Publications

To use microRNAs to downregulate mRNA targets, cells must first process these ~22 nt RNAs from primary transcripts (pri-miRNAs). These transcripts form RNA hairpins important for processing, but additional determinants must distinguish pri-miRNAs from the many other hairpin-containing transcripts expressed in each cell. Illustrating the complexity of this recognition, we show that most Caenorhabditis elegans pri-miRNAs lack determinants required for processing in human cells. To find these determinants, we generated many variants of four human pri-miRNAs, sequenced millions that retained function, and compared them with the starting variants. Our results confirmed the importance of pairing in the stem and revealed three primary-sequence determinants, including an SRp20-binding motif (CNNC) found downstream of most pri-miRNA hairpins in bilaterian animals, but not in nematodes. Adding this and other determinants to C. elegans pri-miRNAs imparted efficient processing in human cells, thereby confirming the importance of primary-sequence determinants for distinguishing pri-miRNAs from other hairpin-containing transcripts.

BACKGROUND

There is a lack of information about posttreatment care among patients with ductal carcinoma in situ (DCIS). This study compares posttreatment care by ethnicity-language and physician specialty among Latina and White women with DCIS.

METHODS

Latina and White women diagnosed with DCIS between 2002 and 2005 identified through the California Cancer Registry completed a telephone survey in 2006. Main outcomes were breast surveillance, lifestyle counseling, and follow-up physician specialty.

KEY RESULTS

Of 742 women (396 White, 349 Latinas), most (90 %) had at least one clinical breast exam (CBE). Among women treated with breast-conserving surgery (BCS; N = 503), 76 % had received at least two mammograms. While 92 % of all women had follow-up with a breast specialist, Spanish-speaking Latinas had the lowest specialist follow-up rates (84 %) of all groups. Lifestyle counseling was low with only 53 % discussing exercise, 43 % weight, and 31 % alcohol in relation to their DCIS. In multivariable analysis, Spanish-speaking Latinas with BCS had lower odds of receiving the recommended mammography screening in the year following treatment compared to Whites (OR 0.5; 95 % CI, 0.2-0.9). Regardless of ethnicity-language, seeing both a specialist and primary care physician increased the odds of mammography screening and CBE (OR 1.6; 95 % CI, 1.2-2.3 and OR 1.9; 95 % CI, 1.3-2.8), as well as having discussions about exercise, weight, and alcohol use, compared to seeing a specialist only.

CONCLUSIONS

Most women reported appropriate surveillance after DCIS treatment. However, our results suggest less adequate follow-up for Spanish-speaking Latinas, possibly due to language barriers or insurance access.

IMPLICATIONS FOR CANCER SURVIVORS

Follow-up with a primary care provider in addition to a breast specialist increases receipt of appropriate follow-up for all women.

BACKGROUND

The prevalence in the United States of dietary supplement use that may be harmful to those with chronic kidney disease (CKD) is unknown. We sought to characterize potentially harmful supplement use by individual CKD status.

STUDY DESIGN

Cross-sectional national survey (National Health and Nutrition Examination Survey, 1999-2008).

SETTING & PARTICIPANTS

Community-based survey of 21,169 nonpregnant noninstitutionalized US civilian adults (aged ≥20 years).

PREDICTOR

CKD status (no CKD, at risk of CKD [presence of diabetes, hypertension, and/or cardiovascular disease], stages 1/2 [albuminuria only (albumin-creatinine ratio ≥30 mg/g)], or stages 3/4 [estimated glomerular filtration rate of 15-59 mL/min/1.73 m(2)]).

OUTCOME

Self-reported use of dietary supplements containing any of 37 herbs the National Kidney Foundation identified as potentially harmful in the setting of CKD.

MEASUREMENTS

Albuminuria and estimated glomerular filtration rate assessed from urine and blood samples; demographics and comorbid conditions assessed by standardized questionnaire.

RESULTS

An estimated 8.0% of US adults reported potentially harmful supplement use within the last 30 days. A lower crude estimated prevalence of potentially harmful supplement use was associated with higher CKD severity (no CKD, 8.5%; at risk, 8.0%; stages 1/2, 6.1%; and stages 3/4, 6.2%; P < 0.001). However, after adjustment for confounders, those with or at risk of CKD were as likely to use a potentially harmful supplement as those without CKD: at-risk OR, 0.93 (95% CI, 0.79-1.09); stages 1/2 OR, 0.83 (95% CI, 0.64-1.08); and stages 3/4 OR, 0.87 (95% CI, 0.63-1.18); all versus no CKD.

LIMITATIONS

Herb content was not available and the list of potentially harmful supplements examined is unlikely to be exhaustive.

CONCLUSIONS

The use of dietary supplements potentially harmful to people with CKD is common regardless of CKD status. Health care providers should discuss the use and potential risks of supplements with patients with and at risk of CKD.

HIV-1 reservoirs preclude virus eradication in patients receiving highly active antiretroviral therapy (HAART). The best characterized reservoir is a small, difficult-to-quantify pool of resting memory CD4(+) T cells carrying latent but replication-competent viral genomes. Because strategies targeting this latent reservoir are now being tested in clinical trials, well-validated high-throughput assays that quantify this reservoir are urgently needed. Here we compare eleven different approaches for quantitating persistent HIV-1 in 30 patients on HAART, using the original viral outgrowth assay for resting CD4(+) T cells carrying inducible, replication-competent viral genomes as a standard for comparison. PCR-based assays for cells containing HIV-1 DNA gave infected cell frequencies at least 2 logs higher than the viral outgrowth assay, even in subjects who started HAART during acute/early infection. This difference may reflect defective viral genomes. The ratio of infected cell frequencies determined by viral outgrowth and PCR-based assays varied dramatically between patients. Although strong correlations with the viral outgrowth assay could not be formally excluded for most assays, correlations achieved statistical significance only for integrated HIV-1 DNA in peripheral blood mononuclear cells and HIV-1 RNA/DNA ratio in rectal CD4(+) T cells. Residual viremia was below the limit of detection in many subjects and did not correlate with the viral outgrowth assays. The dramatic differences in infected cell frequencies and the lack of a precise correlation between culture and PCR-based assays raise the possibility that the successful clearance of latently infected cells may be masked by a larger and variable pool of cells with defective proviruses. These defective proviruses are detected by PCR but may not be affected by reactivation strategies and may not require eradication to accomplish an effective cure. A molecular understanding of the discrepancy between infected cell frequencies measured by viral outgrowth versus PCR assays is an urgent priority in HIV-1 cure research.

Asthma is a common chronic respiratory disease characterized by airway hyperresponsiveness (AHR). The genetics of asthma have been widely studied in mouse and human, and homologous genomic regions have been associated with mouse AHR and human asthma-related phenotypes. Our goal was to identify asthma-related genes by integrating AHR associations in mouse with human genome-wide association study (GWAS) data. We used Efficient Mixed Model Association (EMMA) analysis to conduct a GWAS of baseline AHR measures from males and females of 31 mouse strains. Genes near or containing SNPs with EMMA p-values <0.001 were selected for further study in human GWAS. The results of the previously reported EVE consortium asthma GWAS meta-analysis consisting of 12,958 diverse North American subjects from 9 study centers were used to select a subset of homologous genes with evidence of association with asthma in humans. Following validation attempts in three human asthma GWAS (i.e., Sepracor/LOCCS/LODO/Illumina, GABRIEL, DAG) and two human AHR GWAS (i.e., SHARP, DAG), the Kv channel interacting protein 4 (KCNIP4) gene was identified as nominally associated with both asthma and AHR at a gene- and SNP-level. In EVE, the smallest KCNIP4 association was at rs6833065 (P-value 2.9e-04), while the strongest associations for Sepracor/LOCCS/LODO/Illumina, GABRIEL, DAG were 1.5e-03, 1.0e-03, 3.1e-03 at rs7664617, rs4697177, rs4696975, respectively. At a SNP level, the strongest association across all asthma GWAS was at rs4697177 (P-value 1.1e-04). The smallest P-values for association with AHR were 2.3e-03 at rs11947661 in SHARP and 2.1e-03 at rs402802 in DAG. Functional studies are required to validate the potential involvement of KCNIP4 in modulating asthma susceptibility and/or AHR. Our results suggest that a useful approach to identify genes associated with human asthma is to leverage mouse AHR association data.