Identification of recurrent genetic patterns from targeted sequencing panels with advanced data science: a case-study on sporadic and genetic neurodegenerative diseases.

BACKGROUND: Targeted Next Generation Sequencing is a common and powerful approach used in both clinical and research settings. However, at present, a large fraction of the acquired genetic information is not used since pathogenicity cannot be assessed for most variants. Further complicating this scenario is the increasingly frequent description of a poli/oligogenic pattern of inheritance showing the contribution of multiple variants in increasing disease risk. We present an approach in which the entire genetic information provided by target sequencing is transformed into binary data on which we performed statistical, machine learning, and network analyses to extract all valuable information from the entire genetic profile. To test this approach and unbiasedly explore the presence of recurrent genetic patterns, we studied a cohort of 112 patients affected either by genetic Creutzfeldt-Jakob (CJD) disease caused by two mutations in the PRNP gene (p.E200K and p.V210I) with different penetrance or by sporadic Alzheimer disease (sAD). RESULTS: Unsupervised methods can identify functionally relevant sources of variation in the data, like haplogroups and polymorphisms that do not follow Hardy-Weinberg equilibrium, such as the NOTCH3 rs11670823 (c.3837 + 21 T > A). Supervised classifiers can recognize clinical phenotypes with high accuracy based on the mutational profile of patients. In addition, we found a similar alteration of allele frequencies compared the European population in sporadic patients and in V210I-CJD, a poorly penetrant PRNP mutation, and sAD, suggesting shared oligogenic patterns in different types of dementia. Pathway enrichment and protein-protein interaction network revealed different altered pathways between the two PRNP mutations. CONCLUSIONS: We propose this workflow as a possible approach to gain deeper insights into the genetic information derived from target sequencing, to identify recurrent genetic patterns and improve the understanding of complex diseases. This work could also represent a possible starting point of a predictive tool for personalized medicine and advanced diagnostic applications.

Application of different DNA extraction procedures, library preparation protocols and sequencing platforms: impact on sequencing results.

In this study three DNA extraction procedures, two library preparation protocols and two sequencing platforms were applied to analyse six bacterial cultures and their corresponding DNA obtained as part of a proficiency test. The impact of each variable on sequencing results was assessed using the following parameters: reads quality, assembly and alignment statistics; number of single nucleotide polymorphisms (SNPs), detected applying assembly- and alignment-based strategies; antimicrobial resistance genes (ARGs), identified on de novo assemblies of all sequenced genomes. The investigated nucleic acid extraction procedures, library preparation kits and sequencing platforms do not significantly affect de novo assembly statistics and number of SNPs and ARGs. The only exception was observed for two duplicates, which were associated to one PCR-based library preparation kit. Results from this comparative study can support researchers in the choice toward the available pre-sequencing and sequencing options, and might suggest further comparisons to be performed.

A simple stochastic model for the feedback circuit between p16INK4a and p53 mediated by p38MAPK: implications for senescence and apoptosis.

The mechanisms leading to the cell fate decision between apoptosis and senescence upon DNA damage are still unclear and have stochastic features. Cellular oxidative stress can generate DNA damage and activate the important mitogen-activated protein kinase 14 (p38MAPK) that is involved in pathologies like Alzheimer's disease. Based on experimental evidence we propose a simple network that might operate at the core of the cell control machinery for the choice between apoptosis and senescence involving the cross-talk between p38MAPK, the tumor suppressor protein p53 and the cyclin-dependent kinase inhibitor (p16INK4a). We have performed two types of analyses, deterministic and stochastic, exploring the system's parameter space, in the first, we calculated the fixed points of the deterministic model and, in the second, we numerically integrated the master equation for the stochastic version. The model shows a variety of behaviors dependent on the parameters including states of high expression levels of p53 or p16INK4a that can be associated with an apoptotic or senescent phenotype, respectively, in agreement with experimental data. In addition, we observe both monostable and bistable behavior (where bistability is a phenomenon in which two stable steady states coexist for a fixed set of control parameter values) which here we suggest to be involved in the cell fate decision problem.

Early effects comparison of X-rays delivered at high-dose-rate pulses by a plasma focus device and at low dose rate on human tumour cells.

A comparative study has been performed on the effects of high-dose-rate (DR) X-ray beams produced by a plasma focus device (PFMA-3), to exploit its potential medical applications (e.g. radiotherapy), and low-DR X-ray beams produced by a conventional source (XRT). Experiments have been performed at 0.5 and 2 Gy doses on a human glioblastoma cell line (T98G). Cell proliferation rate and potassium outward currents (IK) have been investigated by time lapse imaging and patch clamp recordings. The results showed that PFMA-3 irradiation has a greater capability to reduce the proliferation rate activity with respect to XRT, while it does not affect IK of T98G cells at any of the dose levels tested. XRT irradiation significantly reduces the mean IK amplitude of T98G cells only at 0.5 Gy. This work confirms that the DR, and therefore the source of radiation, is crucial for the planning and optimisation of radiotherapy applications.

Immune parameters identify Italian centenarians with a longer five-year survival independent of their health and functional status.

Centenarians are rare and exceptional individuals characterized by a peculiar phenotype. They are the best example of healthy aging in humans as most of them have escaped or substantially delayed the onset of major age-related diseases. Within this scenario, the purpose of the present work was to understand if immune status is associated with survival and health status in centenarians. To this aim, 116 centenarians were concomitantly characterized for their immunological, health and functional status, and followed-up for five-year survival. On the basis of previous knowledge we focused on a core of fundamental and basic immune parameters (number of leukocytes, monocytes, total lymphocytes, CD3(+) T lymphocytes, CD4(+) helper T lymphocytes, CD8(+) cytotoxic T lymphocytes, CD19(+) B lymphocytes and plasma levels of IgM), and the most important findings can be summarized as follows: i. a hierarchical cluster analysis was able to define Cluster1 (88 centenarians) and Cluster2 (28 centenarians) characterized by low and high values of all these immune parameters, respectively; ii. centenarians of Cluster2 showed a statistically longer five-year survival and more favorable values of other important immune (naïve, activated/memory and effector/memory T cells) and metabolic (glycemia, insulin and HOMA-IR) parameters, in accord with previous observations that centenarians have a peculiar immune profile, a preserved insulin pathway and a lower incidence of type 2 diabetes; and iii. unexpectedly, parameters related to frailty, as well as functional and cognitive status, did not show any significant correlation with the immune clustering, despite being capable per se of predicting survival. In conclusion, high values of basic immunological parameters and important T cell subsets correlate with five-year survival in centenarians, independent of other phenotypic characteristics. This unexpected biological scenario is compatible with the general hypothesis that in centenarians a progressive disconnection and loss of biological coherence among the different functions of the body occur, where survival/mortality result from the failure of any of these domains which apparently follow an independent age-related trajectory.

Pulsatile intracranial pressure and cerebral autoregulation after traumatic brain injury.

BACKGROUND: Strong correlation between mean intracranial pressure (ICP) and its pulse wave amplitude (AMP) has been demonstrated in different clinical scenarios. We investigated the relationship between invasive mean arterial blood pressure (ABP) and AMP to explore its potential role as a descriptor of cerebrovascular pressure reactivity after traumatic brain injury (TBI). METHODS: We retrospectively analyzed data of patients suffering from TBI with brain monitoring. Transcranial Doppler blood flow velocity, ABP, ICP were recorded digitally. Cerebral perfusion pressure (CPP) and AMP were derived. A new index-pressure-amplitude index (PAx)-was calculated as the Pearson correlation between (averaged over 10 s intervals) ABP and AMP with a 5 min long moving average window. The previously introduced transcranial Doppler-based autoregulation index Mx was evaluated in a similar way, as the moving correlation between blood flow velocity and CPP. The clinical outcome was assessed after 6 months using the Glasgow outcome score. RESULTS: 293 patients were studied. The mean PAx was -0.09 (standard deviation 0.21). This negative value indicates that, on average, an increase in ABP causes a decrease in AMP and vice versa. PAx correlated strong with Mx (R (2) = 0.46, P < 0.0002). PAx also correlated with age (R (2) = 0.18, P < 0.05). PAx was found to have as good predictive outcome value (area under curve 0.71, P < 0.001) as Mx (area under curve 0.69, P < 0.001). CONCLUSIONS: We demonstrated significant correlation between the known cerebral autoregulation index Mx and PAx. This new index of cerebrovascular pressure reactivity using ICP pulse wave information showed to have a strong association with outcome in TBI patients.

Stochastic analysis of a miRNA-protein toggle switch.

Within systems biology there is an increasing interest in the stochastic behavior of genetic and biochemical reaction networks. An appropriate stochastic description is provided by the chemical master equation, which represents a continuous time Markov chain (CTMC). In this paper we consider the stochastic properties of a toggle switch, involving a protein compound (E2Fs and Myc) and a miRNA cluster (miR-17-92), known to control the eukaryotic cell cycle and possibly involved in oncogenesis, recently proposed in the literature within a deterministic framework. Due to the inherent stochasticity of biochemical processes and the small number of molecules involved, the stochastic approach should be more correct in describing the real system: we study the agreement between the two approaches by exploring the system parameter space. We address the problem by proposing a simplified version of the model that allows analytical treatment, and by performing numerical simulations for the full model. We observed optimal agreement between the stochastic and the deterministic description of the circuit in a large range of parameters, but some substantial differences arise in at least two cases: (1) when the deterministic system is in the proximity of a transition from a monostable to a bistable configuration, and (2) when bistability (in the deterministic system) is "masked" in the stochastic system by the distribution tails. The approach provides interesting estimates of the optimal number of molecules involved in the toggle switch. Our discussion of the points of strengths, potentiality and weakness of the chemical master equation in systems biology and the differences with respect to deterministic modeling are leveraged in order to provide useful advice for both the bioinformatician and the theoretical scientist.

Characterization of spinal ganglion neurons in horse (Equus caballus). A morphometric, neurochemical and tracing study.

Spinal ganglion (SG) neurons have been widely described in rodents, and classified according to various criteria. On the basis of such studies, many features of rodent SG neurons have become benchmarks to classify these cells. However, these traits cannot be confirmed in all other species. In the present study, horse SG neurons were morphometrically and neurochemically characterized by detecting the neuronal markers calcitonin gene-related peptide (CGRP), substance P (SP), neuronal nitric oxide synthase (nNOS) and isolectin B4 (IB4) from Griffonia simplicifolia. Moreover, spinal cord staining and tracer studies were also performed injecting Fast Blue tracer in the ileo-cecal junction. The statistical analysis of the histograms related to the cross sectional area of dark and light SG neurons confirmed the presence of the categories of small and large neurons. The staining methods employed yielded the following results: (1) in all triple staining experiments performed, most SG stained neurons were triple-labeled; (2) SP-IR neurons showed the largest percentages of co-localization with the other markers studied; (3) CGRP-IR and IB4-labeled neurons were the SG neurons showing the largest percentages of single staining; (4) nNOS-IR neurons were more represented in horse SGs than in those from rodents; (5) IB4 was widely co-localized with both CGRP and SP. Retrograde tracer investigation combined with neurochemical evaluation showed that in horse, contrarily to rodents, IB4-labeled neurons are widely involved in visceral innervations. The results obtained from the observations of serial stained sections and from a critical analysis of triple-labeling experiments allowed us to conclude that (1) most stained SG neurons co-expressed IB4-nNOS-CGRP-SP neuronal markers, (2) IB4 is not indicated as a marker of non-peptidergic neurons in the horse, (3) horse IB4-labeled neurons are widely involved in visceral sensation, (4) differently from rodents, horse IB4-, CGRP- and SP-labeled fibers share the same spinal cord level terminations.

Cerebral arterial compliance in patients with internal carotid artery disease.

BACKGROUND: A decrease in arterial compliance of the internal carotid artery has been associated with an increased risk in ipsilateral ischaemic stroke. However, so far, no technique has been validated to monitor the compliance of intracerebral arteries (Ca) in patients with carotid artery disease. In this study, we sought to monitor Ca in patients with unilateral symptomatic disease and to determine its variations during changes in PaCO(2). METHODS: We studied 18 patients with unilateral symptomatic internal carotid artery stenosis >50% or occlusion. Patients underwent monitoring of arterial blood pressure (ABP) and middle cerebral artery cerebral blood flow velocities (CBFV) during baseline, hyperventilation and 5%CO(2) inhalation. Ca was calculated from pulsatile amplitudes of ABP and Cerebral arterial blood volume, extracted from the CBFV waveform using a new mathematical model. RESULTS: At baseline, the decrease in Ca on the diseased side was correlated with the degree of stenosis (r = -0.35; P = 0.01). During hypocapnia, Ca was lower compared to baseline on the normal side (P = 0.004) and on the diseased side (P = 0.04). Ca reactivity, reflecting the changes in Ca per changes in 1 mmHg PaCO(2), was lower on the diseased side between baseline and hypocapnia (3.4 vs. 2.6%; P = 0.04). During hypercapnia, no changes in Ca on the diseased (P = 0.8) nor on the normal sides (P = 0.2) were observed. CONCLUSIONS: The decrease in cerebral arterial compliance the side of stenosis/occlusion was correlated with the severity of the internal carotid artery disease. Further studies are needed to determine whether Ca may improve the prediction of ischaemic events in symptomatic and asymptomatic patients.

Systems biology and longevity: an emerging approach to identify innovative anti-aging targets and strategies.

Human aging and longevity are complex and multi-factorial traits that result from a combination of environmental, genetic, epigenetic and stochastic factors, each contributing to the overall phenotype. The multi-factorial process of aging acts at different levels of complexity, from molecule to cell, from organ to organ systems and finally to organism, giving rise to the dynamic "aging mosaic". At present, an increasing amount of experimental data on genetics, genomics, proteomics and other -omics are available thanks to new high-throughput technologies but a comprehensive model for the study of human aging and longevity is still lacking. Systems biology represents a strategy to integrate and quantify the existing knowledge from different sources into predictive models, to be later tested and then implemented with new experimental data for validation and refinement in a recursive process. The ultimate goal is to compact the new acquired knowledge into a single picture, ideally able to characterize the phenotype at systemic/organism level. In this review we will briefly discuss the aging phenotype in a systems biology perspective, showing four specific examples at different levels of complexity, from a systemic process (inflammation) to a cascade-process pathways (coagulation) and from cellular organelle (proteasome) to single gene-network (PON-1), which could also represent targets for anti-aging strategies.

Human models of aging and longevity.

BACKGROUND: The aging phenotype in humans is very heterogeneous and can be described as a complex mosaic resulting from the interaction of a variety of environmental, stochastic and genetic-epigenetic variables. Therefore, each old person must be considered as a singleton, and consequently the definition of 'aging phenotype' is very difficult. OBJECTIVE: We discuss the phenotype of centenarians, the best example of successful aging, as well as other models exploited to study human aging and longevity, such as families enriched in long-living subjects, twins and cohorts of unrelated subjects. METHODS: A critical review of literature available until March 2008. CONCLUSIONS: No single model can be considered the gold standard for the study of aging and longevity, instead the combination of results obtained from different models must be considered in order to better understand these complex phenomena. We propose that a systems biology concept such as that of 'bow-tie' architecture, useful for managing information flow, could help in this demanding task.

Effects of exogenous electromagnetic fields on a simplified ion channel model.

In this paper, we calculate the effect of an exogenous perturbation (an electromagnetic field [EMF] oscillating in the range of microwave frequencies in the range of 1 GHz) on the flux of two ion species through a cylindrical ion channel, implementing a continuous model, the Poisson-Smoluchowski system of equations, to study the dynamics of charged particle density inside the channel. The method was validated through comparison with Brownian dynamics simulations, supposed to be more accurate but computationally more demanding, obtaining a very good agreement. No EMF effects were observed for low field intensities below the level for thermal effects, as the highly viscous regime and the simplicity of the channel do not exhibit resonance phenomena. For high intensities of the external field (>10(5) V/m), we observed slightly different behavior of ion concentration oscillations and ion currents as a function of EMF orientation with respect to the channel axis.

Induced metastable memory in heat shock response.

We studied the dynamics of the Heat Shock Response (HSR) mechanism, and the persistence of a injury-protected state in the cell following the shocks, known as thermotolerance. A series of double shock experiments were performed on Chinese Hamster Ovary (CHO) cells, tracking the dynamics of some components of HSR pathway (the Hsp70 protein level and Hsp70 mRNA transcription rate). The main features of HSR dynamics were well reproduced by a simplified model of the chemical reaction pathways governing the HSR. In particular, the thermotolerance phenomenon could be well characterized by introducing a shock-dependent switch in mRNA halflife, that can be interpreted as a sort of primitive memory at the mRNA level.

Shock wave therapy as an innovative technology in skeletal disorders: study on transmembrane current in stimulated osteoblast-like cells.

Extracorporeal shock wave treatment (ESWT) is successfully used in various musculoskeletal disorders and pathologies. Despite the increasing use of this kind of therapy, some aspects of its mechanism of action are still unclear. In vitro bone cell behavior under ESWT were previously investigated by the present author and MG63 osteoblast-like cells showed an enhancement in proliferation and in the osteoblast differentiation after therapy with a low-energy flux density. The aim of the present study was to evaluate the effect of ESWT on the permeabilization of cell membrane. We characterized physiological changes in the MG63 associated with ESWT generated by an ESW device and patch clamp recording was performed to study ion channels. Experiments were carried out using the whole-cell recording configuration of the patch-clamp technique and the ionic current measurements were performed on cell samples of ESW treated and control groups. The patch-clamp technique showed the effect of ESWT on the amplitude of transmembrane currents. The treatment with ESW enhanced the transmembrane current as well the voltage dependence of Ca-activated and K channels that mediate these currents: the differences between treated cells and control at 80mV were over 1000 pA (p<0.05). These modifications of ion channels activity positively influence cell proliferation (MTT test, p<0.0001) without interfering with the normal synthesis activity of stimulated osteoblasts.

Targeting c-Myc-activated genes with a correlation method: detection of global changes in large gene expression network dynamics.

This work studies the dynamics of a gene expression time series network. The network, which is obtained from the correlation of gene expressions, exhibits global dynamic properties that emerge after a cell state perturbation. The main features of this network appear to be more robust when compared with those obtained with a network obtained from a linear Markov model. In particular, the network properties strongly depend on the exact time sequence relationships between genes and are destroyed by random temporal data shuffling. We discuss in detail the problem of finding targets of the c-myc protooncogene, which encodes a transcriptional regulator whose inappropriate expression has been correlated with a wide array of malignancies. The data used for network construction are a time series of gene expression, collected by microarray analysis of a rat fibroblast cell line expressing a conditional Myc-estrogen receptor oncoprotein. We show that the correlation-based model can establish a clear relationship between network structure and the cascade of c-myc-activated genes.

Leptin concentrations in plasma and follicular fluid from prepubertal gilts as influenced by fasting, refeeding and insulin.

This study's aim was to examine whether fasting and refeeding would influence leptin levels in both plasma and follicular fluid from prepubertal gilts, and whether insulin affects leptin levels in fasting gilts. In experiment 1, four gilts were fasted for 72 h and then refed. Blood samples were withdrawn during normoalimentation, at the end of fasting, and for 4 h after refeeding. All samples were assayed for leptin; alternate samples were assayed for insulin, glucose and non-esterified fatty acids (NEFA). Fasting caused a decrease in leptin, glucose and insulin levels in plasma, while NEFA concentrations increased. In experiment 2, four gilts were given insulin as a bolus (0.2 IU/kg body weight) after 68 h of fasting. Blood samples were collected every 15 min around insulin administration and were assayed for leptin, insulin and glucose. This experiment shows that insulin administration increases leptin levels during fasting. In experiment 3, gilts were ovariectomized during normal alimentation (n=4), after 48 h of fasting (n=4), and after 48 h of realimentation following 48 h of fasting (n=4). Leptin levels in both plasma and follicular fluid collected after 48 h of fasting were significantly lower than those observed during normoalimentation or refeeding. In conclusion, a transient increase in insulin during fasting is effective in restoring leptin concentrations; in addition, leptin levels in follicular fluid parallel those in plasma.

Quantifying the relevance of different mediators in the human immune cell network.

MOTIVATION: Immune cells coordinate their efforts for the correct and efficient functioning of the immune system (IS). Each cell type plays a distinct role and communicates with other cell types through mediators such as cytokines, chemokines and hormones, among others, that are crucial for the functioning of the IS and its fine tuning. Nevertheless, a quantitative analysis of the topological properties of an immunological network involving this complex interchange of mediators among immune cells is still lacking. RESULTS: Here we present a method for quantifying the relevance of different mediators in the immune network, which exploits a definition of centrality based on the concept of efficient communication. The analysis, applied to the human IS, indicates that its mediators differ significantly in their network relevance. We found that cytokines involved in innate immunity and inflammation and some hormones rank highest in the network, revealing that the most prominent mediators of the IS are molecules involved in these ancestral types of defence mechanisms which are highly integrated with the adaptive immune response, and at the interplay among the nervous, the endocrine and the immune systems. CONTACT: claudio.franceschi@unibo.it.

The effect of noise on a class of energy-based learning rules.

Westudy the selectivity properties of neurons based on BCM and kurtosis energy functions in a general case of noisy high-dimensional input space. The proposed approach, which is used for characterization of the stable states, can be generalized to a whole class of energy functions. We characterize the critical noise levels beyond which the selectivity is destroyed. We also perform a quantitative analysis of such transitions, which shows interesting dependency on data set size. We observe that the robustness to noise of the BCM neuron (Bienenstock, Cooper, & Munro, 1982; Intrator & Cooper, 1992) increases as a function of dimensionality. We explicitly compute the separability limit of BCM and kurtosis learning rules in the case of a bimodal input distribution. Numerical simulations show a stronger robustness of the BCM rule for practical data set size when compared with kurtosis.

Cadmium, chromium and lead contamination of Athene noctua, the little owl, of Bologna and Parma, Italy.

A study was conducted to determine cadmium, chromium and lead concentrations in liver and brain of 52 little owls (Athene noctua) from two provinces of Emilia Romagna region, with the aim of furnishing indirect information concerning contamination of their habitat, also considering possible environmental dispersion of the metals. Metal analysis was performed by atomic absorption spectrophotometry with graphite furnace. Variance analysis with sampling area, gender and age shows that no statistical difference was found for gender, while a significant difference (P<0.05) was found for cadmium and lead, but not for chromium, when sampling areas and age were of concern. For all metals highest mean concentrations were found in liver (170 ppb for cadmium, 297 ppb for chromium and 312 ppb for lead). These levels can be considered as indicative of chronic exposure to low and "background" amounts of pollutants and they are of no toxicological concern, as they are always well below the toxic thresholds defined for each metal. The present study can be considered as a starting point for further analyses, aimed to the definition of any possible subtle effect (e.g. effects on enzymes activity) and of any possible correlation between levels of pollutants and appearance of possible adverse effects. It also furnished useful data for diagnostic cases and potentially for monitoring local contamination.