Nathalie Pochet

Distinct physiological states of Plasmodium falciparum in malaria-infected patients

Infection with the malaria parasite Plasmodium falciparum leads to widely different clinical conditions in children, ranging from mild flu-like symptoms to coma and death. Despite the immense medical implications, the genetic and molecular basis of this diversity remains largely unknown. Studies of in vitro gene expression have found few transcriptional differences between different parasite strains. Here we present a large study of in vivo expression profiles of parasites derived directly from blood samples from infected patients. The in vivo expression profiles define three distinct transcriptional states. The biological basis of these states can be interpreted by comparison with an extensive compendium of expression data in the yeast Saccharomyces cerevisiae. The three states in vivo closely resemble, first, active growth based on glycolytic metabolism, second, a starvation response accompanied by metabolism of alternative carbon sources, and third, an environmental stress response. The glycolytic state is highly similar to the known profile of the ring stage in vitro, but the other states have not been observed in vitro. The results reveal a previously unknown physiological diversity in the in vivo biology of the malaria parasite, in particular evidence for a functional mitochondrion in the asexual-stage parasite, and indicate in vivo and in vitro studies to determine how this variation may affect disease manifestations and treatment.

Systematic benchmarking of microarray data classification: assessing the role of non-linearity and dimensionality reduction

MOTIVATION Microarrays are capable of determining the expression levels of thousands of genes simultaneously. In combination with classification methods, this technology can be useful to support clinical management decisions for individual patients, e.g. in oncology. The aim of this paper is to systematically benchmark the role of non-linear versus linear techniques and dimensionality reduction methods. RESULTS A systematic benchmarking study is performed by comparing linear versions of standard classification and dimensionality reduction techniques with their non-linear versions based on non-linear kernel functions with a radial basis function (RBF) kernel. A total of 9 binary cancer classification problems, derived from 7 publicly available microarray datasets, and 20 randomizations of each problem are examined. CONCLUSIONS Three main conclusions can be formulated based on the performances on independent test sets. (1) When performing classification with least squares support vector machines (LS-SVMs) (without dimensionality reduction), RBF kernels can be used without risking too much overfitting. The results obtained with well-tuned RBF kernels are never worse and sometimes even statistically significantly better compared to results obtained with a linear kernel in terms of test set receiver operating characteristic and test set accuracy performances. (2) Even for classification with linear classifiers like LS-SVM with linear kernel, using regularization is very important. (3) When performing kernel principal component analysis (kernel PCA) before classification, using an RBF kernel for kernel PCA tends to result in overfitting, especially when using supervised feature selection. It has been observed that an optimal selection of a large number of features is often an indication for overfitting. Kernel PCA with linear kernel gives better results.

Type I interferons and microbial metabolites of tryptophan modulate astrocyte activity and central nervous system inflammation via the aryl hydrocarbon receptor

Astrocytes have important roles in the central nervous system (CNS) during health and disease. Through genome-wide analyses we detected a transcriptional response to type I interferons (IFN-Is) in astrocytes during experimental CNS autoimmunity and also in CNS lesions from patients with multiple sclerosis (MS). IFN-I signaling in astrocytes reduces inflammation and experimental autoimmune encephalomyelitis (EAE) disease scores via the ligand-activated transcription factor aryl hydrocarbon receptor (AHR) and the suppressor of cytokine signaling 2 (SOCS2). The anti-inflammatory effects of nasally administered interferon (IFN)-β are partly mediated by AHR. Dietary tryptophan is metabolized by the gut microbiota into AHR agonists that have an effect on astrocytes to limit CNS inflammation. EAE scores were increased following ampicillin treatment during the recovery phase, and CNS inflammation was reduced in antibiotic-treated mice by supplementation with the tryptophan metabolites indole, indoxyl-3-sulfate, indole-3-propionic acid and indole-3-aldehyde, or the bacterial enzyme tryptophanase. In individuals with MS, the circulating levels of AHR agonists were decreased. These findings suggest that IFN-Is produced in the CNS function in combination with metabolites derived from dietary tryptophan by the gut flora to activate AHR signaling in astrocytes and suppress CNS inflammation.

Targeting miR-155 restores abnormal microglia and attenuates disease in SOD1 mice.

To investigate miR‐155 in the SOD1 mouse model and human sporadic and familial amyotrophic lateral sclerosis (ALS).

Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing

Although genetic lesions responsible for some mendelian disorders can be rapidly discovered through massively parallel sequencing of whole genomes or exomes, not all diseases readily yield to such efforts. We describe the illustrative case of the simple mendelian disorder medullary cystic kidney disease type 1 (MCKD1), mapped more than a decade ago to a 2-Mb region on chromosome 1. Ultimately, only by cloning, capillary sequencing and de novo assembly did we find that each of six families with MCKD1 harbors an equivalent but apparently independently arising mutation in sequence markedly under-represented in massively parallel sequencing data: the insertion of a single cytosine in one copy (but a different copy in each family) of the repeat unit comprising the extremely long (∼1.5–5 kb), GC-rich (>80%) coding variable-number tandem repeat (VNTR) sequence in the MUC1 gene encoding mucin 1. These results provide a cautionary tale about the challenges in identifying the genes responsible for mendelian, let alone more complex, disorders through massively parallel sequencing.

Association of Brain DNA Methylation in SORL1, ABCA7, HLA-DRB5, SLC24A4, and BIN1 With Pathological Diagnosis of Alzheimer Disease

IMPORTANCE Recent large-scale genome-wide association studies have discovered several genetic variants associated with Alzheimer disease (AD); however, the extent to which DNA methylation in these AD loci contributes to the disease susceptibility remains unknown. OBJECTIVE To examine the association of brain DNA methylation in 28 reported AD loci with AD pathologies. DESIGN, SETTING, AND PARTICIPANTS Ongoing community-based clinical pathological cohort studies of aging and dementia (the Religious Orders Study and the Rush Memory and Aging Project) among 740 autopsied participants 66.0 to 108.3 years old. EXPOSURES DNA methylation levels at individual CpG sites generated from dorsolateral prefrontal cortex tissue using a bead assay. MAIN OUTCOMES AND MEASURES Pathological diagnosis of AD by National Institute on Aging-Reagan criteria following a standard postmortem examination. RESULTS Overall, 447 participants (60.4%) met the criteria for pathological diagnosis of AD. Brain DNA methylation in SORL1, ABCA7, HLA-DRB5, SLC24A4, and BIN1 was associated with pathological AD. The association was robustly retained after replacing the binary trait of pathological AD with 2 quantitative and molecular specific hallmarks of AD, namely, Aβ load and paired helical filament tau tangle density. Furthermore, RNA expression of transcripts of SORL1 and ABCA7 was associated with paired helical filament tau tangle density, and the expression of BIN1 was associated with Aβ load. CONCLUSIONS AND RELEVANCE Brain DNA methylation in multiple AD loci is associated with AD pathologies. The results provide further evidence that disruption of DNA methylation is involved in the pathological process of AD.

Does Estrogen Receptor–Negative/Progesterone Receptor–Positive Breast Carcinoma Exist?

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A targeted functional RNA interference screen uncovers glypican 5 as an entry factor for hepatitis B and D viruses

Chronic hepatitis B and D infections are major causes of liver disease and hepatocellular carcinoma worldwide. Efficient therapeutic approaches for cure are absent. Sharing the same envelope proteins, hepatitis B virus and hepatitis delta virus use the sodium/taurocholate cotransporting polypeptide (a bile acid transporter) as a receptor to enter hepatocytes. However, the detailed mechanisms of the viral entry process are still poorly understood. Here, we established a high‐throughput infectious cell culture model enabling functional genomics of hepatitis delta virus entry and infection. Using a targeted RNA interference entry screen, we identified glypican 5 as a common host cell entry factor for hepatitis B and delta viruses. Conclusion: These findings advance our understanding of virus cell entry and open new avenues for curative therapies. As glypicans have been shown to play a role in the control of cell division and growth regulation, virus–glypican 5 interactions may also play a role in the pathogenesis of virus‐induced liver disease and cancer. (Hepatology 2016;63:35–48)

New models to predict depth of infiltration in endometrial carcinoma based on transvaginal sonography

Preoperative knowledge of the depth of myometrial infiltration is important in patients with endometrial carcinoma. This study aimed at assessing the value of histopathological parameters obtained from an endometrial biopsy (Pipelle® de Cornier; results available preoperatively) and ultrasound measurements obtained after transvaginal sonography with color Doppler imaging in the preoperative prediction of the depth of myometrial invasion, as determined by the final histopathological examination of the hysterectomy specimen (the gold standard).

Occurrence and Outcome of Residual Trophoblastic Tissue A Prospective Study

The purpose of this study was to evaluate the occurrence of residual trophoblastic tissue after miscarriage or delivery, to assess the diagnostic value of sonography with color Doppler examination in the detection of retained tissue, and to define in what cases expectant management may be an option.