Development and Validation of a Bedside Score to Predict Early Death in Cancer of Unknown Primary Patients

Background

We have investigated predictors of 90-day-mortality in a large cohort of non-specific cancer of unknown primary patients.

Methods

Predictors have been identified by univariate and then logistic regression analysis in a single-center cohort comprising 429 patients (development cohort). We identified four predictors that produced a predictive score that has been applied to an independent multi-institutional cohort of 409 patients (validation cohort). The score was the sum of predictors for each patient (0 to 4).

Results

The 90-day-mortality-rate was 33 and 26% in both cohorts. Multivariate analysis has identified 4 predictors for 90-day-mortality: performance status>1 (OR = 3.03, p = 0.001), at least one co-morbidity requiring treatment (OR = 2.68, p = 0.004), LDH>1.5×the upper limit of normal (OR = 2.88, p = 0.007) and low albumin or protein levels (OR = 3.05, p = 0.007). In the development cohort, 90-day-mortality-rates were 12.5%, 32% and 64% when the score was [0–1], 2 and [3]–[4], respectively. In the validation cohort, risks were 13%, 25% and 62% according to the same score values.

Conclusions

We have validated a score that is easily calculated at the beside that estimates the 90-days mortality rate in non-specific CUP patients. This could be helpful to identify patients who would be better served with palliative care rather than aggressive chemotherapy.     

Sporadic Infantile Epileptic Encephalopathy Caused by Mutations in PCDH19 Resembles Dravet Syndrome but Mainly Affects Females

Dravet syndrome (DS) is a genetically determined epileptic encephalopathy mainly caused by de novo mutations in the SCN1A gene. Since 2003, we have performed molecular analyses in a large series of patients with DS, 27% of whom were negative for mutations or rearrangements in SCN1A. In order to identify new genes responsible for the disorder in the SCN1A-negative patients, 41 probands were screened for micro-rearrangements with Illumina high-density SNP microarrays. A hemizygous deletion on chromosome Xq22.1, encompassing the PCDH19 gene, was found in one male patient. To confirm that PCDH19 is responsible for a Dravet-like syndrome, we sequenced its coding region in 73 additional SCN1A-negative patients. Nine different point mutations (four missense and five truncating mutations) were identified in 11 unrelated female patients. In addition, we demonstrated that the fibroblasts of our male patient were mosaic for the PCDH19 deletion. Patients with PCDH19 and SCN1A mutations had very similar clinical features including the association of early febrile and afebrile seizures, seizures occurring in clusters, developmental and language delays, behavioural disturbances, and cognitive regression. There were, however, slight but constant differences in the evolution of the patients, including fewer polymorphic seizures (in particular rare myoclonic jerks and atypical absences) in those with PCDH19 mutations. These results suggest that PCDH19 plays a major role in epileptic encephalopathies, with a clinical spectrum overlapping that of DS. This disorder mainly affects females. The identification of an affected mosaic male strongly supports the hypothesis that cellular interference is the pathogenic mechanism.     

MALDI Imaging Mass Spectrometry: STATE OF THE ART TECHNOLOGY IN CLINICAL PROTEOMICS*

A decade after its inception, MALDI imaging mass spectrometry has become a unique technique in the proteomics arsenal for biomarker hunting in a variety of diseases. At this stage of development, it is important to ask whether we can consider this technique to be sufficiently developed for routine use in a clinical setting or an indispensable technology used in translational research. In this report, we consider the contributions of MALDI imaging mass spectrometry and profiling technologies to clinical studies. In addition, we outline new directions that are required to align these technologies with the objectives of clinical proteomics, including: 1) diagnosis based on profile signatures that complement histopathology, 2) early detection of disease, 3) selection of therapeutic combinations based on the individual patient''s entire disease-specific protein network, 4) real time assessment of therapeutic efficacy and toxicity, 5) rational redirection of therapy based on changes in the diseased protein network that are associated with drug resistance, and 6) combinatorial therapy in which the signaling pathway itself is viewed as the target rather than any single “node” in the pathway.MS has become a versatile tool that we are familiar with in large part due to important electronic and informatics advancements. The ability to obtain the molecular weight is one of the first steps in the identification of a molecule. With the addition of primary structural information mass spectrometry has become a useful technique to identify molecules within complex mixtures.Biological specimens, such as tissues, urine, or plasma, are complex and highly heterogeneous, which makes them inherently difficult to analyze. Further research and developments are necessary to achieve reliable biological models for understanding and studying pathologies. Therefore, it is of primary importance to identify the constituents of these systems and subsequently understand how they function within the framework of the tissue. With regard to clinical proteomics, there is the added dimension of disease, and therefore, the main goal is to characterize the cellular circuitry with a focus on the impact of the disease and/or therapy on these cellular networks.Mass spectrometry has become a centerpiece technology predominantly in the field of proteomics. Nonetheless a more comprehensive understanding of the constituents of biological systems will be aided by determining the constituent distribution. This anatomical dimension has been added through mass spectrometry imaging (MSI)¹ especially using MALDI-MSI.MALDI is an ion source that is well compatible with the introduction of raw materials and surfaces. Shortly after its introduction, MALDI was used for direct tissue profiling. The first applications were neurobiological studies on dissected organs from the mollusk Lymnaea stagnalis (1–8), crustaceans (9), and other mollusks (10, 11). More recently, MALDI was used to generate profiles from tissue sections and ion images using a scanning method to analyze the surface (12) (Fig. 1). This led to the first MALDI MS tissue section imaging micrographs in 1997 (13–15). These studies were followed by 10 years of intense efforts to improve the sensitivity, reproducibility, data processing, tissue preservation, and preparation treatments to fully characterize the proteome leading to a clear improvement of molecular images (16–39) (Fig. 2).Open in a separate windowFig. 1.Schematic representation of the MALDI-MSI work flow. After tissue sectioning and transfer onto a conductive and transparent sample plate, the MALDI matrix is deposited, and data are acquired by recording mass spectra according to a raster of points covering the surface to be analyzed. Mass spectra recorded with their coordinates on the tissue are processed, and molecular images of the localization of molecules can be reconstructed. a.u., arbitrary units; ITO, idium tin oxide.Open in a separate windowFig. 2.Ten years'' evolution from one of the first MALDI images presented in 1999 at the 47th ASMS Conference on Mass Spectrometry and Allied Topics (left) (reprinted with permission of Caprioli and co-workers (84)) and molecular images obtained by our group for mouse stem cells injected in brain tissue sections (right) (M. Wisztorski, C. Meriaux, M. Salzet, and I. Fournier, unpublished results).These developments led to clinical studies using MALDI-MSI technology. Clinical proteomics has many objectives including 1) diagnosis based on signatures as a complement to histopathology, 2) early disease detection, 3) individualized selection of therapeutic combinations that best target the patient''s entire disease-specific protein network, 4) real time assessment of therapeutic efficacy and toxicity, 5) rational redirection of therapy based on changes in the diseased protein network that are associated with drug resistance, and 6) combinatorial therapy in which the signaling pathway itself is viewed as the target rather than any single “node” in the pathway.Based on these key objectives, can we consider MALDI-MSI a mature technology for use in clinical studies? What is the potential impact of this technology in anatomy/pathology and disease? By reviewing each objective, do we have sufficient evidence that MALDI-MSI satisfies the criteria imposed by clinical proteomics? We will now specifically address each of these key points.     

Genome-Wide Association Study Implicates Chromosome 9q21.31 as a Susceptibility Locus for Asthma in Mexican Children

Many candidate genes have been studied for asthma, but replication has varied. Novel candidate genes have been identified for various complex diseases using genome-wide association studies (GWASs). We conducted a GWAS in 492 Mexican children with asthma, predominantly atopic by skin prick test, and their parents using the Illumina HumanHap 550 K BeadChip to identify novel genetic variation for childhood asthma. The 520,767 autosomal single nucleotide polymorphisms (SNPs) passing quality control were tested for association with childhood asthma using log-linear regression with a log-additive risk model. Eleven of the most significantly associated GWAS SNPs were tested for replication in an independent study of 177 Mexican case–parent trios with childhood-onset asthma and atopy using log-linear analysis. The chromosome 9q21.31 SNP rs2378383 (p = 7.10×10⁻⁶ in the GWAS), located upstream of transducin-like enhancer of split 4 (TLE4), gave a p-value of 0.03 and the same direction and magnitude of association in the replication study (combined p = 6.79×10⁻⁷). Ancestry analysis on chromosome 9q supported an inverse association between the rs2378383 minor allele (G) and childhood asthma. This work identifies chromosome 9q21.31 as a novel susceptibility locus for childhood asthma in Mexicans. Further, analysis of genome-wide expression data in 51 human tissues from the Novartis Research Foundation showed that median GWAS significance levels for SNPs in genes expressed in the lung differed most significantly from genes not expressed in the lung when compared to 50 other tissues, supporting the biological plausibility of our overall GWAS findings and the multigenic etiology of childhood asthma.     

Involvement of the Modifier Gene of a Human Mendelian Disorder in a Negative Selection Process

Background

Identification of modifier genes and characterization of their effects represent major challenges in human genetics. SAA1 is one of the few modifiers identified in humans: this gene influences the risk of renal amyloidosis (RA) in patients with familial Mediterranean fever (FMF), a Mendelian autoinflammatory disorder associated with mutations in MEFV. Indeed, the SAA1 α homozygous genotype and the p.Met694Val homozygous genotype at the MEFV locus are two main risk factors for RA.

Methodology/Principal Findings

Here, we investigated Armenian FMF patients and controls from two neighboring countries: Armenia, where RA is frequent (24%), and Karabakh, where RA is rare (2.5%). Sequencing of MEFV revealed similar frequencies of p.Met694Val homozygotes in the two groups of patients. However, a major deficit of SAA1 α homozygotes was found among Karabakhian patients (4%) as compared to Armenian patients (24%) (p = 5.10⁻⁵). Most importantly, we observed deviations from Hardy-Weinberg equilibrium (HWE) in the two groups of patients, and unexpectedly, in opposite directions, whereas, in the two control populations, genotype distributions at this locus were similar and complied with (HWE).

Conclusions/Significance

The excess of SAA1α homozygotes among Armenian patients could be explained by the recruitment of patients with severe phenotypes. In contrast, a population-based study revealed that the deficit of α/α among Karabakhian patients would result from a negative selection against carriers of this genotype. This study, which provides new insights into the role of SAA1 in the pathophysiology of FMF, represents the first example of deviations from HWE and selection involving the modifier gene of a Mendelian disorder.     

Prospective Study of Chikungunya Virus Acute Infection in the Island of La Réunion during the 2005–2006 Outbreak

Background

Chikungunya virus (CHIKV) is a recently re-emerged arthropod borne virus responsible for a massive outbreak in the Indian Ocean and India, and extended to Southeast Asia as well as Italy. CHIKV has adapted to Aedes albopictus, an anthropophilic mosquito species widely distributed in Asia, Europe, Africa and America. Our objective was to determine the clinical and biological features of patients at the acute phase of CHIKV infection.

Methods and Findings

A prospective study enrolled 274 consecutive patients with febrile arthralgia recorded at the Emergency Department of the Groupe Hospitalier Sud-Réunion between March and May 2006. Three groups were defined: one group of 180 viremic patients (positive CHIKV RT-PCR), one group of 34 patients with acute post-viremic infection (negative CHIKV RT-PCR, positive anti-CHIKV IgM and negative IgG), and one group of 46 uninfected patients (negative CHIKV RT-PCR, anti-CHIKV IgM and IgG). Bivariate analyses of clinical and biological features between groups were performed. Patients with CHIKV viremia presented typically with asymmetrical bilateral polyarthralgia (96.5%) affecting the lower (98%) and small joints (74.8%), as well as asthenia (88.6%), headache (70%), digestive trouble (63.3%), myalgia (59%), exanthems (47.8%), conjunctival hyperhemia (23%) and adenopathy (8.9%). Vertigo, cutaneous dysesthesia, pharyngitis and haemorrhages were seldom observed. So far unreported symptoms such as chondrocostal arthralgia (20%), entesopathies (1.6%), talalgia (14%) were also noted. Prurit was less frequent during the viremic than post-viremic phase (13.9% vs. 41.2%; p<0.001), whereas lymphopenia was more frequent (87.6% vs. 39.4%; p<0.001). Others biological abnormalities included leukopenia (38.3%), thrombocytopenia (37.3%), increased ASAT and ALAT blood levels (31.6 and 7.3%, respectively) and hypocalcemia (38.7%). Lymphopenia <1,000/mm³ was very closely associated with viremic patients (Yule coefficient 0.82, positive predictive value 92.3%). Age under 65 was associated with a benign course, as no patients younger than 65 had to be hospitalized (Yule coefficient 0.78).

Conclusions

The diagnosis of CHIKV infection in acute phase is based on commonly accepted clinical criteria (fever and arthralgia), however clinical and biological diffrences exist in acute phase depending on whether or not the patient is within the viremic phase of the infection.     

Filamins Regulate Cell Spreading and Initiation of Cell Migration

Mammalian filamins (FLNs) are a family of three large actin-binding proteins. FLNa, the founding member of the family, was implicated in migration by cell biological analyses and the identification of FLNA mutations in the neuronal migration disorder periventricular heterotopia. However, recent knockout studies have questioned the relevance of FLNa to cell migration. Here we have used shRNA-mediated knockdown of FLNa, FLNb or FLNa and FLNb, or, alternatively, acute proteasomal degradation of all three FLNs, to generate FLN-deficient cells and assess their ability to migrate. We report that loss of FLNa or FLNb has little effect on migration but that knockdown of FLNa and FLNb, or proteolysis of all three FLNs, impairs migration. The observed defect is primarily a deficiency in initiation of motility rather than a problem with maintenance of locomotion speed. FLN-deficient cells are also impaired in spreading. Re-expression of full length FLNa, but not re-expression of a mutated FLNa lacking immunoglobulin domains 19 to 21, reverts both the spreading and the inhibition of initiation of migration.Our results establish a role for FLNs in cell migration and spreading and suggest that compensation by other FLNs may mask phenotypes in single knockout or knockdown cells. We propose that interactions between FLNs and transmembrane or signalling proteins, mediated at least in part by immunoglobulin domains 19 to 21 are important for both cell spreading and initiation of migration.     

Defining ecological thresholds to determine class boundaries in a bioassessment tool: The case of the Eastern Canadian Diatom Index (IDEC)

Most bioassessment tools are based on the Reference Condition Approach (RCA), where the biological integrity of a site is defined by the “distance” between current conditions and its reference condition status. Among them, the Eastern Canadian Diatom Index (IDEC) was developed to evaluate the ecological integrity of streams along an alteration gradient, as a function of the dissimilarity of their diatom community from their suitable reference communities. In the first version of the IDEC, the alteration gradient was arbitrarily divided, like most traditional approaches, into five classes of equal size representing the qualitative statuses of the site. In this article, we propose a remodeling of those classes by introducing ecologically meaningful thresholds, reducing the subjectivity in the determination of the number and the range (widths) of classes. We developed a new approach which uses biotypes issued from a classification technique (Self-Organizing Maps) to determine thresholds between integrity classes of the IDEC. These biotypes represent relatively homogenous ecological entities composed of taxa adapted to a particular biological integrity status. Based on these biotypes, four classes were established. The new limits between classes are now based on the maximum ecological distance between diatom groups, and the transition from one class to another may be related to major ecological thresholds that induce important shifts in community structure. The proposed biotype-based approach allows for the identification of ecologically meaningful differences among biological communities and provides a more relevant interpretation of the community changes along the alteration gradient.     

Exploring the role of galectin 3 in kidney function: a genetic approach

Galectin 3 belongs to a family of glycoconjugate-binding proteinsthat participate in cellular homeostasis by modulating cellgrowth, adhesion, and signaling. We studied adult galectin 3null mutant (Gal 3–/–) and wild-type (WT) mice togain insights into the role of galectin 3 in the kidney. Byimmunofluorescence, galectin 3 was found in collecting duct(CD) principal and intercalated cells in some regions of thekidney, as well as in the thick ascending limbs at lower levels.Compared to WT mice, Gal 3–/– mice had ~11% fewerglomeruli (p < 0.04), associated with kidney hypertrophy(p < 0.006). In clearance experiments, urinary chloride excretionwas found to be higher in Gal 3–/– than in WT mice(p < 0.04), but there was no difference in urinary bicarbonateexcretion, in glomerular filtration, or urinary flow rates.Under chronic low sodium diet, Gal 3–/– mice hadlower extracellular fluid (ECF) volume than WT mice (p <0.05). Plasma aldosterone concentration was higher in Gal 3–/–than in WT mice (p < 0.04), which probably caused the observedincrease in -epithelial sodium channel (-ENaC) protein abundancein the mutant mice (p < 0.001). Chronic high sodium dietresulted paradoxically in lower blood pressure (p < 0.01)in Gal 3–/– than in WT. We conclude that Gal 3–/–mice have mild renal chloride loss, which causes chronic ECFvolume contraction and reduced blood pressure levels.