Whole genome transcript profiling from fingerstick blood samples: a comparison and feasibility study

<p>Abstract</p> <p>Background</p> <p>Whole genome gene expression profiling has revolutionized research in the past decade especially with the advent of microarrays. Recently, there have been significant improvements in whole blood RNA isolation techniques which, through stabilization of RNA at the time of sample collection, avoid bias and artifacts introduced during sample handling. Despite these improvements, current human whole blood RNA stabilization/isolation kits are limited by the requirement of a venous blood sample of at least 2.5 mL. While fingerstick blood collection has been used for many different assays, there has yet to be a kit developed to isolate high quality RNA for use in gene expression studies from such small human samples. The clinical and field testing advantages of obtaining reliable and reproducible gene expression data from a fingerstick are many; it is less invasive, time saving, more mobile, and eliminates the need of a trained phlebotomist. Furthermore, this method could also be employed in small animal studies, i.e. mice, where larger sample collections often require sacrificing the animal. In this study, we offer a rapid and simple method to extract sufficient amounts of high quality total RNA from approximately 70 μl of whole blood collected via a fingerstick using a modified protocol of the commercially available Qiagen PAXgene RNA Blood Kit.</p> <p>Results</p> <p>From two sets of fingerstick collections, about 70 uL whole blood collected via finger lancet and capillary tube, we recovered an average of 252.6 ng total RNA with an average RIN of 9.3. The post-amplification yields for 50 ng of total RNA averaged at 7.0 ug cDNA. The cDNA hybridized to Affymetrix HG-U133 Plus 2.0 GeneChips had an average % Present call of 52.5%. Both fingerstick collections were highly correlated with r²values ranging from 0.94 to 0.97. Similarly both fingerstick collections were highly correlated to the venous collection with r²values ranging from 0.88 to 0.96 for fingerstick collection 1 and 0.94 to 0.96 for fingerstick collection 2.</p> <p>Conclusions</p> <p>Our comparisons of RNA quality and gene expression data of the fingerstick method with traditionally processed sample workflows demonstrate excellent RNA quality from the capillary collection as well as very high correlations of gene expression data.</p

Long-term trends in the foraging ecology and habitat use of an endangered species: an isotopic perspective.

Evaluating long-term drivers of foraging ecology and population productivity is crucial for providing ecological baselines and forecasting species responses to future environmental conditions. Here, we examine the trophic ecology and habitat use of North Atlantic leatherback turtles (St. Croix nesting population) and investigate the effects of large-scale oceanographic conditions on leatherback foraging dynamics. We used bulk and compound-specific nitrogen isotope analysis of amino acids (CSIA-AA) to estimate leatherback trophic position (TP) over an 18-year period, compare these estimates with TP estimates from a Pacific leatherback population, and elucidate the pre-nesting habitat use patterns of leatherbacks. Our secondary objective was to use oceanographic indices and nesting information from St. Croix leatherbacks to evaluate relationships between trophic ecology, nesting parameters, and regional environmental conditions measured by the North Atlantic Oscillation (NAO) and Atlantic Multidecadal Oscillation. We found no change in leatherback TP over time and no difference in TP between Atlantic and Pacific leatherbacks, indicating that differences in trophic ecology between populations are an unlikely driver of the population dichotomy between Pacific and Atlantic leatherbacks. Isotope data suggested that St. Croix leatherbacks inhabit multiple oceanic regions prior to nesting, although, like their conspecifics in the Pacific, individuals exhibit fidelity to specific foraging regions. Leatherback nesting parameters were weakly related to the NAO, which may suggest that positive NAO phases benefit St. Croix leatherbacks, potentially through increases in resource availability in their foraging areas. Our data contribute to the understanding of leatherback turtle ecology and potential mechanistic drivers of the dichotomy between populations of this protected species

Structural and Contextual Patterns in Family Health History Knowledge among African American Adults: A Mixed-Methods Social Network Analysis Study*

Background: Family health history is a strong risk factor for many chronic diseases. Ethnic minorities have been found to have a low awareness of their family health history (FHH), which may pose a contributing factor to health disparities. Purpose: The purpose of this mixed-methods social network analysis study was to identify structural and contextual patterns in African American adults’ FHH knowledge based on interpersonal communication exchanges with their family members. Methods: African American adults completed individually administered family network interviews. Participants’ 3-generation family pedigree served as a visual aid to guide their interview. Our primary outcome of interest for this analysis was whether a family member was reported as someone who talks to the participant about their own (i.e., the family member’s) health, which we refer to as a “personal health informant.” To contextualize quantitative findings, participants were asked to describe how they learned about the health history of the relatives they identified during their interview. Results: Participants (n=37) reported an average family network size of 29.4 relatives (SD = 15.5; Range = 10-67). Each participant, on average, named 17% of their familial network as personal health informants. Multivariate regression results showed that participants were more likely to name an alter as a personal health informant if the alter was female (OR = 2.14, p = 0.0519), from the maternal side of the participant’s family (OR = 1.12, p = 0.0006), had one or more chronic health conditions (OR = 2.41, p = 0.0041), was someone who has discussions with the participant about the participant’s health (OR = 16.28, p < 0.0001), was a source of family health information (OR = 3.46, p = 0.0072), and was someone whose health the participant helps to monitor or track (OR = 5.93, p = 0.0002). Complementary qualitative findings indicate that FHH knowledge is facilitated by open, direct communication among relatives. Personal health informants were described as disclosing information for the purposes of informing others for preventive purposes and for gaining social support. Participants also learned about FHH via other methods, including direct observation, during caretaking, and following a relative’s death. Conclusions: Communication and disclosure practices is an important determinant of African Americans’ FHH knowledge. More culturally and contextually meaningful public health efforts are needed to promote family health history sharing, especially regarding paternal family health history, siblings, and extended relatives

Biomarkers for Early and Late Stage Chronic Allograft Nephropathy by Proteogenomic Profiling of Peripheral Blood

Despite significant improvements in life expectancy of kidney transplant patients due to advances in surgery and immunosuppression, Chronic Allograft Nephropathy (CAN) remains a daunting problem. A complex network of cellular mechanisms in both graft and peripheral immune compartments complicates the non-invasive diagnosis of CAN, which still requires biopsy histology. This is compounded by non-immunological factors contributing to graft injury. There is a pressing need to identify and validate minimally invasive biomarkers for CAN to serve as early predictors of graft loss and as metrics for managing long-term immunosuppression.We used DNA microarrays, tandem mass spectroscopy proteomics and bioinformatics to identify genomic and proteomic markers of mild and moderate/severe CAN in peripheral blood of two distinct cohorts (n = 77 total) of kidney transplant patients with biopsy-documented histology.Gene expression profiles reveal over 2400 genes for mild CAN, and over 700 for moderate/severe CAN. A consensus analysis reveals 393 (mild) and 63 (moderate/severe) final candidates as CAN markers with predictive accuracy of 80% (mild) and 92% (moderate/severe). Proteomic profiles show over 500 candidates each, for both stages of CAN including 302 proteins unique to mild and 509 unique to moderate/severe CAN.This study identifies several unique signatures of transcript and protein biomarkers with high predictive accuracies for mild and moderate/severe CAN, the most common cause of late allograft failure. These biomarkers are the necessary first step to a proteogenomic classification of CAN based on peripheral blood profiling and will be the targets of a prospective clinical validation study

Locus-specific epigenetic remodeling controls addiction- and depression-related behaviors

Chronic exposure to drugs of abuse or stress regulates transcription factors, chromatin-modifying enzymes and histone post-translational modifications in discrete brain regions. Given the promiscuity of the enzymes involved, it has not yet been possible to obtain direct causal evidence to implicate the regulation of transcription and consequent behavioral plasticity by chromatin remodeling that occurs at a single gene. We investigated the mechanism linking chromatin dynamics to neurobiological phenomena by applying engineered transcription factors to selectively modify chromatin at a specific mouse gene in vivo. We found that histone methylation or acetylation at the Fosb locus in nucleus accumbens, a brain reward region, was sufficient to control drug- and stress-evoked transcriptional and behavioral responses via interactions with the endogenous transcriptional machinery. This approach allowed us to relate the epigenetic landscape at a given gene directly to regulation of its expression and to its subsequent effects on reward behavior

Late cardiac events after childhood cancer: Methodological aspects of the pan-european study pancaresurfup

Background and Aim Childhood cancer survivors are at high risk of long-Termadverse effects of cancer and its treatment, including cardiac events. The pan-European PanCareSurFup study determined the incidence and risk factors for cardiac events among childhood cancer survivors. The aim of this article is to describe the methodology of the cardiac cohort and nested case-control study within PanCareSurFup. Methods Eight data providers in Europe participating in PanCareSurFup identified and validated symptomatic cardiac events in their cohorts of childhood cancer survivors. Data onsymptomatic heart failure, ischemia, pericarditis, valvular disease and arrhythmia were collected and graded according to the Criteria for Adverse Events. Detailed treatment data, data on potential confounders, lifestyle related risk factors and general health problems were collected. Results The PanCareSurFup cardiac cohort consisted of 59,915 5-year childhood cancer survivors with malignancies diagnosed between 1940 and 2009 and classified according to the International Classification of Childhood Cancer 3. Different strategies were used to identify cardiac events such as record linkage to population/ hospital or regional based databases, and patient-And general practitioner-based questionnaires. Conclusion The cardiac study of the European collaborative research project PanCareSurFup will provide the largest cohort of 5-year childhood cancer survivors with systematically ascertained and validated data on symptomatic cardiac events. The result of this study can provide information to minimize the burden of cardiac events in childhood cancer survivors by tailoring the follow-up of childhood cancer survivors at high risk of cardiac adverse events, transferring this knowledge into evidence-based clinical practice guidelines and providing a platformfor future research studies in childhood cancer patients. © 2016 Feijen et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

HIV Infection and Women's Sexual Functioning

Objective: To compare sexual problems among HIV-positive and HIV-negative women and describe clinical and psychosocial factors associated with these problems. Design: Data were collected during a study visit of the Women's Interagency HIV Study (WIHS). The WIHS studies the natural and treated history of HIV among women in the United States. Methods: Between October 01, 2006, and March 30, 2007, 1805 women (1279 HIV positive and 526 HIV negative) completed a study visit that included administration of the Female Sexual Function Index. In addition, the visit included completion of standardized interviewer-administered surveys, physical and gynecological examinations, and blood sample collection. Results: Women with HIV reported greater sexual problems than did those without HIV. Women also reported lower sexual function if they were classified as menopausal, had symptoms indicative of depression, or if they reported not being in a relationship. CD4(+) cell count was associated with Female Sexual Function Index scores, such that those with CD4 <= 199 cells per microliter reported lower functioning as compared with those whose cell count was 200 or higher. Conclusions: Given research documenting relationships between self-reported sexual problems and both clinical diagnoses of sexual dysfunction and women's quality of life, greater attention to this issue as a potential component of women's overall HIV care is warranted