DDX47, MeCP2, and other functionally heterogeneous factors protect cells from harmful R loops.

Unscheduled R loops can be a source of genome instability, a hallmark of cancer cells. Although targeted proteomic approaches and cellular analysis of specific mutants have uncovered factors potentially involved in R-loop homeostasis, we report a more open screening of factors whose depletion causes R loops based on the ability of activation-induced cytidine deaminase (AID) to target R loops. Immunofluorescence analysis of γH2AX caused by small interfering RNAs (siRNAs) covering 3,205 protein-coding genes identifies 59 potential candidates, from which 13 are analyzed further and show a significant increase of R loops. Such candidates are enriched in factors involved in chromatin, transcription, and RNA biogenesis and other processes. A more focused study shows that the DDX47 helicase is an R-loop resolvase, whereas the MeCP2 methyl-CpG-binding protein uncovers a link between DNA methylation and R loops. Thus, our results suggest that a plethora of gene dysfunctions can alter cell physiology via affecting R-loop homeostasis by different mechanisms.

A Low-Glycemic, Mediterranean Diet and Lifestyle Modification Program with Targeted Nutraceuticals Reduces Body Weight, Improves Cardiometabolic Variables and Longevity Biomarkers in Overweight Subjects: A 13-Week Observational Trial.

Among the comorbidities of high body mass index, cardiovascular disease continued to be the leading cause of death and disability globally in 2015, while type 2 diabetes remained second. The primary objectives of this observational study were to confirm the safety, tolerability, and efficacy of our calorie-restricted Mediterranean diet with targeted dietary supplementation (PROG1) using globally recognized dietary supplementation. Fifty healthy overweight and obese subjects with cardiometabolic risk factors were assigned a modified Mediterranean diet, including protein shakes and targeted supplementation (PROG2), providing ∼68-76% of subject estimated calorie requirements. Salivary nitrite was assessed weekly and key cardiometabolic metrics were recorded at baseline and weeks 9 and 13. PROG2 was well tolerated with 86% compliance. The most common adverse effects were bloating, flatulence, and constipation, which were self-limiting. Subjects exhibited decreases (P < .01) from baseline of 12% in body weight, 18% in body fat, and 8.8% in waist circumference. Total cholesterol (TC), low-density lipoprotein (LDL) cholesterol, and triglycerides (TG) were reduced (P < .01), respectively, 19%, 22%, and 40%. Lipid ratios of TC/high-density lipoprotein (HDL), TG/HDL, and oxidized LDL (oxLDL)/HDL were decreased 15% (P < .01), 35% (P < .01), and 13% (P < .05), respectively. Inflammation biomarkers, oxLDL and high-sensitivity C-reactive protein, were reduced 17% (P < .01) and 30% (P < .05), respectively. Reductions of 9.0% for systolic (P < .01) and 12% (P < .01) for diastolic blood pressure were noted. In concert, the nitrogen dioxide salivary biomarker for nitric oxide was increased relative to baseline. PROG2 produced a dramatic 50% reduction in subjects meeting cardiometabolic syndrome criteria and a 38% decrease in Framingham 10-year cardiovascular risk. These results confirmed our previous findings that the addition of targeted nutraceutical supplementation to a calorie-restricted Mediterranean diet with lifestyle modifications improves multiple longevity risk factors more effectively than diet and lifestyle modification alone.