Nonalcoholic fatty liver disease is associated with an almost twofold increased risk of incident type 2 diabetes and metabolic syndrome. Evidence from a systematic review and meta-analysis.

BACKGROUND AND AIM: The magnitude of the risk of incident type 2 diabetes (T2D) and metabolic syndrome (MetS) among patients with nonalcoholic fatty liver disease (NAFLD) is poorly known. We gauged the risk of developing T2D and MetS in patients with NAFLD diagnosed by either serum liver enzymes (aminotransferases or gamma-glutamyltransferase [GGT]) or ultrasonography. METHODS: Pertinent prospective studies were identified through extensive electronic database research, and studies fulfilling enrolment criteria were included in the meta-analysis. RESULTS: Overall, in a pooled population of 117020 patients (from 20 studies), who were followed-up for a median period of 5 years (range: 3-14.7 years), NAFLD was associated with an increased risk of incident T2D with a pooled relative risk of 1.97 (95% confidence interval [CI], 1.80-2.15) for alanine aminotransferase, 1.58 (95% CI, 1.43-1.74) for aspartate aminotransferase, 1.86 (95% CI, 1.71-2.03) for GGT (last vs first quartile or quintile), and 1.86 (95% CI, 1.76-1.95) for ultrasonography, respectively. Overall, in a pooled population of 81411 patients (from eight studies) who were followed-up for a median period of 4.5 years (range: 3-11 years), NAFLD was associated with an increased risk of incident MetS with a pooled relative risk of 1.80 (95% CI, 1.72-1.89) for alanine aminotransferase (last vs first quartile or quintile), 1.98 (95% CI, 1.89-2.07) for GGT, and 3.22 (95% CI, 3.05-3.41) for ultrasonography, respectively. CONCLUSIONS: Nonalcoholic fatty liver disease, as diagnosed by either liver enzymes or ultrasonography, significantly increases the risk of incident T2D and MetS over a median 5-year follow-up.

Mapping eQTL networks with mixed graphical Markov models.

Expression quantitative trait loci (eQTL) mapping constitutes a challenging problem due to, among other reasons, the high-dimensional multivariate nature of gene-expression traits. Next to the expression heterogeneity produced by confounding factors and other sources of unwanted variation, indirect effects spread throughout genes as a result of genetic, molecular, and environmental perturbations. From a multivariate perspective one would like to adjust for the effect of all of these factors to end up with a network of direct associations connecting the path from genotype to phenotype. In this article we approach this challenge with mixed graphical Markov models, higher-order conditional independences, and q-order correlation graphs. These models show that additive genetic effects propagate through the network as function of gene-gene correlations. Our estimation of the eQTL network underlying a well-studied yeast data set leads to a sparse structure with more direct genetic and regulatory associations that enable a straightforward comparison of the genetic control of gene expression across chromosomes. Interestingly, it also reveals that eQTLs explain most of the expression variability of network hub genes.

Life expectancy in the immune recovery era: the evolving scenario of the HIV epidemic in northern Italy.

INTRODUCTION: National cohort and intercohort studies have been set to describe the differences of life expectancy (LE) of HIV-infected individuals. OBJECTIVE: The aim of this study was to assess the impact of immune recovery (IR) on LE of patients with HIV undergoing combination antiretroviral therapy. METHODS: In this retrospective observational study, outcome measure was LE of patients with HIV compared with LE of northern Italian population. Group categorizations were as follows: patients with no immune recovery (nIR), patients with IR, patients who are immune maintained, and pre-highly active antiretroviral therapy (HAART) and post-HAART. Abridged life tables were constructed from age-specific mortality rates (per 1000 person years) to estimate LE from the age of 20-55 years. RESULTS: A total of 9671 patients, 71% men, were included. After 2005, we assisted to a rapid increase in the overall rate of patients attaining IR in the community coupled with a progressive decrease of AIDS death, but not of non-AIDS deaths. In a 40-year-old patient, LE was 38.10 years [standard error (SE) = 2.60], 30.08 years (SE = 0.98), and 22.9 (SE = 0.69) in the IR, post-HAART group and nIR, respectively, compared with 41.38 years of the general Italian population. An approximately 5-year gap in LE was observed in IR patients. DISCUSSION: We describe IR at a "community" level, related to calendar year and apparent 10 years after HAART introduction. HAART community IR is significantly influencing LE and is associated with the changing clinical picture of HIV disease. An increasing gradient of LE exists between nIR, post-HAART, and IR groups, with the latter, above the age of 40 years only, reaching LE of general population.

Inference of regulatory networks from microarray data with R and the bioconductor package qpgraph.

Regulatory networks inferred from microarray data sets provide an estimated blueprint of the functional interactions taking place under the assayed experimental conditions. In each of these experiments, the gene expression pathway exerts a finely tuned control simultaneously over all genes relevant to the cellular state. This renders most pairs of those genes significantly correlated, and therefore, the challenge faced by every method that aims at inferring a molecular regulatory network from microarray data, lies in distinguishing direct from indirect interactions. A straightforward solution to this problem would be to move directly from bivariate to multivariate statistical approaches. However, the daunting dimension of typical microarray data sets, with a number of genes p several orders of magnitude larger than the number of samples n, precludes the application of standard multivariate techniques and confronts the biologist with sophisticated procedures that address this situation. We have introduced a new way to approach this problem in an intuitive manner, based on limited-order partial correlations, and in this chapter we illustrate this method through the R package qpgraph, which forms part of the Bioconductor project and is available at its Web site.

Premature age-related comorbidities among HIV-infected persons compared with the general population.

BACKGROUND: Human immunodeficiency virus (HIV)-infected patients may have a greater risk of noninfectious comorbidities (NICMs) compared with the general population. We assessed the prevalence and risk factors for NICMs in a large cohort of HIV-infected adults and compared these findings with data from matched control subjects. METHODS: We performed a case-control study involving antiretroviral therapy (ART)-experienced HIV-infected patients treated at Modena University, Italy, from 2002 through 2009. These patients were compared with age-, sex-, and race-matched adults (control subjects) from the general population included in the CINECA ARNO database. NICMs included cardiovascular disease, hypertension, diabetes mellitus, bone fractures, and renal failure. Polypathology (Pp) was defined as the concurrent presence of ≥2 NICMs. Logistic regression models were constructed to evaluate associated predictors of NICMs and Pp. RESULTS: There were 2854 patients and 8562 control subjects. The mean age was 46 years, and 37% were women. Individual NICM and Pp prevalences in each age stratum were higher among patients than among controls (all P <.001). Pp prevalence among patients aged 41-50 years was similar to that among controls aged 51-60 years (P value was not statistically significant); diabetes mellitus, cardiovascular disease, bone fractures, and renal failure were statistically independent after adjustment for sex, age, and hypertension. Logistic regression models showed that independent predictors of Pp in the overall cohort were (all P < .001) age (odds ratio [OR], 1.11), male sex (OR, 1.77), nadir CD4 cell count <200 cells/µL (OR, 4.46), and ART exposure (OR, 1.01). CONCLUSIONS: Specific age-related NICMs and Pp were more common among HIV-infected patients than in the general population. The prevalence of Pp in HIV-infected persons anticipated Pp prevalence observed in the general population among persons who were 10 years older, and HIV-specific cofactors (lower nadir CD4 cell count and more prolonged ART exposure) were identified as risk factors. These data support the need for earlier screening for NICMs in HIV-infected patients.

Wilks' Λ dissimilarity measures for gene clustering: an approach based on the identification of transcription modules.

Clustering methods are widely used in the analysis of microarray data for their ability to uncover coordinated expression profiles. One important goal of clustering is to discover coregulated genes because it has been postulated that genes targeted by the same transcription factors tend to show similar expression patterns. We focus on agglomerative hierarchical clustering and consider the problem of choosing a dissimilarity measure on the basis of its ability to identify functional modules consisting of a transcription factor and the associated target genes. We first propose two criteria that constitute a theoretical framework for assessing the adequacy and comparing different dissimilarity measures. We show that the proposed criteria allow one to gain insight into the behavior of dissimilarity measures and lead to a ranking of some of the most commonly used dissimilarity measures. Next, we introduce two dissimilarity measures based on the Wilks' Λ statistic and show that, according to the above criteria, they have better performance than the other considered measures. The theoretical results are supported by an applied analysis on both simulated and real data.

Human immunodeficiency virus is the major determinant of steatosis and hepatitis C virus of insulin resistance in virus-associated fatty liver disease.

BACKGROUND AND AIMS: To promote our understanding of the relative contribution of metabolic and viral factors, the independent predictors of fatty liver and insulin resistance (IR) were assessed by comparing patients with nonalcoholic fatty liver disease (NAFLD) to individuals with virus-associated fatty liver disease (VAFLD): human immunodeficiency virus (HIV)-VAFLD, hepatitis C virus (HCV)-VAFLD and HIV-HCV-VAFLD. METHODS: One hundred eighty eight consecutive patients with viral infections (103 HIV, 85 patients with HCV genotype 1 infection: 45 mono-infected and 40 HIV/HCV co-infected) with or without steatosis and 126 NAFLD patients were analyzed. Steatosis was diagnosed by ultrasonography. To assess the odds ratio (OR) of steatosis and IR, HCV and NAFLD, respectively, were used as the reference values. IR was evaluated through homeostasis model (HOMA) and the metabolic syndrome (MetS) using standard criteria. RESULTS: The prevalence of VAFLD was 47%. Multivariate logistic regression analysis was carried out using HCV as the reference. VAFLD was predicted by HIV, HIV/HCV, female gender, waist circumference (WC) and HOMA (OR = 3.99, 3.76, 2.80, 1.08 and 1.18). According to multiple linear regression using NAFLD as the reference, IR was predicted by HCV, HIV and HIV/HCV, WC, triglycerides (coefficient beta = 2.25, 0.99, 1.86, 0.08, 0.05, respectively). In linear models, for any given number of components of MetS, HCV and HCV/HIV-associated fatty liver disease had greater HOMA compared to NAFLD (p <0.001). CONCLUSIONS: Whereas HIV confers a higher risk of steatosis, VAFLD is associated with higher IR than NAFLD and such an effect is specifically linked to HCV rather than to HIV infection.

Reverse engineering molecular regulatory networks from microarray data with qp-graphs.

Reverse engineering bioinformatic procedures applied to high-throughput experimental data have become instrumental in generating new hypotheses about molecular regulatory mechanisms. This has been particularly the case for gene expression microarray data, where a large number of statistical and computational methodologies have been developed in order to assist in building network models of transcriptional regulation. A major challenge faced by every different procedure is that the number of available samples n for estimating the network model is much smaller than the number of genes p forming the system under study. This compromises many of the assumptions on which the statistics of the methods rely, often leading to unstable performance figures. In this work, we apply a recently developed novel methodology based in the so-called q-order limited partial correlation graphs, qp-graphs, which is specifically tailored towards molecular network discovery from microarray expression data with p >> n. Using experimental and functional annotation data from Escherichia coli, here we show how qp-graphs yield more stable performance figures than other state-of-the-art methods when the ratio of genes to experiments exceeds one order of magnitude. More importantly, we also show that the better performance of the qp-graph method on such a gene-to-sample ratio has a decisive impact on the functional coherence of the reverse-engineered transcriptional regulatory modules and becomes crucial in such a challenging situation in order to enable the discovery of a network of reasonable confidence that includes a substantial number of genes relevant to the essayed conditions. An R package, called qpgraph implementing this method is part of the Bioconductor project and can be downloaded from (www.bioconductor.org). A parallel standalone version for the most computationally expensive calculations is available from (http://functionalgenomics.upf.xsedu/qpgraph).

Glomerular filtration rates in HIV-infected patients treated with and without tenofovir: a prospective, observational study.

OBJECTIVES: The aim of our study was to assess the impact of plasma HIV-1 RNA level [viral load (VL)] variation and tenofovir exposure on kidney functions by analysing changes in calculated glomerular filtration rates (GFRs) over a 48 week period in patients with mild renal impairment. PATIENTS AND METHODS: A prospective observational study that included data from all consecutive HIV-infected patients who attended a metabolic clinic was conducted. Included were adult, antiretroviral (ARV)-experienced, tenofovir-naive patients, whose kidney functions were evaluated by calculated GFR using the simplified Modification of Diet in Renal Disease study equation (MDRD). Tenofovir-exposed patients were patients who initiated tenofovir therapy at baseline and tenofovir-unexposed patients were patients whose ARV therapy did not include tenofovir. Participants were stratified into three sub-groups according to the plasma HIV-1 RNA (VL) changes observed: sub-groups 1, 2 and 3 were patients with stable VL < or =50 copies/mL, >0.5 log(10) VL increases and >0.5 VL log(10) decreases, respectively. RESULTS: Ninety-nine patients were enrolled and included in the analysis. Within the tenofovir-unexposed group, GFRs remained stable (ANOVA, P = 0.94) over the follow-up period. Within the tenofovir-exposed group, mean GFR changes varied significantly by sub-group (ANOVA, P < 0.01). In particular, GFR changes in sub-group 3 (+8.4 +/- 12.4 mL/min) were different from those seen in sub-group 1 (-1.0 +/- 8.8 mL/min) (P < 0.05) and sub-group 2 (-4.6 +/- 8.8 mL/min) (P < 0.01). CONCLUSIONS: Observed improvements in GFR that occurred as a consequence of highly active ARV therapy-induced viral suppression may have more than offset any potential negative effects of tenofovir on renal function.

Prevalence of and risk factors for pubic lipoma development in HIV-infected persons.

BACKGROUND: The natural history of HIV-associated body habitus changes is unclear. In this report, we describe a novel manifestation of HIV-associated lipoaccumulation. METHODS: We noted the presence of suprapubic fat pads (pubic lipomas [PLs]) in several patients with preexisting HIV-associated body habitus abnormalities. Subsequently, we evaluated the prevalence of and associated risk factors for development of PLs by undertaking an observational cross-sectional study among patients with known lipodystrophy who attended a metabolic clinic in northern Italy. Inclusion criteria were a physician-confirmed diagnosis of lipodystrophy according to the Multicenter AIDS Cohort Study definition and, for those affected with PL, a readily noticeable PL on physical examination. RESULTS: We evaluated 582 patients with lipodystrophy: 214 female (36.7%) and 368 male (63.3%). The overall PL prevalence was 9.4% (95% confidence interval [CI]: 7.2% to 12.1%; P < 0.0001). PLs were more common among obese than nonobese individuals (34.5%, 95% CI: 17.9% to 5l.3% vs. 8%, 95% CI: 5.9% to 10.6%, respectively; P < 0.0001) and those with preexisting dorsocervical fat pads, commonly called "buffalo humps" (BHs) (18.5%, 95% CI: 12.7% to 25.4% vs. 6.1%, 95% CI: 4.03% to 8.83%, respectively, P < 0.0001; relative risk = 3.02, 95% CI: 1.84% to 4.96%, P < 0.0001). The PL prevalence in the nonobese HIV-infected population (body mass index [BMI] <30, n = 550) was 8.0% (95% CI: 5.9% to 10.6%; P < 0.0001). Logistic regression analyses identified the following factors as associated with a greater likelihood for PL: BMI >30 (beta = 0.18, SE = 0.04; P < 0.001), female gender (beta = 1.06, SE = 0.31; P < 0.001), and shorter duration of HIV infection (beta = -0.005, SE = 0.003; P = 0.04). We used a chain graph model to evaluate risk factors for BH and PL simultaneously. A nonnull interaction between these entities was evident, and this association seemed to be independent of factors positively associated with both (BMI and gender). CONCLUSIONS: PL is a newly recognized manifestation of HIV-associated lipoaccumulation that is more likely to occur among those with coexisting dorsocervical fat pads, suggesting the possibility of a common pathogenesis between the 2 entities. Likewise, PLs are more common among women, obese individuals, and those with a shorter duration of HIV infection. We suggest that PL should be considered part of the HIV-associated lipodystrophy syndrome.

Multidisciplinary approach to the treatment of metabolic and morphologic alterations of HIV-related lipodystrophy.

BACKGROUND: Treatment for metabolic and morphologic alterations in HIV-related lipodystrophy include medical therapy, physical exercise, and surgical interventions. METHOD: We assessed the efficacy and safety of a comprehensive multidisciplinary approach for treating morphological and metabolic alterations of the lipodystrophy syndrome in consecutive patients attending the Metabolic Clinic (MC) of the University of Modena and Reggio Emilia who had at least 2 evaluations over a 48-week period. 245 patients were evaluated: 143 (62.4%) were men, 74 (36.1%) presented with lipoatrophy, 10 (4.9%) with fat accumulation, 93 (45%) with mixed forms, 24 (11.3%) had hypercholesterolemia (LDL >160 mg/dL), 87 (38%) had hypertriglyceridemia (TG >150 mg/dL), 13 (5.7%) had diabetes (glucose >126 mg/dL), and 78 (44%) had insulin resistance (HOMA-IR >4). RESULTS: At follow-up, a significant improvement was observed in both objective and subjective variables. Anthropometric improvement was observed in waist to hip ratio, waist circumference, and right and left cheek dermal thickness measurements. A nonsignificant improvement was observed in fat and lean regional mass by DEXA; CT showed improvement in visceral and subcutaneous adipose tissue. Glucose, HOMA-IR, total cholesterol, and APO B improved. Subjective variables improved in aesthetic satisfaction. CONCLUSION: We conclude that the medical and surgical interventions proposed in this multidisciplinary therapeutic approach are efficacious and safe in the management of lipodystrophy.

Androgen receptor gene CAG and GGC repeat lengths in cryptorchidism.

OBJECTIVE: Cryptorchidism is the most common congenital birth defect in male children, and accumulating evidence suggests that genetic abnormalities may be associated with it. The androgen receptor has two polymorphic sites in exon 1, with different numbers of CAG and GGC repeats, resulting in variable lengths of polyglutamine and polyglycine stretches. Longer CAG repeats result in a reduced androgen receptor transcriptional activity, but the role of the GGC triplets is less clear. In this study we analysed CAG and GGC repeat lengths in men with a history of cryptorchidism, associated or not with impairment of sperm production, in comparison with normal fertile subjects. METHODS: We analysed CAG and GGC repeat lengths in a group of 105 ex-cryptorchid men in comparison with 115 fertile non-cryptorchid men. RESULTS: No difference was found between patients and controls in the mean and median values, and in distribution of CAG and GGC, when considered separately. However, the analysis of the joint distribution of CAG and GGC showed that some combinations are significantly more frequent in men with bilateral cryptorchidism (who frequently presented severe testiculopathies), in a manner similar to that found in idiopathic infertile subjects. CONCLUSIONS: Although further studies are needed to elucidate the possible role of specific CAG/GGC combinations as a causative factor, these data suggest a possible association between androgen receptor gene polymorphisms and cryptorchidism.

Oral carnitine supplementation increases sperm motility in asthenozoospermic men with normal sperm phospholipid hydroperoxide glutathione peroxidase levels.

OBJECTIVE: To clarify the role of carnitine supplementation in idiopathic asthenozoospermia and to look for a rationale for its use in asthenozoospermic patients. DESIGN: Blind clinical study. SETTING: Academic. PATIENT(S): Thirty asthenozoospermic patients divided in two groups according to phospholipid hydroperoxide glutathione peroxidase (PHGPx) levels. INTERVENTION(S): Placebo for 3 months, then oral L-carnitine (2 g/day) for 3 months; semen samples were collected at baseline, after placebo, after carnitine administration, and again after 3 months with no drugs. MAIN OUTCOME MEASURE(S): Evaluation of seminal parameters and determination of seminal PHGPx levels, measured as rescued activity. RESULT(S): When asthenozoospermic subjects were divided in two groups on the basis of PHGPx levels, we observed an improvement of mean sperm motility only in the group of patients with normal PHGPx levels. CONCLUSION(S): Phospholipid hydroperoxide glutathione peroxidase has an important role in male infertility, and carnitine treatment might improve sperm motility in the presence of normal mitochondrial function.