Endometriosis is a highly prevalent disease among women of reproductive age andis frequently associated to infertility. However, the mechanisms underlyingendometriosis-related infertility are still not completely known. Severalstudies have been conducted in order to elucidate this question. Besidesanatomical changes that may impair gametes and embryo transport along the tubes;a smaller ovarian reserve due to advanced endometriosis and endometriomas; and adysregulated hypothalamic-pituitary-ovarian axis, there are pieces of evidencesuggesting that the peritoneal ectopic endometrial foci may induce a localinflammatory response, with the recruitment of macrophages, cytokine release,and reactive oxygen species generation, leading to a pro-oxidant peritonealmicroenvironment. These alterations may be systemically reflected and alsoaffect the follicular microenvironment. A harmful follicular fluid may disruptcumulus cells functions and, consequently, compromise oocyte competence. Thereis also evidence suggesting that the peritoneal fluid of women withendometriosis may alter sperm function. Reduced endometrial receptivity is alsopointed as a possible mechanism involved in endometriosis-related infertility,which needs further investigation. Endometriosis is a disease defined as the presence of endometrial tissue outside theuterine cavity , which iHere, we review and discuss on the role of some possible mechanisms underlying thiscondition, including anatomical changes of the reproductive tract and smallerovarian reserve possibly involved in advanced disease infertility, and also the roleof peritoneal and follicular microenvironments, cumulus cells (CC), sperm function,and endometrial receptivity as possible mechanisms involved in the fertilityimpairment in patients with early endometriosis.Although endometriosis is frequently associated to infertility , the mecper se may affect ovarian reserve (In cases of advanced disease (rAFS III and IV), anatomical changes of thereproductive tract such as peritubal and periovarian adhesions and pelvicdistortions are indicated as limiting factors, which could impair the oocytecapture by the fimbriae, its passage through the tuba, as well as the gameticinteraction and the embryonic path to the uterine cavity ,where pelvic anatomical distortions are not present, raises questions about theinvolvement of other mechanisms in the impairment of fertility in patients withthe disease .In thiset al., 1996; et al., 2013; Evidence from literature suggest that the immune function is possiblydysregulated in endometriosis patients composition of women with endometriosis, such as cytokines  -encoding gene (PTGS2) . Inthis regards, it has been suggested an epigenetic alteration may be involved inCYP19A1 gene deregulation in CC of these patients  expression in the moderate/severe endometriosisgroup compared to women with minimal/mild endometriosis and controls. Itsuggests that advanced disease may induce pronounced OS and stimulate increasedexpression of this antioxidant as an attempt to prevent oxidative damage tooocytes and prolactin secretion . ConsequIn addition, high growth factors, cytokines, activated macrophages, TNF-αconcentrations and OS present in the PF from infertile women with endometriosismay be toxic to sperm function and impaSome authors have also considered the role of the endometrium in infertilityrelated to endometriosis, so that alterations in endometrial receptivity due tolate histological maturation or biochemical disturbances in the eutopicendometrium may compromise embryo implantation in women with the disease .Studies suggest that the endometrium may be functionally altered during theimplantation window in these patients , integriOn the other hand, recent studies have discussed the relevance of endometrialfactor for endometriosis-related infertility (Recently, Although the mechanisms involved in endometriosis-related infertility are still notcompletely understood, some evidences suggest multiple factors that may potentiallyaffect patient's fertility. In addition to the pelvic anatomical alterations likelyto compromise the gametic interaction and the altered steroidogenesis, ovulation anddisrupted ovarian function, peritoneal changes seem to promote a harmful andpro-oxidative microenvironment, which may compromise the CC and the follicularmicroenvironment, affecting folliculogenesis and, possibly, the oocyte competence inwomen with endometriosis. Peritoneal alterations may also damage the spermatozoa anddifficult gametes interaction. The role of compromised endometrial receptivity isstill controversial; however, recent evidence points to a major role of the oocytefactor in impaired fertility of infertile women with endometriosis.


Atherosclerotic cardiovascular disease remains the leading cause of morbidity and mortality worldwide. Atherosclerosis develops over several decades and is mediated by a complex interplay of cellular mechanisms that drive a chronic inflammatory milieu and cell-to-cell interactions between endothelial cells, smooth muscle cells and macrophages that promote plaque development and progression. While there has been significant therapeutic advancement, there remains a gap where novel therapeutic approaches can complement current therapies to provide a holistic approach for treating atherosclerosis to orchestrate the regulation of complex signalling networks across multiple cell types and different stages of disease progression. MicroRNAs (miRNAs) are emerging as important post-transcriptional regulators of a suite of molecular signalling pathways and pathophysiological cellular effects. Furthermore, circulating miRNAs have emerged as a new class of disease biomarkers to better inform clinical diagnosis and provide new avenues for personalised therapies. This review focusses on recent insights into the potential role of miRNAs both as therapeutic targets in the regulation of the most influential processes that govern atherosclerosis and as clinical biomarkers that may be reflective of disease severity, highlighting the potential theranostic (therapeutic and diagnostic) properties of miRNAs in the management of cardiovascular disease. Coronary artery disease (CAD) involves the narrowing or hardening of arteries, restricting blood flow to the heart and resulting in cardiovascular diseases such as angina, myocardial infarction or even sudden death. CAD is driven by atherosclerosis, a multi-faceted disease that develops over several decades that is mediated by a complex interplay between a plethora of cellular mechanisms and interactions between endothelial cells (ECs), smooth muscle cells (SMCs) and inflammatory cells. These mechanisms drive a chronic inflammatory milieu that promotes plaque development and progression, in which lipid build-up in the arteries leads to plaque formation. Despite significant research and therapeutic advances, the impact of atherosclerosis on cardiovascular disease is not fully resolved, highlighting the need for alternate therapies and improved ways to better detect disease progression. MicroRNAs (miRNAs), small non-coding RNAs that simultaneously control the expression of multiple genes, are emerging as powerful clinical biomarkers and therapeutic targets for multi-faceted diseases . miRNA tDuring canonical biogenesis, miRNAs are transcribed by RNA polymerase II, producing a double-stranded hairpin primary (pri)-miRNA transcript . pri-miRCholesterol is an important player in every stage of atherosclerosis development . In the The liver plays a critical role in the production and clearance of lipoproteins. Numerous hepatic-enriched miRNAs are known to regulate lipoprotein metabolism. miR-122 is a crucial regulator of cholesterol and fatty acid synthesis and has been highlighted as a promising target for lowering plasma cholesterol in humans . Cholest−/− mice have elevated hepatic and plasma total and HDL cholesterol levels . A . A 91]. In general, VSMC are thought to contribute to plaque stability via mediating extracellular matrix (ECM) structural elements. However, once undergoing phenotypic changes, VSMCs also contribute to necrotic core development and fibrous cap thinning. miRNAs that mediate changes to the VSMC phenotype by targeting molecules involved in vessel contraction and SMC proliferation and migration could be potential targets to reverse or inhibit the contributions of VSMCs in atherosclerotic plaque progression.Rupture-prone, vulnerable atherosclerotic plaques typically consist of high inflammatory cell content and a large necrotic core covered by a thin fibrous cap. These vulnerable plaques have an increased susceptibility to rupture, often culminating in catastrophic clinical manifestations of myocardial infarction or ischaemic stroke. While the pathophysiology of plaque rupture is not fully understood, it is well accepted that lesion vulnerability is more closely associated with plaque composition than size. There is increasing evidence that miRNAs regulate processes associated with plaque rupture .Apoe−/− mice by promoting SMC proliferation and survival [Local factors regulating SMC proliferation and apoptosis in the vessel wall contribute to the stability of the atherosclerotic fibrous cap, with vulnerable plaques showing increased evidence of SMC death and decreased SMC numbers in the fibrous cap. Numerous miRNAs shown to target SMCs in atherosclerotic plaques could have therapeutic potential in stabilising vulnerable plaques. miR-21 overexpression inhibits ROS-induced SMC apoptosis in vitro  while losurvival .Apoe−/− mice by decreasing VSMC content and inhibiting type I and type III collagen expression [Breakdown of ECM components and the dysregulation of processes involved in regulating collagen structure and content, ECM synthesis and inflammation contribute to fibrous cap thinning and plaque vulnerability . Enhancepression . Converspression .Apoe−/− and Ldlr−/− mice promoted the stabilisation of existing plaques by targeting TIMP3 and VSMC elastin production [ECM structure is also mediated by a network of regulatory elements including matrix metalloproteinases (MMPs) . MMPs cooduction . miR-362oduction . Apoe−/− mice enhanced lesion formation, increased lesional macrophage content and promoted macrophage proliferation after 12 weeks of the high-cholesterol diet. However, inhibition of miR-155 reduced necrotic core formation and the deposition of apoptotic cell debris, preventing the progression of atherosclerosis between 12 and 24 weeks of the high-cholesterol diet [Necrotic core formation is facilitated by cellular apoptosis and death of macrophages/foam cells due to ineffective efferocytosis and an imbalance in healthy versus apoptotic macrophages . Cells urol diet . These svasa vasorum (VV), that infiltrate and progressively destabilise the growing plaque [Although often viewed simplistically as the build-up of cholesterol-rich plaques in the subintimal compartment of the vessel wall, the pathology of atherosclerosis is in fact transmural. In addition to the “inside-out” recruitment of circulating lipoproteins and inflammatory cells from the vessel lumen into plaque, converging lines of evidence point to a parallel “outside-in” pathway to atherogenesis. This involves early and rapid remodelling of the outer vascular layer, or adventitia, consisting of expansion of inflammatory cells and permeable microvessels, called g plaque . VV are g plaque . Accumulating evidence shows that changes in VV characteristics are closely associated with the progression of atherosclerosis . The focAdditionally, the VV serve as the vascular niche for vascular-resident stem cells (VSCs), acting as a stem cell reservoir to supply VSCs, which can differentiate into ECs and VSMCs, into the intima, contributing to atherosclerotic re-modelling . VSCs ha−/− mice have a reduced ability to survive myocardial infarction due to vascular abnormalities and defective angiogenesis [Multiple miRNAs have been shown to regulate endothelial cell (EC) commitment and vasculogenic growth, including that of the VV. The importance of miRNAs in vascular development and angiogenesis was first observed when the enzyme Dicer was inhibited with embryonic lethality observed during early development due to an underdeveloped vascular system ,126. miRogenesis . miR-126ogenesis . Given togenesis . Extensiogenesis ,134, witogenesis . The miRogenesis . FAT4 inogenesis . Endotheogenesis . Furtherogenesis .Numerous miRNAs have also been implicated in SMC differentiation. In addition to their role as modulators of VSMC plasticity, miR-143 and miR-145 are important mediators in the differentiation of multipotent stem cells into the VSMC phenotype . Dicer kCollectively, these studies highlight the role of miRNAs in both the regulation of cardiovascular lineage differentiation and angiogenesis. Under pathophysiological conditions, this may drive the formation of new vessels, including VV into neointimal lesions. While these studies suggest the potential targeting of miRNAs in this space, additional research is required to unravel the involvement of miRNAs in VV growth during atherogenesis.Extensive research has revealed that miRNAs are extremely stable and expressed in the peripheral circulation. miRNAs can be easily obtained and are reliably detected from plasma or serum by non-invasive methods . Given tIn a human study of advanced coronary atherosclerotic plaques, miR-21, miR-92a and miR-99a were found to be upregulated in the circulation . ConsistCirculating miRNAs were also altered in response to established CAD. Patients with CAD had reduced levels of VSMC-enhanced miR-145; EC-enriched miRNAs miR-126, miR-17 and miR-92a; and miR-155, yet expression of cardiomyocyte-enriched miRNAs miR-133 and miR-208a was elevated . CAD is Studies have also reported that some miRNAs have differential expression patterns depending on the disease pathology. miR-126 levels are elevated in patients with atrial fibrillation and heart failure , while cThere has been significant therapeutic advancement in the treatment of atherosclerosis. However, it is evident that there remains a gap where novel therapeutic approaches can complement current therapies such as lipid-lowering drugs  and anti-hypertensive drugs to provide a holistic approach for treating atherosclerosis to orchestrate the regulation of complex signalling networks across multiple cell types and different stages of disease progression. Since their discovery in 2000, there has been significant interest in the potential of miRNAs as both therapeutic targets and clinical diagnostic biomarkers in multi-faceted diseases including atherosclerosis. In vitro and pre-clinical studies to date show that numerous miRNAs have the potential to regulate complex cellular processes across key cardiovascular cell types. We strongly believe that this highlights their clinical potential as emerging therapeutics that can be customised as personalised treatments to specifically target the different stages of atherosclerosis progression. Furthermore, targeted modulation of miRNAs has the capacity to be highly effective for the treatment of atherosclerosis because of their ability to orchestrate a host of complex factors concurrently across multiple cell types. The field of miRNA biology has expanded considerably over the last 20 years and will continue to grow rapidly as miRNA therapeutics enter clinical trials. Furthermore, growing evidence suggest that circulating miRNAs can provide insight into a patients’ specific atherosclerotic disease stage to better inform clinical diagnosis. This highlights the significant potential for the use of miRNAs as theranostic targets, providing an attractive therapeutic approach to facilitate interventions targeted at patient-specific stages of atherosclerosis and the future management of its cardiovascular complications.


The vast-majority of patients that suffers from heart failure hasacute worsening episodes that become more frequent as the disease progresses.Acute heart failure (AHF) refers to rapid onset or worsening of signs and symptoms ofheart failure, often requiring hospitalization and urgent treatment, due to itspotentially life-threatening condition,3, and the immediateinvasive strategy with intent to perform revascularization in patients with both AHF andacute coronary syndrome is recommended in guidelines,5. However, the choicesof revascularization are still controversial subject: either percutaneous coronaryintervention (PCI) or coronary artery bypass grafting (CABG).More than half of these patients are known to have an ischemic etiology, and earlyrevascularization improve clinical outcomesWhich one is better has been long debated. Trials comparing both techniques have shownthat the rates of most adverse clinical outcomes favor CABG, which turns this techniqueas the preferred revascularization strategy in patients with multivessel disease.Unfortunately, most of the trials comparing PCI versus CABG were designed in the settingof stable coronary artery disease. The majority of patients included in these studieshad two vessel disease and preserved left ventricular function, differing from thepatients with AHF. Even so, there’s still no evidence of survival improvement when PCIwas compared to CABG, especially in the long-term comparison.. In this analysis, 717patients received CABG or PCI during the hospitalization for AHF. Adverse outcomes were used for propensity score matching. Theauthors concluded that, compared to PCI, CABG was associated with significant lowerall-cause mortality in patients with AHF. The rate of death from any cause over 4 yearswas lowered by 40% among patients who underwent CABG than those who received PCI. Theseare very impressive results.A recent multicenter prospective cohort study, The Korean Acute Heart Failure Registry,evaluated 5625 patients enrolled prospectively from March 2011 to February2014. After applyinginclusion and exclusion criteria from the Surgical Treatment for Ischemic Heart Failuretrial, the study showed that CABG was associated with improved long-term survival whencompared to PCI in patients with ejection ≤ 35% and 2- or 3-vessel disease. Inthe long-term analysis, CABG was associated with lower incidence of all-cause mortality,being CABG strongly considered in these patients with ischemic cardiomyopathy andmultivessel coronary disease.Another recent multicenter observational analysis between 2004 and 2014 among 7 medicalcenters, reporting to the Northern New England Cardiovascular Disease Study group,evaluated more than 70,000 patients who underwent CABG  versus PCI. The complete revascularization rate, defined as allstenotic main-branch vessels being treated, is always significantly higher in the CABG group than in the PCIgroup in most studies.The better results for surgery might be attributable to the ability to achieve completerevascularization in extensive coronary artery diseasePCI is a well-established strategy and the advance and progress of the stents is beyondquestion. However, for patients that are experiencing signs and symptoms of heartfailure, surgery is still the best and safer option. Besides, after 50 years thesurgical field has also innovated and advanced. The use of multiple arterial grafts thathave superior long-term patency has significantly improved the survival rates. Also,off-pump surgery has reduced aortic manipulation and consequently the rates of strokeand heart failure after surgery on specific patients.It is unquestionable and a very widely known fact that CABG yields better results and therefore a better and longer life ahead forthese patients.


Transcriptomic sequencing (RNA-seq) related applications allow for rapid explorations due to their high-throughput and relatively fast experimental capabilities, providing unprecedented progress in gene functional annotation, gene regulation analysis, and environmental factor verification. However, with increasing amounts of sequenced reads and reference model species, the selection of appropriate reference species for gene annotation has become a new challenge.We proposed a novel approach for finding the most effective reference model species through taxonomic associations and ultra-conserved orthologous (UCO) gene comparisons among species. An online system for multiple species selection (MSS) for RNA-seq differential expression analysis was developed, and comprehensive genomic annotations from 291 reference model eukaryotic species were retrieved from the RefSeq, KEGG, and UniProt databases.Using the proposed MSS pipeline, gene ontology and biological pathway enrichment analysis can be efficiently achieved, especially in the case of transcriptomic analysis of non-model organisms. The results showed that the proposed method solved problems related to limitations in annotation information and provided a roughly twenty-fold reduction in computational time, resulting in more accurate results than those of traditional approaches of using a single model reference species or the large non-redundant reference database.Selection of appropriate reference model species helps to reduce missing annotation information, allowing for more comprehensive results than those obtained with a single model reference species. In addition, adequate model species selection reduces the computational time significantly while retaining the same order of accuracy. The proposed system indeed provides superior performance by selecting appropriate multiple species for transcriptomic analysis compared to traditional approaches.The online version of this article (10.1186/s12859-018-2278-z) contains supplementary material, which is available to authorized users. High-throughput RNA sequencing (RNA-seq) involves the sequencing of cDNA samples using next-generation sequencing instruments, thus permitting the analysis of complete transcriptomes from samples subjected to different experimental conditions. In addition to providing a snapshot of an organism’s transcriptional profile, RNA-seq can also be used to observe changes in gene expression levels by comparing transcriptomes obtained at various time points or from different tissues under different environmental settings . In recenr) sequence database GenBank, maintained by NCBI, contains a popular reference dataset for sequence annotation; thus, several RNA-seq studies performed on novel species have thus far aligned sequences to the nr sequence database for gene function annotation [Although transcriptional data can be obtained using RNA-seq without any prior knowledge of gene sequences, for functional genomic analysis of non-model species, a sequence similarity alignment must be performed with reference sequence datasets containing known gene functions in order to accurately annotate the gene functions of assembled sequences. The most popular gene sequence database is the International Nucleotide Sequence Database Collaboration (INSDC), which regularly updates sequence information from three databases: the National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EMBL-EBI), and the DNA Data Bank of Japan (DDBJ). The non-redundant  for rapid and accurate screening of model species. These UCOs are a set of 357 single-copy genes originating from thaliana –11. In tFinally, differentially expressed gene sets were functionally annotated through gene ontology (GO) and biological pathway enrichment analysis based on multiple species selection. GO is a structural vocabulary system defined by the Gene Ontology Consortium, and it provides a standard vocabulary set for gene function annotation . BiologiFor effective and efficient gene functional analysis in this study, a total of 291 eukaryotic reference model species were verified and selected from the Kyoto Encyclopedia of Genes and Genomes (KEGG) , UniversIn this study, we proposed a system for differential expression analysis of transcriptomic sequencing datasets. The system intelligently selects appropriate reference species for gene functional annotation and functional enrichment analysis. An overview flowchart of the proposed system is shown in Fig. For selection of the most appropriate reference model species, two different approaches were proposed. The first approach is based on information in the NCBI Taxonomy tree, and the other is based on similarity analysis of inter-species UCO protein sequence comparisons. The traditional method of selecting reference species has been constrained by the evolutionary relationships among the query and all candidate species. According to the pipeline, if the query species is present in the NCBI Taxonomy database, the system will reveal all possible reference model species with the shortest branch distances to the query species according to the taxonomic tree. However, the query species may not be present in the taxonomy database or it may possess a large number of closely related species located under the same branch node within the taxonomic tree. In order to efficiently select accurate and sufficient reference species, we proposed a novel approach for identifying suitable reference model species by comparing UCOs between the query and all candidate model species.The NCBI Taxonomy database is the standard nomenclature and classification repository of the INSDC. In the taxonomy tree, there is no clear definition of numeric distances between two nodes. Hence, the evolutionary relationship between any two species can only be represented as their topological locations between nodes on the phylogenetic tree, and accurate evolutionary distances between species pairs cannot be detected from the tree structure. Instead, only relative topological tree structural distances can be used, indicating that a species pair is more related than another species pair with a longer topological tree structural distance. Therefore, in our pipeline, all 291 reference species are compared with the query species to search for their lowest common ancestor (LCA) nodes, and the depths of neighboring nodes are evaluated as a score from the defined taxonomic tree structure. Higher scores represent larger depths from the root and imply that the reference species is located at a relatively lower level compared to that of the query species. The proposed system initially sets a default threshold of three species as a minimum and five as a maximum, but this can be adjusted by the user. The LCA distance between the target species and query species must satisfy that they belong to the same phylum.A. thaliana, humans, mice, yeast, fruit flies, Caenorhabditis elegans, and other eukaryotic organisms. With their widely conserved characteristics, UCO sequence similarities are used as standards for selecting reference model species. The proposed system suggests that a suitable reference model species should possess more similar gene sequences for improved gene annotations during reference mapping procedures. To achieve this goal, we performed BLAST searches for all 291 model species against the defined UCOs to identify all UCO protein sequences in each model species. The BLASTP program was used with an E-value threshold of less than 1.0E-10. All identified UCOs for each of the 291 model species were saved in the UCO database , we performed an experimental test using four non-model species: Corbicula fluminea. In this experiment, the first and second reference species suggest by the taxonomic and UCO approaches were identical (Crassostrea gigas and Lottia gigantea), but the third recommended species was different. The model species Helobdella robusta was suggested by the taxonomic approach, while Branchiostoma floridae was suggested based on UCO comparisons. Therefore, we performed gene annotation analysis separately using each set of three species recommended by the different approaches. Table Crassostrea gigas provided the most comprehensive sequence information in the RefSeq database, but the number of GO and KEGG annotations derived from Crassostrea gigas are significantly lower than those annotated with the other selected model species.Next, we showed the statistics of reference genes and corresponding functional annotations according to the selected model species by our proposed system, and these number would be applied for the following differential expression analysis. The RNA-seq datasets of the first experiment were acquired under both normal and hypoxic conditions for the non-model species Crassostrea gigas (crg); (2) using the top two species suggested by UCO and taxonomic approaches, Crassostrea gigas (crg) and Lottia gigantea (lgi); (3) using the top two species plus H. robusta (hro), as recommended by the taxonomy-based approach; (4) using the top two selected species plus B. floridae (bfo), as recommended by the UCO approach. Figure For gene ontology analysis, we performed four different species selections of gene enrichment analyses for comparison: (1) using a single reference species, P-values. Several studies have reported the identification of GO terms associated with hypoxic environments. For example, the chitin metabolic process, calcium ion binding, and Notch signaling pathway have been shown in previous reports to be strongly associated with such conditions [Based on the identified GO terms obtained from the four different reference model species groups, we specifically investigated GO terms with low nditions , 20. Comnditions . In summP-values less than 0.05 for the various groups of model species, with only significant P-values shown. For example, the cell adhesion molecule (CAM) and prion disease pathways were identified only after increasing the number of reference model species, and both of these pathways have been confirmed to be strongly associated with hypoxia in related research reports [For biological pathway analysis, we performed differential expression analysis using the same four groups of reference species as in the previous section: crg, crg/lgi, crg/lgi/hro, and crg/lgi/bfo. Table  reports , 23. A hCorbicula fluminea under hypoxic conditions, we identified additional significant GO terms, including the Notch signaling pathway, cytoskeletal protein binding, and hydrolase activity. These GO terms have been found to be associated with hypoxia in reported studies. For biological pathway analysis, additional significant biological pathways were identified, such as the CAM pathway, by increasing the number of multiple species selected as well. Therefore, appropriate selection of multiple species for transcriptomic analysis can reduce required computational time and unnecessary searches against the non-redundant gene dataset. Taking the Corbicula fluminea RNA-seq datasets as an example , we applied the non-redundant gene dataset  and the 4 selected model species including Crassostrea gigas, Lottia gigantea, H. robusta, and B. floridae as our target reference datasets individually. The TBLASTX algorithms were performed under a Linux server with 2 CPU(8 cores), 128GB RAM, and 16 multiple thread settings. The results showed that the proposed method solved problems related to limitations in annotation information and provided a roughly twenty-fold reduction in computational time when selected 3 model species according to taxonomic or UCO approaches. In addition, selecting multiple appropriate species as reference model species helps to reduce missing annotation information, allowing for more comprehensive results than those obtained with a single model reference species. We have developed an integrated system that combines the multiple model species selection pipeline and enrichment analysis of differentially expressed genes. This includes a total of 291 reference model species that were initially selected from the intersection of the RefSeq, KEGG, and UniProt online databases. Corresponding genomes, gene annotations, UCO genes, GO terms, and KEGG pathways were initially constructed and integrated into the proposed system. However, due to different naming architectures among the three databases and an increased number of curated genomes recently, additional model species present in the three databases should be carefully verified and added to the system in the future for a more comprehensive system.This paper proposes a novel approach for efficiently identifying appropriate reference model species by analyzing taxonomic relationships and comparing UCOs. Based on UCO genes largely conserved across all eukaryotic organisms, accurate evolutionary distances are calculated using sequence alignment and applied to compensate for indistinguishable characteristics of the taxonomic tree. In this study, we performed RNA-seq experiments in four non-model species, and our results confirmed that evolutionary distances between species could be ascertained using UCO gene sets. We also performed enrichment analysis of the identified differentially expressed genes using GO and biological pathway approaches. For example, though GO analysis of Additional file 1:The identified UCO datasets for 291 candidate reference model species . (FASTA 46754 kb)


A successful prostate cancer must be capable of changing its phenotype in response to a variety of microenvironmental influences, such as adaptation to treatment or successful proliferation at a particular metastatic site. New cell phenotypes emerge by selection from the large, genotypically heterogeneous pool of candidate cells present within any tumor mass, including a distinct stem cell-like population. In such a multicellular model of human prostate cancer, flexible responses are primarily governed not only by de novo mutations but appear to be dominated by a combination of epigenetic controls, whose application results in treatment resistance and tumor relapse. Detailed studies of these individual cell populations have resulted in an epigenetic model for epithelial cell differentiation, which is also instructive in explaining the reported high and inevitable relapse rates of human prostate cancers to a multitude of treatment types. Human prostate cancer has a deserved reputation for being amongst the most heterogeneous of human tumors . HeterogWhilst such heterogeneity is generally accepted, it is rarely reflected in molecular studies of the cancers, either at the phenotypic or genotypic levels ,4,5. TheThe current approach to tumor heterogeneity, deep sequencing of genomic DNA, has identified a degree of genomic and clonal variations, and increasing levels of mutations between treatment naïve tumors  and aggrIn contrast to tumors where there is a known chemical etiological agent , prostate cancers have a relatively low rate of single base pair changes within the tumor mass . In factGene expression patterns are equally heterogeneous in both normal and malignant prostate glands where, as a cell becomes more defined, gene expression is not only more restricted, but is considerably enhanced. For example, the expression of genes for proteins secreted by the non-dividing, terminally differentiated prostatic luminal cells  is governed by promoters whose activity is many thousand-fold higher than those of maintenance genes such as those required in basal cells . Some maEven in human tissues where great care has been taken to micro-dissect the epithelial component, there remains a gross element of heterogeneity according to the basal or luminal origin of the epithelial cells. In normal prostate, the luminal epithelial fraction comprises around 50% of the cellular epithelial population, whereas basal epithelial cells form the remainder within a gland. In cancers, this ratio is extremely skewed: more than 99% of the cancer mass is a luminal-like cell, which is incompletely differentiated (whilst expressing androgen receptor and prostate-specific antigen) but has gained the ability to replicate in an uncontrolled fashion. However, within the tumor mass, there also remains a small population (fewer than 1% of cells) with a basal-like phenotype . Given tOthers have reported similar cell fractionation protocols, which indicated that a basal cell was the likely origin for the most aggressive and malignant prostate cancers. A human basal cell of origin ,30,31 isThe cell of origin (COO) of prostate cancer has been briefly discussed above. Logically, given the time required to develop a cancer, the COO should be long-lived in order to accumulate necessary changes. The slow turnover of prostate stem cells can also explain the slow progression and late-onset of prostate cancer (reviewed in ). MathemThe cancer stem cell (CSC) hypothesis states that not all of the cells in the tumor are able to reconstitute the tumor mass after dissociation and that a sub-population of cells are responsible for tumor initiation, and post-treatment relapse. The CSCs have been termed stem-like cells, since their properties, and some phenotypic characteristics replicate the tissue-renewing stem cells in normal cell systems. It is assumed that the pool of CSCs, which is between 0.01% and 0.1% of a prostate cancer mass lies at the apex of an aberrant differentiation hierarchy see .The more traditional view of carcinogenesis is embodied in the stochastic mechanism which proposes that the definitive carcinogenic event is initiated by an oncogene or tumor suppressor gene. The mutation is “fixed” in the population by subsequent mitosis, resulting in a daughter cell whose tumor propagation potential matches that of the initiating cell. Subsequent mutations and accumulation of different genetic lesions within the initiated “field” produced clones with growth advantages that can be traced to the founder event. There is now increasing evidence in prostate cancer (reviewed in Reference ) to showIt is likely that the CSC and stochastic hypotheses are not mutually exclusive. Experimental evidence requires the initiating events to occur in longer lived and largely quiescent stem/progenitor cells, establishing pre-tumor development  which maSince our original hypothesis was that in both normal and malignant prostate, the bulk of the cells is derived from an original  stem cell , it is iOur second assumption was that genes whose expression is changing during the differentiation process ought to be co-regulated in some way. Therefore, we re-analyzed our initial gene expression data on the basis of a high pair-wise correlation A i.e., gHowever, such simplistic mechanisms cannot explain all of the co-regulations seen within the four expression groups during basal cell differentiation. An equally powerful regulator of co-expression would also seem to be high levels of a restricted number of transcription factors  which cohttps://www.proteinatlas.org/ENSG00000184012-TMPRSS2.In terms of gene expression responses and co-regulation, the TMPRSS2 gene   was cleaIdentification of the cognate binding sites within promoters for transcription factors and the range of differentiation-associated transcription factors , has posMost current therapies for prostate cancer are directed against replicating differentiated cells , but theIn a purely theoretical analysis of cell fate determination in development, Conrad Waddington  visualizWaddington formulated these hypotheses in the complete absence of any potential epigenetic mechanisms in development or indeed cancer . We now In evolutionary terms, a permanent change such as mutation or deletion of a gene is clearly a strategy for many species. In cancer, however, a permanent response to drug treatments such as AR gene amplification/mutation  or DHFR Returning to Waddington’s original Landscape, on to which the various epithelial cell types in normal and malignant prostate have been superimposed B, it is Small non-coding RNAs, such as the more than 2000 microRNAs (miRNA) encoded in the human genome are a major mediator of epigenetic gene expression control . BearingIncreased miRNA expression has also been linked to oncogenic changes—suppressing tumor suppressor genes there (onco-miRNAs) whereas some are downregulated, permitting the expression of known oncogenes (suppressor miRNAs). Unlike many other studies in common tumor types, there has been little consensus about the most significant miRNA expression changes in prostate cancer (reviewed by Reference ), whilstWhen miRNA levels were studied in purified cell fractions from multiple normal and malignant prostate tissues B, there The miRNA expression profiles showed that (i) a miRNA signature was conserved in stem cells from BPH, PCa, and CRPC, implying that miRNAs play their most important role in regulation of essential SC properties such as self-renewal, prolonged proliferation, and a hard-wired capacity to differentiate, regardless of the pathological origins of the cells. (ii) The prostate SC miRNA signature overlapped considerably with that from human embryonic SCs (hESCs)  e.g., hiGiven the strong link between differentiated state and miRNA expression in this study, a number of the previously prostate cancer (both primary and CRPC) -associated miRNA identified in Rane et al.,  had prevFinally, since multiple miRNAs implicated in the hESC maintenance program are conserved in adult human prostate epithelial SCs, this strengthens the evidence for a stem-like status for CD133+/CD44+/a2b1 integrin high cells—a status which is ultimately acquired by malignant cells in CRPC after multiple rounds of androgen-based therapies, emphasizing the basal stem-like nature of these advanced. and broadly incurable cancers .Bioinformatic analysis to identify the most significant changes in expression has recently been compromised in unfractionated tumor biopsies in a paper describing the expression of the onco-miRNAs 143/145 in normal mouse colon . PreviouWe sought to minimize the impact of our study of epithelial differentiation, by restricting the candidate genes suppressed by miRNA control after referral to a range of existing algorithms (MiRWALK) to those which were actually expressed in prostate epithelium . SecondlIt has been suggested in studies of other cancer types, that both the induction of a more stem-like state and chromatin status play a dual role in radio-resistance ,88,89,90Phenotypic plasticity, and the generation of cells with a stem-like phenotype from more differentiated cells, has also been implicated in therapy resistance. Since our miRNA dataset implied such a close relationship between treatment-resistant cells (CRPC) and that miRNA could perturb differentiated state. Here, our candidate selection was driven by the set of transcription factors identified earlier: i.e., RXR, Rock2, vitamin D receptor, GCRs, TAZ serum response factor and HSF1. Within the set of miRNA over-expressed in SC, one miRNA: miR548c-3p had a high potential to control the differentiation-linked transcription factor expression set. This miRNA is overexpressed approximately fivefold in SCs compared with more differentiated cells, and its overexpression has been associated with poor patient survival . When miStem cells contain bivalent or “poised” chromatin, which share active and repressive histone binding ,94. The 2β1integrinhi) sustained less DNA damage and were, therefore, more resistant to radiation than the more differentiated transit amplifying (TA) and committed basal (CB) cells [The existence of condensed or bivalent chromatin has been proposed as a response and resistance mechanism to a number of therapies for cancer ,98,99. PB) cells . In retiB) cells , prefereB) cells  as definLike many other stresses, hypoxia  also resMany miRNAs play a variety of roles in resistance to chemotherapy, and the Gene Ontology link from our linked profiling of mRNA/miRNA implied that the same feature would apply to radiotherapy-induced DNA damage repair ,28. miR-When expression was studied in both cell lines and primary tissue-derived cells, inhibition of miR-99a/miR-100 prevented p53 dependent apoptosis in irradiated PCa cells. In a similar manner to HDAC inhibitor treatment (see above), suppression of miR-99a/100 results in relaxation of damaged chromatin by both histone acetylation and recruitment of DNRCA1 and RAD51 . Of the Expression of PARP1 whose inhibition was recently shown to increase survival times a subset of PCa patients , is anotControl of cell fate really cannot be explained by any single transcription factor see . Whilst Persistent changes to DNA are stabilized by CpG hypermethylation in many cancer types (reviewed by Reference ) includiThe ability of CpG methylations to control the expression of many genes in cancer has been extensively reviewed . GlutathGene expression studies, closely coupled to genome-wide CpG methylations in prostate tissues have found that there was a relatively low correlation between the two phenomena, unlike similar studies in established cell lines . In fracAs a test of this hypothesis, we have recently carried out a genome-wide DNA sequencing of bisulfite-modified DNA extracted from multiple cell types, enriched according to their phenotype . In contSince these signatures had the cell and patient-specific elements removed, they were then applied to existing CpG methylation data in the TCGA prostate cancer database . UnfortuSecondly, since the original tissues used to establish the signatures were from high Gleason grade samples, we next asked whether this signature was able to distinguish tumors with a poor outcome from those which remained organ-confined. Again, all of the relevant clinical outcomes were included in the TCGA information. By using 60% of the database information as a training set, we were able to devise a 17 DMR signature for patients whose cancers were likely to have spread. This resulted in a 76% detection rate for poorer outcomes, but from an original radical prostatectomy sample, i.e., at an earlier time before conventional technology such as MRI scanning could be used to locate micro-metastases. Thus, malignancy seems to be fixed in the CpG methylation patterns from an early time in cancer development. With more patients and matching of methylated CpG technologies  this analysis could offer an early diagnosis of the most malignant prostate cancers.The analysis also had a sounder mechanistic basis than an empirical serum PSA level increase. The cancer-related hypermethylated regions detected in the luminal compartments were normally in upstream enhancer regions, outside of CpG islands, Shores and Shelves . As deteEpigenetic control of gene expression is normally considered at the single gene level . However, most mammalian cells are diploid and prostate cancer cells are normally either quasi-diploid (hormone naïve) or aneuploid (CRPC), containing at least two copies of all non-sex chromosomes. One notable exclusion is the X-encoded androgen receptor with its critical role in PCa, although amplification of X and AR genes is seen in CRPC . The selHigh-resolution genome sequencing has now provided unprecedented details about the allelic nature of oncogene activation in prostate cancers, where most mutagenic changes are heterozygous, retaining a copy of the normal allele . AccordiThe presence of the normal allele is rarely considered when determining new potential therapeutic targeting and indeed understanding the cancer. As normal cells and tissues develop from a stem cell origin, virtually every cell inactivates one chromosomal copy by epigenetic mechanisms. Patches of clonally derived cells are also present in most tissues, for example, multiple cell patches containing inherited mitochondrial DNA mutations in the normal prostate .An elegant single cell transcript analysis of allelic expression in developing mouse embryos showed mono-allelic expression of 12% to 24% of autosomal genes . A generDifferent cancer cells are likely to display variant allelic preferences between genes. Such Random Monoallelic Expression (RME) is distinct from expression controls established by aberrant promoter methylation, or locus deletion detected in cancers. In RME, the alleles of a specific gene can be (i) biallelically, (ii) maternal monoallelically, (iii) paternal monoallellically expressed or (iv) completely silenced. The expressed allele is stably retained after mitosis and differentiation in non-stem daughter cells ,143. FroIn the majority of genes displaying RME, regulation of allelic choice is, however, not controlled by strand-specific methylation ,144 of pTumorigenic RME has been reported in peripheral mononuclear blood cells from chronic lymphocytic leukemia patients with DAPK1 haploinsufficiency , whereasThe expression of TMPRSS2—which provides the promoter for the TMPRSS2-ERG fusion, presents in about 50% of organ-confined prostate cancers, the commonest genetic abnormality in prostate cancer, ,53 is stWithin a mass of identical cancer cells, epigenetic control of RME can both silence tumor suppressor loci and activate oncogenic alleles. However, it is now clear that tumors are not a homogeneous mass of identical cells. Pre-tumor progression, where mutations accumulate in a phenotypically silent manner has been proposed as the source of the multiple cooperating driver mutations in the final tumor. It is perhaps significant that treatment-naive prostate cancers have relatively few p53 mutations , to rendThe latter events are illustrated schematically in There is a prominent role for each of the major epigenetic control mechanisms in prostate epithelial cell differentiation. Histone modifications and changes to chromatin configuration provide the initial overall control of transcription and the selection of allelic preferences in gene expression. A cell stage-specific representation of this is shown in We have defined a set of transcription factors, including the critical Rock 2 kinase, which controls transcription of non-overlapping gene sets . These mThe SC state appears to be one of “active” quiescence, where expression at high levels of many miRNAs, and the existence of bivalent and/or poised chromatin (controlled by simultaneous binding of repressive and activating modified histones) indicates a cell which can react rapidly to changes in microenvironment/cell division, to produce a more differentiated daughter cell. Genomic methylation plays a less important, but not insignificant role, as SC are generally hypomethylated, with only a few clusters of hypermethylated chromatin. Some of these CpG clusters influence the SC adhesive properties i.e., sensing changes to the microenvironment, which may define fate after asymmetric division. However, the patterns of differential CpG methylation between normal and malignant cells from the same patient lie out-with the normally screened CpG “islands” can provide significant information about cellular processes involved in both carcinogenesis and differentiation, particularly if carried out on a patient-specific basis using matched normal and malignant tissues. In terms of understanding prostate cancer, and devising more effective and longer-lasting treatments, we need to consider the phenotype of not only the majority cell population within normal and malignant prostate epithelium but also minor populations such as progenitors and stem-like cells. The stem-like cells provide a strong argument in favor of an intrinsic therapy-resistant cell in cancers, rather than induction of resistance by the therapies. Since the ability to differentiate appears to be hard-wired- into all such stem-like cells, one solution would be to deplete or eliminate the SC by inducing differentiation, as shown in acute promyelocytic leukemia where pre-treatment with retinoic acid results in a more differentiated cell, which can be killed effectively by traditional chemotherapies.Treatment with inhibitors of histone deacetylase, (at a concentration about 100-fold lower than that used in cytotoxic cancer treatments) resulted in a 40% increase in SC radio-sensitivity, whilst not affecting the more differentiated and radiosensitive cells. The in vitro data strongly promotes the use of HDAC inhibitors (at sub-toxic doses) as radio-sensitizers in prostate cancer treatments.Radiotherapy (and chemotherapy) patients are often treated with glucocorticoids to counteract the side-effects of treatment. In our studies of miR99a/100 in primary PCa, pre-treatment with dexamethasone stimulated miR99a/100, reducing SMARC expression and decreased radiotherapy responses, whereas combination treatment with the GCR inhibitor Mifepristone increased radio-sensitivity by stimulating the expression levels of miR-99a/100 and decreasing SMARC-induced chromatin condensation. Therefore, the clinical use of GCR inhibitors should clinically enhance radiotherapy and perhaps reduce tumor relapse.Overexpression of exogenous miR-548c-3p, which is highly expressed in PCa SC, made radiosensitive CB cells more resistant to irradiation, by induction of a more stem-like state. Thus, inhibition of the SC-preserving activity of high miR-548c-3p levels should also increase clinical radiotherapy efficacy.Exploitation of this fundamental property of the resistant stem-like population i.e., a focus on cellular differentiation in prostate cancer, rather than the traditional description of cancer as a fast-growing cell, has now yielded three potentially novel strategies to improve treatment efficacy:To paraphrase what Waddington so beautifully illustrated almost 80 years ago: by getting stem-like cells in cancer to roll down into epigenetic valleys, we can perhaps kill more of them by conventional means. The challenge faced by researchers wishing to translate similar findings into clinical practice is the similarity between the epigenetic control of normal and malignant cell differentiation. Preservation of normal stem cell function, not only in the target organ, but elsewhere in the body remains difficult to predict, and off-target effects may take some time to manifest themselves if affecting slowly cycling stem cells. A major feature of Waddington’s Hypothesis was the prediction of developmental plasticity mediated by epigenetic control. Mutational changes to the cancer genome are essentially irreversible and rather stupid evolutionary strategies and are mainly exploited by prostate cancers as a response to therapy. A smart tumor cell will maintain its options in a changing tumor microenvironment .Finally, the data from prostate and other cancers provides insights to be gained from a cell fractionation approach to complex tissues, prior to deep sequencing or similar analyses, and its ability to generate genuinely novel targets for cancer therapy. Recent data also clearly indicate the compromise offered by analysis of established cell lines, which have been selected for their ability to grow (sometimes more than 40 years ago), compared to tissues. The high quantity, high heterogeneity, high depth approaches to the analysis of tissues also present problems with interpretation—requiring large numbers of cells. Rather, current efforts to miniaturize key assays such as genomic methylation, chromatin immunoprecipitation, and better fidelity DNA/RNA sequencing from single cells are all key to the study of minor cell populations.With major pharmaceutical companies seemingly focused on generating biosimilar drugs in a restricted pool of therapeutics, offering life extensions of months and at a high cost in many cases, relative to either standard of care or placebo treatments, the ability to kill more of the disparate cell types in a tumor based on epigenetic mechanisms, in a “low mutation” primary cancer such as prostatic adenocarcinomas.


The prevalence of overweight and obesity is on the rise around the world. Common comorbidities associated with obesity, particularly diabetes, hypertension, and heart disease have an impact on social and financial systems. Appropriate lifestyle and behavior interventions are still the crucial cornerstone to weight loss success, but maintaining such a healthy lifestyle is extremely challenging. Abundant natural materials have been explored for their obesity treatment potential and widely used to promote the development of anti-obesity products. The weight loss segment is one of the major contributors to the overall revenue of the dietary supplements market. In this review, the anti-obesity effects of different dietary or herbal products, and their active ingredients and mechanisms of action against obesity will be discussed. Obesity and overweight are major contributors to the global burden of chronic diseases and complications, including cardiovascular diseases, diabetes, and cancer. In 2014, it was reported by World Health Organization (WHO) that more than 1.9 billion adults were overweight, and of these over 600 million were obese. Once mainly a concern for higher income countries, overweight and obesity are also on the rise in low and middle income countries, especially in urban areas [There are many different options for obesity treatments, including dietary control, exercise, life-style changes, prescription weight-loss medications, and weight-loss surgeries . AccordiIn 2007, the Nutrition Business Journal showed that the aggregate market value of dietary supplement reached nearly 20 billion dollars in sales for the USA. It was estimated that there was at least a 700 million dollars market for weight loss products alone in 2008 . By the Anti-obesity drugs have been studied profoundly for decades. The need for adjunctive therapies for weight loss has accelerated the progress in the pharmaceutical industry worldwide. In USA, four FDA-approved oral weight loss drugs have been developed, including orlistat , Contrave , Belviq (lorcaserin hydrochloride), and Qsymia (phentermine and topiramate extended-release). These clinical medications manipulate body weight by increasing energy expenditure, suppressing appetite, or inhibiting pancreatic lipase to decrease lipid absorption in the intestine ,8.Weight loss drugs may appear to be a solution to obesity. However, possible side effects or adverse drug reactions are always a big public health concern and also a major barrier to the development of new drug products. For example, in 1997, two weight loss drugs, fenfluramine (part of the popular fen-phen) and dexfenfluramine (Redux), were withdrawn from the market because of their possible detrimental effects to heart valves. In 2010, sibutramine (Meridia) was also withdrawn due to an increased risk of heart attacks and strokes. In the same year, in response to the occasional reports of severe liver injury with the use of weight loss drug “Xenical”, FDA approved a revised drug label in which safety information about its potential side-effect was noticed.As mentioned in the ESCP Guideline, pharmacological obesity treatment should be intended only for patients with BMI > 30 or BMI ≥ 27 with comorbidity [In face of the adverse side effects of synthetic drugs, natural products are now preferably used due to their effectiveness in managing overweight and many other chronic disorders. For example, traditional herbal medicines with a long history of use along with other natural substances might suppress appetite and promote weight loss. It was in general believed that these natural materials could be relatively more economical with little to no toxic side effects when compared with the synthetic ones .Excessive adiposity can primarily be attributed to an imbalance in energy homeostasis, in which the consequences of excessive food intake are not balanced by increased energy expenditure . That isThere has been a rise in satiety-enhancing products on sale in the food supplement marketplace. The biological mechanisms of appetite and satiety are regulated by a complex interaction of neurological and hormonal signals. Many studies have revealed that some food ingredients could provide satiety enhancing effects and be beneficial for weight control . The mecA line of evidence indicates that neural signal peptides like serotonin, histamine, dopamine, and their associated receptor activities are associated with satiety regulation. These neural signal peptides and their receptors could be potential target areas for the development of supplement products that treat obesity through energy intake reduction by increasing satiety .One of the promising strategies for treating obesity is to interfere with fat absorption along the gastrointestinal tract directly . There has been long-standing interest in discovering and developing inhibitors for nutrient digestion and absorption. The underlying concept is that for any dietary fat being absorbed in human intestine, the fat should be broken down enzymatically by the action of pancreatic lipase. Pancreatic lipase activity is therefore widely considered as one of the most important indicators for the determination of the anti-obesity potential of natural products .Streptomyces toxytricini [As a key enzyme in dietary triglyceride absorption, pancreatic lipase hydrolyzes triglyceride to monoglyceride and fatty acids. Some substances have been confirmed to have capabilities to interact directly with intestinal lipases themselves. One well known example is tetrahydrolipstatin (orlistat), a derivative of the naturally-occurring lipase inhibitor isolated from ytricini . It is aytricini ,17.Sibiraea angustata extracts on adipocyte differentiation has also revealed that the expression of both C/EBPβ and PPARγ were significantly inhibited leading to a decrease in the lipid content of adipocyte cells [Adipocytes play a central role in the maintenance of lipid homeostasis and energy balance. They have a particular large capacity to store triglycerides as well as to release free fatty acids in response to changing energy demands. As adipocyte tissue growth is associated with both the hyperplasia and hypertrophy of adipocytes, this has led to the development of natural products in anti-obesity therapy that specifically target adipogenesis inhibition. Some research has also suggested that adipocyte differentiation could be inhibited by the blockade of several transcription factors such as C/EBPβ (CCAAT/enhancer binding protein beta) and PPARγ (peroxisome proliferator-activated receptor gamma) . A studyte cells .An increase in the rate of lipolysis stimulates triglyceride hydrolysis and hence diminishes fat storage and combats obesity. The key points to enhance lipolysis have been discussed in many studies. For instance, activation of β-adrenergic receptor initiatively triggered lipolysis in white adipocytes and non-shivering thermogenesis in brown fat . An actiThe growing threat of obesity to global health has encouraged scientists and researchers to put more effort into finding an efficient anti-obesity ingredient. Numerous potential materials from natural sources have been investigated along with their active ingredients. These natural materials are mostly derived from plants, including fruits, vegetables, grains, and herbs. The biological benefits of these natural materials are basically contributed by the presence of an abundant amount of phytochemicals, fibers, and unsaturated fatty acids . Some seCurcuma longa) and mulberry leaf , to treat obese patients. Recently, herbal therapies are not only popular in Asia, but also more and more common in the Western world. This is the reason why herbal materials could be another major category of anti-obesity products [The anti-obesity products in the market can be classified into three categories: (1) food ingredients; (2) herbal ingredients; and (3) other functional supplements. Developing functional products from what people usually consume in their daily life is probably the most popular segment in the functional supplement industry. Products made from fruits , grains (soybean), vegetables, or beverage drinks (tea leaves) are relatively safer and more acceptable to consumers. Nowadays, traditional Chinese medical practitioners use herbal remedies that usually are combinations of different herbs, such as turmeric  leaves are also popular in functional food market. The major bioactive ingredients constituent in green tea, accounting for up to 35% of the dry weight, is polyphenols. They may include flavonols, flavones, and flavan-3-ols (catechins). A number of clinical trials have revealed the beneficial effects of catechins (270 to 1200 mg/day), e.g., reduced body weight, lowered serum leptin levels, and reduced absorption of fatty acid. Another bioactive constituent in tea leaves is caffeine, which influences somatic nervous system activity and acts synergistically with catechins to increase energy expenditure and fat oxidation. Apart from green tea, other herbal tea materials such as maté tea (Ilex paraguariensis), rooibos , and honeybush (Cyclopia intermedia) have also been studied for their roles in obesity prevention and lipid metabolism [Anti-obesity products derived from green tea  inhibition of proliferation of precursor cells; (2) increase of apoptosis effect; (3) inhibition of pancreatic lipase activity; and (4) increase in energy expenditure . Some sePolyphenols are functional compounds that have anti-carcinogenic, anti-oxidant, anti-bacterial, and anti-viral activities . In the Naturally occurring phenolic acids comprise two classes: hydroxycinnamic acids and hydroxybenzoic acids. Hydroxycinnamic acid derivatives, i.e., coumaric acid, caffeic acid, and ferulic acid, are present mainly in the form of simple esters with glucose or quinic acid. The most commonly occurring acid derivative is chlorogenic acid. In the investigations of dietary phenolic acids on mouse pre-adipocytes, chlorogenic and coumaric acids effectively exerted inhibitory effects on cell growth and enhanced apoptosis. A recent study evaluating the effects of ferulic acid administration on lipid metabolism of mice has found that it could suppress the weight gain due to inhibition of fatty acid biosynthesis .Flavonoids are abundantly present in nature. They have been proven to have the positive effects on anti-obesity. Six subgroups of flavonoids are summarized in Phytosterols, which encompass plant-derived sterols and stanols, are compounds structurally similar to cholesterol. They occur in high concentrations in vegetable oils such as corn, soybean, and sunflower oil . Plant sAlkaloids are generally defined as basic , nitrogen-containing organic constituents commonly found in plants. Alkaloids such as capsaicin and caffeine have been reported to be able to significantly increase energy expenditure, reduce appetite, and inhibit both adipocyte differentiation and pancreatic lipase. Most of these alkaloids are α-adrenergic agonists although some of them have β-adrenergic agonist properties.The potential anti-obesity effects of PUFAs might be explained by their performance in the following aspects: a balance between energy intake and energy expenditure, lipid metabolism, status of adipocytes, and neuroendocrine system . It has Some anti-obesity products are rich in different types of dietary fiber, such as pectin, gum, cellulose, and soluble dietary fiber. In 1970, Heaton summarized the anti-obesity functions of dietary fiber. He has found that dietary fiber could act like a physiologic obstacle to lower energy intake by three mechanisms: (1) displacement of other nutrients in the diet by dietary fiber; (2) providing satiety and reducing appetite; and (3) inhibiting food absorption in small intestine .Furthermore, recent studies have revealed that viscosity and fermentability are two important physicochemical properties that are closely related to the beneficial physiological effects of dietary fiber . Many soMany protein supplements such as whey, casein and soy protein have been sold and marketed as an anti-obese product for a long while. Going on a high-protein daily diet could help people lose weight and prevents weight gain rebound . ProteinDietary calcium is an important factor in the maintenance of skeletal integrity, blood calcium level, and modulation of chronic diseases risks. Several authors have reported that a high intake of calcium may increase fecal fat excretion and energy expenditure . The mecEscherichia coli and Enterobacter cloaca B29) might trigger high fat diet-induced obesity [Lactobacillus gasseri SBT2055 and Bifidobacterium breve B-3) to decrease body weight and body fat in obese patients has been proven by several clinical studies [Some studies have provided evidence to support the hypothesis that gut microbes are involved in the development of type 2 diabetes mellitus and obesity . Lipopol obesity . The abi studies ,75. Mech studies . Using pObesity is a complex, chronic disorder caused by an interaction of contributing factors, including dietary, lifestyle, genetic, and environmental factors. Appropriate lifestyle and behavior interventions are the fundamentals of weight loss success, but maintaining such a healthy lifestyle is extremely challenging. The use of some natural anti-obesity products could be considered as a supportive tool to keep obese people holding on their weight-loss goals. It is also possible that the combination of multiple natural products could confer a synergistic activity that increases their anti-obesity action on multiple targets, offering advantages over chemical treatments in terms of serious side-effects. Natural materials may give not only anti-obesity effect but also other health benefits, such as anti-diabetic and anti-hyperlipidemic activities. It is anticipated that the availability of many natural sources will provide a beneficial basis for developing novel anti-obesity products.


Cyclospora cayetanensis through ingestion of fecally contaminated food or water. Symptoms of cyclosporiasis might include watery diarrhea (most common), loss of appetite, weight loss, cramping, bloating, increased gas, nausea, and fatigue. Typically, increased numbers of cases are reported in the United States during spring and summer; since the mid-1990s, outbreaks have been identified and investigated almost every year. Past outbreaks have been associated with various types of imported fresh produce   sold at a convenience store chain in the Midwest; 250 laboratory-confirmed cases were reported in persons with exposures in three states (illness onset mid-May–mid-June)  were identified among persons in two different states who became ill during June. Investigation of one cluster, for which the state health department conducted an ingredient-specific case-control study, found consumption of basil to be significantly associated with illness. A formal analytic study was not conducted for the other cluster, but all patients reported consuming basil. Three clusters associated with Mexican-style restaurants in the Midwest have resulted in reports of 53 confirmed cases in persons who became ill during May–August. Analytic studies were conducted for two clusters; consumption of cilantro was found to be significantly associated with illness in both. Although a formal analytic study was not possible for the third cluster, all 32 identified patients reported consuming cilantro at the restaurant. FDA traceback of the basil and cilantro from these clusters is ongoing. Additional clusters associated with Mexican-style restaurants were identified in multiple states; but investigations to determine a single vehicle of infection were unsuccessful because of small case counts, limited exposure information, or because fresh produce items (including cilantro) were served as components of other dishes .C. cayetanensis. As of October 1, 2018, a total of 2,299 laboratory-confirmed cyclosporiasis casesMany cases could not be directly linked to an outbreak, in part because of the lack of validated molecular typing tools for The 2,299 domestically acquired, laboratory-confirmed cases reported in persons who became ill during May–August 2018 are markedly higher than the numbers of cases reported for the same period in 2016 (174) and 2017 (623). This increase might be due, in part, to changes in diagnostic testing practices, including increased use of gastrointestinal molecular testing panels.C. cayetanensis. Persons with diarrheal illness that lasts >3 days or who have any other concerning symptoms should see a health care provider if they think they might have become ill from eating contaminated food.Consumers should continue to enjoy fresh produce as part of a well-balanced diet. To reduce risk from most causes of foodborne illness and other contaminants, CDC recommends washing fresh fruits and vegetables with clean running water; however, washing, including use of routine chemical disinfection or sanitizing methods, is unlikely to kill


Nowadays, hadrontherapy is increasingly used for the treatment of various tumors, in particular of those resistant to conventional radiotherapy. Proton and carbon ions are characterized by physical and biological features that allow a high radiation dose to tumors, minimizing irradiation to adjacent normal tissues. For this reason, radioresistant tumors and tumors located near highly radiosensitive critical organs, such as skull base tumors, represent the best target for this kind of therapy. However, also hadrontherapy can be associated with radiation adverse effects, generally referred as acute, early-delayed and late-delayed. Among late-delayed effects, the most severe form of injury is radiation necrosis. There are various underlying mechanisms involved in the development of radiation necrosis, as well as different clinical presentations requiring specific treatments. In most cases, radiation necrosis presents as a single focal lesion, but it can be multifocal and involve a single or multiple lobes simulating brain metastasis, or it can also involve both cerebral hemispheres. In every case, radiation necrosis results always related to the extension of radiation delivery field. Multiple MRI techniques, including diffusion, perfusion imaging, and spectroscopy, are important tools for the radiologist to formulate the correct diagnosis. The aim of this paper is to illustrate the possible different radiologic patterns of radiation necrosis that can be observed in different MRI techniques in patients treated with hadrontherapy for tumors involving the skull base. The images of exemplary cases of radiation necrosis are also presented. Hadrontherapy provides a more beneficial dose distribution to tumors than conventional radiotherapy.Among late-delayed adverse effects, radiation necrosis is the most severe one.Clinical presentation of radiation-related injury is often asymptomatic or slightly symptomatic.Late-delayed focal lesions are typically contrast-enhancing areas with necrotic core.Radiation-related brain lesions generally show high signal intensity on ADC maps.Since the discovery of X-rays by Röntgen in 1895, photon and electron beams have been widely used in the management of malignant tumors as a conventional radiotherapy (RT) and they currently play a crucial role in the treatment of brain and skull base tumors, either used alone or as adjuvant therapy, combined with surgery and chemotherapy , 4114, 4rPH represents the maximum change in signal intensity as contrast agent passes through capillary vascularization; peak values are first calculated by the difference in one region of interest before and after contrast administration, then obtaining a ratio with those of the healthy counterpart .rPH has been proven to be highly correlated to rCBV , 53 and Studies conducted on patients treated for glioblastoma multiforme to evaluate any differences in these hemodynamic parameters between groups with histologically proven tumor recurrences and others with radiation necrosis, showed how mean, minimum, and maximum values of rPH and rCBV were significantly higher in tumor recurrence; rPH values higher than 2.17 were observed only in recurrent tumors .Tissutal vascular permeability can be measured by PSR, which is an additional parameter that provides information about contrast agent leakage through capillary circle, while higher rPSR values are expected in radiation necrosis compared to recurrent tumors, in literature is reported a large degree of rPSR values overlapping between the two ; this asIn DCE MRI, rapidly acquired T1-weighted sequences are performed to detect changes in signal during the passage of contrast bolus through vessels, which can be influenced from overall perfusion, microvascularization permeability, and extracellular volume.Ktrans (volume transfer constant between blood plasma and extravascular extracellular space), ve (volume of the extravascular extracellular space per unit volume of tissue), and kep  [DCE-MRI is based on a two-compartmental (plasma space and extravascular-extracellular space) pharmacokinetic model. The simplest and widely used model is the Kety/Tofts one, which makes it possible to estimate rans/ve) , 56.Ktrans, the most measured DCE parameter, can have different interpretations depending on blood flow and permeability. When there is very high permeability, the flux of gadolinium-based contrast agent is limited only by flow, and thus Ktrans mainly reflects blood flow. In conditions of very low permeability, the gadolinium-based contrast agent cannot leak easily into the extravascular-extracellular space, and thus Ktrans mainly reflects permeability. Despite this complexity, Ktrans appears to reproducibily measure permeability in glioma patients [Ktrans values are expected [Ktrans values are expected in tumor recurrence. However, the radiation-induced endothelial damage could lead to an increased capillary permeability in radiation necrosis with feedback of Ktrans values higher than expected [patients  and DCE-expected , 58 whilexpected .In comparison to DSC, some advantages have been reported for DCE, such as higher spatial resolution and no susceptibility to artifacts. Nevertheless, the main hindrance with DCE is represented by the non-linear relationship between T1 signal intensity and contrast agent concentration; even if pharmacokinetic models (such as Tofts-Kermode model) have been developed to outflank this issue, DCE remains incline to errors in quantifying hemodynamic parameters.Ktrans). They also reported that a combination of T1 and T2 perfusion parameters showed no significant improvement in diagnostic accuracy compared with CBV.In particular, in order to differentiate tumor recurrence and radiation necrosis in treated high-grade gliomas, Zakhari et al.  reportedIn a retrospective review of 40 patients using DSC and DCE, Seeger et al.  reportedFor all these evidences, the utilization of DCE in common practice is limited.N-acetylaspartate (NAA), choline (Cho), creatine (Cr), lipid, and lactate [Magnetic resonance spectroscopy (MRS) measures the relative compositions of various metabolites in brain tissue, most commonly including  lactate .NAA represents neuronal density and it decreases in case of neuronal injury or death; creatine level is the result of cellularity and cellular metabolism; choline is representative of cellular turnover and proliferative activity since it is a metabolite found in cell membrane biosynthesis; lipids and lactate are the products of anaerobic metabolism and cell destruction, therefore they are not normally present in brain tissue .Radiation-induced lesions may show a variety of MRS findings, changing over time, which range from only a mild decrease in NAA to very low or undetectable levels of all metabolites .In particular, the NAA decrease which occurs early after treatment has been suggested to be related either to neuronal damage, such as neuronal cell death due to apoptosis, or to neuronal dysfunction secondary to the irradiation .Radiation necrosis has been reported to determine variable changes in choline and creatine levels –65. For As a result, some studies report a transitory inversion of Cho/NAA ratio which may reflect brain injury occurring early after radiation treatment , 69.Observations of a decrease in both the Cho and the Cho compounds as well as a decrease in the Cho/Creatine (Cr) ratio have also been reported in irradiated brain , 71.However, the typical spectrum in delayed cerebral necrosis shows a generalized decrease of Cho, Cr, and NAA .Lactate and lipid peaks start to manifest at approximately week 4 after radiation therapy and continue to increase during the delayed phase of radiation changes, likely as a consequence of the liberation of intracellular lipid bodies and of cell membrane damage due to massive cellular destruction  Figs. 11g and 4eA more recent study on tissue-based, untargeted metabolomics analysis to examine differential metabolic profiles of radiation necrosis in comparison to tumoral tissue, identified multiple candidate metabolites which could assist in the diagnosis. For example, alpha-tocopherol and citric acid were most significantly elevated in radiation necrosis compared with tumor, while proline and UDP-glucuronic acid were most elevated in tumoral tissue compared with radiation necrosis .In conclusion, hadrontherapy is increasingly used for the treatment of various tumors resistant to conventional radiotherapy or located near highly radiosensitive critical organs. In particular, skull base tumors such as clival chordomas, chondrosarcomas, sinonasal malignancies, and adenoid cystic carcinomas with perineural spread are currently treated with hadrontherapy.Radiation can be associated with adverse effects generally referred to as acute, early-delayed, and late-delayed. Among late-delayed effects, the most severe form of injury is radiation necrosis.Brain radiation-induced necrosis can present with heterogeneous radiological features and with different patterns. Multiple MRI techniques including diffusion, perfusion imaging, and spectroscopy play an important role in the evaluation and diagnosis of brain radiation necrosis. Radiologist should be aware of the typical imaging manifestations of brain radiation necrosis, which are described in this paper.


Metabolic reprogramming is a common cancer cell phenotype as it sustains growth and proliferation. Targeting metabolic activities offers a wide range of therapeutic possibilities which are applicable to acute myeloid leukemia (AML). Indeed, in addition to the IDH1/2-mutated AML model which established the proof-of-concept for specifically targeting metabolic adaptations in AML, several recent reports have expanded the scope of such strategies in these diseases. This review highlights recent findings on metabolic deregulation in AML and summarizes their implications in leukemogenesis. Acute myeloid leukemias (AMLs) are characterized by abnormal proliferation/survival of hematopoietic progenitors blocked in their differentiation. Recent advances in AML biology, especially in the field of their mutational landscape led to the development of targeted therapies . It was This review will therefore highlight the implication of metabolism in normal hematopoiesis and then will focus on the pathways recently reported to be deregulated and potentially targetable in AML.Metabolism supports a set of flexible processes that allow energy production in cells according to their needs which are highly dependent on their state of proliferation, differentiation or quiescence. Hematopoietic stem cells (HSCs) are totipotent cells which ensure the maintenance of the blood system. The balance between HSC self-renewal and lineage differentiation is mainly regulated by transcription factors and cytokines but cell metabolism is also a key player of these processes. In order to maintain their survival and their quiescent state in the hypoxic niche, HSCs adapt their metabolism . This loConsistently with the important role of the balance between different metabolic pathways in the regulation of HSC maintenance or differentiation, metabolic dysfunctions are also involved in leukemogenesis . Metabolin vivo  forces AML cells to up-regulate GLUT5 transporter expression, allowing them to use fructose as alternative substrate for glycolysis. A blockage of fructose uptake reduces leukemogenesis and potentiates the cytotoxicity of cytarabine . FinallyGlycolysis is thus a frequently upregulated metabolic pathway to which AML cells become dependent for their growth, creating therefore a metabolic vulnerability which can be therapeutically exploited.in vivo and is currently evaluated in relapsed/refractory AML (NCT02882321) (Although oxidative phosphorylation (OXPHOS) is the most efficient mechanism for energy generation, its relative slowness and propensity to induce a high level of ROS production during mitochondrial ATP production leads cancer cells to mainly rely on aerobic glycolysis. Notably however, cancer cell subsets with different dependencies in terms of energy-generating pathways can coexist within tumors. Accordingly, leukemic stem cells (LSCs), in contrast to normal hematopoietic stem cells (HSCs), are deficient in glycolysis use and depend upon BCL2-mediated oxidative respiration for maintenance, suggesting that a selective eradication of these cells may be possible by targeting OXPHOS with BCL2 inhibitors . Direct 2882321) . Further2882321) .Plasticity of cancer cells allowing metabolic adaptations to balance between glycolysis and oxidative metabolism is frequently observed. In AML, mTORC1 inhibition induces metabolic reprograming from a glycolytic to an oxidative process by promoting the TCA cycle through an increase of acetyl-CoA (instead of lactate) production from pyruvate. This leads to a switch of AML cells sensitivity from glycolysis to OXPHOS inhibition, which was therapeutically exploited by concomitant mTORC1 and OXPHOS inhibition . Metabolde novo synthesis of lipid membrane components and the elimination of potentially toxic lipids , a dropped mammalian cholesterol metabolite. DDA is a partial agonist on liver-X-receptor (LXR) which induces lethal autophagy eristics . Sphingo, Ye et al. identified a subpopulation of LSCs that expressed the fatty acid transporter CD36, which is enriched in the adipocyte tissue, allowing these cells to become chemo-resistant. Mechanistically, LSCs induce lipolysis in adipocytes which, in turn, creates a ME that supports LSCs maintenance by fueling their FAO . Notablysurvival .With glucose, glutamine is the main nutrient source for the growth/survival of cancer cells. Glutamine supports tumor growth through its transformation to α-KG, which feeds the TCA cycle, and by contributing to leucine import into the cells, which activates the amino-acid/Rag/Rac/mTORC1 signaling pathway . L-asparAML cells are also dependent on exogenous arginine due to their deficiency in the argininosuccinate synthetase-1 (ASS1) enzyme, which allows cells to synthesize arginine from citrulline. This deficiency confers a proliferative advantage to cancer cells but also a selective addiction of these cells to the extracellular availability of this amino acid which can be exploited by arginine-depleting agents such as pegylated arginine deiminase (ADI-PEG20) . ClinicaA crucial field of research is to find how to eradicate LSCs by targeting metabolic deregulations. As mentioned earlier, LSCs harbor a selective dependence on OXPHOS which makes them sensitive to BCL2 inhibition  whereas Metabolic pathways are deregulated in AML cells and play a critical role in leukemogenesis, contributing to chemoresistance and disease relapse. These mechanisms constitute therefore potent targets for AML treatment. However, metabolic abnormalities are multiple and heterogeneous among AML patients. Furthermore, the high plasticity of AML cells that enables them to adapt their metabolism and ensure their survival under selective inhibition of some pathways, and interactions of these cells with the BMME supporting their metabolic pathways, must be taken into account in the development of therapeutic strategies. Targeting specific metabolic addictions of leukemic cells must be privileged. In this regard, a very promising strategy is the synergistic effect observed with BCL2 inhibitors and hypomethylating agents , 81. GivAll authors listed have made a substantial, direct and intellectual contribution to the work, and approved it for publication.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.