Development and validation of a universal blood donor genotyping platform: a multinational prospective study.

Each year, blood transfusions save millions of lives. However, under current blood-matching practices, sensitization to non-self-antigens is an unavoidable adverse side effect of transfusion. We describe a universal donor typing platform that could be adopted by blood services worldwide to facilitate a universal extended blood-matching policy and reduce sensitization rates. This DNA-based test is capable of simultaneously typing most clinically relevant red blood cell (RBC), human platelet (HPA), and human leukocyte (HLA) antigens. Validation was performed, using samples from 7927 European, 27 South Asian, 21 East Asian, and 9 African blood donors enrolled in 2 national biobanks. We illustrated the usefulness of the platform by analyzing antibody data from patients sensitized with multiple RBC alloantibodies. Genotyping results demonstrated concordance of 99.91%, 99.97%, and 99.03% with RBC, HPA, and HLA clinically validated typing results in 89 371, 3016, and 9289 comparisons, respectively. Genotyping increased the total number of antigen typing results available from 110 980 to >1 200 000. Dense donor typing allowed identification of 2 to 6 times more compatible donors to serve 3146 patients with multiple RBC alloantibodies, providing at least 1 match for 176 individuals for whom previously no blood could be found among the same donors. This genotyping technology is already being used to type thousands of donors taking part in national genotyping studies. Extraction of dense antigen-typing data from these cohorts provides blood supply organizations with the opportunity to implement a policy of genomics-based precision matching of blood.

Risk of childhood wheeze and asthma after respiratory syncytial virus infection in full-term infants.

BACKGROUND: Most studies addressing the association between RSV and recurrent wheezing (RW) and asthma have been conducted in patients at risk for lung morbidity. Data in full-term infants are limited. METHODS: The risk of RW/asthma during the first 5 years of life in full-term infants hospitalized with RSV during the first year (Y) of life was estimated using 2010-16 data from three claims databases in USA (Truven MarketScan Commercial Claims and Encounters Database [CCAE], Truven Health MarketScan Multi-State Medicaid [MDCD], and Optum Clinformatics Extended Data Mart-Socio-Economic Status [SES]). Full-term infants with and without RSV infection and ≥ 2 years of continuous health plan enrollment from birth were included. Incidence rates of RW/asthma, cumulative incidence, adjusted incidence rate ratios (aIRR), and odds ratios (aOR) were calculated. RESULTS: During the 16-year study, 38,494 (CCAE), 62 846 (MDCD), and 23 099 (SES) matched infant pairs were included in each cohort. In the CCAE database, RW/asthma incidence/1000 patient-years (69.7 vs 28.7, aIRR: 2.4 [2.3-2.5]); cumulative incidence (17.6%-25.2% vs 5.0%-11.4%); and aOR (Y2: 4.1 [3.9-4.4]; Y3: 3.2 [3.0-3.3]; Y4: 2.9 [2.7-3.1]; Y5: 2.6 [2.5-2.9]) were higher in the RSV vs. non-RSV cohort. Results in the SES insured population were comparable, while cumulative incidence and aIRR were higher in the Medicaid population (MDCD). CONCLUSION: Although there are limitations in this study, including possible coding errors and missing covariates, we showed that full-term infants with severe RSV infection during the first year of life, spanning several respiratory seasons and a geographically diverse population, are at significant risk of RW/asthma during childhood.

Traumatic posterior atlantoaxial dislocation without related fractures of C1-C2.

Posterior dislocation without any associated fracture of odontoid is exceedingly rare and only 11 cases have been reported so far. A 32 year old male presented with pain, stiffness in neck, difficulty in breathing, associated lacerations on face and deformity of mandible and inability to open mouth. His plain radiographs, CT scan, MRI demonstrated a posterior dislocation of the atlas with respect of axis and a flake of bone from odontoid process on CT scan. He was successfully managed by closed reduction, C1C2 lateral mars pedicular screw stabilization and inter facetal fusion with synthetic bone graft substitute. At 10 months followup he had lost only 30° cervical rotation. The case is reported in view of rarity and to discuss the treatment rationale.

Label-free detection of biomolecular interactions using BioLayer interferometry for kinetic characterization.

The analysis of biomolecular interactions is key in the drug development process. Label-free biosensor methods provide information on binding, kinetics, concentration, and the affinity of an interaction. These techniques provide real-time monitoring of interactions between an immobilized ligand (such as a receptor) to an analyte in solution without the use of labels. Advances in biosensor design and detection using BioLayer Interferometry (BLI) provide a simple platform that enables label-free monitoring of biomolecular interactions without the use of flow cells. We review the applications of BLI in a wide variety of research and development environments for quantifying antibodies and proteins and measuring kinetics parameters.

Modulation of alpha interferon anti-hepatitis C virus activity by ISG15.

ISG15 has recently been reported to possess antiviral properties against viruses, both in vivo and in vitro. Knock-down of ISG15 gene expression by small interfering RNA followed by alpha interferon (IFN-alpha) treatment in Huh-7 cells resulted in an increased phenotypic sensitivity to IFN-alpha, as determined by measuring hepatitis C virus (HCV) RNA replication inhibition in stably transfected HCV replicon cells and in cells infected with genotype 1a HCVcc (infectious HCV). This IFN-alpha-specific effect, which was not observed with IFN-gamma, correlated with an increase in expression of the IFN-alpha-inducible genes IFI6, IFITM3, OAS1 and MX1, whereas the expression of the non-IFN-alpha-inducible genes PTBP-1 and JAK1 remained unchanged. It has previously been reported that, unlike ISG15 knock-down, increased sensitivity to IFN-alpha after knock-down of USP18 occurs through the prolonged phosphorylation of STAT-1. Combination knock-down of ISG15 and USP18 resulted in a moderate increase in IFN-alpha-inducible gene expression compared with single ISG15 or USP18 knock-down. Furthermore, the phenotype of increased gene expression after ISG15 knock-down and IFN-alpha treatment was also observed in non-hepatic cell lines A549 and HeLa. Taken together, these results reveal a novel function for ISG15 in the regulation of the IFN-alpha pathway and its antiviral effect.

Simultaneous modeling of concentration-effect and time-course patterns in gene expression data from microarrays.

BACKGROUND: Time-course and concentration-effect experiments with multiple time-points and drug concentrations provide far more valuable information than experiments with just two design-points (treated vs. control), as commonly performed in most microarray studies. Analysis of the data from such complex experiments, however, remains a challenge. MATERIALS AND METHODS: Here we present a semi-automated method for fitting time profiles and concentration-effect patterns, simultaneously, to gene expression data. The submodels for time-course included exponential increase and decrease models with parameters, such as initial expression level, maximum effect, and rate-constant (or half-time). The submodel for concentration-effect was a 4-parameter Hill model. RESULTS: The method was applied to an Affymetrix HG-U95Av2 dataset consisting of 51 arrays. The specific study focused on the effects of two platinum drugs, cisplatin and oxaliplatin, on A2780 human ovarian carcinoma cells. Replicates were available at most time points and concentrations. Eighteen genes were selected, and after selection, time-course and concentration-effect were modeled simultaneously. CONCLUSION: Comparisons of model parameters helped to distinguish genes with different expression patterns between the two drug treatments. This overall paradigm can help in understanding the molecular mechanisms of the agents, and the timing of their actions.

Platinum drug effects on the expression of genes in the polyamine pathway: time-course and concentration-effect analysis based on Affymetrix gene expression profiling of A2780 ovarian carcinoma cells.

PURPOSE: As a follow-up to our previous findings that platinum drugs induce a key enzyme in polyamine catabolism, gene expression profiling and mathematical modeling were used to define the effects of cisplatin and oxaliplatin on the expression of polyamine metabolic pathway genes in A2780 human ovarian carcinoma cells. METHODS: Time-course and concentration-effect experiments were each carried out with cisplatin or oxaliplatin in two separate experiments and cells subjected to gene expression profiling using Affymetrix array technology. Time-course data were modeled using exponential increase and decrease models. Concentration-effect data were modeled using a four parameter Hill model. RESULTS: Gene expression profiling of human ovarian carcinoma A2780 cells after exposure to either cisplatin or oxaliplatin indicates that the expression of several genes involved in polyamine pathway is affected by the platinum drugs. Mathematical/Statistical modeling of the data from time-course and concentration-effect experiments of gene expression from nine polyamine pathway genes represented on the HGU95Av2 chip, indicates that three biosynthetic pathway genes (SAMDC, ODC1 and SRM) are down-regulated and one catabolic pathway gene (SSAT) is up-regulated. Expression changes were similar for different probesets for a given gene on the array. Studies on the induction of SSAT by platinum drugs suggested by the Affymetrix data have been previously validated from this laboratory (Hector et al. in Mol Cancer Ther 3:813-822, 2004). Here, the effects of oxaliplatin exposure on SAMDC and ODC observed by Affymetix are validated with real time QRT-PCR. CONCLUSION: The data indicate a concerted effect of platinum drugs on the polyamine metabolic pathway with down-regulation in the expression of several enzyme genes involved in biosynthesis and many-fold up-regulation in expression of SSAT, an acetylating enzyme gene that is critically involved in polyamine catabolism and export.

TIMP1 and SERPIN-A overexpression and TFF3 and CRABP1 underexpression as biomarkers for papillary thyroid carcinoma.

BACKGROUND: No molecular pathways or specific genes are consistently associated with sporadic cases of papillary thyroid carcinoma (PTC), despite that it is the most common thyroid malignancy. Nodular goiter is an enlargement of the thyroid that is a compensatory response to a perturbation in normal thyroid homeostasis. It has been disputed in the literature that patients presenting with goiter have a higher incidence of PTC. The identification of molecular events that are common to both goiter and PTC could explain the overlap of these two disorders. METHODS: We used high-density oligonuleotide arrays to perform molecular profiling of PTC and nodular goiter with paired normal samples. RESULTS: Specifically, increased expression of SERPIN-A (proteinase inhibitor-alpha antitrypsin) and TIMP 1 (tissue inhibitor of metalloproteinase 1) identified these as candidate molecular biomarkers for PTC. Decreases in the CRABP1 (cellular retinoic acid binding protein 1) and TFF3 (trefoil factor 3) expression levels identified these as candidate molecular biomarkers as well. The same analysis was performed to identify genes showing specific alterations in goiter tissues. CONCLUSIONS: This is the first report to our knowledge that compares the gene expression profiles of PTC and goiter. Our results suggest that PTC and goiter share very limited overlap in transcript expression.

Identification of differentially expressed genes in clinically distinct groups of serous ovarian carcinomas using cDNA microarray.

To identify changes in gene expression in serous epithelial ovarian cancers (SEOC), we utilized cDNA microarrays consisting of 2382 genes with cancer related properties to analyze tumors from 20 patients with defined clinical out-comes. The significance analysis of microarrays method was used to determine differentially expressed genes, leading to the identification of 134 up-regulated and 231 down-regulated genes overall. By increasing the stringency of the statistical selection criteria, 41 over-expressed and 51 under-expressed genes were identified. The median duration of follow-up of the 20 patients was 16.8 months with a median progression free survival of 7.0 months. We found 11 genes that were differentially over-expressed in patients with recurrent disease, and 3 genes (homo sapiens mRNA for Ins P3 5-phophatase, lipoma HMGIC fusion partner-like 2 and CD63 melanoma 1 antigen) in patients who were dead of disease. Subsequently, we examined the distribution of the differentially expressed genes in the cDNA library database from adult human tumor and normal tissues using the DigiNorthern method to identify a subset of genes with relatively restricted tissue distribution. Finally, protein expression of 5 selected genes were further examined using immunohistochemistry applied on a tissue microarray prepared from an independent panel of 93 SEOC tissues. The results provided validation for 2 under-expressed genes (E2F transcription factor 5 and CK14) and 3 over-expressed genes (Bcl2-like 1, COX-2, CD63). Our study demonstrates differential gene expression in clinically distinct groups of SEOC using cDNA microarray. These genes may potentially be useful as biomarkers and/or targets for therapeutic intervention.

Identification of novel cellular targets in biliary tract cancers using global gene expression technology.

Biliary tract carcinoma carries a poor prognosis, and difficulties with clinical management in patients with advanced disease are often due to frequent late-stage diagnosis, lack of serum markers, and limited information regarding biliary tumor pathogenesis. RNA-based global analyses of gene expression have led to the identification of a large number of up-regulated genes in several cancer types. We have used the recently developed Affymetrix U133A gene expression microarrays containing nearly 22,000 unique transcripts to obtain global gene expression profiles from normal biliary epithelial scrapings (n = 5), surgically resected biliary carcinomas (n = 11), and biliary cancer cell lines (n = 9). Microarray hybridization data were normalized using dCHIP (http://www.dCHIP.org) to identify differentially up-regulated genes in primary biliary cancers and biliary cancer cell lines and their expression profiles was compared to that of normal epithelial scrapings using the dCHIP software as well as Significance Analysis of Microarrays or SAM (http://www-stat.stanford.edu/ approximately tibs/SAM/). Comparison of the dCHIP and SAM datasets revealed an overlapping list of 282 genes expressed at greater than threefold levels in the cancers compared to normal epithelium (t-test P <0.1 in dCHIP, and median false discovery rate <10 in SAM). Several pathways integral to tumorigenesis were up-regulated in the biliary cancers, including proliferation and cell cycle antigens (eg, cyclins D2 and E2, cdc2/p34, and geminin), transcription factors (eg, homeobox B7 and islet-1), growth factors and growth factor receptors (eg, hepatocyte growth factor, amphiregulin, and insulin-like growth factor 1 receptor), and enzymes modulating sensitivity to chemotherapeutic agents (eg, cystathionine beta synthase, dCMP deaminase, and CTP synthase). In addition, we identified several "pathway" genes that are rapidly emerging as novel therapeutic targets in cancer (eg, cytosolic phospholipase A2, an upstream target of the cyclooxygenase pathway, and ribosomal protein S6 kinase and eukaryotic translation initiation factor 4E, two important downstream mediators of the mitogenic Akt/mTOR signaling pathway). Overexpression of selected up-regulated genes was confirmed in tissue microarrays of biliary cancers by immunohistochemical analysis (n = 4) or in situ hybridization (n = 1), and in biliary cancer cell lines by reverse transcriptase PCR (n = 2). The majority of genes identified in the present study has not been previously reported in biliary cancers, and represent novel potential screening and therapeutic targets of this cancer type.

Observation of matter wave beat phenomena in the macrodomain for electrons moving along a magnetic field.

We report here the observations that exhibit the existence of matter wave phenomena with wavelength in the macrodomain of a few centimeters, for electrons moving along a magnetic field from an electron gun to a collector plate situated behind a grounded grid. These are in accordance with the predictions of a quantumlike theory for charged particles in the classical macrodomain, given by one of the authors [R. K. Varma, Phys. Rev. A 31, 3951 (1985)] with a recent generalization [R. K. Varma, Phys. Rev. E 64, 036608 (2001)]. The beats correspond to two closely spaced "frequencies" in the system, with the beat frequency given, in accordance with the characteristics of a wave phenomena, by the difference between the two frequencies. The beats ride as a modulation over a discrete energy band structure obtained with only one frequency present. The frequency here corresponds to the distance between the electron gun and the detector plate as it characterizes the variation in the energy band structure as the electron energy is swept. The second "frequency" corresponds to the gun-grid distance. These observations of the beats of matter waves in this experiment, with characteristics in accordance with the wave algorithm, then establish unambiguously the existence of macroscopic matter waves for electrons propagating along a magnetic field.