Synovial Sarcoma Chromatin Dynamics Reveal a Continuum in SS18:SSX Reprograming.

Synovial sarcoma (SyS) is an aggressive soft-tissue malignancy characterized by a pathognomonic chromosomal translocation leading to the formation of the SS18::SSX fusion oncoprotein. SS18::SSX associates with mammalian BAF complexes suggesting deregulation of chromatin architecture as the oncogenic driver in this tumour type. To examine the epigenomic state of SyS we performed comprehensive multi-omics analysis on 52 primary pre-treatment human SyS tumours. Our analysis revealed a continuum of epigenomic states across the cohort at fusion target genes independent of rare somatic genetic lesions. We identify cell-of-origin signatures defined by enhancer states and reveal unexpected relationships between H2AK119Ub1 and active marks. The number of bivalent promoters, dually marked by the repressive H3K27me3 and activating H3K4me3 marks, has strong prognostic value and outperforms tumor grade in predicting patient outcome. Finally, we identify SyS defining epigenomic features including H3K4me3 expansion associated with striking promoter DNA hypomethylation in which SyS displays the lowest mean methylation level of any sarcoma subtype. We explore these distinctive features as potential vulnerabilities in SyS and identify H3K4me3 inhibition as a promising therapeutic strategy.

Prediction Model Performance With Different Imputation Strategies: A Simulation Study Using a North American ICU Registry.

OBJECTIVES: To evaluate the performance of pragmatic imputation approaches when estimating model coefficients using datasets with varying degrees of data missingness. DESIGN: Performance in predicting observed mortality in a registry dataset was evaluated using simulations of two simple logistic regression models with age-specific criteria for abnormal vital signs (mentation, systolic blood pressure, respiratory rate, WBC count, heart rate, and temperature). Starting with a dataset with complete information, increasing degrees of biased missingness of WBC and mentation were introduced, depending on the values of temperature and systolic blood pressure, respectively. Missing data approaches evaluated included analysis of complete cases only, assuming missing data are normal, and multiple imputation by chained equations. Percent bias and root mean square error, in relation to parameter estimates obtained from the original data, were evaluated as performance indicators. SETTING: Data were obtained from the Virtual Pediatric Systems, LLC, database (Los Angeles, CA), which provides clinical markers and outcomes in prospectively collected records from 117 PICUs in the United States and Canada. PATIENTS: Children admitted to a participating PICU in 2017, for whom all required data were available. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Simulations demonstrated that multiple imputation by chained equations is an effective strategy and that even a naive implementation of multiple imputation by chained equations significantly outperforms traditional approaches: the root mean square error for model coefficients was lower using multiple imputation by chained equations in 90 of 99 of all simulations (91%) compared with discarding cases with missing data and lower in 97 of 99 (98%) compared with models assuming missing values are in the normal range. Assuming missing data to be abnormal was inferior to all other approaches. CONCLUSIONS: Analyses of large observational studies are likely to encounter the issue of missing data, which are likely not missing at random. Researchers should always consider multiple imputation by chained equations (or similar imputation approaches) when encountering even only small proportions of missing data in their work.

Mobile Text Messaging to Improve Medication Adherence and Viral Load in a Vulnerable Canadian Population Living With Human Immunodeficiency Virus: A Repeated Measures Study.

BACKGROUND: Combination antiretroviral therapy (cART) as treatment for human immunodeficiency virus (HIV) infection is effective and available, but poor medication adherence limits benefits, particularly in vulnerable populations. In a Kenyan randomized controlled trial, a weekly text-messaging intervention (WelTel) improved cART adherence and HIV viral load (VL). Despite growing evidence for short message service (SMS) text-message interventions in HIV care, there is a paucity of data utilizing these interventions in marginalized or female cohorts. OBJECTIVE: This study was undertaken to assess whether the standardized WelTel SMS text-message intervention applied to a vulnerable, predominantly female, population improved cART adherence and VL. METHODS: We conducted a repeated measures study of the WelTel intervention in high-risk HIV-positive persons by measuring change in VL, CD4 count, and self-reported adherence 12 months before and 12 months after the WelTel intervention was introduced. Inclusion criteria included VL ≥200 copies/mL, indication for treatment, and meeting vulnerability criteria. Participants were given a mobile phone with unlimited texting (where required), and weekly check-in text messages were sent for one year from the WelTel computer platform. Clinical data were collected for control and intervention years. Participants were followed by a multidisciplinary team in a clinical setting. Outcomes were assessed using Wilcoxon signed ranks tests for change in CD4 and VL from control year to study end and mixed-effects logistic regressions for change in cART adherence and appointment attendance. A secondary analysis was conducted to assess the effect of response rate on the outcome by modeling final log10 VL by number of responses while controlling for mean log10 VL in the control year. RESULTS: Eighty-five participants enrolled in the study, but 5 withdrew (final N=80). Participants were predominantly female (90%, 72/80) with a variety of vulnerabilities. Mean VL decreased from 1098 copies/mL in the control year to 439 copies/mL at study end (P=.004). Adherence to cART significantly improved (OR 1.14, IQR 1.10-1.18; P<.001), whereas appointment attendance decreased slightly with the intervention (OR 0.81, IQR 0.67-0.99; P=.03). A response was received for 46.57% (1753/3764) of messages sent and 9.62% (362/3764) of text messages sent were replied to with a problem. An outcome analysis examining relationship between reply rate and VL did not meet statistical significance (P=.07), but may be worthy of investigating further in a larger study. CONCLUSIONS: WelTel may be an effective tool for improving cART adherence and reducing VLs among high-risk, vulnerable HIV-positive persons. TRIAL REGISTRATION: Clinicaltrials.gov NCT02603536; https://clinicaltrials.gov/ct2/show/NCT02603536 (Archived by WebCite at http://www.webcitation.org/6qK57zCwv).