The development of Alzheimer's dementia (AD) accompanies both central and peripheral metabolic disturbance, but the metabolic basis underlying AD and metabolic markers predictive of AD risk remain to ...be determined. It is also unclear whether the metabolic changes in the peripheral blood and brain are overlapping in relation to AD. The present study addresses these questions by targeted metabolomics in both antemortem blood and postmortem brain samples in 2 community-based longitudinal cohorts of aging and dementia. We found that higher serum levels of 3 acylcarnitines, including decanoylcarnitine (C10), pimelylcarnitine (C7-DC), and tetradecadienylcarnitine (C14:2), significantly predict a lower risk of incident AD (composite hazard ratio = 0.368, 95% CI 0.207, 0.653) after an average of 4.5-year follow-up, independent of age, sex, and education. In addition, baseline serum levels of ten glycerophospholipids, one amino acid, and 5 acylcarnitines predict the longitudinal change in cognitive functions. Moreover, 28 brain metabolites were associated with AD phenotypes. Of the putative metabolites identified in the serum and brain, 4 metabolites (3 glycerophospholipids PC aa C30:0, PC ae C34:0, PC ae C36:1 and 1 acylcarnitine C14:2) were present in both the postmortem brain and antemortem blood, but only one metabolite (C14:2) was associated with AD in the same direction (i.e., protective). Partial correlation and network analyses suggest a potential tissue-specific regulation of metabolism, although other alternatives exist. Together, we identified significant associations of both central and peripheral metabolites with AD phenotypes, but there seems to be little overlap between the 2 tissues.
•Blood metabolites increase AD risk prediction beyond traditional clinical factors.•Metabolic disturbance could be implicated in AD pathology.•We found little overlap between peripheral and central metabolisms in relation to AD.•Metabolomics analysis of the blood and brain of same individuals.
Recent advances in large-scale gene expression profiling necessitate concurrent development of biostatistical approaches to reveal meaningful biological relationships. Most analyses rely on ...significance thresholds for identifying differentially expressed genes. We use an approach to compare gene expression datasets using 'threshold-free' comparisons. Significance cut-offs to identify genes shared between datasets may be too stringent and may miss concordant patterns of gene expression with potential biological relevance. A threshold-free approach gaining popularity in several research areas, including neuroscience, is Rank-Rank Hypergeometric Overlap (RRHO). Genes are ranked by their p-value and effect size direction, and ranked lists are compared to identify significantly overlapping genes across a continuous significance gradient rather than at a single arbitrary cut-off. We have updated the previous RRHO analysis by accurately detecting overlap of genes changed in the same and opposite directions between two datasets. Here, we use simulated and real data to show the drawbacks of the previous algorithm as well as the utility of our new algorithm. For example, we show the power of detecting discordant transcriptional patterns in the postmortem brain of subjects with psychiatric disorders. The new R package, RRHO2, offers a new, more intuitive visualization of concordant and discordant gene overlap.
Abstract Background Impairments in certain cognitive processes (e.g., working memory) are typically most pronounced in schizophrenia (SZ), intermediate in bipolar disorder (BP) and least in major ...depressive disorder (MDD). Given that working memory depends, in part, on neural circuitry that includes pyramidal cells in layer 3 (L3) and layer 5 (L5) of the dorsolateral prefrontal cortex (DLPFC), we sought to determine if transcriptome alterations in these neurons were shared or distinctive for each diagnosis. Methods Pools of L3 and L5 pyramidal cells in the DLPFC were individually captured by laser-microdissection from 19 matched tetrads of unaffected comparison, SZ, BP and MDD subjects and the mRNA was subjected to transcriptome profiling by microarray. Results In DLPFC L3 and L5 pyramidal cells, transcriptome alterations were numerous in SZ subjects, but rare in BP and MDD subjects. The leading molecular pathways altered in SZ subjects involved mitochondrial energy production and the regulation of protein translation. In addition, we did not find any significant transcriptome signatures related to psychosis or suicide. Conclusions In concert, these findings suggest that molecular alterations in DLPFC L3 and L5 pyramidal cells might be characteristic of the disease process(es) operative in individuals diagnosed with SZ and thus might contribute to the circuitry alterations underlying cognitive dysfunction in individuals with this disorder.
Schizophrenia is associated with disrupted cognitive control and sleep-wake cycles. Here we identify diurnal rhythms in gene expression in the human dorsolateral prefrontal cortex (dlPFC), in ...schizophrenia and control subjects. We find significant diurnal (24 h) rhythms in control subjects, however, most of these transcripts are not rhythmic in subjects with schizophrenia. Instead, subjects with schizophrenia have a different set of rhythmic transcripts. The top pathways identified in transcripts rhythmic only in subjects with schizophrenia are associated with mitochondrial function. Importantly, these rhythms drive differential expression patterns of these and several other genes that have long been implicated in schizophrenia (including BDNF and GABAergic-related transcripts). Indeed, differential expression of these transcripts is only seen in subjects that died during the night, with no change in subjects that died during the day. These data provide insights into a potential mechanism that underlies changes in gene expression in the dlPFC with schizophrenia.
Estrogen receptor alpha (ER) is the oncogenic driver for ER+ breast cancer (BC). ER antagonists are the standard-of-care treatment for ER+ BC; however, primary and acquired resistance to these agents ...is common. CBP and p300 are critical ER co-activators and their acetyltransferase (KAT) domain and acetyl-lysine binding bromodomain (BD) represent tractable drug targets, but whether CBP/p300 inhibitors can effectively suppress ER signaling remains unclear. We report that the CBP/p300 KAT inhibitor A-485 and the BD inhibitor GNE-049 downregulate ER, attenuate estrogen-induced c-Myc and Cyclin D1 expression, and inhibit growth of ER+ BC cells through inducing senescence. Microarray and RNA-seq analysis demonstrates that A-485 or EP300 (encoding p300) knockdown globally inhibits expression of estrogen-regulated genes, confirming that ER inhibition is an on-target effect of A-485. Using ChIP-seq, we report that A-485 suppresses H3K27 acetylation in the enhancers of ER target genes (including MYC and CCND1) and this correlates with their decreased expression, providing a mechanism underlying how CBP/p300 inhibition downregulates ER gene network. Together, our results provide a preclinical proof-of-concept that CBP/p300 represent promising therapeutic targets in ER+ BC for inhibiting ER signaling.
The estrogen receptor alpha (ESR1) is an important gene transcriptional regulator, known to mediate the effects of estrogen. Canonically, ESR1 is activated by its ligand estrogen. However, the role ...of unliganded ESR1 in transcriptional regulation has been gaining attention. We have recently shown that ligand-free ESR1 is a key regulator of several cytochrome P450 (CYP) genes in the liver, however ligand-free ESR1 has not been characterized genome-wide in the human liver. To address this, ESR1 ChIP-Seq was conducted in human liver samples and in hepatocytes with or without 17beta-estradiol (E2) treatment. We identified both ligand-dependent and ligand-independent binding sites throughout the genome. These two ESR1 binding categories showed different genomic localization, pathway enrichment, and cofactor colocalization, indicating different ESR1 regulatory function depending on ligand availability. By analyzing existing ESR1 data from additional human cell lines, we uncovered a potential ligand-independent ESR1 activity, namely its co-enrichment with the zinc finger protein 143 (ZNF143). Furthermore, we identified ESR1 binding sites near many gene loci related to drug therapy, including the CYPs. Overall, this study shows distinct ligand-free and ligand-bound ESR1 chromatin binding profiles in the liver and suggests the potential broad influence of ESR1 in drug metabolism and drug therapy.
Proteolysis targeting chimeras (PROTACs) are heterobifunctional small molecules that utilize the ubiquitin proteasome system (UPS) to degrade proteins of interest (POI). PROTACs are potentially ...superior to conventional small molecule inhibitors (SMIs) because of their unique mechanism of action (MOA, i.e., degrading POI in a sub-stoichiometric manner), ability to target "undruggable" and mutant proteins, and improved target selectivity. Therefore, PROTACs have become an emerging technology for the development of novel targeted anticancer therapeutics. In fact, some of these reported PROTACs exhibit unprecedented efficacy and specificity in degrading various oncogenic proteins and have advanced to various stages of preclinical and clinical development for the treatment of cancer and hematologic malignancy. In this review, we systematically summarize the known PROTACs that have the potential to be used to treat various hematologic malignancies and discuss strategies to improve the safety of PROTACs for clinical application. Particularly, we propose to use the latest human pan-tissue single-cell RNA sequencing data to identify hematopoietic cell type-specific/selective E3 ligases to generate tumor-specific/selective PROTACs. These PROTACs have the potential to become safer therapeutics for hematologic malignancies because they can overcome some of the on-target toxicities of SMIs and PROTACs.
Fusion transcripts are formed by either fusion genes (DNA level) or trans-splicing events (RNA level). They have been recognized as a promising tool for diagnosing, subtyping and treating cancers. ...RNA-seq has become a precise and efficient standard for genome-wide screening of such aberration events. Many fusion transcript detection algorithms have been developed for paired-end RNA-seq data but their performance has not been comprehensively evaluated to guide practitioners. In this paper, we evaluated 15 popular algorithms by their precision and recall trade-off, accuracy of supporting reads and computational cost. We further combine top-performing methods for improved ensemble detection.
Fifteen fusion transcript detection tools were compared using three synthetic data sets under different coverage, read length, insert size and background noise, and three real data sets with selected experimental validations. No single method dominantly performed the best but SOAPfuse generally performed well, followed by FusionCatcher and JAFFA. We further demonstrated the potential of a meta-caller algorithm by combining top performing methods to re-prioritize candidate fusion transcripts with high confidence that can be followed by experimental validation.
Our result provides insightful recommendations when applying individual tool or combining top performers to identify fusion transcript candidates.
With the rapid advances and prevalence of high-throughput genomic technologies, integrating information of multiple relevant genomic studies has brought new challenges. Microarray meta-analysis has ...become a frequently used tool in biomedical research. Little effort, however, has been made to develop a systematic pipeline and user-friendly software. In this article, we present MetaOmics, a suite of three R packages MetaQC, MetaDE and MetaPath, for quality control, differentially expressed gene identification and enriched pathway detection for microarray meta-analysis. MetaQC provides a quantitative and objective tool to assist study inclusion/exclusion criteria for meta-analysis. MetaDE and MetaPath were developed for candidate marker and pathway detection, which provide choices of marker detection, meta-analysis and pathway analysis methods. The system allows flexible input of experimental data, clinical outcome (case-control, multi-class, continuous or survival) and pathway databases. It allows missing values in experimental data and utilizes multi-core parallel computing for fast implementation. It generates informative summary output and visualization plots, operates on different operation systems and can be expanded to include new algorithms or combine different types of genomic data. This software suite provides a comprehensive tool to conveniently implement and compare various genomic meta-analysis pipelines.
http://www.biostat.pitt.edu/bioinfo/software.htm
ctseng@pitt.edu
Supplementary data are available at Bioinformatics online.
Kava beverages are typically prepared from the root of Piper methysticum. They have been consumed among Pacific Islanders for centuries. Kava extract preparations were once used as herbal drugs to ...treat anxiety in Europe. Kava is also marketed as a dietary supplement in the U.S. and is gaining popularity as a recreational drink in Western countries. Recent studies suggest that kava and its key phytochemicals have anti-inflammatory and anticancer effects, in addition to the well-documented neurological benefits. While its beneficial effects are widely recognized, rare hepatotoxicity had been associated with use of certain kava preparations, but there are no validations nor consistent mechanisms. Major challenges lie in the diversity of kava products and the lack of standardization, which has produced an unmet need for quality initiatives. This review aims to provide the scientific community and consumers, as well as regulatory agencies, with a broad overview on kava use and its related research. We first provide a historical background for its different uses and then discuss the current state of the research, including its chemical composition, possible mechanisms of action, and its therapeutic potential in treating inflammatory and neurological conditions, as well as cancer. We then discuss the challenges associated with kava use and research, focusing on the need for the detailed characterization of kava components and associated risks such as its reported hepatotoxicity. Lastly, given its growing popularity in clinical and recreational use, we emphasize the urgent need for quality control and quality assurance of kava products, pharmacokinetics, absorption, distribution, metabolism, excretion, and foundational pharmacology. These are essential in order to inform research into the molecular targets, cellular mechanisms, and creative use of early stage human clinical trials for designer kava modalities to inform and guide the design and execution of future randomized placebo controlled trials to maximize kava's clinical efficacy and to minimize its risks.
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