Project description:While gene panel sequencing is becoming widely used for cancer risk prediction, its clinical utility with respect to predicting aggressive prostate cancer (PrCa) is limited by our current understanding of the genetic risk factors associated with predisposition to this potentially lethal disease phenotype. This study included 837 men diagnosed with aggressive PrCa and 7261 controls (unaffected men and men who did not meet criteria for aggressive PrCa). Rare germline pathogenic variants (including likely pathogenic variants) were identified by targeted sequencing of 26 known or putative cancer predisposition genes. We found that 85 (10%) men with aggressive PrCa and 265 (4%) controls carried a pathogenic variant (<i>p</i> < 0.0001). Aggressive PrCa odds ratios (ORs) were estimated using unconditional logistic regression. Increased risk of aggressive PrCa (OR (95% confidence interval)) was identified for pathogenic variants in <i>BRCA2</i> (5.8 (2.7-12.4)), <i>BRCA1</i> (5.5 (1.8-16.6)), and <i>ATM</i> (3.8 (1.6-9.1)). Our study provides further evidence that rare germline pathogenic variants in these genes are associated with increased risk of this aggressive, clinically relevant subset of PrCa. These rare genetic variants could be incorporated into risk prediction models to improve their precision to identify men at highest risk of aggressive prostate cancer and be used to identify men with newly diagnosed prostate cancer who require urgent treatment.
Project description:Most existing dimensionality reduction and clustering packages for single-cell RNA-seq (scRNA-seq) data deal with dropouts by heavy modeling and computational machinery. Here, we introduce CIDR (Clustering through Imputation and Dimensionality Reduction), an ultrafast algorithm that uses a novel yet very simple implicit imputation approach to alleviate the impact of dropouts in scRNA-seq data in a principled manner. Using a range of simulated and real data, we show that CIDR improves the standard principal component analysis and outperforms the state-of-the-art methods, namely t-SNE, ZIFA, and RaceID, in terms of clustering accuracy. CIDR typically completes within seconds when processing a data set of hundreds of cells and minutes for a data set of thousands of cells. CIDR can be downloaded at https://github.com/VCCRI/CIDR .
Project description:In this study, we will apply a multi-staged approach to reveal genes harboring rare variants that are associated with aggressive PCa. Whole-exome sequencing (Aim 1a) of 2,700 aggressive cases and 2,700 non-aggressive cases of European ancestry will be conducted followed by rare variant analysis of single sites and gene burden testing to identify novel susceptibility loci/genes for aggressive disease. We will validate the most significantly associated genes (~500) through targeted sequencing in an additional 7,500 aggressive and 7,500 non-aggressive cases (Aim 1b). Next, we will investigate the clinical predictive utility of the genes/variants identified in 2,300 cases in the STHM3 trial who are undergoing biopsy based on PSA and genetic risk score stratification (Aim 2). Last, we will examine whether the genes identified in Aim 1 contribute to the greater risk of aggressive PCa in 4,000 men of African ancestry (Aim 3). Through this tiered approach we expect... (for more see dbGaP study page.)
Project description:BACKGROUNDMalaria pathogenicity is determined, in part, by the adherence of Plasmodium falciparum-infected erythrocytes to the microvasculature mediated via specific interactions between P. falciparum erythrocyte membrane protein (PfEMP1) variant domains and host endothelial receptors. Naturally acquired antibodies against specific PfEMP1 variants can play an important role in clinical protection against malaria.METHODSWe evaluated IgG responses against a repertoire of PfEMP1 CIDR domain variants to determine the rate and order of variant-specific antibody acquisition and their association with protection against febrile malaria in a prospective cohort study conducted in an area of intense, seasonal malaria transmission.RESULTSUsing longitudinal data, we found that IgG antibodies against the pathogenic domain variants CIDR?1.7 and CIDR?1.8 were acquired the earliest. Furthermore, IgG antibodies against CIDR?3 were associated with reduced prospective risk of febrile malaria and recurrent malaria episodes.CONCLUSIONThis study provides evidence that acquisition of IgG antibodies against PfEMP1 variants is ordered and demonstrates that antibodies against CIDR?1 domains are acquired the earliest in children residing in an area of intense, seasonal malaria transmission. Future studies will need to validate these findings in other transmission settings and determine the functional activity of these naturally acquired CIDR variant-specific antibodies.TRIAL REGISTRATIONClinicalTrials.gov NCT01322581.FUNDINGDivision of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH.
Project description:BACKGROUND:During the erythrocytic cycle, Plasmodium falciparum malaria parasites express P. falciparum Erythrocyte Membrane Protein 1 (PfEMP1) that anchor the infected erythrocytes (IE) to the vascular lining of the host. The CIDR?1 domain of PfEMP1 is responsible for binding host endothelial protein C receptor (EPCR), and increasing evidence support that this interaction triggers severe malaria, accounting for the majority of malaria-related deaths. In high transmission regions, children develop immunity to severe malaria after the first few infections. This immunity is believed to be mediated by antibodies targeting and inhibiting PfEMP1, causing infected erythrocytes to circulate and be cleared in the spleen. The development of immunity to malaria coincides with acquisition of broad antibody reactivity across the CIDR?1 protein family. Altogether, this identifies CIDR?1 as an important vaccine target. However, the antigenic diversity of the CIDR?1 domain family is a challenge for vaccine development. METHODS:Immune responses in mice vaccinated with Virus-Like Particles (VLP) presenting CIDR?1 antigens were investigated. Antibody reactivity was tested to a panel of recombinant CIDR?1 domains, and the antibodies ability to inhibit EPCR binding by the recombinant CIDR?1 domains was tested in Luminex-based multiplex assays. RESULTS:VLP-presented CIDR?1.4 antigens induced a rapid and strong IgG response capable of inhibiting EPCR-binding of multiple CIDR?1 domains mainly within the group A CIDR?1.4-7 subgroups. CONCLUSIONS:The study observations mirror those from previous CIDR?1 vaccine studies using other vaccine constructs and platforms. This suggests that broad CIDR?1 antibody reactivity may be achieved through vaccination with a limited number of CIDR?1 variants. In addition, this study suggest that this may be achieved through vaccination with a human compatible VLP vaccine platform.
Project description:Most severe Plasmodium falciparum infections are experienced by young children. Severe symptoms are precipitated by vascular sequestration of parasites expressing a particular subset of the polymorphic P. falciparum erythrocyte membrane protein 1 (PfEMP1) adhesion molecules. Parasites binding human endothelial protein C receptor (EPCR) through the CIDR?1 domain of certain PfEMP1 were recently associated with severe malaria in children. However, it has remained unclear to which extend the EPCR-binding CIDR?1 domains epitomize PfEMP1 expressed in severe malaria. Here, we characterized the near full-length transcripts dominating the var transcriptome in children with severe malaria and found that the only common feature of the encoded PfEMP1 was CIDR?1 domains. Such genes were highly and dominantly expressed in both children with severe malarial anaemia and cerebral malaria. These observations support the hypothesis that the CIDR?1-EPCR interaction is key to the pathogenesis of severe malaria and strengthen the rationale for pursuing a vaccine or adjunctive treatment aiming at inhibiting or reducing the damaging effects of this interaction.
Project description:The Staphylococcus aureus LysR-type transcriptional regulator, CidR, activates the expression of two operons including cidABC and alsSD that display pro- and anti-death functions, respectively. Although several investigations have focused on the functions of different genes associated with these operons, the collective role of the CidR regulon in staphylococcal physiology is not clearly understood. Here we reveal that the primary role of this regulon is to limit acetate-dependent potentiation of cell death in staphylococcal populations. Although both CidB and CidC promote acetate generation and cell death, the CidR-dependent co-activation of CidA and AlsSD counters the effects of CidBC by redirecting intracellular carbon flux towards acetoin formation. From a mechanistic standpoint, we demonstrate that CidB is necessary for full activation of CidC, whereas CidA limits the abundance of CidC in the cell.
Project description:The death and lysis of a subpopulation of <i>Staphylococcus aureus</i> cells during biofilm development benefit the whole bacterial population through the release of an important component of the biofilm matrix, extracellular DNA. Previously, we have demonstrated that these processes are affected by the gene products of the <i>cidABC</i> operon, the expression of which is controlled by the LysR-type transcriptional regulator, CidR. In this study, we characterized <i>cis</i>- and <i>trans</i>-acting elements essential for the induction of the <i>cidABC</i> operon. In addition to a CidR-binding site located within the <i>cidABC</i> promoter region, sequence analysis revealed the presence of a putative catabolite responsive element (<i>cre</i> box), suggestive of the involvement of the catabolite control protein A (CcpA) in the regulation of <i>cidABC</i> expression. This was confirmed using electrophoretic mobility shift assays and real-time reverse transcriptase PCR analysis demonstrating the direct positive control of <i>cidABC</i> transcription by the master regulator of carbon metabolism. Furthermore, the importance of CcpA and the identified <i>cre</i> site for the induction of the <i>cidABC</i> operon was demonstrated by examining the expression of P <i><sub>cidABC</sub>-lacZ</i> reporter fusions in various mutant strains in which the genes involved in carbon metabolism and carbon catabolite repression were disrupted. Together the results of this study demonstrate the necessity of both transcriptional regulators, CidR and CcpA, for the induction of the <i>cidABC</i> operon and reveal the complexity of molecular interactions controlling its expression.<b>IMPORTANCE</b> This work focuses on the characterization of <i>cis</i>- and <i>trans</i>-acting elements essential for the induction of the <i>cidABC</i> operon in <i>S. aureus</i> The results of this study are the first to demonstrate the synergistic control of <i>cidABC</i> expression by transcriptional regulators CidR and CcpA during carbohydrate metabolism. We established that the full induction of <i>cidABC</i> expression depends on the metabolic state of bacteria and requires both CidR and CcpA. Together, these findings delineate regulatory control of <i>cidABC</i> expression under different metabolic conditions and provide important new insights into our understanding of cell death mechanisms during biofilm development in <i>S. aureus</i>.