.

RESEARCH AIM

To estimate the likelihood that maternal dairy and soy avoidance will resolve rectal bleeding in an exclusively breastfed infant.

METHODS

This was a prospective, longitudinal, one-group pre/post study involving mothers of exclusively breastfed infants at least 2 weeks but less than 6 months of age with a positive stool guaiac test in the absence of an intestinal lesion or other explanation for the blood. Participants agreed to follow a dairy and soy elimination/rechallenge protocol, maintain a food diary, and have their infant re-tested at 3-week intervals to determine the outcome of the dietary changes. One participant was lost to follow-up, leaving a final sample size of N = 19.

RESULTS

All infants continued to test positive for blood in the stool after their mothers eliminated foods containing dairy or soy. Therefore, 0% (0/19) of infants responded to their mother's restricted diet, 95% confidence interval (one-sided [0%, 15%]).

CONCLUSION

Given these results, we must call into question the rationale for advising breastfeeding mothers to eliminate dairy and soy from their diet in response to their infant's unexplained rectal bleeding.

CHANGING TO BASAL-BOLUS INSULIN THERAPY FOR THE INPATIENT MANAGEMENT OF HYPERGLYCEMIA-A NATURAL EXPERIMENT

Objective: Most acute-care hospitals have transitioned from sliding-scale to basal-bolus insulin therapy to manage hyperglycemia during hospitalization, but there is limited scientific evidence demonstrating better short-term clinical outcomes using the latter approach. The present study sought to determine if using basal-bolus insulin therapy favorably affects these outcomes in noncritical care settings and, if so, whether the magnitude of benefit differs in patients with known versus newly diagnosed type 2 diabetes. Methods: This natural experiment compared outcomes in 10,120 non-critically ill adults with type 2 diabetes admitted to an academic teaching hospital before and after hospital-wide implementation of a basal-bolus insulin therapy protocol. A group of 30,271 inpatients without diabetes (type 1 or 2) served as controls. Binomial models were used to compare percentages of patients with type 2 diabetes who were transferred to intensive care, experienced complications, or died in the hospital before and after implementation of the protocol, controlling for changes in the control group. The analysis also evaluated before-after changes in length of stay and glucometric indicators. Results: Implementation of basal-bolus therapy did not reduce intensive care use (the primary outcome), complications, mortality, or median length of stay, except in patients with newly diagnosed diabetes (n = 234), who experienced a statistically significant decline in the incidence of complications (P<.01). The absence of effect in previously diagnosed patients was observed in spite of a 32% decline (from 3.7% to 2.5%) in the proportion of inpatient days with hypoglycemia <70 mg/dL (P<.01) and a 16% decline (from 13.5% to 11.3%) in the proportion of days with hyperglycemia >300 mg/dL (P<.01). Conclusion: Despite achieving significant reductions in both hyperglycemia and hypoglycemia, use of basal-bolus insulin therapy to manage hyperglycemia in non-critically ill hospitalized patients did not improve short-term clinical outcomes, except in the small minority of patients with newly diagnosed diabetes. The optimal management of hyperglycemia for improving these outcomes has yet to be determined. Abbreviation: ICD-9 = International Classification of Diseases-Ninth Revision.

Repeated lipopolysaccharide exposure leads to placental endotoxin tolerance

PROBLEM

Placental infection induces increased levels of pro-inflammatory cytokines, which have been implicated in the pathogenesis of pre-term labor. Endotoxin tolerance is a phenomenon in which exposure to a dose of endotoxin makes tissue less responsive to subsequent exposures. The objective of our study was to determine whether repeated exposure to endotoxin will induce a tolerant phenotype in normal human second-trimester placental tissue.

METHODS OF STUDY

Human second-trimester placental explants from elective termination of pregnancy were cultured and exposed to endotoxin (LPS). After 24 hours, the media was collected for analysis, and the explants were re-exposed to LPS after adding fresh media for another 24 hours. This process was repeated for a total of 4 LPS doses. The media was collected from each day and analyzed for cytokine levels.

RESULTS

The first LPS treatment stimulated the secretion of the pro-inflammatory cytokines IL-1β and TNF-α. However, their production was significantly diminished with repeated LPS doses. Production of the anti-inflammatory cytokines, IL-1ra and IL-10, was also stimulated by the first LPS treatment, but secretion was more gradually and moderately decreased with repeated LPS doses compared to the pro-inflammatory cytokines. The ratios of the anti-inflammatory/pro-inflammatory mediators (IL-1ra/IL-1β and IL-10/TNF-α) indicate a progressively more anti-inflammatory milieu with repeated LPS doses.

CONCLUSION

Repeated LPS exposure of human second-trimester placental tissues induced endotoxin tolerance. We speculate that endotoxin tolerance at the maternal-fetal interface will protect the fetus from exaggerated inflammatory responses after repeated infectious exposure.

Risk of Death in Infants Who Have Experienced a Brief Resolved Unexplained Event: A Meta-Analysis

OBJECTIVE

To estimate an upper bound on the risk of death after a brief resolved unexplained event (BRUE), a sudden alteration in an infant's breathing, color, tone, or responsiveness, previously labeled "apparent life-threatening event" (ALTE).

STUDY DESIGN

The meta-analysis incorporated observational studies of patients with ALTE that included data on in-hospital and post-discharge deaths with at least 1 week of follow-up after hospital discharge. Pertinent studies were identified from a published review of the literature from 1970 through 2014 and a supplementary PubMed query through February 2017.

RESULTS

The 12 included studies (n = 3005) reported 12 deaths, of which 8 occurred within 4 months of the event. Applying a Poisson-normal random effects model to the 8 proximate deaths using a 4-month time horizon yielded a post-ALTE mortality rate of about 1 in 800, which constitutes an upper bound on the risk of death after a BRUE.

CONCLUSIONS

This risk is about the same as the baseline risk of death during the first year of life. The meta-analysis therefore supports the return-home approach advocated in a recently published clinical practice guideline-not routine hospitalization-for BRUE patients who have been evaluated in the emergency department and determined to be at lower risk.

Corneal abrasion following anaesthesia for non-ocular surgical procedures: A case-controlled study

The aim of this study was to identify risk factors associated with perioperative corneal abrasion at a single hospital in Mineola, New York (United States). A chart review was conducted of patients with perioperative corneal abrasion following non-ocular surgery and age-matched controls between June 2011 and November 2013. An age-stratified logistic regression model evaluated the association between corneal abrasion and potentially predisposing variables. The adjusted odds of a corneal abrasion occurring were 4.6 times greater for patients having surgery for ≥ 3 hours (p=0.001) and 3.6 times greater for patients with pre-existing ocular disease (p=0.02). Gender, diabetes status, surgical procedure or position were not found to be associated with the occurrence of a corneal abrasion. Corneal abrasions were associated with longer procedures and history of pre-existing ocular disease. No significant association between body positioning or surgical site and perioperative corneal abrasion was found. The study concludes that a longer duration of surgical procedure and pre-existing ocular disease are risk factors for perioperative corneal abrasion.

Palliative Care in New York State Nursing Homes: A Descriptive Study

Objective:

To describe the current landscape of palliative care (PC) in nursing homes (NHs) in New York State (NYS).

Measurements:

A statewide survey was completed by 149 respondents who named 61 different NHs as their workplace. Questions were related to presence, type, and composition of PC programs; perceptions of PC; barriers to implementing PC; and qualifying medical conditions.

Results:

Hospice is less available than palliative or comfort care programs, with three-fourths of NYS NH responded providing a PC program. In general, medical directors and physicians were more similar in perspective about the role/impact of PC compared to nursing and others. There was general agreement about the positive impact and role of PC in the NH. Funding and staffing were recognized as barriers to implementing PC.

Conclusion:

There is growing penetration of PC programs in NH facilities in NYS, with good perception of the appropriate utilization of PC programs. Financial reimbursement and staffing are barriers to providing PC in the NH and need to be addressed by the health-care system.

Resveratrol counters systemic lupus erythematosus-associated atherogenicity by normalizing cholesterol efflux

Resveratrol is a bioactive molecule used in dietary supplements and herbal medicines and consumed worldwide. Numerous investigations by our group and others have indicated cardioprotective and anti-inflammatory properties of resveratrol. The present study explored potential atheroprotective actions of resveratrol on cholesterol efflux in cultured human macrophages exposed to plasma from systemic lupus erythematosus (SLE) patients. These results were confirmed in ApoE(-/-)Fas(-/-) double knockout mice, displaying a lupus profile with accelerated atherosclerosis. Resveratrol treatment attenuated atherosclerosis in these mice. THP-1 human macrophages were exposed to 10% pooled or individual plasma from patients who met diagnostic criteria for SLE. Expression of multiple proteins involved in reverse cholesterol transport (ABCA1, ABCG1, SR-B1, and cytochrome P450 27-hydroxylase) was assessed using QRT-PCR and Western blotting techniques. Ten-week-old ApoE(-/-)Fas(-/-) double knockout mice (n = 30) were randomly divided into two equal groups of 15, one of which received 0.01% resveratrol for 10 consecutive weeks. Atherosclerosis progression was evaluated in murine aortas. Bone marrow-derived macrophages (BMDM) were cultured and expression of cholesterol efflux proteins was analyzed in each group of mice. Our data indicate that inhibition of cholesterol efflux by lupus plasma in THP-1 human macrophages is rescued by resveratrol. Similarly, administration of resveratrol in a lupus-like murine model reduces plaque formation in vivo and augments cholesterol efflux in BMDM. This study presents evidence for a beneficial role of resveratrol in atherosclerosis in the specific setting of SLE. Therefore, resveratrol may merit investigation as an additional resource available to reduce lipid deposition and atherosclerosis in humans, especially in such vulnerable populations as lupus patients.

Impact of computerized physician order entry alerts on prescribing in older patients

BACKGROUND

A computerized physician order entry (CPOE) system provides opportunity for real-time alerts to prescribers. Winthrop University Hospital began using CPOE in 2009.

OBJECTIVE

We sought to improve prescribing among older hospitalized patients by adding alerts to the CPOE system for potentially inappropriate medications.

METHODS

In January 2011, informational alerts were integrated into the CPOE system for selected high-risk medications: diphenhydramine, metoclopramide, and all antipsychotics. We evaluated the effect of these alerts on prescribing frequency by comparing the number of prescriptions during the second quarters of 2010 ("pre-alert") with the second quarters of 2011 through 2013 ("post-alert"). Prescribing patterns were evaluated through a pharmacy database of medication orders. Frequency of prescribing was adjusted for total discharges. A comparison was made to ages 18-64 years, and comparing "as needed" vs standing orders.

RESULTS

In the 65 years of age and older group, there were significant reductions in prescription rates pre-alert vs post-alert for diphenhydramine (p < 0.001) and metoclopramide (p < 0.001). There was no decrease in prescription rates for antipsychotics in older patients (p = 0.80). In the younger comparison group, no decreases in prescription rates for those drugs were observed. Our analysis is based on numbers of written prescriptions and not actual doses administered; therefore, no conclusions concerning the effect of these alerts on communication or documentation of risk/benefits of these medications can be ascertained.

CONCLUSION

The data suggest that prescribing rates for drugs with the least efficacy and potential for harm and with alternative agents (i.e., diphenhydramine and metoclopramide) can be modified by CPOE alerts for older patients.

Predictive properties of DNA methylation patterns in primary tumor samples for osteosarcoma relapse status

Osteosarcoma is the most common primary malignant bone tumor in children. Validated biological markers for disease prognosis available at diagnosis are lacking. No genome-wide DNA methylation studies linked to clinical outcomes have been reported in osteosarcoma to the best of our knowledge. To address this, we tested the methylome at over 1.1 million loci in 15 osteosarcoma biopsy samples obtained prior to the initiation of therapy and correlated these molecular data with disease outcomes. At more than 17% of the tested loci, samples obtained from patients who experienced disease relapse were more methylated than those from patients who did not have recurrence while patients who did not experience disease relapse had more DNA methylation at fewer than 1%. In samples from patients who went on to have recurrent disease, increased DNA methylation was found at gene bodies, intergenic regions and empirically-annotated candidate enhancers, whereas candidate gene promoters were unusual for a more balanced distribution of increased and decreased DNA methylation with 6.6% of gene promoter loci being more methylated and 2% of promoter loci being less methylated in patients with disease relapse. A locus at the TLR4 gene demonstrates one of strongest associations between DNA methylation and 5 y event-free survival (P-value = 1.7 × 10(-6)), with empirical annotation of this locus showing promoter characteristics. Our data indicate that DNA methylation information has the potential to be predictive of outcome in pediatric osteosarcoma, and that both promoters and non-promoter loci are potentially informative in DNA methylation studies.

Sample size determination for three-level randomized clinical trials with randomization at the first or second level

Clinical trials in the context of comparative effectiveness research (CER) are often conducted to evaluate health outcomes under real-world conditions and standard health care settings. In such settings, three-level hierarchical study designs are increasingly common. For example, patients may be nested within treating physicians, who in turn are nested within an urgent care center or hospital. While many trials randomize the third-level units (e.g., centers) to intervention, in some cases randomization may occur at lower levels of the hierarchy, such as patients or physicians. In this article, we present and verify explicit closed-form sample size and power formulas for three-level designs assuming randomization is at the first or second level. The formulas are based on maximum likelihood estimates from mixed-effect linear models and verified by simulation studies. Results indicate that even with smaller sample sizes, theoretical power derived with known variances is nearly identical to empirically estimated power for the more realistic setting when variances are unknown. In addition, we show that randomization at the second or first level of the hierarchy provides an increasingly statistically efficient alternative to third-level randomization. Power to detect a treatment effect under second-level randomization approaches that of patient-level randomization when there are few patients within each randomized second-level cluster and, most importantly, when the correlation attributable to second-level variation is a small proportion of the overall correlation between patient outcomes.

High-resolution chromatin immunoprecipitation (ChIP) sequencing reveals novel binding targets and prognostic role for SOX11 in mantle cell lymphoma

Sex determining region Y-box 11 (SOX11) expression is specific for mantle cell lymphoma (MCL) as compared with other non-Hodgkin's lymphomas. However, the function and direct-binding targets of SOX11 in MCL are largely unknown. We used high-resolution chromatin immunoprecipitation sequencing to identify the direct target genes of SOX11 in a genome-wide, unbiased manner and elucidate its functional significance. Pathway analysis identified WNT, PKA and TGF-beta signaling pathways as significantly enriched by SOX11-target genes. Quantitative chromatin immunoprecipitation sequencing and promoter reporter assays confirmed that SOX11 directly binds to individual genes and modulates their transcription activities in these pathways in MCL. Functional studies using RNA interference demonstrate that SOX11 directly regulates WNT in MCL. We analyzed SOX11 expression in three independent well-annotated tissue microarrays from the University of Wisconsin (UW), Karolinska Institute and British Columbia Cancer Agency. Our findings suggest that high SOX11 expression is associated with improved survival in a subset of MCL patients, particularly those treated with intensive chemotherapy. Transcriptional regulation of WNT and other biological pathways affected by SOX11-target genes may help explain the impact of SOX11 expression on patient outcomes.

Akt inhibitors MK-2206 and nelfinavir overcome mTOR inhibitor resistance in diffuse large B-cell lymphoma

PURPOSE

The mTOR pathway is constitutively activated in diffuse large B-cell lymphoma (DLBCL). mTOR inhibitors have activity in DLBCL, although response rates remain low. We evaluated DLBCL cell lines with differential resistance to the mTOR inhibitor rapamycin: (i) to identify gene expression profile(s) (GEP) associated with resistance to rapamycin, (ii) to understand mechanisms of rapamycin resistance, and (iii) to identify compounds likely to synergize with mTOR inhibitor.

EXPERIMENTAL DESIGN

We sought to identify a GEP of mTOR inhibitor resistance by stratification of eight DLBCL cell lines with respect to response to rapamycin. Then, using pathway analysis and connectivity mapping, we sought targets likely accounting for this resistance and compounds likely to overcome it. We then evaluated two compounds thus identified for their potential to synergize with rapamycin in DLBCL and confirmed mechanisms of activity with standard immunoassays.

RESULTS

We identified a GEP capable of reliably distinguishing rapamycin-resistant from rapamycin-sensitive DLBCL cell lines. Pathway analysis identified Akt as central to the differentially expressed gene network. Connectivity mapping identified compounds targeting Akt as having a high likelihood of reversing the GEP associated with mTOR inhibitor resistance. Nelfinavir and MK-2206, chosen for their Akt-inhibitory properties, yielded synergistic inhibition of cell viability in combination with rapamycin in DLBCL cell lines, and potently inhibited phosphorylation of Akt and downstream targets of activated mTOR.

CONCLUSIONS

GEP identifies DLBCL subsets resistant to mTOR inhibitor therapy. Combined targeting of mTOR and Akt suppresses activation of key components of the Akt/mTOR pathway and results in synergistic cytotoxicity. These findings are readily adaptable to clinical trials.

Dynamics of cell-mediated immune responses to cytomegalovirus in pediatric transplantation recipients

CMI responses, combined with quantification of CMV DNA (DNAemia), may identify transplantation recipients at risk for invasive disease. PBMC were collected in pediatric transplantation candidates at one, three, and six months post-transplant in 10 subjects (six renal, three cardiac, one stem cell) and at single time points in eight HC and 14 children greater than one yr post-transplant (LTTx). Cells were stimulated with anti-CD3mAb or CMV pp65 peptide pools and responses assessed by IFNG enzyme-linked immunosorbent spot assay and cytokine secretion. IFNG responses to anti-CD3mAb were significantly lower pretransplant relative to HC and were further decreased at one and three months post-transplant, but recovered to levels comparable to HC by six months. Responses to pp65 among CMV-seropositive recipients followed a similar pattern but recovered by three months. CMV-seropositive LTTx and HC showed a Th1 cytokine response to pp65 stimulation. Three LTTx subjects developed CMV DNAemia; two demonstrated decreased responses to anti-CD3mAB (and pp65 in the CMV seropositive subject) at the onset of DNAemia, which recovered as DNAemia resolved. Monitoring CMI in children is feasible and may provide an adjunct biomarker to predict CMV progression and recovery.

Late-replicating heterochromatin is characterized by decreased cytosine methylation in the human genome

Heterochromatin is believed to be associated with increased levels of cytosine methylation. With the recent availability of genome-wide, high-resolution molecular data reflecting chromatin organization and methylation, such relationships can be explored systematically. As well-defined surrogates for heterochromatin, we tested the relationship between DNA replication timing and DNase hypersensitivity with cytosine methylation in two human cell types, unexpectedly finding the later-replicating, more heterochromatic regions to be less methylated than early replicating regions. When we integrated gene-expression data into the study, we found that regions of increased gene expression were earlier replicating, as previously identified, and that transcription-targeted cytosine methylation in gene bodies contributes to the positive correlation with early replication. A self-organizing map (SOM) approach was able to identify genomic regions with early replication and increased methylation, but lacking annotated transcripts, loci missed in simple two variable analyses, possibly encoding unrecognized intergenic transcripts. We conclude that the relationship of cytosine methylation with heterochromatin is not simple and depends on whether the genomic context is tandemly repetitive sequences often found near centromeres, which are known to be heterochromatic and methylated, or the remaining majority of the genome, where cytosine methylation is targeted preferentially to the transcriptionally active, euchromatic compartment of the genome.

Septin 9 isoform expression, localization and epigenetic changes during human and mouse breast cancer progression

Introduction

Altered expression of Septin 9 (SEPT9), a septin coding for multiple isoform variants, has been observed in several carcinomas, including colorectal, head and neck, ovarian and breast, compared to normal tissues. The mechanisms regulating its expression during tumor initiation and progression in vivo and the oncogenic function of its different isoforms remain elusive.

Methods

Using an integrative approach, we investigated SEPT9 at the genetic, epigenetic, mRNA and protein levels in breast cancer. We analyzed a panel of breast cancer cell lines, human primary tumors and corresponding tumor-free areas, normal breast tissues from reduction mammoplasty patients, as well as primary mammary gland adenocarcinomas derived from the polyoma virus middle T antigen, or PyMT, mouse model. MCF7 clones expressing individual GFP-tagged SEPT9 isoforms were used to determine their respective intracellular distributions and effects on cell migration.

Results

An overall increase in gene amplification and altered expression of SEPT9 were observed during breast tumorigenesis. We identified an intragenic alternative promoter at which methylation regulates SEPT9_v3 expression. Transfection of specific GFP-SEPT9 isoforms in MCF7 cells indicates that these isoforms exhibit differential localization and affect migration rates. Additionally, the loss of an uncharacterized SEPT9 nucleolar localization is observed during tumorigenesis.

Conclusions

In this study, we found conserved in vivo changes of SEPT9 gene amplification and overexpression during human and mouse breast tumorigenesis. We show that DNA methylation is a prominent mechanism responsible for regulating differential SEPT9 isoform expression and that breast tumor samples exhibit distinctive SEPT9 intracellular localization. Together, these findings support the significance of SEPT9 as a promising tool in breast cancer detection and further emphasize the importance of analyzing and targeting SEPT9 isoform-specific expression and function.

Widespread hypomethylation occurs early and synergizes with gene amplification during esophageal carcinogenesis

Although a combination of genomic and epigenetic alterations are implicated in the multistep transformation of normal squamous esophageal epithelium to Barrett esophagus, dysplasia, and adenocarcinoma, the combinatorial effect of these changes is unknown. By integrating genome-wide DNA methylation, copy number, and transcriptomic datasets obtained from endoscopic biopsies of neoplastic progression within the same individual, we are uniquely able to define the molecular events associated progression of Barrett esophagus. We find that the previously reported global hypomethylation phenomenon in cancer has its origins at the earliest stages of epithelial carcinogenesis. Promoter hypomethylation synergizes with gene amplification and leads to significant upregulation of a chr4q21 chemokine cluster and other transcripts during Barrett neoplasia. In contrast, gene-specific hypermethylation is observed at a restricted number of loci and, in combination with hemi-allelic deletions, leads to downregulatation of selected transcripts during multistep progression. We also observe that epigenetic regulation during epithelial carcinogenesis is not restricted to traditionally defined “CpG islands,” but may also occur through a mechanism of differential methylation outside of these regions. Finally, validation of novel upregulated targets (CXCL1 and 3, GATA6, and DMBT1) in a larger independent panel of samples confirms the utility of integrative analysis in cancer biomarker discovery.

The incidence of esophageal adenocarcinoma (EA) is increasing at an alarming pace in the United States. Distinct pathological stages of Barrett's metaplasia and low- and high-grade dysplasia can be seen preceding malignant transformation. These precursor lesions provide a unique in vivo model for deepening our understanding the early steps in human neoplasia. By integrating genome-wide DNA methylation, copy number, and transcriptomic datasets obtained from endoscopic biopsies of neoplastic progression within the same individual, we are uniquely able to define the molecular events associated progression of Barrett esophagus. We show that the predominant change during this process is loss of DNA methylation. We show that this global hypomethylation occurs very early during the process and is seen even in preinvasive lesions. This loss of DNA methylation drives carcinogenesis by cooperating with gene amplifications in upregulating proteins during this process. Finally we uncovered proteins that upregulated by loss of methylation or gene amplification (CXCL1 and 3, GATA6, and DMBT1) and show their relevance by validating their levels in larger independent panel of samples, thus confirming the utility of integrative analysis in cancer biomarker discovery.

DNA methylation alterations in multiple myeloma as a model for epigenetic changes in cancer

Epigenetics refers to heritable modifications of the genome that are not a result of changes in the DNA sequence and result in phenotypic changes. These changes can be stably transmitted through cell division and are potentially reversible. Epigenetic events are very important during normal development wherein a single progenitor cell proliferates and differentiates into various somatic cell types. This process occurs through modification of the genome without changing the genetic code. Because epigenetic control of gene expression is so important, aberrant epigenetic regulation can lead to disease and cancer. This article reviews epigenetic changes seen in cancer by examining epigenetic changes commonly found in multiple myeloma, a common hematologic malignancy of plasma cells. Epigenetic control of gene expression can be exerted by changes in DNA methylation, histone modifications, and expression of noncoding RNAs. Each of these regulatory mechanisms interacts with the others at different genomic locations and can be measured quantitatively within the cell, requiring that we consider these mechanisms not individually but as a biological system. DNA methylation was the earliest discovered epigenetic regulator and has been the focus of most investigations in cancer. We have thus focused on DNA methylation changes in the pathogenesis of multiple myeloma, which promises to become an excellent model for systems biological studies of epigenomic dysregulation in human disease.

A randomized trial to assess anti-HIV activity in female genital tract secretions and soluble mucosal immunity following application of 1% tenofovir gel

Background

Preclinical and early phase clinical microbicide studies have not consistently predicted the outcome of efficacy trials. To address this gap, candidate biomarkers of microbicide pharmacodynamics and safety were evaluated in a double-blind, placebo-controlled trial of tenofovir gel, the first microbicide to demonstrate significant protection against HIV acquisition.

Methods

30 women were randomized to apply a single daily dose of tenofovir or placebo gel for 14 consecutive days. Anti-HIV activity was measured in cervicovaginal lavage (CVL) on Days 0, 3, 7, 14 and 21 by luciferase assay as a surrogate marker of pharmacodynamics. Endogenous activity against E. coli and HSV-2 and concentrations of immune mediators were quantified in CVL as candidate biomarkers of safety. Tenofovir levels were measured in CVL and blood.

Results

A significant increase in anti-HIV activity was detected in CVL from women who applied tenofovir gel compared to their endogenous anti-HIV activity in genital tract secretions on Day 0 and compared to activity in CVL from women in the placebo group. The activity correlated significantly with CVL concentration of tenofovir (r = 0.6, p<0.001) and fit a sigmoid E_max pharmacodynamic model. Anti-HIV activity in CVL from women who applied tenofovir persisted when virus was introduced in semen, whereas endogenous anti-HIV activity decreased. Tenofovir did not trigger an inflammatory response or induce sustained loss in endogenous antimicrobial activity or immune mediators.

Conclusions

Tenofovir gel had no deleterious impact on soluble mucosal immunity. The increased anti-HIV activity in CVL, which persisted in the presence of semen and correlated with tenofovir concentration, is consistent with the efficacy observed in a recent clinical trial. These results promote quantified CVL anti-HIV activity as a surrogate of tissue pharmacodynamics and as a potential biomarker of adherence to product. This simple, feasible and inexpensive bioassay may promote the development of models more predictive of microbicide efficacy.

Trial Registration

ClinicalTrials.gov NCT00594373

LINE-1 activity in facultative heterochromatin formation during X chromosome inactivation

During X chromosome inactivation (XCI), Xist RNA coats and silences one of the two X chromosomes in female cells. Little is known about how XCI spreads across the chromosome, although LINE-1 elements have been proposed to play a role. Here we show that LINEs participate in creating a silent nuclear compartment into which genes become recruited. A subset of young LINE-1 elements, however, is expressed during XCI, rather than being silenced. We demonstrate that such LINE expression requires the specific heterochromatic state induced by Xist. These LINEs often lie within escape-prone regions of the X chromosome, but close to genes that are subject to XCI, and are associated with putative endo-siRNAs. LINEs may thus facilitate XCI at different levels, with silent LINEs participating in assembly of a heterochromatic nuclear compartment induced by Xist, and active LINEs participating in local propagation of XCI into regions that would otherwise be prone to escape.

Prognostic and predictive value of 16p12.1 and 16q22.1 copy number changes in human breast cancer

The present study investigated DNA copy number changes mapping to the p and q arms of chromosome 16 in breast cancer with the goal to determine their potential in identifying breast cancer patients with poor prognosis. We identified the minimal overlapping regions on chromosome 16 that are commonly deleted and amplified in breast tumors. Fluorescence in situ hybridization was used to screen a custom-made breast carcinoma tissue microarray representing all tumor grades, in order to detect DNA copy number changes mapping to 16p12.1 and 16q22.1. We generated 16q/16p ratios for each patient and examined the correlation between DNA copy number alterations and the patients' clinical and pathological parameters. We observed lower q/p ratios in grade I invasive carcinomas, compared with grade III carcinomas, which consistently showed high q/p ratios (P < 0.0091 and 0.0075). In addition, age adjusted for grade analysis revealed that tumors from younger patients (<45 yr) had significantly higher q/p ratios, suggesting that in younger individuals those tumors might be more aggressive (P < 0.0001). The finding that higher q/p ratios occur in younger patients offers a tool to identify high-risk individuals most likely to proceed to high grade.

Experimental intrauterine growth restriction induces alterations in DNA methylation and gene expression in pancreatic islets of rats

Intrauterine growth restriction (IUGR) increases susceptibility to age-related diseases, including type 2 diabetes (T2DM), and is associated with permanent and progressive changes in gene expression. Our study was designed to test whether epigenomic dysregulation mediates the cellular memory of this intrauterine event. To test this hypothesis, we isolated pancreatic islets from control and IUGR (induced by bilateral uterine artery ligation at day 18 of fetal life) animals at 7 weeks of age. Using the HELP (HpaII tiny fragment enrichment by ligation-mediated PCR) assay, we generated the first DNA methylation map at almost 1 million unique sites throughout the rat genome in normal pancreatic islet cells, allowing us to identify the changes that occur as a consequence of IUGR. We validated candidate dysregulated loci with quantitative assays of cytosine methylation and gene expression. IUGR changes cytosine methylation at approximately 1,400 loci (false discovery rate of 4.2%) in male rats at 7 weeks of age, preceding the development of diabetes and thus representing candidate loci for mediating the pathogenesis of metabolic disease that occurs later in life. Epigenetic dysregulation occurred preferentially at conserved intergenic sequences, frequently near genes regulating processes known to be abnormal in IUGR islets, such as vascularization, beta-cell proliferation, insulin secretion, and cell death, associated with concordant changes in mRNA expression. These results demonstrate that epigenetic dysregulation is a strong candidate for propagating the cellular memory of intrauterine events, causing changes in expression of nearby genes and long term susceptibility to type 2 diabetes.

Cytosine methylation dysregulation in neonates following intrauterine growth restriction

Background

Perturbations of the intrauterine environment can affect fetal development during critical periods of plasticity, and can increase susceptibility to a number of age-related diseases (e.g., type 2 diabetes mellitus; T2DM), manifesting as late as decades later. We hypothesized that this biological memory is mediated by permanent alterations of the epigenome in stem cell populations, and focused our studies specifically on DNA methylation in CD34+ hematopoietic stem and progenitor cells from cord blood from neonates with intrauterine growth restriction (IUGR) and control subjects.

Methods and Findings

Our epigenomic assays utilized a two-stage design involving genome-wide discovery followed by quantitative, single-locus validation. We found that changes in cytosine methylation occur in response to IUGR of moderate degree and involving a restricted number of loci. We also identify specific loci that are targeted for dysregulation of DNA methylation, in particular the hepatocyte nuclear factor 4α (HNF4A) gene, a well-known diabetes candidate gene not previously associated with growth restriction in utero, and other loci encoding HNF4A-interacting proteins.

Conclusions

Our results give insights into the potential contribution of epigenomic dysregulation in mediating the long-term consequences of IUGR, and demonstrate the value of this approach to studies of the fetal origin of adult disease.

Cytosine methylation dysregulation in neonates following intrauterine growth restriction

BACKGROUND

Perturbations of the intrauterine environment can affect fetal development during critical periods of plasticity, and can increase susceptibility to a number of age-related diseases (e.g., type 2 diabetes mellitus; T2DM), manifesting as late as decades later. We hypothesized that this biological memory is mediated by permanent alterations of the epigenome in stem cell populations, and focused our studies specifically on DNA methylation in CD34+ hematopoietic stem and progenitor cells from cord blood from neonates with intrauterine growth restriction (IUGR) and control subjects.

METHODS AND FINDINGS

Our epigenomic assays utilized a two-stage design involving genome-wide discovery followed by quantitative, single-locus validation. We found that changes in cytosine methylation occur in response to IUGR of moderate degree and involving a restricted number of loci. We also identify specific loci that are targeted for dysregulation of DNA methylation, in particular the hepatocyte nuclear factor 4alpha (HNF4A) gene, a well-known diabetes candidate gene not previously associated with growth restriction in utero, and other loci encoding HNF4A-interacting proteins.

CONCLUSIONS

Our results give insights into the potential contribution of epigenomic dysregulation in mediating the long-term consequences of IUGR, and demonstrate the value of this approach to studies of the fetal origin of adult disease.

Experimental approaches to the study of epigenomic dysregulation in ageing

In this review, we describe how normal ageing may involve the acquisition of epigenetic errors over time, akin to the accumulation of genetic mutations with ageing. We describe how such experiments are currently performed, their limitations technically and analytically and their application to ageing research.

Introduction to epigenomics and epigenome-wide analysis

Epigenetics is the study of heritable change other than those encoded in DNA sequence. Cytosine methylation of DNA at CpG dinucleotides is the most well-studied epigenetic phenomenon, although epigenetic changes also encompass non-DNA methylation mechanisms, such as covalent histone modifications, micro-RNA interactions, and chromatin remodeling complexes. Methylation changes, both global and gene specific, have been observed to be associated with disease, particularly in cancer.This chapter begins with a general overview of epigenomics, and then focuses on understanding and analyzing genome-wide cytosine methylation data. There are many microarray-based techniques available to measure cytosine methylation across the genome, as well as gold-standard techniques based on sequencing bisulfite converted DNA, which is used to measure methylation in a smaller, more targeted set of loci. We have provided an overview of many of the current technologies - their advantages, limitations, and recent improvements. Regardless of which technology is used, the goal is to produce a set of methylation measurements that are highly consistent with true methylation levels of the corresponding set of CpG dinucleotides.Identifying all loci with aberrant methylation or hypomethylation in disease, or in natural processes such as aging, requires the comparison of methylation levels across many samples. In such studies, the development of methylation-based diagnostic tools may be of interest, potentially to be used as early disease detection strategies based on a set of sentinel loci. In addition, the identification of loci with potentially reversible methylation events may result in new therapeutic options. Given the vast number of measurable sites, prioritization of candidate loci is an important and complex issue and rests on a foundation of appropriate statistical testing and summarization. Coupled with statistical estimates of importance, the genomic context of each locus measured may offer important information about the mechanisms by which epigenetic changes impact disease and allows us further refinement of candidate loci. We will conclude this chapter by identifying issues in building methylation-based models for prediction and potential directions of further statistical research in epigenetics.

CG dinucleotide periodicities recognized by the Dnmt3a-Dnmt3L complex are distinctive at retroelements and imprinted domains

The Dnmt3a and Dnmt3L genes are critical mediators of cytosine methylation during gametogenesis, with major actions noted at transposable elements and imprinted loci. The Dnmt3a-Dnmt3L complex was recently described to have preferential activity at CG dinucleotides located 8-10 bp apart. Because cytosine methylation is heterogeneously distributed in the genome, we tested whether this relative sequence preference explains the effects of mutation of the Dnmt3a and Dnmt3L genes using bioinformatic analysis. We found that the human and mouse genomes are significantly enriched in a CG dinucleotide periodicity of 2 bp, leading to an increased frequency of CGs spaced 8 bp apart that represent widespread targets for this protein complex. When we broke down the human and mouse genomes by annotation, we found that this significant 2-bp periodicity and increased 8-bp periodicity are maintained in Alu SINEs in both species. The 8-bp periodicity was mapped genome-wide, identifying enrichment at the promoters of both paternally and maternally methylated imprinted genes and at CG dinucleotide-enriched sequences. We conclude that CG dinucleotide periodicity helps to explain some but not all of the relative sequence specificity of mutations of Dnmt3a or Dnmt3L in the establishment of germline cytosine methylation patterns.

The Einstein Center for Epigenomics: studying the role of epigenomic dysregulation in human disease

There is increasing interest in the role of epigenetic and transcriptional dysregulation in the pathogenesis of a range of human diseases, not just in the best-studied example of cancer. It is, however, quite difficult for an individual investigator to perform these studies, as they involve genome-wide molecular assays combined with sophisticated computational analytical approaches of very large datasets that may be generated from various resources and technologies. In 2008, the Albert Einstein College of Medicine in New York, USA established a Center for Epigenomics to facilitate the research programs of its investigators, providing shared resources for genome-wide assays and for data analysis. As a result, several avenues of research are now expanding, with cancer epigenomics being complemented by studies of the epigenomics of infectious disease and a neuroepigenomics program.

CG dinucleotide clustering is a species-specific property of the genome

Cytosines at cytosine-guanine (CG) dinucleotides are the near-exclusive target of DNA methyltransferases in mammalian genomes. Spontaneous deamination of methylcytosine to thymine makes methylated cytosines unusually susceptible to mutation and consequent depletion. The loci where CG dinucleotides remain relatively enriched, presumably due to their unmethylated status during the germ cell cycle, have been referred to as CpG islands. Currently, CpG islands are solely defined by base compositional criteria, allowing annotation of any sequenced genome. Using a novel bioinformatic approach, we show that CG clusters can be identified as an inherent property of genomic sequence without imposing a base compositional a priori assumption. We also show that the CG clusters co-localize in the human genome with hypomethylated loci and annotated transcription start sites to a greater extent than annotations produced by prior CpG island definitions. Moreover, this new approach allows CG clusters to be identified in a species-specific manner, revealing a degree of orthologous conservation that is not revealed by current base compositional approaches. Finally, our approach is able to identify methylating genomes (such as Takifugu rubripes) that lack CG clustering entirely, in which it is inappropriate to annotate CpG islands or CG clusters.

Outcomes after treatment of cervical intraepithelial neoplasia among women with HIV

OBJECTIVE

To describe outcomes after treatment of cervical intraepithelial neoplasia (CIN) in women with HIV.

MATERIALS AND METHODS

Women in two prospective cohort studies, the Women's Interagency HIV Study (WIHS) and the HIV Epidemiology Research Study (HERS), were followed every 6 months after treatment of CIN using human papillomavirus (HPV) testing and cytology with colposcopy as indicated. Identification of CIN or a squamous intraepithelial lesion (SIL) within 6 months was defined as treatment failure and later disease as recurrence.

RESULTS

Follow-up was available for 170 HIV-seropositive and 15 HIV-seronegative women. Treatment failed in 84 (45%) women (79 HIV seropositive and 5 HIV seronegative). Failure was more likely in women with lower CD4 counts (CD4 < 200 cells/microL: odds ratio [OR] = 2.96; 95% CI = 1.4-6.2) and detectable HPV DNA (OR 8.20; 95% CI = 1.8-37.4; p = .01). After successful treatment, recurrence-free probabilities at 1,2, 3, and 5 years were .79, .64, .49, and .34, respectively. HIV-seronegative women were less likely to recur than HIV-seropositive women (p = .03). In multivariable analysis of HIV-positive women, recurrence was more likely among women treated for CIN 2,3 (hazard ratio [HR] = 2.4; 95% CI = 1.4-4.8), those with CD4 count of less than 200 cells/microL (HR = 2.9; 95% CI = 1.3-6.5) and those with HPV after treatment (HR 2.9; 95% CI = 1.4-6.1); oncogenic HPV was more strongly associated with recurrence than nononcogenic HPV (p(trend) = .009). Most failures and recurrences were low grade, but one adenocarcinoma was diagnosed 4.2 years after therapy for CIN 1.

CONCLUSION

Treatment failure and recurrence are common in women with HIV but are usually low grade.

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.