Within-subject biological variation estimates using an indirect data mining strategy. Spanish multicenter pilot study (BiVaBiDa)

OBJECTIVES

The estimates of biological variation (BV) have traditionally been determined using direct methods, which present limitations. In response to this issue, two papers have been published addressing these limitations by employing indirect methods. Here, we present a new procedure, based on indirect methods that analyses data collected within a multicenter pilot study. Using this method, we obtain CV_I estimates and calculate confidence intervals (CI), using the EFLM-BVD CV_I estimates as gold standard for comparison.

METHODS

Data were collected over a 18-month period for 7 measurands, from 3 Spanish hospitals; inclusion criteria: patients 18-75 years with more than two determinations. For each measurand, four different strategies were carried out based on the coefficient of variation ratio (rCoeV) and based on the use of the bootstrap method (OS1, RS2 and RS3). RS2 and RS3 use symmetry reference change value (RCV) to clean database.

RESULTS

RS2 and RS3 had the best correlation for the CV_I estimates with respect to EFLM-BVD. RS2 used the symmetric RCV value without eliminating outliers, while RS3 combined RCV and outliers. When using the rCoeV and OS1 strategies, an overestimation of the CV_I value was obtained.

CONCLUSIONS

Our study presents a new strategy for obtaining robust CV_I estimates using an indirect method together with the value of symmetric RCV to select the target population. The CV_I estimates obtained show a good correlation with those published in the EFLM-BVD database. Furthermore, our strategy can resolve some of the limitations encountered when using direct methods such as calculating confidence intervals.

Evaluación crítica y meta-análisis de estudios de variación biológica para albúmina glicosilada, glucosa y HbA1c

Objetivos

A lo largo de los años se han publicado numerosos artículos sobre variación biológica (VB) de diferente calidad. Los objetivos de este trabajo fueron realizar una revisión sistemática y una evaluación crítica de los estudios de VB para albúmina glicosilada y proporcionar datos actualizados de VB para glucosa y HbA_1c, incluyendo prestigiosos estudios recientemente publicados como el Estudio de Variación Biológica Europea (EuBIVAS).

Métodos

Se hizo una búsqueda bibliográfica sistemática para identificar estudios sobre VB, encontrándose 9 estudios no incluidos en la primera revisión: 4 para albúmina glicosilada, 3 para glucosa y 3 para HbA_1c. Se realizó una evaluación crítica de los estudios relevantes, utilizando la herramienta Biological Variation Data Critical Appraisal Checklist (BIVAC). Se obtuvieron los estimados globales de VB mediante meta-análisis de los estudios que cumplían los requisitos BIVAC, realizados en individuos sanos con estudios de diseño similar.

Resultados

Un estudio recibió el grado A, dos el B y 6 el C. en la mayoría de los casos el grado C se asoció a deficiencias en el análisis estadístico de los datos. Los estimados de VB para albúmina glicosilada fueron: CV_I = 1,4%(1,2–2,1) y CV_G = 5,7%(4,7–10,6); para HbA_1c, CV_I = 1,2%(0,3–2,5), CV_G = 5,4%(3,3–7,3) y para glucosa, CV_I = 5,0%(4,1–12,0), CV_G = 8,1%(2,7–10,8) no difirieron de los estimados globales previamente descritos.

Conclusiones

La evaluación crítica y clasificación de los estudios de VB a tenor de su calidad metodológica, seguido de un meta-análisis, genera estimados de VB robustos y fiables. Este estudio proporciona datos de VB para albúmina glicolisada, glucosa y HbA_1c actualizados y basados en la evidencia científica.

Critical appraisal and meta-analysis of biological variation estimates for kidney related analytes

Objective

Kidney markers are some of the most frequently used laboratory tests in patient care, and correct clinical decision making depends upon knowledge and correct application of biological variation (BV) data. The aim of this study was to review available BV data and to provide updated BV estimates for the following kidney markers in serum and plasma; albumin, creatinine, cystatin C, chloride, potassium, sodium and urea.

Content

Relevant studies were identified from a historical BV database as well as by systematic literature searches. Retrieved publications were appraised by the Biological Variation Data Critical Appraisal Checklist (BIVAC). Meta-analyses of BIVAC compliant studies with similar design were performed to deliver global estimates of within-subject (CVI) and between-subject (CVG) BV estimates. Out of the 61 identified papers, three received a BIVAC grade A, four grade B, 48 grade C, five grade D grade and one was not appraised as it did not report numerical BV estimates. Most studies were identified for creatinine (n=48). BV estimates derived from the meta-analysis were in general lower than previously reported estimates for all analytes except urea. For some measurands, BV estimates may be influenced by age or states of health, but further data are required.

Summary

This review provides updated global BV estimates for kidney related measurands. For all measurands except for urea, these estimates were lower than previously reported.

Outlook

For the measurands analyzed in this review, there are sufficient well-designed studies available to publish a trustworthy estimate of BV. However, for a number of newly appearing kidney markers no suitable data is available and additional studies are required.

Critical appraisal and meta-analysis of biological variation studies on glycosylated albumin, glucose and HbA1c

OBJECTIVES

Numerous biological variation (BV) studies have been performed over the years, but the quality of these studies vary. The objectives of this study were to perform a systematic review and critical appraisal of BV studies on glycosylated albumin and to deliver updated BV estimates for glucose and HbA_1c, including recently published high-quality studies such as the European Biological Variation study (EuBIVAS).

METHODS

Systematic literature searches were performed to identify BV studies. Nine publications not included in a previous review were identified; four for glycosylated albumin, three for glucose, and three for HbA_1c. Relevant studies were appraised by the Biological Variation Data Critical Appraisal Checklist (BIVAC). Global BV estimates were derived by meta-analysis of BIVAC-compliant studies in healthy subjects with similar study design.

RESULTS

One study received BIVAC grade A, 2B, and 6C. In most cases, the C-grade was associated with deficiencies in statistical analysis. BV estimates for glycosylated albumin were: CV_I=1.4% (1.2-2.1) and CV_G=5.7% (4.7-10.6), whereas estimates for HbA_1c, CV_I=1.2% (0.3-2.5), CV_G=5.4% (3.3-7.3), and glucose, CV_I=5.0% (4.1-12.0), CV_G=8.1% (2.7-10.8) did not differ from previously published global estimates.

CONCLUSIONS

The critical appraisal and rating of BV studies according to their methodological quality, followed by a meta-analysis, generate robust, and reliable BV estimates. This study delivers updated and evidence-based BV estimates for glycosylated albumin, glucose and HbA_1c.

Systematic review of the biological variation data for diabetes related analytes

BACKGROUND

Objective interpretation of laboratory test results used to diagnose and monitor diabetes mellitus in part requires the application of biological variation data (BVD). The quality of published BVD has been questioned. The aim of this study was to quality assess publications reporting BVD for diabetes-related analytes using the Biological Variation Data Critical Appraisal Checklist (BIVAC); to assess whether published BVD are fit for purpose and whether the study design and population attributes influence BVD estimates and to undertake a meta-analysis of the BVD from BIVAC-assessed publications.

METHODS

Publications reporting data for glucose, HbA_1c, adiponectin, C-peptide, fructosamine, insulin like growth factor 1 (IGF-1), insulin like growth factor binding protein 3 (IGFBP-3), insulin, lactate and pyruvate were identified using a systematic literature search. These publications were assessed using the BIVAC, receiving grades A, B, C or D, where A is of highest quality. A meta-analysis of the BVD from the assessed studies utilised weightings based upon BIVAC grades and the width of the data confidence intervals to generate global BVD estimates.

RESULTS

BIVAC assessment of 47 publications delivered 1 A, 3 B, 39C and 4 D gradings. Publications relating to adiponectin, C-peptide, IGF-1, IGFBP-3, lactate and pyruvate were all assessed as grade C. Meta-analysis enabled global BV estimates for all analytes except pyruvate, lactate and fructosamine.

CONCLUSIONS

This study delivers updated and evidence-based BV estimates for diabetes-related analytes. There remains a need for delivery of new high-quality BV studies for several clinically important analytes.

Review of Methods to Study Gene Expression Regulation Applied to Asthma

Gene expression regulation is the cellular process that controls, increasing or decreasing, the expression of gene products (RNA or protein). A complex set of interactions between genes, RNA molecules, protein, and other components determined when and where specific genes are activated and the amount of protein or RNA produced. Here, we focus on several methods to study gene regulation applied to asthma and allergic research such as: Western Blot to identify and quantify proteins, electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) to study protein interactions with nucleic acids, and RNA interference (RNAi) by which gene expression could be silenced.

Retinoic Acid Modulates PTGDR Promoter Activity

BACKGROUND AND OBJECTIVE

Vitamin A has been linked to the development of allergic diseases although its role is not fully understood, Retinoic acid (RA), a metabolite of Vitamin A, has been previously associated with the prostaglandin pathway, and PTGDR, a receptor of PGD2, has been proposed as a candidate gene in allergy and asthma. Considering the role of PTGDR in allergy, the goal of this study was to analyze the effect of RA on the activation of the promoter region of the PTGDR gene.

METHODS

A549 lung epithelial cells were transfected with 4 combinations of genetic variants of the PTGDR promoter and stimulated with all-trans RA (ATRA); luciferase assays were performed using the Dual Luciferase Reporter System, and real-time quantitative polymerase chain reaction was used to measure the expression of PTGDR, CYP26A1, RARA, RARB, RARG, and RXRA in basal A549 cell cultures and after ATRA treatment. We also performed an in silico analysis.

RESULTS

After ATRA treatment increased expression of CYP26A1 (12-fold) and RARB (4-fold) was detected. ATRA activated PTGDR promoter activity in transfected cells (P<.001) and RA response element sequences were identified in silico in this promoter region.

CONCLUSIONS

RA modulated PTGDR promoter activity. Differential response to RA and to new treatments based on PTGDR modulation could depend on genetic background in allergic asthmatic patients.

Mouse Models Applied to the Research of Pharmacological Treatments in Asthma

Models developed for the study of asthma mechanisms can be used to investigate new compounds with pharmacological activity against this disease. The increasing number of compounds requires a preclinical evaluation before starting the application in humans. Preclinical evaluation in animal models reduces the number of clinical trials positively impacting in the cost and in safety. In this chapter, three protocols for the study of drugs are shown: a model to investigate corticoids as a classical treatment of asthma; a protocol to test the effects of retinoic acid (RA) on asthma; and a mouse model to test new therapies in asthma as monoclonal antibodies.

General and Specific Mouse Models for Asthma Research

To study the complexity of human asthma disease, the development of different animal models is needed. Among all different laboratory animals, mice represent a useful tool for the development of asthma. This chapter will describe protocols for designing different animal models applied to the studying of asthma phenotypes.

Gene Silencing Delivery Methods: Lipid-Mediated and Electroporation Transfection Protocols

The RNA interference (RNAi) plays an important role in regulation of gene expression. It is a mechanism used by many organisms to silence the expression of genes that control different processes in the cell. The double strand (ds) RNA molecule inhibits gene expression of a targeted gene with high specificity and selectivity.Different types of small ribonucleic acid molecules, microRNA (miRNA), small interfering RNA (siRNA), short hairpin RNA (shRNA), and the piwi RNA (piRNA) are involved in the RNA interference. RNAi is a relevant research tool in cell cultures and in vivo experiments because synthetic dsRNA introduced into cells can selectively silence specific target genes.Here, we describe a general guide for gene silencing mediated by siRNA, focusing on the most used delivery methods: lipid-mediated and electroporation transfection.

Protocols for Exosome Isolation and RNA Profiling

Exosomes are small extracellular vesicles of multivesicular bodies derived from the cell endosome. Molecules have a characteristic composition both in the membrane and in the carried load. These particles are located in the culture medium of cells in vitro and in vivo body fluids, being synthesized by almost all kind of cells. The most characteristic molecule transported within is the RNA with a large clinical potential. In this chapter, the methodology for isolation of exosomes and subsequent purification of the RNA is reviewed.

p73 plays a role in erythroid differentiation through GATA1 induction

The TP73 gene gives rise to transactivation domain-p73 isoforms (TAp73) as well as DeltaNp73 variants with a truncated N terminus. Although TAp73alpha and -beta proteins are capable of inducing cell cycle arrest, apoptosis, and differentiation, DeltaNp73 acts in many cell types as a dominant-negative repressor of p53 and TAp73. It has been proposed that p73 is involved in myeloid differentiation, and its altered expression is involved in leukemic degeneration. However, there is little evidence as to which p73 variants (TA or DeltaN) are expressed during differentiation and whether specific p73 isoforms have the capacity to induce, or hinder, this differentiation in leukemia cells. In this study we identify GATA1 as a direct transcriptional target of TAp73alpha. Furthermore, TAp73alpha induces GATA1 activity, and it is required for erythroid differentiation. Additionally, we describe a functional cooperation between TAp73 and DeltaNp73 in the context of erythroid differentiation in human myeloid cells, K562 and UT-7. Moreover, the impaired expression of GATA1 and other erythroid genes in the liver of p73KO embryos, together with the moderated anemia observed in p73KO young mice, suggests a physiological role for TP73 in erythropoiesis.