Gaussian Process-based prediction of memory performance and biomarker status in ageing and Alzheimer's disease-A systematic model evaluation.

Neuroimaging markers based on Magnetic Resonance Imaging (MRI) combined with various other measures (such as genetic covariates, biomarkers, vascular risk factors, neuropsychological tests etc.) might provide useful predictions of clinical outcomes during the progression towards Alzheimer's disease (AD). The use of multiple features in predictive frameworks for clinical outcomes has become increasingly prevalent in AD research. However, many studies do not focus on systematically and accurately evaluating combinations of multiple input features. Hence, the aim of the present work is to explore and assess optimal combinations of various features for MR-based prediction of (1) cognitive status and (2) biomarker positivity with a multi-kernel learning Gaussian process framework. The explored features and parameters included (A) combinations of brain tissues, modulation, smoothing, and image resolution; (B) incorporating demographics & clinical covariates; (C) the impact of the size of the training data set; (D) the influence of dimensionality reduction and the choice of kernel types. The approach was tested in a large German cohort including 959 subjects from the multicentric longitudinal study of cognitive impairment and dementia (DELCODE). Our evaluation suggests the best prediction of memory performance was obtained for a combination of neuroimaging markers, demographics, genetic information (ApoE4) and CSF biomarkers explaining 57% of outcome variance in out-of-sample predictions. The highest performance for Aß42/40 status classification was achieved for a combination of demographics, ApoE4, and a memory score while usage of structural MRI further improved the classification of individual patient's pTau status.

An RNA interference screen identifies new avenues for nephroprotection.

This corrects the article DOI: 10.1038/cdd.2015.128.

An RNA interference screen identifies new avenues for nephroprotection.

Acute kidney injury is a major public health problem, which is commonly caused by renal ischemia and is associated with a high risk of mortality and long-term disability. Efforts to develop a treatment for this condition have met with very limited success. We used an RNA interference screen to identify genes (BCL2L14, BLOC1S2, C2ORF42, CPT1A, FBP1, GCNT3, RHOB, SCIN, TACR1, and TNFAIP6) whose suppression improves survival of kidney epithelial cells in in vitro models of oxygen and glucose deprivation. Some of the genes also modulate the toxicity of cisplatin, an anticancer agent whose use is currently limited by nephrotoxicity. Furthermore, pharmacological inhibition of TACR1 product NK1R was protective in a model of mouse renal ischemia, attesting to the in vivo relevance of our findings. These data shed new light on the mechanisms of stress response in mammalian cells, and open new avenues to reduce the morbidity and mortality associated with renal injury.

5-HTTLPR/rs25531 polymorphism and neuroticism are linked by resting state functional connectivity of amygdala and fusiform gyrus.

The s/s-genotype of the 5-HTTLPR polymorphism and the personality trait of neuroticism have both been associated with experiences of negative affect, anxiety and mood disorders, as well as an emotional processing bias towards negative facial emotions. On a neural level, this bias can be characterized by altered amygdala and fusiform gyrus (FFG) activity during perception of negative facial expressions. Using resting-state functional magnetic resonance imaging in a multi-center-sample of 178 healthy subjects of European descent, this study investigated the association of 5-HTTLPR (short s- and long l-allele) including the genotype of the single nucleotide polymorphism (SNP) rs25531 (A/G) within this region polymorphism, and trait neuroticism on resting-state functional connectivity (rs-FC) between amygdala and the FFG. Moreover, we aimed to identify additional brain regions with associations of 5-HTTLPR/rs25531 (combined according to its expression; low: s/s; high: l(A)/l(A); intermediate: s/l(A), s/l(G), l(G)/l(G), l(A)/l(G)) and trait neuroticism to amygdala rs-FC. Separate analyses for 5-HTTLPR/rs25531 and neuroticism (controlling for age, gender, handedness, and research site) revealed that s/s-homozygotes and individuals high in neuroticism obtained altered amygdala rs-FC in the right occipital face area, which is considered to be a "core component" of the face processing system. Importantly, effects of neuroticism were replicated across three independent research sites. Additionally, associations of 5-HTTLPR/rs25531 genotype and amygdala rs-FC were observed in the anterior and posterior cingulate cortex, whereas neuroticism was not related to rs-FC in these areas. The presented data implies that 5-HTTLPR/rs25531 variants and neuroticism are linked by resting state functional connectivity of amygdala and fusiform gyrus and suggests that variants of 5-HTTLPR/rs25531 genotype and different levels of neuroticism may partly account for altered processing of negative facial emotions.

Epistatic interaction of genetic depression risk variants in the human subgenual cingulate cortex during memory encoding.

Recent genome-wide association studies have pointed to single-nucleotide polymorphisms (SNPs) in genes encoding the neuronal calcium channel CaV1.2 (CACNA1C; rs1006737) and the presynaptic active zone protein Piccolo (PCLO; rs2522833) as risk factors for affective disorders, particularly major depression. Previous neuroimaging studies of depression-related endophenotypes have highlighted the role of the subgenual cingulate cortex (CG25) in negative mood and depressive psychopathology. Here, we aimed to assess how recently associated PCLO and CACNA1C depression risk alleles jointly affect memory-related CG25 activity as an intermediate phenotype in clinically healthy humans. To investigate the combined effects of rs1006737 and rs2522833 on the CG25 response, we conducted three functional magnetic resonance imaging studies of episodic memory formation in three independent cohorts (N=79, 300, 113). An epistatic interaction of PCLO and CACNA1C risk alleles in CG25 during memory encoding was observed in all groups, with carriers of no risk allele and of both risk alleles showing higher CG25 activation during encoding when compared with carriers of only one risk allele. Moreover, PCLO risk allele carriers showed lower memory performance and reduced encoding-related hippocampal activation. In summary, our results point to region-specific epistatic effects of PCLO and CACNA1C risk variants in CG25, potentially related to episodic memory. Our data further suggest that genetic risk factors on the SNP level do not necessarily have additive effects but may show complex interactions. Such epistatic interactions might contribute to the 'missing heritability' of complex phenotypes.

Prefrontal dopamine and the dynamic control of human long-term memory.

Dopaminergic projections to the prefrontal cortex support higher-order cognitive functions, and are critically involved in many psychiatric disorders that involve memory deficits, including schizophrenia. The role of prefrontal dopamine in long-term memory, however, is still unclear. We used an imaging genetics approach to examine the hypothesis that dopamine availability in the prefrontal cortex selectively affects the ability to suppress interfering memories. Human participants were scanned via functional magnetic resonance imaging while practicing retrieval of previously studied target information in the face of interference from previously studied non-target information. This retrieval practice (RP) rendered the non-target information less retrievable on a later final test-a phenomenon known as retrieval-induced forgetting (RIF). In total, 54 participants were genotyped for the catechol-O-methyltransferase (COMT) Val(108/158)Met polymorphism. The COMT Val(108/158)Met genotype showed a selective and linear gene-dose effect on RIF, with the Met allele, which leads to higher prefrontal dopamine availability, being associated with greater RIF. Mirroring the behavioral pattern, the functional magnetic resonance imaging data revealed that Met allele carriers, compared with Val allele carriers, showed a greater response reduction in inhibitory control areas of the right inferior frontal cortex during RP, suggesting that they more efficiently reduced interference. These data support the hypothesis that the cortical dopaminergic system is centrally involved in the dynamic control of human long-term memory, supporting efficient remembering via the adaptive suppression of interfering memories.

The BDNF-Val66Met polymorphism: implications for susceptibility to multiple sclerosis and severity of disease.

Neurodegeneration following inflammatory injury is considered to be a pathological correlate of irreversible disability in patients with multiple sclerosis. The availability of neurotrophins could influence the probability or rate of disease progression and the time of onset. The BDNF-Val66Met-polymorphism leads to altered intracellular transport and secretion of BDNF, and is thus a logical candidate for a gene that influences susceptibility and, more specifically, the clinical course of multiple sclerosis. In order to test this hypothesis we genotyped the polymorphism in 951 UK multiple sclerosis trio families, but found no evidence for association before (p=0.63) or after stratification for clinical course (p=0.73).

Measures of hippocampal volumes, diffusion and 1H MRS metabolic abnormalities in temporal lobe epilepsy provide partially complementary information.

We assessed whether interictal measures of hippocampal volume, hippocampal diffusion and metabolic abnormalities yield correlated or complementary information about hippocampal pathology in patients with temporal lobe epilepsy (TLE). Volumes, apparent diffusion coefficients (ADC) and ratios of N-acetyl-aspartate (NAA) to Creatine/Phosphocreatine (Cr) and Choline (Cho) were measured from each hippocampus during one magnetic resonance imaging (MRI) session in patients with TLE. Structural MRI showed unilateral hippocampal sclerosis (HS) in 13 patients and was normal in the remaining nine patients. Pearson's correlation (two-tailed) between ADC values and NAA/(Cr + Cho) ratios was significant (P = 0.04, r = -0.45) for the hippocampus ipsilateral to the epileptogenic zone as determined on the basis of interictal and ictal scalp EEG recordings. This finding was driven by a very high correlation between the two measures in the presence of HS (P < 0.001, r = -0.96). Furthermore, ipsilateral ADC values but not NAA/(Cr + Cho) ratios were correlated with disease duration (P = 0.001, r = 0.67). Hippocampal volumes did not correlate with either ADC values, NAA/(Cr + Cho) ratios or disease duration. These data suggest that hippocampal volumes, NAA/(Cr + Cho) ratios and ADC values capture partially complementary aspects of hippocampal pathology.

A multivariate, spatiotemporal analysis of electromagnetic time-frequency data of recognition memory.

Electromagnetic indices of "fast" (above 12 Hz) oscillating brain activity are much more likely to be considerably attenuated by time-averaging across multiple trials than "slow" (below 12 Hz) oscillating brain activity. To the extent that both types of oscillations represent the activity of temporally and topographically separable neural populations, time averaging can cause a loss of brain activity information that is important both conceptually and for multimodal integration with hemodynamic techniques. To address this issue for recognition memory, simultaneous electroencephalography (EEG) and whole-head magnetoencephalography (MEG) recordings of explicit word recognition from 11 healthy subjects were analyzed in two different ways. First, the time course of neural oscillations ranging from theta (4.5 Hz) to gamma (42 Hz) frequencies were identified using single-trial continuous wavelet transforms. Second, traditional analyses of amplitude variations of time-averaged EEG and MEG signals, event-related potentials (ERPs), and fields (ERFs) were performed and submitted to distributed source analyses. To identify data patterns that covaried with the difference between correctly recognized studied (old) words and correctly rejected nonstudied (new) words, a multivariate statistical tool, partial least squares (PLS), was applied to both types of analyses. The results show that ERPs and ERFs are mainly displaying those neural indices of recognition memory that oscillate in the theta (4.5-7.5 Hz), alpha (8-11.5), and to some extent in the beta1 (12-19.5 Hz) frequency range. The sources of the ERPs/ERFs were in good agreement with the topography of theta/alpha/beta 1 oscillations in being confined to the anterior temporal lobe at 400 ms and being distributed across temporal, parietal, and occipital areas between 500 and 700 ms. Gamma oscillations covaried either positively or negatively with theta/alpha/beta1 oscillations. A positive covariance, for instance, was detected over left anterior temporal sensors as early as 200-350 ms and is compatible with studies in rodents showing that gamma and theta oscillations emerge together out of the interaction of the hippocampus and the entorhinal and perirhinal cortices. Fast beta oscillations (20-29.5 Hz), on the other hand, did not strongly covary with slow oscillations and were likely to arise from neural populations not adequately represented in ERPs/ERFs. In summary, by providing a more comprehensive description of electromagnetic signals, time-frequency data are of potential benefit for integrating electrophysiological and hemodynamic indices of brain activity and also for integrating human and animal electrophysiology.

Role of p53 and p21waf1/cip1 in senescence-like terminal proliferation arrest induced in human tumor cells by chemotherapeutic drugs.

Exposure of human tumor cell lines to moderate doses of anticancer agents induces terminal proliferation arrest accompanied by morphologic and enzymatic changes that resemble senescence of normal cells. We have investigated the role of p53 and p21waf1/cip1 in the induction of this response in drug-treated tumor cells. Doxorubicin treatment induced the senescence-like phenotype (SLP) and its associated terminal growth arrest in wild-type HCT116 colon carcinoma cells; this response was strongly decreased but not abolished in HCT116 lines with homozygous knockout of p53 or p21. Transduction of HT1080 fibrosarcoma cells with a genetic inhibitor of p53 also decreased the induction of SLP and increased drug-induced mitotic cell death. To determine if drug-stimulated p21 expression was responsible for senescence-like growth arrest, we have expressed different levels of p21 from an inducible promoter. While high-level overexpression of p21 was sufficient to induce SLP in HT1080 cells, the levels of p21 expressed in doxorubicin-treated cells could account for only a fraction of doxorubicin-induced SLP. Our results indicate that p53 and p21 act as positive regulators of senescence-like terminal proliferation arrest, but their function is neither sufficient nor absolutely required for this treatment response in tumor cells.

P-glycoprotein function involves conformational transitions detectable by differential immunoreactivity.

The MDR1 P-glycoprotein (Pgp), a member of the ATP-binding cassette family of transporters, is a transmembrane ATPase efflux pump for various lipophilic compounds, including many anti-cancer drugs. mAb UIC2, reactive with the extracellular moiety of Pgp, inhibits Pgp-mediated efflux. UIC2 reactivity with Pgp was increased by the addition of several Pgp-transported compounds or ATP-depleting agents, and by mutational inactivation of both nucleotide-binding domains (NBDs) of Pgp. UIC2 binding to Pgp mutated in both NBDs was unaffected in the presence of Pgp transport substrates or in ATP-depleted cells, whereas the reactivities of the wild-type Pgp and Pgps mutated in a single NBD were increased by these treatments to the level of the double mutant. These results indicate the existence of different Pgp conformations associated with different stages of transport-associated ATP hydrolysis and suggest trapping in a transient conformation as a mechanism for antibody-mediated inhibition of Pgp.

Efficient recovery and regeneration of integrated retroviruses.

We report a rapid and efficient PCR-based rescue procedure for integrated recombinant retroviruses. Full-length proviral DNA is amplified by long-range PCR using a pair of primers derived from the long terminal repeats (LTR), and virus is regenerated by transfecting retrovirus-packaging cells with the PCR-derived provirus. The viral yield from the PCR product is similar to that from the retroviral plasmid vector, and the representation of different inserts is accurately maintained in the recovered retroviral population. This procedure is suitable for expression cloning from retroviral libraries and should be applicable to the analysis of natural retrovirus populations.

Identification of p53 genetic suppressor elements which confer resistance to cisplatin.

Loss of p53 function is associated with the acquisition of cisplatin resistance in the human ovarian adenocarcinoma A2780 cell line. Selection for cisplatin resistance of A2780 cells was used to isolate genetic suppressor elements (GSEs) from a retroviral library expressing random fragments of human or murine TP53 cDNA. Six GSEs were identified, encoding either dominant negative mutant peptides or antisense RNA molecules which corresponded to various regions within the TP53 gene. Both types of GSE induced cisplatin resistance when introduced individually into A2780 cells. Expression of antisense GSEs led to decreased intracellular levels of p53 protein. One sense GSE induced loss of p53-mediated activities such as DNA damage induced cell cycle arrest and apoptosis. A synthetic peptide, representing the predicted amino acid sequence of this GSE, conferred resistance to cisplatin when introduced into A2780 cells and inhibited the sequence specific DNA binding activity of p53 protein in vitro. Overall, these results directly indicate that inactivation of p53 function confers cisplatin resistance in these human ovarian tumour cells. We have identified short structural domains of p53 which are capable of independent functional interactions and highlighted the efficacy of this approach to discriminate biologically active GSEs from a random fragment library.

Applications of green fluorescent protein as a marker of retroviral vectors.

The Green Fluorescent Protein (GFP) of Aequorea victoria is used as a vital fluorescent tag for the detection and isolation of genetically modified cells. Several modified variants of GFP were tested as marker genes in retroviral vectors containing different backbones and promoter combinations. Constructs allowing for reliable detection of GFP fluorescence and the expression of a cotransduced gene from a strong promoter were identified. Cells harboring such constructs are detectable by flow cytometry, fluorescence microscopy and multi-well fluorescence reading. GFP expression in transduced cells is stable both in vitro and in vivo, and long-term dynamics of GFP-positive fractions in a mixed population can be used to monitor the biological effects of a cotransduced gene. Selection of cells with the highest GFP fluorescence enriches for multiply infected cells. The use of different GFP variants allows one to monitor simultaneously two cell populations transduced with vectors carrying GFPs that differ in their fluorescence intensity or spectral properties and to identify doubly transduced cells. In addition, transcription of an inducible promoter positioned in the opposite orientation to GFP can be monitored by the inhibition of GFP fluorescence. Thus, GFP provides a useful marker for gene transfer by retroviral vectors and extends the range of applications for retroviral transduction.

From Morvan's fibrillary chorea to the "mal des ardents".

The authors present a case of Morvan's fibrillary chorea. We compare this observation with cases in the past such as the "mal des ardents", the plague of Athens, acrodynia and the epidemic of Pont St Esprit which were all characterized clinically by pain, burning sensations, hallucinations and insomnia. Since aetiological aspects remain uncertain, the similarity in clinical observations establishes a close relationship between the "mal des ardents" and the clinical features of our patient.

Effects of infection rate and selection pressure on gene expression from an internal promoter of a double gene retroviral vector.

Many commonly used retroviral vectors express one gene from the viral long terminal repeat (LTR) promoter and another gene from an internal promoter. We have investigated factors affecting the expression of the luciferase reporter gene from the internal cytomegalovirus-derived promoter of the retroviral vector, LNCX, which contains a LTR-driven neo gene as a selectable marker. A subline of human HT1080 cells, expressing the murine ecotropic receptor, was infected with retrovirus generated by transient transfection of BOSC 23 packaging cells. Mass populations of cells infected under conditions resulting in different initial infection rates (IIR) and selected with G418, showed highly variable luciferase activity. Luciferase expression in cell populations with IIR < or = 5% was generally low; many populations with IIR < 1% had marginal or no luciferase activity. The loss of luciferase expression in low-IIR populations was associated with G418 selection. In contrast, cell populations with IIR > or = 6% showed higher luciferase expression, which was strongly correlated with the IIR. Southern hybridization analysis showed that most cells of the low-IIR populations carried one integrated provirus, with a high incidence of structural rearrangements that abolished luciferase activity. In contrast, populations with IIR > or = 6% contained two or more copies of integrated provirus per cell, and their luciferase activity correlated with the provirus copy number. Luciferase expression was relatively stable in the populations with IIR > 1% maintained in the absence of G418. Increasing the selective concentration of G418 or prolonged maintenance of cell populations in the presence of G418 resulted in higher incidence of provirus rearrangements and decreased luciferase expression. These results indicate that the negative effect of selection for the LTR-driven gene on gene expression from an internal promoter depends on the selection stringency and can be obviated by increasing the infection rate.

Differential over-expression of mdr1 genes in multidrug-resistant rat glioblastoma cell lines selected with doxorubicin or vincristine.

We have compared the pharmacological and molecular characteristics of 2 cell lines derived from the C6 rat glioblastoma, and selected for resistance either to doxorubicin (C6 0.5 line) or to vincristine (C6 IV line). Each line displays a preferential 400-fold resistance towards the drug used for selection, the C6 IV line being especially weakly resistant to doxorubicin (13-fold). Verapamil completely restored doxorubicin sensitivity in the C6 IV line as well as vincristine resistance in the C6 0.5 line, but could not completely reverse doxorubicin resistance in the C6 0.5 line or vincristine resistance in the C6 IV line. This suggests that specific mechanisms of resistance against each drug were added to a common P-glycoprotein-mediated multidrug-resistance mechanism. Doxorubicin efflux was total within 2 hr in the C6 IV line, whereas it remained 8 to 10% of drug in the C6 0.5 line 4 hr after drug removal, despite a more rapid efflux of the drug in the first 30 min. This 2-compartment behavior could be related to a special sub-cellular distribution of doxorubicin in C6 0.5 cells. Northern and Western blot analysis of the mdrI gene and of the P-glycoprotein expressed by the 2 resistant cell lines made it possible to quantify their degree of over-expression; when compared with the C6 wild strain, the C6 0.5 line over-expressed both the mdrI gene and the P-glycoprotein to a slightly higher level than the C6 IV line. Northern and Western blot analysis also suggested that C6 0.5 cell preferentially over-expressed the mdrIa gene, whereas the C6 IV cells preferentially over-expressed the mdrIb gene. This differential over-expression was confirmed after polymerase-chain-reaction amplification of the cDNA sequences transcribed from total RNA extracted from the 2 lines. It can be concluded therefore that the mdrIa gene product is more efficient than the mdrIb gene product in extruding anti-cancer drugs from the cells; and that the mdrIb gene product might preferentially extrude vincristine rather than doxorubicin.

Pharmacological and molecular characterization of intrinsic and acquired doxorubicin resistance in murine tumor cell lines.

We have studied the pharmacological parameters of doxorubicin resistance in three lines of murine cells selected by long-term culture in the presence of this drug or vincristine. A line originating from rat hepatoma spontaneously presented an intrinsic doxorubicin resistance as compared to the other lines, originating from a rat glioblastoma and from simian-virus-40-transformed mouse hepatocytes. This intrinsic resistance, as well as the doxorubicin resistance exhibited by the vincristine-selected glioblastoma variant, could be entirely attribute to decreased drug accumulation due to drug efflux. In contrast, the doxorubicin-selected variants of the three lines exhibited an intracellular tolerance to this drug. Despite a reduction in drug accumulation when exposed to the same amount of doxorubicin, they accumulated 6-12 times more doxorubicin than wild lines when submitted to equitoxic exposures. Verapamil could restore in these lines the doxorubicin accumulation observed in sensitive lines but could not restore doxorubicin cytotoxicity. Quantitative evaluation of P-glycoprotein expression by Western blotting with the C219 antibody indicated that the wild hepatoma line overexpressed P-glycoprotein by a factor of 5 in comparison with the other wild lines, and that the vincristine-selected glioblastoma variant overexpressed this protein almost as much as the doxorubicin-selected variants. These observations favor the existence of P-glycoprotein-independent mechanisms of doxorubicin resistance, which are added to the classical multidrug-resistant phenotype in doxorubicin-selected highly resistant variant cell lines.

Doxorubicin-induced lipid peroxidation and glutathione peroxidase activity in tumor cell lines selected for resistance to doxorubicin.

Doxorubicin-induced lipid peroxidation was evaluated in four human or murine cell strains in culture and in their doxorubicin-resistant variants, by the quantification of malondialdehyde produced after a 2-h incubation of cells with the drug. Significantly increased malondialdehyde levels were obtained 24 h after doxorubicin treatment in three of the wild-type cell lines with doses as low as 0.05-0.1 micrograms/ml, which is within an order of magnitude of the concentration of the drug which inhibits cell growth by 50%. This production of malondialdehyde was abolished in two doxorubicin-resistant strains, even with high doses of drug (100-300 micrograms/ml), but was maintained in the third resistant line. No malondialdehyde production was observed in the fourth cell line, sensitive or resistant. It is remarkable that an enhancement of selenium-dependent and non-selenium-dependent glutathione peroxidase activities was exhibited during the acquisition of resistance to doxorubicin in the two first lines, but not in the third, whereas a constitutively high non-selenium-dependent glutathione peroxidase activity existed in the doxorubicin-sensitive and doxorubicin-resistant variants of the fourth cell line. Gene expression of selenium-dependent glutathione peroxidase and of glutathione S-transferase pi, which is known partially to bear a non-selenium-dependent glutathione peroxidase activity, were correlated with the corresponding enzyme activities. It appears, therefore, that the already known enhancement of glutathione peroxidase activity and expression in doxorubicin-resistant cell lines has a quantifiable consequence upon doxorubicin-induced lipid peroxidation and may have consequences in the mechanism of resistance to this drug.