Pancreatic cancer prognosis is predicted by an ATAC-array technology for assessing chromatin accessibility

Unlike other malignancies, therapeutic options in pancreatic ductal adenocarcinoma (PDAC) are largely limited to cytotoxic chemotherapy without the benefit of molecular markers predicting response. Here we report tumor-cell-intrinsic chromatin accessibility patterns of treatment-naïve surgically resected PDAC tumors that were subsequently treated with (Gem)/Abraxane adjuvant chemotherapy. By ATAC-seq analyses of EpCAM+ PDAC malignant epithelial cells sorted from 54 freshly resected human tumors, we show here the discovery of a signature of 1092 chromatin loci displaying differential accessibility between patients with disease free survival (DFS) < 1 year and patients with DFS > 1 year. Analyzing transcription factor (TF) binding motifs within these loci, we identify two TFs (ZKSCAN1 and HNF1b) displaying differential nuclear localization between patients with short vs. long DFS. We further develop a chromatin accessibility microarray methodology termed "ATAC-array", an easy-to-use platform obviating the time and cost of next generation sequencing. Applying this methodology to the original ATAC-seq libraries as well as independent libraries generated from patient-derived organoids, we validate ATAC-array technology in both the original ATAC-seq cohort as well as in an independent validation cohort. We conclude that PDAC prognosis can be predicted by ATAC-array, which represents a low-cost, clinically feasible technology for assessing chromatin accessibility profiles.

Geospatial Distribution and Predictors of Mortality in Hospitalized Patients With COVID-19: A Cohort Study

BACKGROUND

The global coronavirus disease 2019 (COVID-19) pandemic offers the opportunity to assess how hospitals manage the care of hospitalized patients with varying demographics and clinical presentations. The goal of this study was to demonstrate the impact of densely populated residential areas on hospitalization and to identify predictors of length of stay and mortality in hospitalized patients with COVID-19 in one of the hardest hit counties internationally.

METHODS

This was a single-center cohort study of 1325 sequentially hospitalized patients with COVID-19 in New York between March 2, 2020, to May 11, 2020. Geospatial distribution of study patients' residences relative to population density in the region were mapped, and data analysis included hospital length of stay, need and duration of invasive mechanical ventilation (IMV), and mortality. Logistic regression models were constructed to predict discharge dispositions in the remaining active study patients.

RESULTS

The median age of the study cohort (interquartile range [IQR]) was 62 (49-75) years, and more than half were male (57%) with history of hypertension (60%), obesity (41%), and diabetes (42%). Geographic residence of the study patients was disproportionately associated with areas of higher population density (r s = 0.235; P = .004), with noted "hot spots" in the region. Study patients were predominantly hypertensive (MAP > 90 mmHg; 670, 51%) on presentation with lymphopenia (590, 55%), hyponatremia (411, 31%), and kidney dysfunction (estimated glomerular filtration rate < 60 mL/min/1.73 m2; 381, 29%). Of the patients with a disposition (1188/1325), 15% (182/1188) required IMV and 21% (250/1188) developed acute kidney injury. In patients on IMV, the median (IQR) hospital length of stay in survivors (22 [16.5-29.5] days) was significantly longer than that of nonsurvivors (15 [10-23.75] days), but this was not due to prolonged time on the ventilator. The overall mortality in all hospitalized patients was 15%, and in patients receiving IMV it was 48%, which is predicted to minimally rise from 48% to 49% based on logistic regression models constructed to project disposition in the remaining patients on ventilators. Acute kidney injury during hospitalization (odds ratioE, 3.23) was the strongest predictor of mortality in patients requiring IMV.

CONCLUSIONS

This is the first study to collectively utilize the demographics, clinical characteristics, and hospital course of COVID-19 patients to identify predictors of poor outcomes that can be used for resource allocation in future waves of the pandemic.

Advances in molecular classification of renal neoplasms

Kidney neoplasms are classified by light microscopy using the World Health Organization (WHO) system. The WHO system defines histopathologic tumor subtypes with distinct clinical behavior and underlying genetic mutations. In adults, the common malignant subtypes are variants of renal cell carcinoma (RCC). Histopathologic classification is critical for clinical management of RCC, but is becoming more complex with recognition of novel tumor subtypes, development of procedures yielding small diagnostic biopsies, and emergence of molecular therapies directed at tumor gene activity. Therefore, classification systems based on gene expression are likely to become essential for diagnosis, prognosis and treatment of kidney tumors. Recent DNA microarray studies have shown that clinically relevant renal tumor subtypes are characterized by distinct gene expression profiles, which are useful for discovery of novel diagnostic and prognostic biomarkers. In this review, we summarize the WHO classification system for renal tumors, general applications of microarray technology in cancer research, and specific microarray studies that have advanced knowledge of renal tumor diagnosis, prognosis, therapy and pathobiology.

Medicaid, welfare dependency, and work: is there a causal link?

Medicaid exerts a strong "pull" on potential welfare recipients, increasing the probability that a number of single mothers will apply for and stay on welfare in order to be covered by Medicaid. However, the availability of private health insurance coverage exerts a strong positive influence on women's decisions to work and a strong negative effect on welfare participation rates. If private insurance coverage were as comprehensive as Medicaid and readily available at all jobs, its impact on promoting work would be substantially greater than is the impact of Medicaid in promoting the use of welfare.

The effect of the U.S. welfare system on marital status

"An issue of long-standing importance in the U.S. welfare system has been its lack of neutrality with respect to family composition, which generally provides payments only to female-headed families--that is, families with no able-bodied male present. Using data from 1969 to 1985 to examine the issue, this study finds that (1) the simple cross-sectional correlations between marital status and welfare benefits are almost always in the expected direction but are generally weak in significance; (2) that the magnitude and significance of the correlations have nevertheless grown over time; and (3) that the correlations for men are no weaker and usually stronger, especially for blacks, than those for women."

Determination of Lead and Cadmium in Foods by Anodic Stripping Voltammetry: II. Collaborative Study

A dry ash anodic stripping voltammetric method for determining lead and cadmium in foods was collaboratively studied by 20 laboratories. The food commodities studied were strained green beans, beef (baby food), fish (mackerel), infant formula (milk base), apple juice, and cereal (wheat farina). Each collaborator analyzed 3 commodities, each consisting of 2 duplicate lead and cadmium fortification levels, for a total of 4 samples for each commodity. The low fortification levels ranged from 0.03 to 0.08 ppm for cadmium and from 0.05 to 0.15 ppm for lead. The high fortification levels ranged from 0.12 to 0.28 ppm for cadmium and from 0.24 to 0.45 ppm for lead. Each commodity was analyzed by 10 collaborators. The average overall reproducibilities of the low level fortifications were 247c for lead and 21% for cadmium; for the high level fortifications, average overall reproducibilities were 18% for lead and 16% for cadmium. The average accuracies of the collaborative results as measured by comparison to reference values were 96 and 97% for cadmium and lead, respectively. This method has been adopted official first action.