Functional analysis of the CRINKLY4 gene family in Arabidopsis thaliana and Viviparous1 promoter in Zea mays

The cereal endosperm is an excellent system to study cell differentiation and fate specification. The aleurone of maize is one cell layer and requires continuous positional cues to specify and maintain its identity. A genetic hierarchy is implicated in this process. CRINKLY4 ( Cr4), a receptor-like kinase, belongs to cell fate-specifying genes and is required to specify aleurone cell identity. Viviparous1 ( Vp1), a B3 domain-containing transcription factor, functions late in development to regulate the expression of C1 in aleurone cells. It also plays an important regulatory role in late embryogenesis and seed maturation with abscisic acid (ABA).;The Arabidopsis genome encodes ACR4, an ortholog of CR4, and four AtCRRs. ACR4 and AtCRR1 and 2 are mainly expressed in developing young tissues. The kinase domain of ACR4 was shown to be a serine/threonine kinase and had ability to phosphorylate the non-functional kinase domain of AtCRR2. T-DNA insertion mutants of acr4 showed a phenotype restricted to the integument and seed coat, while mutants of atcrrs did not show obvious phenotype and triple mutants of acr4, atcrr1 and 2 had similar phenotype as acr4, suggesting that Arabidopsis might have a redundant function and the hypothetical redundant function is not encoded by AtCRRs.;Vp1 functions in ABA regulated processes. Its expression is regulated by ABA, high salinity and osmoticum. The induction of Vp1 expression by ABA does not require de novo protein synthesis. The sequence analysis of 958 bp of the Vp1 promoter identified a potential ABRC (ABA response complex), which consists a predicted ABRE (ABA response element) and a CE1L (coupling element 1-like) element. Electrophoretic mobility shift assay (EMSA) confirmed that the ABRE and CE1L specifically bound proteins in 20 DAP embryo nuclear protein extracts. ABA or osmoticum induce nuclear protein interaction with the ABRE. The ABRE was also shown to be critical for the induction of Vp1 expression by ABA in a transient gene expression experiment. Sequence analysis and EMSA experiments also identified several other binding sites such as: VPP1, AtMYB2 and ZIP1. This provides a starting point to further study the regulation of Vp1 expression

Set Based Association Testing in High Dimensional Genomic Studies

The last decade has ushered in an era of high dimensional, high volume data. In particular with the biotechnological revolution of the era, high-dimensional genomic studies of various designs have provided investigators with the tools to study thousands or even millions of genomic features simultaneously. These studies have shed new light on the underlying mechanisms of complex diseases. The accumulated knowledge of these complex relationships between genes has led scientists to formalize pathways and graphical networks that visually and succinctly give descriptions of the geometry of these relationships. With such knowledge, it has become possible to develop procedures for statistical inference, not just at the individual genes level, but at the more meaningful gene-set level. The focus of this thesis is the development of new statistical procedures for such gene-set analysis. After presenting an overview at the introduction, we give a comprehensive review of the literature relevant developments in the thesis in Chapter 2. In Chapter 3, we develop a Bayesian procedure that incorporates information contained in a gene graphical network, viewed as a directed graph, into the construction of prior distributions and we use the derived posterior distributions to construct statistical tests at the gene-set level. Our procedure extends the work of Pan (2006) and Wei and Pan (2008) which did not use the direction as information in the graphical network, but rather used undirected graphs and assumed a mixture model for the distribution to generate the posterior distribution of the mixing parameters via the use of a Markov random field. We demonstrate the gain in statistical power of our procedure over Pan and Wei\u27s in an application to detect differentially expressed genes, and gene-sets by analyzing a data set that compares favorable risk and poor risk defined by cytogenetics in adults with acute myeloid leukemia (AML). To enhance comprehension of the vast and complex information in high-dimensional data from genomic studies, it is sometimes useful and desirable to have a procedure that relates such data to specific endpoints. In this regards, association tests are highly desirable. In Chapter 4, we propose a procedure which we label `Projection onto Orthogonal Space Testing (POST)\u27 as a flexible method for testing association of gene sets and pathways with specific phenotypic endpoints while adjusting for other factors and variables as needed. In a simulation study, we demonstrate that POST has better operating characteristics than other methods recently developed to address the same objective. Thus we feel that POST does not only help to better understand treatment responses, but also prioritizes pathways for further study. We expect that POST will be especially valuable in clinical studies where cohorts with moderate to large sample sizes have rich high-dimensional data. Another new procedure for association testing which we label \u27Locus Based Integrated Testing(LOCIT)\u27 and an extension of the procedure -LOCITO- are introduced in Chapter 5. LOCIT is designed to test association of multiple forms of genomic data within a locus with an endpoint of interest in genomic studies. Given different forms of genomic data such as SNP genotypes, gene expression, and methylation levels, LOCIT performs one test per locus, taking several features at the locus into consideration. To illustrate the efficacy of LOCIT, we apply the procedure to a set consisting of SNP genotypes and gene profiling in an AML cohort to identify loci /genes that are associated with clinical outcomes. In chapter 6, we summarize our development of gene-set level association tests and outline future directions of our research in this area

The potential of epigallocatechin gallate in the chemoprevention and therapy of hepatocellular carcinoma

Hepatocellular carcinoma (HCC), one of the most notorious malignancies globally, has a high fatality and poor prognosis. Though remarkable breakthroughs have been made in the therapeutic strategies recently, the overall survival of HCC remains unsatisfactory. Consequently, the therapy of HCC remains a great challenge. Epigallocatechin gallate (EGCG), a natural polyphenol extracted from the leaves of the tea bush, has been extensively investigated for its antitumor effects. In this review, we summarize the previous literature to elucidate the roles of EGCG in the chemoprophylaxis and therapy of HCC. Accumulating evidence has confirmed EGCG prevents and inhibits the hepatic tumorigenesis and progression through multiple biological mechanisms, mainly involving hepatitis virus infection, oxidative stress, proliferation, invasion, migration, angiogenesis, apoptosis, autophagy, and tumor metabolism. Furthermore, EGCG enhances the efficacy and sensitivity of chemotherapy, radiotherapy, and targeted therapy in HCC. In conclusion, preclinical studies have confirmed the potential of EGCG for chemoprevention and therapy of HCC under multifarious experimental models and conditions. Nevertheless, there is an urgent need to explore the safety and efficacy of EGCG in the clinical practice of HCC

The crosstalk among the physical tumor microenvironment and the effects of glucose deprivation on tumors in the past decade

The occurrence and progression of tumors are inseparable from glucose metabolism. With the development of tumors, the volume increases gradually and the nutritional supply of tumors cannot be fully guaranteed. The tumor microenvironment changes and glucose deficiency becomes the common stress environment of tumors. Here, we discuss the mutual influences between glucose deprivation and other features of the tumor microenvironment, such as hypoxia, immune escape, low pH, and oxidative stress. In the face of a series of stress responses brought by glucose deficiency, different types of tumors have different coping mechanisms. We summarize the tumor studies on glucose deficiency in the last decade and review the genes and pathways that determine the fate of tumors under harsh conditions. It turns out that most of these genes help tumor cells survive in glucose-deprivation conditions. The development of related inhibitors may bring new opportunities for the treatment of tumors

Dietary inflammatory index, and depression and mortality risk associations in U.S. adults, with a special focus on cancer survivors

IntroductionA higher risk for depression and mortality is associated with the inflammatory potential of diet measured through the Dietary Inflammatory Index (DII). The roles of DII in the risk of depression and death in cancer survivors were unclear. We aimed to examine the association between energy-adjusted DII (E-DII) score and risk of depression, and mortality using data from the 2007–2018 National Health and Nutrition Examination Survey (NHANES), with a special focus on cancer survivors.MethodsThe 24-h dietary recall interview was used as a basis to calculate the E-DII score and the Patient Health Questionnaire-9 (PHQ-9) was used to measure the depressive outcomes. Logistic regression analyses were performed to determine the association between quartiles of E-DII score and depression. Cox proportional hazard regression and competing risk analyses were used to estimate the risks of quartiles of E-DII score or depression on mortality.ResultsA total of 27,447 participants were included; including 24,694 subjects without cancer and 2,753 cancer survivors. The E-DII score and depression were not distributed differently between the two groups. However, the E-DII scores were positively associated with within each group’s depression (all P trend < 0.001) and participants with higher E-DII scores had a higher risk of depression (subjects without cancer: ORQ4vsQ1: 2.17, 95% CI: 1.75–2.70; cancer survivors: ORQ4vsQ1: 1.78, 95% CI: 1.09–2.92). The median follow-up time were 87 person-months, a total of 1,701 (4.8%) and 570 (15.2%) all-cause deaths in subjects without cancer and cancer survivors were identified by the end of 2019. The highest E-DII scores quartile was associated with the highest risk of all-cause (HRQ4vsQ1: 1.90, 95% CI: 1.54–2.35) and cardiovascular disease (CVD) cause death (HRQ4vsQ1: 2.50, 95% CI: 1.69–2.3.7) in the subjects without cancer. Moreover, participants with depressive symptoms had higher all-cause mortality (HR: 1.29, 95% CI: 1.04–1.59). No significant correlation was found for E-DII scores or depression with all-cause, cancer-cause or CVD-cause mortality in cancer survivors.ConclusionOur findings demonstrate that E-DII score was positively associated with depression risk. A higher E-DII score or depressive symptom may increase the risks of all-cause and CVD-cause mortality only among general subjects

Functional analysis of the CRINKLY4 gene family in Arabidopsis thaliana and Viviparous1 promoter in Zea mays

The cereal endosperm is an excellent system to study cell differentiation and fate specification. The aleurone of maize is one cell layer and requires continuous positional cues to specify and maintain its identity. A genetic hierarchy is implicated in this process. CRINKLY4 ( Cr4), a receptor-like kinase, belongs to cell fate-specifying genes and is required to specify aleurone cell identity. Viviparous1 ( Vp1), a B3 domain-containing transcription factor, functions late in development to regulate the expression of C1 in aleurone cells. It also plays an important regulatory role in late embryogenesis and seed maturation with abscisic acid (ABA).;The Arabidopsis genome encodes ACR4, an ortholog of CR4, and four AtCRRs. ACR4 and AtCRR1 and 2 are mainly expressed in developing young tissues. The kinase domain of ACR4 was shown to be a serine/threonine kinase and had ability to phosphorylate the non-functional kinase domain of AtCRR2. T-DNA insertion mutants of acr4 showed a phenotype restricted to the integument and seed coat, while mutants of atcrrs did not show obvious phenotype and triple mutants of acr4, atcrr1 and 2 had similar phenotype as acr4, suggesting that Arabidopsis might have a redundant function and the hypothetical redundant function is not encoded by AtCRRs.;Vp1 functions in ABA regulated processes. Its expression is regulated by ABA, high salinity and osmoticum. The induction of Vp1 expression by ABA does not require de novo protein synthesis. The sequence analysis of 958 bp of the Vp1 promoter identified a potential ABRC (ABA response complex), which consists a predicted ABRE (ABA response element) and a CE1L (coupling element 1-like) element. Electrophoretic mobility shift assay (EMSA) confirmed that the ABRE and CE1L specifically bound proteins in 20 DAP embryo nuclear protein extracts. ABA or osmoticum induce nuclear protein interaction with the ABRE. The ABRE was also shown to be critical for the induction of Vp1 expression by ABA in a transient gene expression experiment. Sequence analysis and EMSA experiments also identified several other binding sites such as: VPP1, AtMYB2 and ZIP1. This provides a starting point to further study the regulation of Vp1 expression.</p