MicroRNA global profiling in cystic fibrosis cell lines reveals dysregulated pathways related with inflammation, cancer, growth, glucose and lipid metabolism, and fertility: an exploratory study.

BACKGROUND AND AIM: Cystic fibrosis (CF), is due to CF transmembrane conductance regulator (CFTR) loss of function, and is associated with comorbidities. The increasing longevity of CF patients has been associated with increased cancer risk besides the other known comorbidities. The significant heterogeneity among patients, suggests potential epigenetic regulation. Little attention has been given to how CFTR influences microRNA (miRNA) expression and how this may impact on biological processes and pathways. METHODS: We assessed the changes in miRNAs and subsequently identified the affected molecular pathways using CFBE41o-, and IB3 human immortalized cell lines since they reflect the most common genetic mutations in CF patients, and 16HBE14o- cells were used as controls. RESULTS: In the CF cell lines, 41 miRNAs showed significant changes (FC (log2) ≥ +2 or FC (log2) ≤ -2 and p-value≤0.05). Gene target analysis evidenced 511 validated miRNA target genes. Gene Ontology analysis evidenced cancer, inflammation, body growth, glucose, and lipid metabolism as the biological processes most impacted by these miRNAs. Protein-protein interaction and pathway analysis highlighted 50 significantly enriched pathways among which RAS, TGF beta, JAK/STAT and insulin signaling. CONCLUSIONS: CFTR loss of function is associated with changes in the miRNA network, which regulates genes involved in the major comorbidities that affect CF patients suggesting that further research is warranted.

Correction to: Parma consensus statement on metabolic disruptors.

CORRECTION: After publication of the article [1], it has been brought to our attention that the thirteenth author of this article has had their name spelt incorrectly. In the original article the spelling "Laura Rizzir" was used. In fact the correct spelling should be "Laura Rizzi".

miR-146a, miR-155, miR-370, and miR-708 Are CFTR-Dependent, Predicted FOXO1 Regulators and Change at Onset of CFRDs.

CONTEXT: Cystic fibrosis-related diabetes (CFRD) is the most frequent and severe co-morbidity in cystic fibrosis (CF). Presentation and severity are quite variable. OBJECTIVE: To investigate changes in microRNAs (miRNAs) due to CF transmembrane conductance regulator malfunctioning in vitro, to study the circulating levels of selected miRNAs in serum samples from patients, and to assess their relationships in different age groups with genotype, glucose tolerance state, and at onset of CFRD. Design/Setting/Patients/Interventions: Transcriptional profiling of all known miRNAs in CFBE41o- cells, in their normal counterparts (16HBE14o- cells), and in IB3 cells was performed. A set of miRNAs was differentially expressed in the CF cells. By in silico analysis, four miRNAs (miR-146a, miR-155, miR-370, and miR-708) were selected as potential regulators of the FOXO1 gene. Seventy-four CF patients and 50 healthy subjects whose glucose tolerance was characterized by an oral glucose tolerance test were enrolled in the study, and the identified miRNAs were quantified in serum by quantitative RT-PCR. Main Outcome Measurements/Results: A total of 111 miRNAs were differentially expressed in the two CF cell lines. miR-155, miR-370, and miR-708 were up-regulated and miR-146a was down-regulated in vitro, whereas in vivo, miR-146a, miR-155, and miR-370 were up-regulated, and miR-708 was down-regulated. These changes showed relationships with genotype, glucose tolerance state, and onset of CFRD. CONCLUSIONS: The data showed significant changes in miRNAs dependent on genotype and glucose tolerance state in CF patients and highlighted some miRNAs of importance in CFRD at onset. miRNAs could explain some of the variability observed in CF.

HMGB1 Is Increased by CFTR Loss of Function, Is Lowered by Insulin, and Increases In Vivo at Onset of CFRD.

CONTEXT: Cystic fibrosis-related diabetes (CFRD) is associated with worsening of inflammation and infections, and the beginning of insulin treatment is debated. OBJECTIVES: To verify high-mobility group box 1 protein (HMGB1) levels in CF patients according to glucose tolerance state, and analyze relationships with insulin secretion and resistance. To verify, in an in vitro model, whether HMGB1 gene expression and protein content were affected by insulin administration and whether these changes were dependent on CF transmembrane conductance regulator (CFTR) loss of function. PATIENTS AND METHODS: Forty-three patients in stable clinical conditions and 35 age- and sex-matched controls were enrolled. Glucose tolerance was established in patients based on a 5 point oral glucose tolerance test (OGTT). Fasting glucose to insulin ratio (FGIR), HOMA-IR index, whole-body insulin sensitivity index (WIBISI), and the areas under the curve for glucose (AUCG) and insulin (AUCI) were calculated. HMGB1 was assayed in serum, in cell lysates and conditioned media using a specific ELISA kit. For the in vitro study we used CFBE41o- cells, homozygous for the F508del mutation, and 16HBE14o- as non-CF control. HMGB1 gene expression was studied by real-time RT-PCR. Cells were stimulated with insulin at 2.5 and 5 ng/mL. The CFTR inhibitor 172 and CFTR gene silencing were used to induce CFTR loss of function in 16HBE14o- cells. RESULTS: HMGB1 levels were increased at onset of CFRD (5.04 ± 1.2 vs 2.7 ± 0.3 ng/mL in controls; P < .05) and correlated with FGIR (R = +0.43; P = .038), and AUCI (R = +0.43; P = .013). CFTR loss of function in the 16HBE14o- cells increased HMGB1 and was lowered by insulin. CONCLUSION: HMGB1 was increased in CF patients with deranging glucose metabolism and showed relationships with indexes of glucose metabolism. The increase in HMGB1 was related to CFTR loss of function, and insulin lowered HMGB1. Further research is required to verify whether HMGB1 could potentially be a candidate marker of onset of CFRD and to establish when to start insulin treatment.

Data Mining of Determinants of Intrauterine Growth Retardation Revisited Using Novel Algorithms Generating Semantic Maps and Prototypical Discriminating Variable Profiles.

OBJECTIVES: Intra-uterine growth retardation is often of unknown origin, and is of great interest as a "Fetal Origin of Adult Disease" has been now well recognized. We built a benchmark based upon a previously analysed data set related to Intrauterine Growth Retardation with 46 subjects described by 14 variables, related with the insulin-like growth factor system and pro-inflammatory cytokines, namely interleukin-6 and tumor necrosis factor-α. DESIGN AND METHODS: We used new algorithms for optimal information sorting based on the combination of two neural network algorithms: Auto-contractive Map and Activation and Competition System. Auto-Contractive Map spatializes the relationships among variables or records by constructing a suitable embedding space where 'closeness' among variables or records reflects accurately their associations. The Activation and Competition System algorithm instead works as a dynamic non linear associative memory on the weight matrices of other algorithms, and is able to produce a prototypical variable profile of a given target. RESULTS: Classical statistical analysis, proved to be unable to distinguish intrauterine growth retardation from appropriate-for-gestational age (AGA) subjects due to the high non-linearity of underlying functions. Auto-contractive map succeeded in clustering and differentiating completely the conditions under study, while Activation and Competition System allowed to develop the profile of variables which discriminated the two conditions under study better than any other previous form of attempt. In particular, Activation and Competition System showed that ppropriateness for gestational age was explained by IGF-2 relative gene expression, and by IGFBP-2 and TNF-α placental contents. IUGR instead was explained by IGF-I, IGFBP-1, IGFBP-2 and IL-6 gene expression in placenta. CONCLUSION: This further analysis provided further insight into the placental key-players of fetal growth within the insulin-like growth factor and cytokine systems. Our previous published analysis could identify only which variables were predictive of fetal growth in general, and identified only some relationships.

Parma consensus statement on metabolic disruptors.

A multidisciplinary group of experts gathered in Parma Italy for a workshop hosted by the University of Parma, May 16-18, 2014 to address concerns about the potential relationship between environmental metabolic disrupting chemicals, obesity and related metabolic disorders. The objectives of the workshop were to: 1. Review findings related to the role of environmental chemicals, referred to as "metabolic disruptors", in obesity and metabolic syndrome with special attention to recent discoveries from animal model and epidemiology studies; 2. Identify conclusions that could be drawn with confidence from existing animal and human data; 3. Develop predictions based on current data; and 4. Identify critical knowledge gaps and areas of uncertainty. The consensus statements are intended to aid in expanding understanding of the role of metabolic disruptors in the obesity and metabolic disease epidemics, to move the field forward by assessing the current state of the science and to identify research needs on the role of environmental chemical exposures in these diseases. We propose broadening the definition of obesogens to that of metabolic disruptors, to encompass chemicals that play a role in altered susceptibility to obesity, diabetes and related metabolic disorders including metabolic syndrome.

Di-(2-ethylhexyl) phthalate metabolites in urine show age-related changes and associations with adiposity and parameters of insulin sensitivity in childhood.

OBJECTIVES: Phthalates might be implicated with obesity and insulin sensitivity. We evaluated the levels of primary and secondary metabolites of Di-(2-ethylhexyl) phthalate (DEHP) in urine in obese and normal-weight subjects both before and during puberty, and investigated their relationships with auxological parameters and indexes of insulin sensitivity. DESIGN AND METHODS: DEHP metabolites (MEHP, 6-OH-MEHP, 5-oxo-MEHP, 5-OH-MEHP, and 5-CX-MEHP), were measured in urine by RP-HPLC-ESI-MS. Traditional statistical analysis and a data mining analysis using the Auto-CM analysis were able to offer an insight into the complex biological connections between the studied variables. RESULTS: The data showed changes in DEHP metabolites in urine related with obesity, puberty, and presence of insulin resistance. Changes in urine metabolites were related with age, height and weight, waist circumference and waist to height ratio, thus to fat distribution. In addition, clear relationships in both obese and normal-weight subjects were detected among MEHP, its products of oxidation and measurements of insulin sensitivity. CONCLUSION: It remains to be elucidated whether exposure to phthalates per se is actually the risk factor or if the ability of the body to metabolize phthalates is actually the key point. Further studies that span from conception to elderly subjects besides further understanding of DEHP metabolism are warranted to clarify these aspects.

miR-196a expression in human and canine osteosarcomas: a comparative study.

Osteosarcoma (OS) is the most common primary malignant bone tumour in dogs and humans. MicroRNAs are short non-coding RNA molecules involved in post-transcriptional gene expression. Here, we compared the effects of miR-196a deregulation in human and canine OS cells after having observed a more uniform distribution and stronger down-expression in the human specimens. Cell response to miR-196a transfection was different in human and canine OS. A decreased proliferation rate was seen in human MG63 and 143B OS cells, while no appreciable changes occurred in canine DAN cells. Transient decrease of motility was highly remarkable and longer in MG63, concomitant with decreased levels of annexin1, a target of miR-196a promoting cell migration and invasion. In conclusion, the effects of miR-196a over-expression on tumour cell response may be strictly related to species and cell type. Further studies are needed to define the impact of miRNA deregulation on OS development.

FOXO1 content is reduced in cystic fibrosis and increases with IGF-I treatment.

Cystic fibrosis-related diabetes is to date the most frequent complication in cystic fibrosis (CF). The mechanisms underlying this condition are not well understood, and a possible role of insulin resistance is debated. We investigated insulin signal transduction in CF. Total insulin receptor, IRS1, p85 PI3K, and AKT contents were substantially normal in CF cells (CFBE41o-), whereas winged helix forkhead (FOX)O1 contents were reduced both in baseline conditions and after insulin stimulation. In addition, CF cells showed increased ERK1/2, and reduced ß2 arrestin contents. No significant change in SOCS2 was observed. By using a CFTR inhibitor and siRNA, changes in FOXO1 were related to CFTR loss of function. In a CF-affected mouse model, FOXO1 content was reduced in the muscle while no significant difference was observed in liver and adipose tissue compared with wild-type. Insulin-like growth factor 1 (IGF-I) increased FOXO1 content in vitro and in vivo in muscle and adipose tissue. In conclusion; we present the first description of reduced FOXO1 content in CF, which is compatible with reduced gluconeogenesis and increased adipogenesis, both features of insulin insensitivity. IGF-I treatment was effective in increasing FOXO1, thereby suggesting that it could be considered as a potential treatment in CF patients possibly to prevent and treat cystic fibrosis-related diabetes.

A validated biorepository of retina and choroid tissues for gene expression studies.

Research studies on pathologies affecting the posterior segment of the eye are usually carried out either in animal models or cell lines of human origin that mimic the molecular patterns occurring in the human retina-pigment epithelium-choroid (RPC) complex in vivo. As this is not always the case, we were prompted to validate a biorepository of RPC tissues for research purposes. A PubMed literature search on "retina," "choroid," "bio-bank," or "biorepository" as keywords did not lead to any publication describing the collection and banking of samples from the RPC complex for research purposes. The possibility to obtain access to a validated collection of high quality human RPC tissues as starting material is likely to lead to more appropriate findings and treatments, which eventually may improve human ocular health. Here we show that when tissues are harvested (T <25 hours from donor death) and stored appropriately, RNAs are not degraded (RNA Integrity Number Values >8.0) and express specific genes and molecular/biochemical pathways occurring in the RPC complex. These quality controlled tissues/RNAs comprising the biorepository could therefore be used for gene expression studies by research scientists and clinicians interested in testing their hypotheses in a more appropriate setting, thus replacing studies performed on less relevant animal models and cells in vitro, and directly extrapolating the findings to human pathophysiology.

Artificial Neural Networks, and Evolutionary Algorithms as a systems biology approach to a data-base on fetal growth restriction.

One of the specific aims of systems biology is to model and discover properties of cells, tissues and organisms functioning. A systems biology approach was undertaken to investigate possibly the entire system of intra-uterine growth we had available, to assess the variables of interest, discriminate those which were effectively related with appropriate or restricted intrauterine growth, and achieve an understanding of the systems in these two conditions. The Artificial Adaptive Systems, which include Artificial Neural Networks and Evolutionary Algorithms lead us to the first analyses. These analyses identified the importance of the biochemical variables IL-6, IGF-II and IGFBP-2 protein concentrations in placental lysates, and offered a new insight into placental markers of fetal growth within the IGF and cytokine systems, confirmed they had relationships and offered a critical assessment of studies previously performed.

Human RNA integrity after postmortem retinal tissue recovery.

PURPOSE: To assess the parameters for postmortem retinal tissue recovery and processing that affect the quality of RNA extracted from the retina/retinal pigment epithelium (RPE) complex. METHODS: RNA was extracted from retina/RPE samples. The RNA quality was determined based on qualitative/quantitative measurements made with a Bioanalyzer (Agilent) and on the expression of a long retinal gene (RPE65). After a pilot analysis on rats, ocular RNA was extracted from human donor eyeballs (group A) explanted according to conventional procedures for cornea transplantation. In a second experiment, another group of human donor eyeballs (group B) were processed in a much shorter time. The postmortem interval (T) comprised two periods: T1, the time between a donor's death and enucleation, and T2, the time between eyeball explantation and immersion of the excised retina/RPE sample in preservative solution (T = T1 + T2). RESULTS: A short T2 was correlated with good quality of RNA extracted from the retina/RPE complex (p = 0.043) and successful expression of a tissue-specific gene (p = 0.007). No other parameter appeared to influence RNA quality. CONCLUSIONS: The time between eyeball explantation and immersion of the retina/RPE sample in preservative solution was the chief parameter affecting the quality of RNA extracted from the retina/RPE complex.

MicroRNA cloning and sequencing in osteosarcoma cell lines: differential role of miR-93.

BACKGROUND: Studies show that abnormalities in non-coding genes can contribute to carcinogenesis; microRNA levels may modulate cancer growth and metastatic diffusion. METHOD: MicroRNA libraries were built and sequenced from two osteosarcoma cell lines (MG-63 and 143B), which differ in proliferation and transmigration. By cloning and transfection, miR-93, expressed in both cell lines, was then investigated for its involvement in osteosarcoma progression. RESULTS: Six of the 19 miRNA identified were expressed in both cell lines with higher expression levels of miR-93 in 143B and in primary osteosarcoma cultures compared to normal osteoblasts. Interestingly, levels of miR-93 were significantly higher in metastases from osteosarcoma than in paired primary tumours. When 143B and MG-63 were transfected with miR-93, clones appeared to respond differently to microRNA overexpression. Ectopic expression of miR-93 more significantly increased cell proliferation and invasivity in 143B than in MG-63 clones. Furthermore, increased mRNA and protein levels of E2F1, one of the potential miR-93 targets, were seen in osteosarcoma cellular clones and its involvement in 143B cell proliferation was confirmed by E2F1 silencing. CONCLUSION: Although further studies are needed to evaluate miRNA involvement in osteosarcoma progression, miR-93 overexpression seems to play an important role in osteosarcoma cell growth and invasion.

Differential distribution of aggrecan isoforms in perineuronal nets of the human cerebral cortex.

Aggrecan is a component of the CNS extracellular matrix (ECM) and we show here that the three primary alternative spliced transcripts of the aggrecan gene found in cartilage are also present in the adult CNS. Using a unique panel of core protein-directed antibodies against human aggrecan we further show that different aggrecan isoforms are deposited in perineuronal nets (PNNs) and neuropil ECM of Brodmann's area 6 of the human adult cerebral cortex. According to their distribution pattern, the identified cortical aggrecan isoforms were subdivided into five clusters spanning from cluster 1, comprised isoforms that appeared widespread throughout the cortex, to cluster 5, which was an aggrecan-free subset. Comparison of brain and cartilage tissues showed a different relative abundance of aggrecan isoforms, with cartilage-specific isoforms characterizing cluster 5, and PNN-associated isoforms lacking keratan sulphate chains. In the brain, isoforms of cluster 1 were disclosed in PNNs surrounding small-medium interneurons of layers II-V, small-medium pyramidal neurons of layers III and V and large interneurons of layer VI. Aggrecan PNNs enveloped both neuron bodies and neuronal processes, encompassing pre-terminal nerve fibres, synaptic boutons and terminal processes of glial cells and aggrecan was also observed in continuous 'coats' associated with satellite, neuron-associated cells of a putative glial nature. Immunolabelling for calcium-binding proteins and glutamate demonstrated that aggrecan PNNs were linked to defined subsets of cortical interneurons and pyramidal cells. We suggest that in the human cerebral cortex, discrete, layer-specific PNNs are assembled through the participation of selected aggrecan isoforms that characterize defined subsets of cortical neurons.

Instability of mitochondrial DNA and MRI and clinical correlations in malignant gliomas.

Mutations and instability of mitochondrial DNA (mtDNA) are frequent in tumors but their pathogenic relevance is not established. To assess their role in the clinical management of malignant gliomas we have studied the D loop of mtDNA in 42 such tumors. Alterations were found in 36% of the cases. The MRI and the clinical follow-up of these patients suggest that these mutations are not associated with increased aggressiveness. mtDNA could be amplified from post-surgical tumor cavities in patients undergoing a loco-regional treatment. These results imply that mtDNA mutations are unlikely to play a role in diagnostic or prognostic evaluations of gliomas: their detection, however, could be of use for the clinical follow-up of malignant gliomas.