Genetic testing for inherited eye conditions in over 6,000 individuals through the eyeGENE network

Genetic testing in a multisite clinical trial network for inherited eye conditions is described in this retrospective review of data collected through eyeGENE®, the National Ophthalmic Disease Genotyping and Phenotyping Network. Participants in eyeGENE were enrolled through a network of clinical providers throughout the United States and Canada. Blood samples and clinical data were collected to establish a phenotype:genotype database, biorepository, and patient registry. Data and samples are available for research use, and participants are provided results of clinical genetic testing. eyeGENE utilized a unique, distributed clinical trial design to enroll 6,403 participants from 5,385 families diagnosed with over 30 different inherited eye conditions. The most common diagnoses given for participants were retinitis pigmentosa (RP), Stargardt disease, and choroideremia. Pathogenic variants were most frequently reported in ABCA4 (37%), USH2A (7%), RPGR (6%), CHM (5%), and PRPH2 (3%). Among the 5,552 participants with genetic testing, at least one pathogenic or likely pathogenic variant was observed in 3,448 participants (62.1%), and variants of uncertain significance in 1,712 participants (30.8%). Ten genes represent 68% of all pathogenic and likely pathogenic variants in eyeGENE. Cross‐referencing current gene therapy clinical trials, over a thousand participants may be eligible, based on pathogenic variants in genes targeted by those therapies. This article is the first summary of genetic testing from thousands of participants tested through eyeGENE, including reports from 5,552 individuals. eyeGENE provides a launching point for inherited eye research, connects researchers with potential future study participants, and provides a valuable resource to the vision community.     

ASK1 associates with troponin T and induces troponin T phosphorylation and contractile dysfunction in cardiomyocytes

There is increasing support for the idea that excessive production of proinflammatory mediators such as tumor necrosis factor (TNF) and reactive oxygen species (ROS) contribute to the pathogenesis of cardiac dysfunction. However, the mechanisms by which cytokine/ROS production mediates cardiac dysfunction have not been established. Given that apoptosis signal-regulating kinase 1 (ASK1) is highly expressed in cardiac muscle and that ASK1 is an important mediator in the signaling pathways induced by tumor necrosis factor, interleukin-1, and ROS, we used the yeast two-hybrid system with ASK1 as bait to identify ASK1 substrates from a human heart cDNA library. The cDNA encoding the cardiac troponin T (cTnT) was isolated. ASK1 specifically interacted with cTnT, but not cTnI, in vitro and in vivo via the C-terminal ASK1 domain. ASK1 specifically phosphorylated cTnT in vitro and in vivo. Mutations in cTnT (T194/S198) at an ASK1-phosphorylation consensus sequence significantly reduced phosphorylation by ASK1. ROS-induced ASK1 activation, cTnT phosphorylation, and contractile dysfunction in cardiomyocytes showed similar kinetics. Moreover, overexpression of constitutively active ASK1 induces cTnT phosphorylation and inhibits shortening and calcium transient in adult cardiomyocytes. We conclude that ASK1 plays an important role in regulation of cardiac contractile function by phosphorylating cTnT and may participate in cytokine/ROS-induced pathogenesis of cardiomyopathy and heart failure.     

Elevated Fecal Candida Counts in Patients with Antibiotic-Associated Diarrhea: Role of Soluble Fecal Substances

To assess the role of soluble fecal substances in the elevation of fecal Candida counts in patients with antibiotic-associated diarrhea (AAD), we investigated the growth of Candida albicans in vitro in serially diluted stool fluids from patients with AAD and healthy subjects. There were significantly higher Candida albicans counts in stool fluids diluted 1:10 from AAD patients than in healthy subjects and the phosphate-buffered saline growth control, which may be due to reduced soluble Candida inhibitors and increased availability of growth factors and nutrients.     

Muscularity in adult humans: Proportion of adipose tissue‐free body mass as skeletal muscle

Muscularity, or the proportion of adipose tissue‐free body mass (ATFM) as skeletal muscle (SM), provides valuable body composition information, especially for age‐related SM loss (i.e., sarcopenia). Limited data from elderly cadavers suggest a relatively constant SM/ATFM ratio, 0.540 ± 0.046 for men (mean ± SD, n = 6) and 0.489 ± 0.049 for women (n = 7). The aim of the present study was to examine the magnitude and constancy of the SM/ATFM ratio in healthy adults. Whole‐body SM and ATFM were measured using multi‐scan magnetic resonance imaging. The SM/ATFM ratio was 0.528 ± 0.036 for men (n = 139) and 0.473 ± 0.037 for women (n = 165). Multiple regression analysis indicated that the SM/ATFM ratio was significantly influenced by sex, age, body weight, and race. The four factors explained 50% of the observed between individual variation in the SM/ATFM ratio. After adjusting for age, body weight, and race, men had a larger SM/ATFM ratio than women. Both older men and women had a lower SM/ATFM ratio than younger subjects, although the relative reduction was greater in men. After adjustment for sex, age, and body weight, there were no significant differences in the SM/ATFM ratios between Asian, Caucasian, and Hispanic subjects. In contrast, African‐American subjects had a significantly greater SM/ATFM ratio than subjects in the other three groups. In addition, the SM/ATFM ratio was significantly lower in AIDS patients than corresponding values in healthy subjects. Am. J. Hum. Biol. 13:612–619, 2001. © 2001 Wiley‐Liss, Inc.     

Muco-cutaneous colonization and nosocomial infections caused by methicillin-resistant Staphylococcus aureus and Acinetobacter baumanii in intensive care patients

This study was designed to assess the frequency and risk factors for colonization with MRSA and A. baumanii in the intensive care unit, and to analyse the relationship between colonization and infection with MRSA or A. baumanii. During a 24-day survey period, colonization was studied weekly with nasal, throat and digit skin swabs; nosocomial infections were routinely monitored according to CDC recommendations. Clinical data and invasive procedures were registered during a one-year non-epidemic period; 103 ICU patients hospitalized for more than 7 days were prospectively included. We investigated acquired colonization and nosocomial infection with SAMR or A. baumanii for 87 patients not colonized by SAMR or A. baumanii on admission. The colonization acquisition rate was 56% for MRSA and 27% for A. baumanii. Infection incidence (cases per 1,000 patient-days) was 6.46 for MRSA and 1.61 for A. baumanii. On univariate analysis, acquired MRSA colonization was associated with longer ICU stays, longer mechanical ventilation and longer central venous catheterization. Multivariate analysis only showed an association with longer ICU stay. Acquired A. baumanii colonization was associated with SAPSII, longer mechanical ventilation, and longer central venous catheterization in univariate analysis. Multivariate analysis only showed an association with SAPSII and longer mechanical ventilation. In this study, SAMR or A. baumanii infections were not associated with colonization or clinical setting or invasive procedures.     

Cervical specimen order and performance measures of Chlamydia trachomatis diagnostic testing

The orders of three endocervical specimens of 3,561 women for Chlamydia trachomatis testing were randomized to determine whether test performance measures of two nucleic acid amplification tests and a DNA probe were affected by swab order. Specimen collection order did not appear to affect the diagnostic accuracy of these tests.     

High rate of transfer of Staphylococcus aureus from parental skin to infant gut flora

Many Swedish infants carry Staphylococcus aureus in their intestinal microflora. The source of this colonization was investigated in 50 families. Infantile S. aureus strains were isolated from rectal swabs and stool samples at 3 days and at 1, 2, 4, and 8 weeks of age. The strains were identified by using the random amplified polymorphic DNA method and compared to strains from swab cultures of the mothers' hands, nipples, and nares and from the fathers' hands and nares. Maternal stool samples were also obtained at a later stage to compare infant and adult intestinal S. aureus colonization. Although 60% of 1-month-old children had S. aureus in the stools, this was true of only 24% of the mothers. The median population numbers in colonized individuals also differed: 10(6.8) CFU/g of feces among infants at 2 weeks of age versus 10(3.2) CFU/g of feces in the mothers. Of S. aureus strains in the stools of 3-day-old infants, 90% were identical to a parental skin strain. A total of 96% of infants whose parents were S. aureus skin carriers had S. aureus in their feces and 91% had the same strain as at least one of the parents. In comparison, only 37% of infants to S. aureus-negative parents had S. aureus in the stool samples. Thus, infantile intestinal S. aureus colonization was strongly associated with parental skin S. aureus carriage (P = 0.0001). These results suggest that S. aureus on parental skin establish readily in the infantile gut, perhaps due to poor competition from other gut bacteria.     

Papillomas and atypical papillomas in breast core needle biopsy specimens: risk of carcinoma in subsequent excision

We sought to define the risk associated with papillomas and atypical papillomas in breast core needle biopsy specimens from a series of approximately 8,500 biopsies performed during 8 years. From a total of 62 papillary lesions (including papillomas and atypical papillomas), 40 (65%) had histologic follow-up. Overall, 15 (38%) of 40 patients had ductal carcinoma in situ (12 cases) or invasive carcinoma at excision (3 cases). Eight cases diagnosed as papilloma had benign follow-up. Slides were available for review in 38 cases and reclassified into benign papilloma with florid hyperplasia and no or minimal atypia (18 cases), papilloma with separate foci of atypical ductal hyperplasia (7 cases), and severely atypical papillomas "suspicious" for papillary carcinoma (13 cases). Carcinoma was identified in 0 (0%), 2 (29%), and 12 (92%) cases, respectively. We conclude that while atypical papillary lesions and papillomas with associated atypical ductal hyperplasia in breast core needle biopsy specimens are associated with a risk of carcinoma, lesions diagnosed as papilloma or papilloma with no or minimal atypia are benign and do not need to be excised.     

Comparison of in vitro and in vivo alpha/beta ratios for prostate cancer

Parallel in vitro and in vivo studies provide insight into the relationship between clinical response and intrinsic cellular radiosensitivity and may aid in the development of predictive assays. Compilations of radiosensitivity parameters from in vitro experiments can also be used to examine the potential effectiveness of alternative or new treatment plan designs until enough clinical data become available to directly estimate the requisite radiosensitivity parameters. In this work, survival data for six prostate cancer cell lines (ten datasets total) have been extracted from the literature and re-analysed using the linear-quadratic (LQ) survival model. The paired bootstrap technique for regression is used to compute 95% confidence intervals for the estimated radiosensitivity parameters. LQ radiosensitivity parameters derived from the in vitro data are then compared to radiosensitivity parameters derived from clinical data for prostate cancer. Estimates of alpha range from 0.09 to 0.35 Gy(-1) (all cell lines), and the alpha/beta ratio ranges from 1.09 to 6.29 Gy (all cell lines). Point estimates of the repair half-time (PPC-1, TSU-Pr1, PC-3 and DU-145 cell lines) range from 5.7 to 8.9 h (95% confidence interval from 0.26 h to 10.7 h). Differences in the radiosensitivity parameters determined from the data reported by different laboratories are as large as or larger than the differences in radiosensitivity parameters observed among the various prostate cell lines. The reported studies demonstrate that even seemingly small corrections for dose rate effects, such as those expected in high dose rate (HDR) experiments, can sometimes have a significant impact on estimates of alpha and alpha/beta. By neglecting dose rate effects in the analysis of HDR experiments, estimates of the alpha/beta, ratio may be too high by factors as large as 1.3 to 6.2. The half-time for repair derived from the in vitro experiments appears significantly larger (slower repair rate) than estimates derived from the clinical data. However, the prostate radiosensitivity parameters alpha and alpha/beta may be approximately the same in vitro and in vivo. Most of the in vitro data are consistent with an alpha/beta ratio for prostate cancer less than 3 or 4 Gy.