Publications

Genome-wide association studies have identified over 70 single-nucleotide polymorphisms (SNPs) associated with breast cancer. A subset of these SNPs are associated with quantitative expression of nearby genes, but the functional effects of the majority remain unknown. We hypothesized that some risk SNPs may regulate alternative splicing. Using RNA-sequencing data from breast tumors and germline genotypes from The Cancer Genome Atlas, we tested the association between each risk SNP genotype and exon-, exon-exon junction- or transcript-specific expression of nearby genes. Six SNPs were associated with differential transcript expression of seven nearby genes at FDR < 0.05 (BABAM1, DCLRE1B/PHTF1, PEX14, RAD51L1, SRGAP2D and STXBP4). We next developed a Bayesian approach to evaluate, for each SNP, the overlap between the signal of association with breast cancer and the signal of association with alternative splicing. At one locus (SRGAP2D), this method eliminated the possibility that the breast cancer risk and the alternate splicing event were due to the same causal SNP. Lastly, at two loci, we identified the likely causal SNP for the alternative splicing event, and at one, functionally validated the effect of that SNP on alternative splicing using a minigene reporter assay. Our results suggest that the regulation of differential transcript isoform expression is the functional mechanism of some breast cancer risk SNPs and that we can use these associations to identify causal SNPs, target genes and the specific transcripts that may mediate breast cancer risk.

BACKGROUND

Severe sepsis and septic shock are a major health concern worldwide. The objective of this study is to determine if Severe Sepsis Best Practice Alert (SS-BPA) implementation was associated with improved processes of care and clinical outcomes among patients with severe sepsis or septic shock presenting to the emergency department (ED).

METHODS

This is a single-center, before-and-after observational study. The intervention group (n = 103) consisted of adult patients presenting to the ED with severe sepsis or septic shock during a 7-month period after implementation of the SS-BPA. The control group (n = 111) consisted of patients meeting the same criteria over a prior 7-month period. The SS-BPA primarily acts by automated, real-time, algorithm-based detection of severe sepsis or septic shock via the electronic medical record system. The primary outcome was in-hospital mortality. Secondary outcomes included hospital length of stay (LOS), time to antibiotic administration, and proportion of patients who received antibiotics within the target 60 minutes.

RESULTS

Time to antibiotics was significantly reduced in the SS-BPA cohort (29 vs 61.5 minutes, P < .001). In addition, there was a higher proportion of patients who received antibiotics within 60 minutes (76.7 vs 48.6%; P < .001). On multivariable analysis, in-hospital mortality was not significantly reduced in the intervention group (odds ratio, 0.64; 95% confidence interval, 0.26-1.57). Multivariable analysis of LOS indicated a significant reduction among patients in the SS-BPA cohort (geometric mean ratio, 0.66; 95% confidence interval, 0.53-0.82).

CONCLUSION

Implementation of the SS-BPA for severe sepsis or septic shock among ED patients is associated with significantly improved timeliness of antibiotic administration and reduced hospital LOS.

Progression to AIDS is driven by CD4 T cell depletion, mostly involving pyroptosis elicited by abortive HIV infection of CD4 T cells in lymphoid tissues. Inefficient reverse transcription in these cells leads to cytoplasmic accumulation of viral DNAs that are detected by the DNA sensor IFI16, resulting in inflammasome assembly, caspase-1 activation, and pyroptosis. Unexpectedly, we found that peripheral blood-derived CD4 T cells naturally resist pyroptosis. This resistance is partly due to their deeper resting state, resulting in fewer HIV-1 reverse transcripts and lower IFI16 expression. However, when co-cultured with lymphoid-derived cells, blood-derived CD4 T cells become sensitized to pyroptosis, likely recapitulating interactions occurring within lymphoid tissues. Sensitization correlates with higher levels of activated NF-κB, IFI16 expression, and reverse transcription. Blood-derived lymphocytes purified from co-cultures lose sensitivity to pyroptosis. These differences highlight how the lymphoid tissue microenvironment encountered by trafficking CD4 T lymphocytes dynamically shapes their biological response to HIV.

Cigarette smoking is increasingly recognized as an indicator for inferior adherence to antiretroviral therapy (ART) among HIV-positive patients. Given the limited body of work on this issue, we aimed to explore the relations between cigarette smoking, nicotine dependence, and ART adherence in Vietnam. A cross-sectional study of 1050 HIV-positive people was conducted from January to September 2013 in Hanoi (the capital) and Nam Dinh (a rural city). Adherence to ART during the last 30 days was measured by the 100-point visual analog scale (VAS). Smoking history and nicotine dependence (Fagerstrom Test of Nicotine Dependence) were self-reported by participants. Multiple logistic regression was performed to examine the association of current smoking and nicotine dependence with ART nonadherence. Using the established VAS cut point of 95 to indicate adequate adherence, the prevalence of ART nonadherence was 30.9%. Approximately 35.5% of the sample reported current smoking. No association between smoking status and ART nonadherence was found. However, participants with greater nicotine dependence (OR = 1.1, 95%CI = 1.0-1.2 per unit increase) were more likely to be nonadherent. Also, individuals who were female (OR = 1.70, 95%CI = 1.19-2.42), receiving ART in Nam Dinh (OR = 1.6, 95%CI = 1.1-2.4), and currently feeling anxiety (OR = 1.6, 95% CI = 1.2-2.1) had a higher likelihood of ART nonadherence. Additionally, current smokers reporting current pain (OR = 1.9, 95%CI = 1.2-3.1) were more likely to be nonadherent. Conversely, protective factors included living with a spouse/partner (OR = 0.5, 95%CI = 0.3-0.7) and having more than a high school education (OR = 0.4, 95%CI = 0.1-1.0). Given the high prevalence of suboptimal adherence and current smoking among HIV-positive patients, screening for smoking status and nicotine dependence during ART treatment may help to improve patients' adherence to medication. More efforts should be targeted to women, patients with mental health problems, and ART clinics in rural areas.