Testing Multiple Hypotheses through IMP weighted FDR Based on a Genetic Functional Network with Application to a New Zebrafish Transcriptome Study

In genome-wide studies, hundreds of thousands of hypothesis tests are performed simultaneously. Bonferroni correction and False Discovery Rate (FDR) can effectively control type I error but often yield a high false negative rate. We aim to develop a more powerful method to detect differentially expressed genes. We present a Weighted False Discovery Rate (WFDR) method that incorporate biological knowledge from genetic networks. We first identify weights using Integrative Multi-species Prediction (IMP) and then apply the weights in WFDR to identify differentially expressed genes through an IMP-WFDR algorithm. We performed a gene expression experiment to identify zebrafish genes that change expression in the presence of arsenic during a systemic Pseudomonas aeruginosa infection. Zebrafish were exposed to arsenic at 10 parts per billion and/or infected with P. aeruginosa. Appropriate controls were included. We then applied IMP-WFDR during the analysis of differentially expressed genes. We compared the mRNA expression for each group and found over 200 differentially expressed genes and several enriched pathways including defense response pathways, arsenic response pathways, and the Notch signaling pathway

The Blk pathway functions as a tumor suppressor in chronic myeloid leukemia stem cells

A therapeutic strategy for treating cancer is to target and eradicate cancer stem cells (CSCs) without harming their normal stem cell counterparts. The success of this approach relies on identification of molecular pathways that selectively regulate CSC function. Using BCR-ABL-induced chronic myeloid leukemia (CML) as a disease model for CSCs, we show that BCR-ABL down-regulates the B lymphoid kinase (Blk) gene through c-Myc in leukemia stem cells (LSCs) in CML mice and that Blk functions as a tumor suppressor in LSCs but does not affect normal hematopoietic stem cells (HSCs) or hematopoiesis. Blk suppresses LSC function through a pathway involving an upstream regulator, Pax5, and a downstream effector, p27. Inhibition of this Blk pathway accelerates CML development, whereas increased activity of the Blk pathway delays CML development. Blk also suppresses human CML stem cells. Our results demonstrate the feasibility of selectively targeting LSCs, an approach that should be applicable to other cancers

Genetic Influences on Eight Psychiatric Disorders Based on Family Data of 4 408 646 Full and Half-siblings, and Genetic Data of 333 748 Cases and Controls

Background. Most studies underline the contribution of heritable factors for psychiatric disorders. However, heritability estimates depend on the population under study, diagnostic instruments, and study designs that each has its inherent assumptions, strengths, and biases. We aim to test the homogeneity in heritability estimates between two powerful, and state of the art study designs for eight psychiatric disorders. Methods. We assessed heritability based on data of Swedish siblings (N = 4 408 646 full and maternal half-siblings), and based on summary data of eight samples with measured genotypes (N = 125 533 cases and 208 215 controls). All data were based on standard diagnostic criteria. Eight psychiatric disorders were studied: (1) alcohol dependence (AD), (2) anorexia nervosa, (3) attention deficit/hyperactivity disorder (ADHD), (4) autism spectrum disorder, (5) bipolar disorder, (6) major depressive disorder, (7) obsessive-compulsive disorder (OCD), and (8) schizophrenia. Results. Heritability estimates from sibling data varied from 0.30 for Major Depression to 0.80 for ADHD. The estimates based on the measured genotypes were lower, ranging from 0.10 for AD to 0.28 for OCD, but were significant, and correlated positively (0.19) with national sibling-based estimates. When removing OCD from the data the correlation increased to 0.50. Conclusions. Given the unique character of each study design, the convergent findings for these eight psychiatric conditions suggest that heritability estimates are robust across different methods. The findings also highlight large differences in genetic and environmental influences between psychiatric disorders, providing future directions for etiological psychiatric research

Toll-Like Receptor Signaling in the Zebrafish, Danio rerio: Evidence of Evolving Function

Mechanistic studies aimed at describing the way lower vertebrates like zebrafish utilize Toll-like receptors have not been extensively undertaken. In this dissertation, zebrafish TRIF is shown to signal in a manner that differs from what has been shown in mammals. Zebrafish TRIF is smaller than mammalian homologs and possesses significant sequence gaps in its N- and C-termini, calling into question whether it can interact with proteins deemed essential to signal transduction in mammals. Through co-immunoprecipitation, zebrafish TRIF was shown not to interact with zebrafish TRAF6 but was shown to interact with RIPl and TBKl. Overexpression of full-length zebrafish TRIF activates NF-KB and type I interferon (IFN); however, the way zebrafish TRIF signals differs from mammalian homologs. Through overexpression of mutants, it was determined that zebrafish TRIF relies upon its TIR domain and C-terminus for both NF-KB and IFN signaling. It was observed that an N-terminal deletion of TRIF exhibited the most potent IFN upregulation, calling into question TBKl\u27s in zebrafish TRIF signaling. Taken together, the data indicate that NF-KB signaling is RHIM domain-dependent and IFN signaling is TBK1-independent. This dissertation also explored the role of TLR4 signaling in zebrafish. Lipopolysaccharide (LPS), the ligand that activates TLR4 pathways in mammals, induces interleukin 1 and tumor-necrosis factor - alpha in zebrafish; however, this response must be regulated by an alternative LPS receptor. Zebrafish TLR4a (zfTLR4a) and TLR4b failed to respond to LPS stimulation, as measured by NF-KB activation. zfTLR4a and zfTLR4a, unlike mammalian TLR4s, also cannot be made constitutively active, which argues for their potential roles as co-receptors. zfTLR4a-GFP and zfTLR4b-GFP exhibited alternative localization patterns, indicating that, despite their sequence similarities, they may play alternative roles in the cell. Unlike mammals, zebrafish cannot be induced to express IFN by LPS. The functional inability of TLR4 to recognize LPS and thereby activate NF-KB and IFN has not been replaced by the other TLRs. The discovery, through analysis of synteny across vertebrates, that the TIR domain containing adaptor TRAM, which is essential for TLR4-mediated LPS induction of IFN, is not present in nonmammals may also contribute to the absence of LPS-inducible IFN activation in zebrafish

Tamazepam and alcohol: evaluation of a saliva drug-screening device

Abstract not available

A tumor suppressor function of the Msr1 gene in leukemia stem cells of chronic myeloid leukemia

We have shown that Alox5 is a critical regulator of leukemia stem cells (LSCs) in a BCR-ABL-induced chronic myeloid leukemia (CML) mouse model, and we hypothesize that the Alox5 pathway represents a major molecular network that regulates LSC function. Therefore, we sought to dissect this pathway by comparing the gene expression profiles of wild type and Alox5(-/-) LSCs. DNA microarray analysis revealed a small group of candidate genes that exhibited changes in the levels of transcription in the absence of Alox5 expression. In particular, we noted that the expression of the Msr1 gene was upregulated in Alox5(-/-) LSCs, suggesting that Msr1 suppresses the proliferation of LSCs. Using CML mouse model, we show that Msr1 is downregulated by BCR-ABL and this down-regulation is partially restored by Alox5 deletion, and that Msr1 deletion causes acceleration of CML development. Moreover, Msr1 deletion markedly increases LSC function through its effects on cell cycle progression and apoptosis. We also show that Msr1 affects CML development by regulating the PI3K-AKT pathway and beta-Catenin. Together, these results demonstrate that Msr1 suppresses LSCs and CML development. The enhancement of the tumor suppressor function of Msr1 may be of significance in the development of novel therapeutic strategies for CML

Novel interactions between FOXM1 and CDC25A regulate the cell cycle.

FOXM1 is a critical regulator of the G1/S and G2/M cell cycle transitions, as well as of the mitotic spindle assembly. Previous studies have suggested that FOXM1 regulates CDC25A gene transcription, but the mechanism remains unknown. Here, we provide evidence that FOXM1 directly regulates CDC25A gene transcription via direct promoter binding and indirect activation of E2F-dependent pathways. Prior literature reported that CDC25B and CDC25C activate CDK1/cyclinB complexes in order to enable phosphorylation of FOXM1. It was unknown if CDC25A functions in a similar manner. We report that FOXM1 transcriptional activity is synergistically enhanced when co-expressed with CDC25A. The increase is dependent upon CDK1 phosphorylation of FOXM1 at T600, T611 and T620 residues. We also report a novel protein interaction between FOXM1 and CDC25A via the C-terminus of FOXM1. We demonstrate that the phosphorylation of Thr 600 and Thr 611 residues of FOXM1 enhanced this interaction, and that the interaction is dependent upon CDC25A phosphatase activity. Our work provides novel insight into the underlying mechanisms by which FOXM1 controls the cell cycle through its association with CDC25A