The antiphospholipid antibody syndrome is a systemic, acquired, immune-mediated disorder characterized by episodes of venous, arterial, or microcirculation thrombosis and/or pregnancy abnormalities, associated with the persistent presence of autoantibodies, confirmed at least in two occasions 12 weeks apart, directed to molecular complexes consisting of phospholipids and proteins. Antiphospholipid antibody syndrome should always be considered as a potential diagnosis especially for young patients presenting with a history of thrombotic events, in particular when they occur without any obvious external trigger or any inherited thrombophilic mutation (even if 2006 criteria do not exclude antiphospholipid antibody syndrome in patients with other inherited or acquired prothrombotic conditions), or for women with recurrent pregnancy losses or later fetal deaths. Many other disorders are able to mimic antiphospholipid antibody syndrome, so a broad range of alternative diagnoses should be investigated and ruled out during clinical workup. Antiphospholipid antibody syndrome (APS) is a systemic, autoimmune, acquired disorder characterized by venous and/or arterial thrombosis and/or pregnancy morbidities, associated with the positivity, confirmed at least in two occasions 12 weeks apart, of such autoantibodies directed toward molecular complexes of phospholipids and proteins. A broad range of different diagnoses should be investigated and ruled out during diagnostic workup, because many other disorders are able to mimic APS. This entity should always be considered especially in young patients with history of thrombotic events without inherited thrombophilic mutation or external trigger or in women with recurrent pregnancy losses or later fetal deaths. According to 2006 Miyakis classification criteria, the presence of other inherited or acquired prothrombotic conditions does not exclude APS diagnosis. On the other hand, the identification of patients with the so-called APS “noncriteria” is important because these patients have often an autoimmune disorder that can evolve into a true APS during followup [Patients with usual clinical manifestations of APS associated with positivity of antiphospholipid antibodies (aPL): thrombotic events in typical districts such as deep vein thrombosis of the lower limbs, pulmonary embolism, myocardial infarction, and stroke or typical pregnancy disorders. This is the typical APS.Patients with unusual clinical presentation of typical manifestations of APS associated with positivity of aPL: for example, thrombotic events in atypical districts, particularly liver, renal, adrenal, and mesenteric vessels or cerebral venous sinuses with unclear presentation and difficult diagnosis.Female patients with incomplete clinical manifestations of obstetric APS associated with positivity of aPL: pregnancy disorders not completely fulfilling Miyakis criteria .Patients with noncriteria clinical manifestations of APS associated with positivity of aPL: for example, nonthrombotic pulmonary or cardiac involvement, ocular, neurological, osteoarticular, and hematological manifestations.In (a) situation, diagnosis is usually simple. However, special attention deserves the exclusion of certain conditions, such as microangiopathic syndromes or systemic lupus erythematosus (SLE).In clinical practice, according to these classification criteria, it is possible to identify the following situations.In (b) condition, the absence of nonspecific clinical manifestations  could make APS diagnosis more complex.In (c) and (d) cases the patient who presents noncriterial, but suggestive, clinical features deserves a careful followup to detect early “clinical criteria” and to establish the best treatment.Particular attention must be paid to those forms characterized by typical thrombotic events or pregnancy disorders in the absence of other causes, without aPL positivity ; probably, at the present time laboratory tests are inadequate to detect all APS patients since recently the existence of “noncriterial” potentially diagnostic antibodies has been proposed .For diagnostic algorithm, see Thrombotic events in APS can involve both arterial and venous vessels of any size and district, sometimes requiring a broad number of medical conditions to be ruled out see .Thrombotic microangiopathic syndromes include thrombotic thrombocytopenic purpura (TTP), hemolytic uremic syndrome (HUS), and hemolysis, elevated liver enzymes, and low platelets (HELLP) syndrome; these disorders are characterized by platelet consumption, intravascular hemolysis with schistocytes due to red cell fragmentation, and clinical/laboratory findings of organ dysfunction; histologically they are all marked by small vessel occlusion with hyaline thrombi and fibrin deposition. Interestingly, aPL have not been rarely detected in these conditions and on the other hand APS does not infrequently show some degree of microangiopathic involvement, especially in its catastrophic form; indeed, catastrophic antiphospholipid syndrome (CAPS) is considered the most devastating manifestation of APS, fatal up to 50% of cases and characterized by multiple organ dysfunction developing in a few days, due to intravascular microthrombosis. For all these conditions the term MAPS (microangiopathic antiphospholipid syndrome) has been proposed , 5.Moschowitz syndrome, the eponym of TTP, is mainly characterized by fever, microangiopathic hemolytic anemia, thrombocytopenia, and severe neurological involvement, while renal involvement is quite rare; diagnostic markers are considered the presence of high levels of circulating ultralarge von Willebrand factor (ULVWF) multimers and schistocytes. Of note, in acquired autoimmune form, the presence of antibodies against the metalloproteinase ADAMTS13 could be useful for differential diagnosis; on the other hand aPL have been occasionally reported in TTP patients .Interestingly in TTP 90% of deaths are from myocardial infarction (due to platelet thrombi in the coronary circulation). Myocardial infarction is also a frequent manifestation of arterial thrombosis in APS.In clinical practice APS rarely presents a severe thrombocytopenia such as in TTP.HUS is clinically characterized by microvascular thrombosis with consequent tissue ischemia and necrosis with renal failure, thrombocytopenia, and microangiopathic anemia. There are two distinct forms: (a) diarrhea-associated HUS, typically correlated with Shiga-like toxin-producing bacteria (STEC-HUS), and (b) atypical HUS (diarrhea nonassociated) which represents a frequent form of HUS in adults , 8.Clinical issues for differential diagnosis are mainly represented by the rapid onset of renal involvement and the presence of microangiopathic anemia with thrombocytopenia associated with episodes of diarrhea. aPL are usually not found in this condition.HELLP syndrome is more common in multiparous women between the 27th and the 37th week of gestation; clinically, it is characterized by gastrointestinal involvement , generalized edema, signs of hemolysis, elevated liver enzymes, severe thrombocytopenia, and signs of renal failure. Of note severe hypertension is not usually found in HELLP syndrome, helping to distinguish it from preeclampsia (even if they can coexist in about 70–80% of cases) .Differential diagnosis is complicated by the evidence that also APS patients can experience HELLP syndrome during pregnancy .Another clinical condition, potentially very severe, characterized by thrombocytopenia and multiple thrombotic occlusions of small vessels, is heparin induced thrombocytopenia (HIT), which should be suspected early during heparin treatment .type I HIT, with favorable prognosis, occurs in approximately 10% of patients undergoing both low molecular weight heparin (LMWH) and unfractionated heparin (UH) therapy. It occurs very early usually within the first four/five days of therapy (thought to be caused by direct platelet activation from heparin) and resolves without treatment and without any complication since it is not associated with thrombotic events;type II HIT, which involved 1–5% of patients undergoing heparin therapy (more frequently using unfractionated heparin compared to LMWH), is associated with microthrombosis involving multiple districts affecting both the arterial and the venous vessels . Diagnostic marker is considered a platelet count which falls by about 50% compared to baseline after 5–15 days from the beginning of heparin therapy. Of note in type II HIT the production of specific antiplatelet antibodies (i) may not be associated with thrombocytopenia or (ii) may be associated with thrombocytopenia but not with thrombotic complications or (iii) may be associated with both thrombocytopenia and thrombosis.The pathogenesis of HIT has been recently better defined: during the early phase heparin binds to platelet factor 4 (PF4), generating a complex (heparin-PF4) toward which IgG antibodies are produced and this complex is also able to activate platelets via FcγRIIa receptor, causing microthrombosis and thrombocytopenia.Two major forms have been described:The detection of antibodies to heparin-PF4 complex for HIT laboratory diagnosis can be performed using either a serotonin release assay (SRA), with low sensitivity and high specificity for HIT, or an ELISA test, more sensitive but less specific for HIT. Of note the diagnosis not only is based on these tests but also is currently based on probability according to a compatible clinical scenario .HIT treatment requires immediate discontinuation of heparin and the beginning of an alternative anticoagulation strategy with direct thrombin inhibitor, heparinoids or pentasaccharides.Both APS and HIT can present thrombocytopenia  and thrombosis, but anamnestic clues  and the absence of aPL could help in diagnostic workup.Disseminated intravascular coagulation (DIC) is characterized by microvascular thrombosis, possibly leading to consumptive coagulopathy and bleeding, which can in turn lead to multiple organ failure; it is secondary to surgery, chronic inflammatory diseases or malignancies, and sepsis. Laboratory markers of DIC are thrombocytopenia, prolonged clotting times, increased levels of fibrin degradation products, and reduced plasma fibrinogen.Differential diagnosis with APS could be difficult, because DIC is able to both mimic and complicate APS, especially in its catastrophic form (CAPS), which is characterized by disseminated intravascular thrombosis resulting in multiorgan failure; an aid in clinical practice could be the evidence that more frequently DIC presents thrombotic and hemorrhagic complications at the same time .However, one should keep in mind that the main clinical presentation in DIC is hemorrhage and sepsis is the most common cause.For clinical and laboratory findings in microangiopathic syndromes, DIC and HIT, see In Miyakis criteria the term “secondary APS” is considered inappropriate because SLE and APS may represent a different spectrum of the same disease, underlying the strong relation existing between these conditions .Indeed not only SLE patients could present aPL positivity associated with vascular involvement or obstetrical disease, but also APS patients could present some SLE features, such as autoimmune hemolytic anemia and mild reduction in complement, anti-nuclear antibodies (ANA); interestingly, these patients can be considered as APS patients who likely will evolve into SLE over time.Renal involvement in APS patients is not infrequent; markers to distinguish SLE renal involvement from APS ones are a significant titer of circulating ANA, the presence of other autoantibody specificities such as anti-native DNA, anti-Sm or anti-C1q, complement consumption, and specific histological findings from renal biopsy.Given that both APS and SLE could present similar neurological symptoms and MR findings, another clinical challenge is the differential diagnosis with Neuro-SLE . This diBehçet syndrome (BS) is a systemic vasculitis characterized by mucocutaneous, ocular, and neurological involvement. Moreover a significant proportion of Behçet patients results very prone to recurrent vascular thrombosis, which could represent the main clinical manifestation of the disease, so complicating the differential diagnosis with APS; due to its primary inflammatory vascular origin, the thrombotic events in BS need corticosteroid or immunosuppressive therapy rather than anticoagulation .Noteworthily the inappropriate use of anticoagulants in BS could be harmful if used in patients with clinically occult pulmonary artery aneurisms, since the risk of rupture is very high in this setting .Of note as APS also BS can be responsible for cerebral venous sinus thrombosis and parenchymal lesions , 19. NeuIn summary aPL can be found in Behçet patients with doubtful clinical significance . HoweverThrombotic manifestations of APS may have an unclear clinical presentation when they occur in atypical sites.Cerebral ischemic events are the main neurological manifestations of APS, while cerebral venous thrombosis is considered rare events but must always be considered in diagnostic workup because signs and symptoms may be unclear and diagnosis may be difficult without a specific approach .Kidney manifestations are less frequent and less recognized in APS than in SLE patients and mainly differ for their primary vascular involvement with only secondary glomerular damage , 24. IndThromboses of arterial or venous districts such as sovraepatic (Budd-Chiari syndrome), portal, mesenteric and more rarely of the splenic veins are the main events of gastrointestinal involvement in APS patients; differential diagnosis in these cases should be myeloproliferative disorders and in such cases the determination of JAK2 is crucial . Henoch-Adrenal insufficiency secondary to acute vascular infarction is the main, even though rare, manifestation of APS but diagnosis can be hard .Pregnancy disorders not completely fulfilling Miyakis criteria  may raise the suspicion of APS; however, many other clinical conditions must be excluded, such as anatomic dysfunction, endocrine disorders, coagulopathies, or other autoimmune diseases, for example, SLE, autoimmune thyroiditis, or celiac disease .Differential diagnosis results more complex for such noncriterial clinical clues whose presence does not allow, according to Miyakis consensus, a diagnosis of definite APS, even though this clinical presentation strongly suggests the suspicion of APS or the potential evolution over time towards it. These patients represent a significant proportion of subjects to be prospectively evaluated in order to detect early manifestations of definite disease.β2GPI of IgM isotype) could be present also in MS patients, making in some cases the differential diagnosis between the two conditions more difficult. Usually the diagnosis of demyelinating disease is supported by the presence of lesions involving the periventricular and corpus callosumareas and the detection of oligoclonal bands from cephalospinal fluid [Brain MR imaging could be similar for morphology and location in multiple sclerosis (MS) and APS with SNC involvement ; moreoveal fluid , 34.Devic's syndrome, nowadays known as neuromyelitis optica (NMO), is considered a distinct disorder from MS, since it recognizes a different inflammatory pathway and the presence of aquaporin-4 (anti-NMO) antibodies is considered the main pathogenetic player and a diagnostic biomarker. In particular testing patients for anti-NMO antibodies is strongly recommended in subjects who present severe optic neuritis  and/or with transverse myelitis longitudinally extended, defined as a spinal inflammatory lesion involving at least three consecutive vertebrae .NMO can coexist with SLE and APS in the same patient; diagnose NMO typical ocular/spinal pattern investigating the presence of anti-NMO is crucial, since this lead to the correct treatment with plasmapheresis or other immunosuppressive treatment .Livedo, acrocyanosis, and peripheral ulcers represent the most likely cutaneous manifestations of APS , 38.Livedo of the limbs, the most characteristic cutaneous manifestation in APS patients, is histologically marked by partial or complete lumen occlusion of small or medium caliber arteries of dermo-hypodermis without perivascular inflammatory infiltrates. Of note only livedo racemosa (irregular and interrupted borders) is associated with pathological conditions such as APS, while livedo reticularis (circular and continuous borders) is considered a benign condition and is more commonly encountered during clinical practice .A debate exists about differential diagnosis between APS and Sneddon's syndrome, since both are characterized by the presence of cerebrovascular accidents and cutaneous manifestations such as peripheral ulcers and livedo. Markers for differential diagnosis could be considered in Sneddon's syndrome patients as follows: the presence of high blood pressure, the extent of livedo , and the absence of circulating aPL. Skin biopsy can show in selected circumstances histological findings of endothelial cell proliferation and occlusion of the small cutaneous vessels, more related to Sneddon's syndrome .Heart valves dysfunctions, generally of the mitral valve, ranging from mild valve thickening to the typical nonbacterial thrombotic lesions (Libman-Sacks endocarditis) have been demonstrated by echocardiographic studies . CardiomThe main pulmonary nonthrombotic manifestations in APS patients are considered as follows: intra-alveolar hemorrhage, acute respiratory distress syndrome (ARDS), and fibrosing alveolitis , 44.Of note, aPL are often associated with chronic thromboembolic pulmonary hypertension .Amaurosis fugax is the most frequent manifestation, generally without pathological fundoscopic findings, and it may represent, rather than an ocular dysfunction, a warning bell of cerebrovascular disease . On the other hand severe ocular events which may occur in APS patients are artery or vein thrombosis, retinal vascular occlusive retinopathy, and ischemic optic neuropathy, although none of them is included in Miyakis criteria. Of note, other immunological conditions, such as giant cell arteritis (GCA), are able to induce ischemic optic neuropathy with rapidly progressive and severe visual impairment, but usually in APS inflammatory markers are normal. APS must be considered in differential diagnosis especially in young patients presenting with ocular vasoocclusive disease without any traditional thrombophilic risk factors , 47.Thrombocytopenia, previously included in classification criteria, is nowadays considered a noncriterial APS manifestation and is found in approximately 30–40% of APS patients, justifying aPL screening in every patient with idiopathic thrombocytopenia. Noteworthy is that APS-associated thrombocytopenia is generally less severe than SLE ones and rarely requires aggressive treatment . In the Articular symptoms are rare APS manifestations and, if present, could always raise the suspicion of an associated connective tissue disease. Moreover, especially in CAPS patients, aseptic bone necrosis, in particular of the femoral head, could be considered .The pathogenesis of aseptic osteonecrosis is not yet definitely understood; however, it is believed that microthrombosis or vasculopathy is involved .


The papers in the “Hydrothermal Vent” research topic cover a range of microbiological research in deep and shallow hydrothermal environments, from high temperature “black smokers,” to diffuse flow habitats and episodically discharging subsurface fluids, to the hydrothermal plumes. Together they provide a snapshot of current research interests in a field that has evolved rapidly since the discovery of hydrothermal vents in 1977.Sulfurimonas and Sulfurovum, were also found in cool, diffusive flow at the same location, Axial Seamount on the Juan de Fuca Ridge  similar to those seen in deep-sea vents; however proteobacterial lineages that are distinct from those of deep-sea vents were also detected. In contrast, in the deeper sediment layers of this sample vent field, Price et al. (2-rich, low-pH fluids, the sulfate-reducing microbial communities show maximal activities at a distinctly lower pH range than at less acidic control sites not impacted by CO2-rich vent fluids.While deep-sea hydrothermal vent sites are difficult to access and to sample, shallow water hydrothermal vents that can be reached by scuba divers provide an accessible alternative environment to study. Perhaps the best-investigated of these shallow-water vents are found on the coast of the Greek island Milos in the Aegean Sea, where hot, briny, reducing, COi et al.  show thae et al.  find Epse et al. , as they2, or assimilate them into microbial biomass; these communities feature prominently in metagenomic analyses of hydrocarbon-rich Guaymas chimneys (He et al., in-situ colonization chambers that were placed into surficial hydrothermal sediments on the seafloor (Callac et al., Among deep-sea vent sites, the sediment-covered Guaymas Basin hydrothermal vents in the central Gulf of California is unusual; the buried organic matter in these sediments are hydrothermally processed to petroleum compounds, low-molecular weight organic acids, short-chain alkanes, methane and ammonia. These substrates sustain a unique microbial ecosystem that combines the characteristics of communities from hydrocarbon seeps and mid-ocean ridge hydrothermal vents. Meyer and colleagues demonstrate that the microbial populations in Guaymas sediments show a high degree of microbial connectivity and population overlap within an area of a few 100 m—a consequence of vigorous venting, rapid dispersal via bottom currents, and closely spaced hydrothermal features (Meyer et al., 2 assimilation pathways that coexist in the endosymbiont, the Calvin-Benson-Bassham and the reverse TCA cycle (Thiel et al., Persephonella from different vent sites in the Okinawa Trough and in the distant Southern Mariana Trench in the western Pacific undergo sympatric speciation. Similarly, Wagner et al. (Thermoanaerobacter uzonensis, from different terrestrial hot spring locations within the Uzon Caldera in Kamtchatka. In this case, genetic divergence did not correlate with geographic separation on these short distances of mostly a few 100 m. Sylvan et al. (Mariprofundus ferrooxidans, fall into different 16S rRNA phylotypes of Zetaproteobacteria from the Southern Mariana Arc, the Hawaiian hot spot, and from the Vai'lulu/Tonga Arc/East Lau Spreading Center/Kermadec Arc. This study shows that the Zetaproteobacteria from these sites form mutually intertwined microclusters on the 16S rRNA gene level, suggesting more detailed genomic analyses to explore their biogeography in fine resolution (Singer et al., Hydrothermal vents are suitable model systems to explore microbial biogeography because they are island habitats in the deep sea; their thermophilic, chemosynthetic or special substrate-adapted microbial inhabitants likely cannot survive, and certainly cannot thrive in the cold, oxidized sediments and bottom waters of the deep sea that separate hydrothermal hot spots. In this volume several papers evaluate the controls of microbial community structure, geographic distance vs. environmental selection pressures in different habitats such as tubeworm trophosomes, sulfides, and ferric iron hydroxides. Sulfur-oxidizing endosymbionts of vestimentiferan tubeworms, which thrive in seep and vent habitats, showed a clear separation into different Gulf of Mexico and Mediterranean genotypes by 16S rRNA gene, mitochondrial cytochrome C oxidase, and functional genes of the two coexisting COr et al.  use multn et al.  describeThis research topic includes methodological assessments. Molecular surveys of biogeographic patterns and dominant microbial populations depend critically on the molecular tools used. To document inherent methodological biases, Hoshino and Inagaki  perform Marinobacter and find that these versatile bacteria—commonly regarded as aerobes or fermenters—include nitrate-reducing and metal-reducing representatives from low-temperature vents, marine sediments and mid-ocean ridge basalts. This genus is therefore well-suited to colonize aerobic- to-anoxic gradients in most marine environments, including hydrothermal vents. Likewise, the Thaumarchaeota—marine archaea that are ubiquitous in the cold and oxic marine water column—have been found in surficial marine sediments, hydrothermal plumes, and hot spring sediments. Ragon et al. (The last two contributions to this research topic discuss microbial groups that are not commonly considered as components of hydrothermal microbiota, marine heterotrophic bacteria and pelagic marine archaea. When cosmopolitan, heterotrophic marine bacteria appear in molecular diversity surveys of hydrothermal vents or other extreme habitats, they are regarded as “hitchhikers” or potentially contaminants from entrainment of seawater. Handley and Lloyd  examine n et al.  report aThese papers represent a sampler of ongoing microbiological research in hydrothermal environments, and demonstrate the wide multidisciplinary context of this field. Hydrothermal vents are not disconnected in time and space from the wider deep-sea ecosystem, without geological and biogeographical context. The research papers assembled here integrate geology, biogeochemistry, microbial physiology, microbial genomics and systematics across spatial scales that zoom in and out depending on the research question at hand. Perhaps no other field is so intertwined with the geological and geochemical evolution of the oceans, and promises so many biochemical and physiological discoveries still to be made within the unexhausted richness of extreme microbial life.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.


Genetic understanding of complex traits has developed immensely over the past decade but remains hampered by incomplete descriptions of contribution to phenotypic variance. Gene-environment (GxE) interactions are one of these contributors and in the guise of diet and physical activity are important modulators of cardiometabolic phenotypes and ensuing diseases.We mined the scientific literature to collect GxE interactions from 386 publications for blood lipids, glycemic traits, obesity anthropometrics, vascular measures, inflammation and metabolic syndrome, and introduce CardioGxE, a gene-environment interaction resource. We then analyzed the genes and SNPs supporting cardiometabolic GxEs in order to demonstrate utility of GxE SNPs and to discern characteristics of these important genetic variants. We were able to draw many observations from our extensive analysis of GxEs. 1) The CardioGxE SNPs showed little overlap with variants identified by main effect GWAS, indicating the importance of environmental interactions with genetic factors on cardiometabolic traits. 2) These GxE SNPs were enriched in adaptation to climatic and geographical features, with implications on energy homeostasis and response to physical activity. 3) Comparison to gene networks responding to plasma cholesterol-lowering or regression of atherosclerotic plaques showed that GxE genes have a greater role in those responses, particularly through high-energy diets and fat intake, than do GWAS-identified genes for the same traits. Other aspects of the CardioGxE dataset were explored.Overall, we demonstrate that SNPs supporting cardiometabolic GxE interactions often exhibit transcriptional effects or are under positive selection. Still, not all such SNPs can be assigned potential functional or regulatory roles often because data are lacking in specific cell types or from treatments that approximate the environmental factor of the GxE. With research on metabolic related complex disease risk embarking on genome-wide GxE interaction tests, CardioGxE will be a useful resource. Over the last decade, hundreds of genetic loci have been described as contributors to complex traits and human diseases. Yet, often a large proportion of the heritability of many traits remains ill defined. Contributors to phenotypic variance include: inability of small sample sizes to detect variants with small effects, disease markers not in complete linkage disequilibrium (LD) with the causal variant thus underestimating heritability , heritabThe cell and the organism as a whole are consistently challenged to maintain homeostasis in the face of a wide array of stimuli or perturbations, both health-promoting and disease-causing. To accomplish homeostasis, adjustments to molecular parameters must be enacted that correspond to the stimulatory challenge, which typically includes altered protein function or gene expression. This all amounts to continual changes to the phenotypes of the cell or organism and it is the timeliness and efficiency of these phenotypic adjustments that determine health and healthy aging. This process can be termed phenotypic flexibility, a phenomenon which is a central concept of the gene-environment interaction . A gene-The genetic basis of transcription rates, particularly as responses to stimuli, and transcription differences between individuals is now widely recognized as commonplace, with important consequences on disease outcomes. Expression quantitative trait loci (eQTL) are currently seen as one important source linking discovery of disease genes to functional mechanisms that are the basis of complex traits . SimilarOur 2011 report cataloged 554 GxE interactions, 377 of which contained common traits and environmental factors, that reached statistical significance and were pertinent to nutrition, cardiovascular diseases, blood lipids and type 2 diabetes mined from 184 scientific reports . We invehttp://www.quertle.info with search terms including genetic variation , “interaction,” or an environmental factor  and, after reading and manual parsing of the data, were incorporated into the update presented here. Specifically, data fields captured included SNPs tested for GxE interactions, the assigned gene for the SNP, common aliases of the SNP, risk allele, phenotype, modifying environmental factor, population ethnicity/origin and PubMed identifier. We excluded all reports on children and adolescents, and any GxE studies examining non-alcoholic fatty liver disease and other phenotypes that are peripherally affiliated with cardiometabolic dysfunction, including atrial fibrillation, cardiomyopathies and response to lipid-lowering, glucose-homeostasis and other medications.The description of literature mining and building this dataset has been described . Brieflyr2 ≥ 0.80, and return all variants contained in the LD block of the input SNP [z-test.To demonstrate the utility of GxE SNPs within the CardioGxE dataset and interactions they represent, and to offer insight into potential mechanisms of function, we performed a series of comparisons to other biomedical genomics data. These comparisons to test for enrichment included roles in main-effect associations to disease phenotypes, transcriptional control , adaptation, and in maintaining metabolic homeostasis in a set of pertinent tissues and cell types. To initiate these analyses, we created two separate SNP datasets based on LD: one for GxE SNPs and another from genome-wide association studies (GWAS) SNPs for the same cardiometabolic traits but not including any SNPs for which there is GxE evidence. Genomic coordinates (dbSNP138) for the region spanning 300 kb and centered on each SNP were determined. A bash shell script was written to retrieve iteratively all 1000 Genomes Project SNP data (accessed 04/10/2014) within this region from the CEU population using tabix and vcftools , pipe thnput SNP . These SZ-score test was conducted.Two measures of positive selection signals for GxE SNPs, integrated haplotype score (iHS)  and globcis or trans eQTL data, we collected significant hits from 5 published eQTL experiments [To determine if a GxE SNP or one in LD had evidence of eriments -24. A PeOn the basis of our earlier microRNA (miR) target SNP database , we furtp <0.05, plus those tests that are not significant. The CardioGxE catalog is composed of 1187 significant GxEs (in 189 genes) and 13770 with no significant interaction observed. By far, most reports examined populations of European ancestry. Of 1187 significant GxEs, 1013 (85.2%) involve the typically measured lifestyle choices or environmental factors of physical activity or inactivity, smoking, alcohol consumption and diet. Dietary measures include macronutrient intakes, either as daily amounts or as percent of total energy, of carbohydrates, both simple and complex; protein; and fat, sub-divided into total fat, saturated fatty acid (SFA), mono-unsaturated fatty acid (MUFA), and poly-unsaturated fatty acid (PUFA), with the latter further categorized as N-3 or N-6, omega-3 or omega-6, respectively. Of 1187 significant GxEs, 992 (83.6%) include the commonly measured phenotypes of blood lipids , glycemic traits , obesity anthropometrics , vascular measures (diastolic and systolic blood pressure), inflammation (C-reactive protein or CRP), and metabolic syndrome, or changes in these values in response to an intervention, typically dietary.All GxE interaction tests for cardiometabolic traits from 386 published scientific reports identified by literature mining are presented in Additional file We then trimmed the data to those significant GxEs that contain both common phenotypes and environmental factors producing a list of 654 different significant cardiometabolic GxEs. These GxEs are different in terms of any data parameter including population, or the direction or threshold of the environmental term constituting the GxE interaction. This dataset, although smaller than the 1187 total GxEs mined from the literature, allows for much more direct comparisons to other biomedical and genomics datasets. In our 2011 report, we described 554 different GxE interactions from 184 publications . In thatThe National Human Genome Research Institute (NHGRI) maintains a Clinical Genomic Database , a manuaGWAS have been powerful interrogators of the genome, identifying genetic sources of phenotypic variance and disease risk. However, the contribution to phenotype variance that could be explained solely by main effect associations for many cardiometabolic traits was quite small . We reasr2 threshold set to 0.80 yielding a set of 3381 GxE SNPs. We then compared these GxE SNPs to SNPs supporting main effect associations to cardiometabolic phenotypes in two important resources. Of 759 SNPs with associations to cardiometabolic phenotypes in the GWAS catalog [In order to compare GxE SNPs to SNPs supporting main effect associations, we first compiled a list of SNPs in high LD with the lead GxE SNP. This was done with data from the 1000 Genomes Project in the CEU population with an  catalog , only 36 catalog . FurtherEpistasis also has been offered as a contributor to the observed variance in disease phenotypes ,6. Some ABCA1 and LPL markers as each having GxE interactions for HDL-C, but always with environmental factors not shared with the other gene. Two, a knowledge-driven screen of GWAS data reported an interaction between LIPC and HMGCR for HDL-C [HMGCR are cataloged here. Additional literature mining revealed several gene-gene interactions acting on cardiometabolic traits. We identified just five examples for which the genes containing the epistasis relationship also participate in GxE interactions for the same phenotype and environmental factor. These include LEPxLEPR on obesity [ADRB2xADRB3 on BMI [APOExCETP on HDL-C [CETPxLIPC on HDL-C [PPARAxPPARG on small dense LDL [Of eleven significant gene-gene interaction models discovered in a cohort in which epistasis was examined as a source for phenotypic variance for HDL-C , only twor HDL-C , but no  obesity  and a ch3 on BMI  and a BMon HDL-C  and GxE on HDL-C  and GxE ense LDL  and a LDComparisons of risk allele frequencies across diverse populations have established appreciable directional differentiation for blood lipid and T2DM risk allele frequencies ,56. The p <0.001, two sample z-test).Three resources were used to investigate relationships between cardiometabolic GxEs and adaptation to climate and geography. First, two genome-wide studies have examined associations between genetic variants and climatic and geographical characteristics, including latitude, seasonality, precipitation, solar radiation and temperature ,59. SecoANGPTL4 and PPARA, both expressed in adipocytes, were identified as showing adaptation to high altitude in Tibetans [UCP1 and UCP2 genes are described as having undergone adaptation to temperature, specifically cold resistance [LIPE and physical activity. This gene resides within a region identified as having been subject to a selective sweep in Ethiopian highlanders with respect to hypoxia tolerance adaptation [It is a challenge to understand fully the relationships between factors driving adaptation to a given climate or geographical feature and the phenotype-environment pairings observed in published GxE interactions. Nonetheless, some examples deserve attention. GxE genes Tibetans ,69 and aTibetans ,71. The sistance , and paraptation . OverallTLR1 recently was described as having been under selective pressure in Roma gypsy and European populations in response to Yersinia pestis, the agent of plague [TLR4 variants support GxE interactions with obesity traits and smoking in an Argentinean population of European ancestry [Although the work presented here does not explore relationships between genes under selective pressure from pathogen exposure and genes that support cardiometabolic GxE interactions , such inf plague . TLR4 vaancestry . IdentifHomo sapiens species and are not detected as specific to populations of a single ancestry and thus may be observed as main effect associations. Three, the environmental factors driving selection at the GxE or GWAS loci could be quite different, but although these factors remain unknown, interpretation of this result is hindered. In addition, we observed no significant enrichment for Fst or iHS signals in LD blocks supporting HDL-C or physical activity GxEs compared to all cardiometabolic GxEs (data not shown). However, because a genetic marker that associates with HDL-C levels, or any other trait, may either support an as yet untested GxE interaction or a GxE for another, even unrelated phenotype, any enrichment of HDL-C GxE loci under selection compared to main effect loci cannot be fully known.In other work, we examined our catalog of GxE variants and the GWAS-based main effect SNPs for signals of recent positive selection in populations of European ancestry with data from the 1000 Genome Selection Browser . As noteANGPTL3, APOA4, APOA5, CPT1A, CPT1B, PPARA and PPARD. In non-European populations 252 different GxE tests with any of these seven genes have been performed and 33 (13.1%) were significant; in populations with European ancestry 437 such tests were performed giving 95 (21.7%) significant GxE interactions. This difference between ancestries is significant  with certain implications for cardiometabolic disease risk. Furthermore, this may lend support to adaptation by Europeans to geographical specificities of that continent, but does not dismiss the possibility of complex population structure in Africa at the time of divergence of the human and Neanderthal lineages [Seeking to add further support to the hypothesis that many environment-sensitive genes and their variants that function in human disease have been or are under selective adaptation, a theme we have explored with respect to heart disease risk , we examlineages .Regarding physiological and biological pathways, the phenotypes forming the GxE interactions cataloged here are generally well understood. Also, within many GxE genes there are interactions involving the same phenotype but with different environmental factors or involving the same environmental factor acting upon several phenotypes. Lastly, pathway analysis based on environmental factors, in our opinion, will be more robust once GxE GWIS results are collected and the involved variants are fully characterized. For these reasons, we opted not to perform a traditional test of pathway or gene ontology enrichment for sets of GxE genes, for example for all GxEs affecting triglycerides (TG) or all GxEs pertaining to SFA intake or even all TG-SFA GxEs, but to examine the GxE gene function in the context of metabolic syndrome (MetS). To accomplish this, we mined from a series of 12 electronic posters depicting MetS in six organs or tissues and six cell types  whether Second, a comparison to pathways relevant to metabolic syndrome and metabolic homeostasis  showed tAPOB) and rs1800588 (LD with rs1077834 mapping to LIPC). This is about a 4.9-fold  enrichment over triglyceride GxE SNPs supporting eQTL not in liver. Similarly, we found a significant enrichment of HDL-C GxE SNPs supporting liver eQTL (p <0.01), including rs34367192 (LD with rs10495562 mapping to ADAM17), rs6720173 (LD with rs3792009 mapping to ABCG5), and rs1800588 and rs2070895 (both in LD with rs1077834 mapping to LIPC). Lastly, for LDL-C traits, we observed a significant enrichment of LDL-C GxE SNPs supporting liver eQTL (p <0.01), including rs34367192 (LD with rs10495562 mapping to ADAM17), rs1800591 (LD with rs11937107 mapping to MTTP), and rs2070895 (LD with rs1077834 mapping to LIPC). All liver eQTL SNPs discussed here associate with mRNAs for the gene to which the SNP maps, except for rs7575840 associating with a transcript just upstream of APOB. No GxE SNPs for total cholesterol support eQTL in liver. Although the reported incidences of liver-based eQTL are small and dictate caution regarding interpretation, the consistency of the above enrichments is intriguing and suggested a comparison between GxE and GWAS signals for tissue-specific eQTL.We reasoned that SNPs forming GxE interactions for phenotypes that are highly relevant to a particular tissue will more frequently support allele-specific gene expression in that tissue, with a rationale similar to that showing SNPs associated with type 2 diabetes and related traits are enriched in islet cell-specific enhancers . Thus, ap-value of enrichment in the GWAS samples. Nonetheless, these results overall may be indicative of main effect SNPs exerting function in a tissue or cell type principal to that phenotype and the GxE SNP could be sensing differentials in environmental factors in other or peripheral tissues. Alternatively, the observation of no enrichment could indicate that there are equal effects on transcription across sources of trait variation, but these may operate in different tissues with respect to GxE and main effect. For example, brain and gut eQTL are not readily available for such analyses and GxEs may function in those organs with influences on hunger, satiety, lipid catabolism, cholesterol synthesis, or nutrient absorption. Lastly and perhaps most importantly, eQTL data are lacking for the response to a challenge that closely mimics the environmental factor in the GxE equation.In order to assess the impact of the eQTL in main effects compared to environmental interactions, we tested whether CardioGxE-based LD blocks for a given trait are more likely to share a liver eQTL than GWAS-based markers. We examined LD blocks from both GxE and GWAS sources for all cardiometabolic traits and each of four main blood lipids for overlap with liver eQTL. Specifically, a comparison of GxE LD blocks and those GWAS LD blocks not overlapping with the GxE set showed no significant enrichment in liver eQTL associations, with one exception Table . NotablyHuman microRNAs (miRs) have emerged as important epigenetic regulators of cardiometabolic traits ,80. GeneA miR SNP confidence score was created by counting for each SNP the number of supported algorithms, datasets or tables supporting a genetic effect of miR-mediated regulation in order to rank the likelihood that a SNP is a miR regulatory SNP. Confidence scores for the GxE miR SNPs and their proxies ranged from 0–13. We collected all potential  regulatory miRs for each SNP with a miRSNP confidence score >3 (13 lead and 46 proxy SNPs) and identified the most frequently participating miRs among GxE miR SNPs  either create or destroy a CpG dinucleotide, double the percent across all dbSNP135 data (22%). In addition, we find that 16 of these 79 variants map to within 3 kb of a CpG island, as downloaded from the UCSC genome browser. These results identify an accumulation of such CpG-altering SNPs (CGS), a type of SNP with particular relationships to DNA methylation ,85, in cp <0.001  and personal genetics , the impBMI: Body mass index; CAD: Coronary artery disease; CEU: Utah residents with ancestry from northern and western Europe, from the Centre d’Etude du Polymorphisme Humain collection; CGS: CpG-altering SNP; CVD: Cardiovascular disease; DBP: Diastolic blood pressure; eQTL: Expression quantitative trait locus; EWAS: Environment-wide association study; Fst: Fixation statistics; GWAS: Genome-wide association study; GWIS: Genome-wide interaction study; GxE: Gene by environment (interaction); HDL: High-density lipoprotein; HDL-C: High-density lipoprotein cholesterol; HOMA-IR: Homeostasis model assessment-estimated insulin resistance; iHS: Integrated haplotype score; LD: Linkage disequilibrium; LDL: Low-density lipoprotein; LDL-C: Low-density lipoprotein cholesterol; MetS: Metabolic syndrome; miR: microRNA; MUFA: Mono-unsaturated fatty acid; NHANES: National Health and Nutrition Examination Survey; PUFA: Poly-unsaturated fatty acid; SBP: Systolic blood pressure; SFA: Saturated fatty acid; SNP: Single nucleotide polymorphism; T2DM: Type 2 diabetes mellitus; TG: Triglyceride; VLDL: Very low-density lipoprotein.The authors declare that they have no competing interests.LDP conceived of the study, managed the project, performed all analyses not specifically mentioned here, and wrote the manuscript. LDP and BAB mined the literature and populated the updated database. KR acquired the LD SNPs, and mined eQTL data, and LDP analyzed and interpreted those results. BEC and HSD compared GxE SNPs to GWAS databases. RH mined for cardiometabolic GxE-epistasis overlap. PDN identified GxE variants and genes under selection from climatic and geographical features. CQL identified GxE variants showing adaptation by Fst and iHS. MetS pathway analysis was undertaken by BAB. Identification of the GxE SNP effects on miR-mRNA interactions was performed by YCL. Analysis of GxE SNPs affecting potential CpG islands was done by YM. LDP and JMO have given final approval of the published version of this report, and provided financial support. All authors aided in interpretation of results, and read and revised the manuscript.The CardioGxE catalog of gene-environment interactions for cardiometabolic phenotypes.Click here for file


Lobular breast cancer is not only the second most common breast cancer subtype, known for decades, but also a tumour entity that still poses many unresolved questions. These include questions about the targets and cooperation partners of E-cadherin, the best model systems for translational research, and the best tools for detection, surveillance and therapy. Leading experts review the molecular and cellular bases, the model systems, the histopathology and profiling approaches, risk factors, imaging tools and therapeutic options for lobular breast cancer. Numerous commentaries or reviews about lobular breast cancer begin with the phrase 'the most frequent special subtype of human breast cancer' or some variation of it. Often the statement follows that lobular breast cancer typically has  a better prognosis. However, gynaecological oncologists from time to time see patients with a reasonably small, nearly indolent looking breast tumour classified by the pathologist as 'lobular' which, at some point, develops into a highly aggressive, principally unmanageable metastatic disease. As well as this, some might say 'anecdotal', evidence contradicting the usual phrase about the 'typically better prognosis', comprehensive studies on really large cohorts also do not support this view . The lonCDH1 gene promoter. More than a few people in the field argue that loss of E-cadherin staining together with the characteristic growth pattern are defining characteristics of lobular breast cancer, a unique association between histology and genetics in breast cancer. However, this view is contested by the, admittedly small, group of E-cadherin-negative bona fide invasive-ductal breast carcinomas .CDH1 knock-out models , leavinThe peculiar growth pattern (due to loss of proper cell-cell contacts?) directly translates into challenges for the clinical detection of lobular breast cancer by physical examination or imaging because in many patients the tumour mass is so diffuse that it might evade timely and reliable detection (see Johnson and colleagues in this series ).in situ' and so on) and overt invasive malignancy and the underlying driver mutations .CDH1 germline mutations and the risk of lobular breast cancer development is much more complex .A further unresolved topic regarding invasive lobular breast cancer is the contradiction between the very high proportion of estrogen receptor (ER)-positive lobular breast cancer specimens (more than 90 % depending on the study) and the comparably low efficiency of anti-estrogen therapy in this patient cohort compared with invasive ductal breast cancer with a much lower proportion of ER-positive specimens . This iBreast Cancer Research might assume. Therefore, a timely update on the molecular and cellular bases of this somewhat elusive disease, proper model systems to study it, genetic and non-genetic risk factors causing it, methods to detect it, and protocols to treat it seems to be warranted.These observations and clinical experiences hint at the fact that 'lobular breast cancer' is far less understood than many readers of http://breast-cancerresearch.com/series/LBCThis article is part of a series on Lobular breast cancer, edited by Ulrich Lehmann. Other articles in this series can be found at


Whereas aberrant brain connectivity is likely the core pathology of autism-spectrum disorder (ASD), studies do not agree as to whether hypo- or hyper-connectivity is the main underlying problem. Recent functional imaging studies have shown that, in most young ASD patients, cerebral cortical regions appear hyperconnected, and cortical thickness/brain size is increased. Collectively, these findings indicate that developing ASD brains may exist in an altered neurotrophic milieu. Consistently, some ASD patients, as well as some animal models of ASD, show increased levels of brain-derived neurotrophic factor (BDNF). However, how BDNF is upregulated in ASD is unknown. To address this question, we propose the novel hypothesis that a putative zinc-metalloprotease-BDNF (ZMB) axis in the forebrain plays a pivotal role in the development of hyperconnectivity and megalencephaly in ASD.We have previously demonstrated that extracellular zinc at micromolar concentrations can rapidly increase BDNF levels and phosphorylate the receptor tyrosine kinase TrkB via the activation of metalloproteases. The role of metalloproteases in ASD is still uncertain, but in fragile X syndrome, a monogenic disease with an autistic phenotype, the levels of MMP are increased. Early exposure to lipopolysaccharides (LPS) and other MMP activators such as organic mercurials also have been implicated in ASD pathogenesis. The resultant increases in BDNF levels at synapses, especially those involved in the zinc-containing, associative glutamatergic system may produce abnormal brain circuit development. Various genetic mutations that lead to ASD are also known to affect BDNF signaling: some down-regulate, and others up-regulate it. We hypothesize that, although both up- and down-regulation of BDNF may induce autism symptoms, only BDNF up-regulation is associated with the hyperconnectivity and large brain size observed in most young idiopathic ASD patients.To test this hypothesis, we propose to examine the ZMB axis in animal models of ASD. Synaptic zinc can be examined by fluorescence zinc staining. MMP activation can be measured by in situ zymography and Western blot analysis. Finally, regional levels of BDNF can be measured. Validating this hypothesis may shed light on the central pathogenic mechanism of ASD and aid in the identification of useful biomarkers and the development of preventive/therapeutic strategies. Autism spectrum disorder (ASD) is a heterogeneous developmental disorder of the brain characterized by impaired communication, abnormal sociability, restricted interests, and stereotyped behaviors . In mostAlthough the majority of ASD cases remain idiopathic, recent years have witnessed dazzling progress towards an understanding of the underlying neurobiological mechanisms. In about 10% of cases, the etiology of ASD has a monogenic basis, such as fragile X syndrome (FMR1 gene), Rett syndrome (MECP2 gene) or tuberous sclerosis (TSC1 and 2 genes), each of which causes autistic symptoms in affected individuals -7]. How. How7]. ASD is considered primarily a disorder of brain circuitry. Hence, many investigators have sought to explain ASD symptoms by searching for abnormal synaptic functions. For instance, Geschwind and colleagues suggested that ASD brains have an imbalance in excitatory/inhibitory neurotransmission . In addiAs discussed above, earlier studies on brain connectivity in ASD suggested hypoconnectivity as the core functional pathology of ASD. Using fMRI, Just et al. first provided experimental evidence for hypoconnectivity in ASD ,21]. Th. Th21]. More recently, Supekar and colleagues examined young ASD patients using task-free fMRI and found hyperconnectivity throughout the brain . In addiConsistent with the hyperconnectivity theory, Markram and Markram proposed the “intense world hypothesis”, initially based on their findings obtained in the valproate model of autism in rats . They foTaken together, these studies strongly suggest that, at least during early brain development, overall hyperconnectivity rather than hypoconnectivity is the main circuit abnormality in most ASD brains.Kanner first noted that some autistic children have macrocephaly . Since tSome cross-sectional studies indicate that the increased brain growth in ASD may be age dependent. Courchesne et al. reported that increased gray and white matter volume may occur largely during early childhood, followed by normalization to control values at older age . This agAlthough it is not certain whether more neurons and/or glial cells  are generated during the brain growth spurt in ASD, various trophic factors, including epidermal growth factor (EGF) and insulin-like growth factor 1 (IGF1), have been proposed to be involved ,41]. Ho. Ho41]. BDNF is a potent neurotrophic factor that belongs to the neurotrophin (NT) family. Other members of the family include nerve growth factor (NGF), NT3, and NT4/5. The mature form of BDNF is generated from proBDNF by proteolysis ,44]. Wh. Wh44]. MECP2 gene result in a reduction in BDNF levels in the brain, indicating that a deficiency in BDNF may contribute to the pathology of Rett syndrome ,,,. Members4,. MembeSimilar mechanisms may be applicable to other models. As discussed above, thimerosal and valproate are capable of causing zinc dyshomeostasis. It would thus be interesting to determine whether zinc dyshomeostasis also occurs in other models of ASD, especially those that are linked to megalencephaly and hyperconnectivity.On the basis of published findings, described above, and our own preliminary results, we propose the novel hypothesis that an abnormality in the putative zinc-metalloprotease-BDNF (ZMB) axis plays a crucial role in the development of ASD. As discussed above, this hypothesis is easily testable in animal models and, if validated, could mechanistically account for megalencephaly and hyperconnectivity—puzzling aspects of ASD that are currently unresolved. To date, evidence for this hypothesis is admittedly sparse. Still, considering the immensity of the problems posed by ASD in current neuroscience and medicine, we believe the hypothesis is worth pursuing.The central feature of the hypothesis is that diverse causes of ASD—environmental or genetic—converge on upregulation of the ZMB axis during early brain development. Whereas upregulation of BDNF may result directly from epigenetic changes, as are possibly induced by the known histone deacetylase inhibitor valproate, in many cases, perhaps even in the valproate model, metalloprotease activation may be involved. Inflammation may release synaptic zinc and activate metalloproteases in microglial cells. Environmental toxins such as thimerosal may also release synaptic zinc and, at the same time, directly activate neuronal and/or microglial metalloproteases Figure . Activat+/− male and female mice to produce ZnT3+/+, ZnT3+/− and ZnT3−/− offspring. Accordingly, injection of valproate into a pregnant mouse should reveal whether the levels of ZnT3 or synaptic zinc affect manifestation of the ASD phenotype. MMP activity and BDNF levels could be measured concurrently by zymography and Western blotting/immunocytochemistry, respectively. If the hypothesis is correct, ZnT3-null offspring should exhibit diminished MMP activation and lower BDNF expression than ZnT3 WT or heterozygous mice.Tests of the ZMB hypothesis should begin with various animal models of ASD. Three parameters—synaptic zinc, MMP activity and BDNF expression levels—can be relatively easily measured. First, it should be determined whether synaptic zinc or ZnT3 affects outcome in these ASD models. For instance, ZnT3 dosage effects could be tested by crossing ZnT3Shanks are postsynaptic proteins whose expression may be controlled by zinc levels ,107],,. HoweverIf validated, this theory could be translated to human cases, facilitating the search for early biomarkers as well as therapeutic measures capable of halting progression of the ASD pathology.It has been demonstrated that levels of BDNF in the CNS and peripheral blood (platelets) are closely correlated ,67],,. HoweverIf early biochemical diagnosis is indeed feasible, then preventative measures may be developed. Provided that the ZMB axis hypothesis is validated, drugs that interfere with actions of synaptic zinc such as clioquinol, or metalloprotease inhibitors such as minocycline, may prove effective in reducing the incidence of ASD. These approaches could, and should, be tested in various animal models of ASD. Successful results may be readily translatable to humans, since some of these drugs are currently in clinical use.In addition to its practical significance, validating the ZMB axis hypothesis would likely provide insight into normal brain development and open up new avenues for the study of ASD mechanisms.It has long been known that some ASD children have large heads/brains, but the clinical and/or neurobiological significance of this finding has received relatively little scrutiny until recently. Pathological studies have shown that both gray and white matter increase in volume, suggesting that ASD brains may be under increased trophic influence. This finding is made more interesting by the recent demonstration that ASD brains are likely hyperconnected, which further supports the concept of increased trophic influence. An increasing body of evidence suggests that BDNF upregulation plays a key role in the increased trophic effects in ASD. In several animal models of ASD, BDNF expression is significantly increased. Moreover, in human ASD patients, blood levels of BDNF may be increased. Case control studies on hair samples from young ASD patients also described increased level of zinc ,115]. A. A115]. ASD: Autism spectrum disorderBDNF: Brain-derived neurotrophic factorZMB: Zinc-metalloprotease-BDNFfMRI: Functional magnetic resonance imagingThe authors declare that they have no competing interests.JYK conceived and organized the central idea and wrote the manuscript. JSL, HRB, and MHY performed experiments, gathered data, and wrote the manuscript. All authors read and approved the final manuscript.


Reactive oxygen species (ROS) are known to have many roles in the propagation of the inflammatory process. Indeed increased leucocyte ROS have been implicated in a number of autoinflammatory diseases .To use genetic mapping, next generation sequencing and functional studies to identify the genetic cause for a severe unclassified autoinflammatory disease mimicking Wegener's granulomatosis in a consanguineous family.Three affected children in a Pakistani family suffered from a severe and unusual autoinflammatory syndrome, presenting in the first year of life with recurrent fevers, erythema nodosum-like rash, severe oromucocutaneous ulceration, systemic inflammation, and massively elevated serum IgD, without mutation in MVK. One of the affected children also suffered from multifocal sterile osteomyelitis with bony lytic lesions and died at age 12 months from bronchopneumonia, and acute cervical myelopathy from cervical vertebral collapse. The two older children were resistant to treatment with corticosteroids, colchicine, several different DMARDs, anakinra and infliximab. Both were cured by allogeneic haematopoietic stem cell transplantation (HSCT) in their teenage years and remain well and off all treatment approximately 6 years later. We performed homozygosity mapping in the three affected siblings, two unaffected siblings and their unaffected parents; followed by targeted capture and re-sequencing of an identified region of homozygosity. To study protein function, we used small interfering and short hairpin RNA knockdowns in THP1 cells. THP1 cell lines were also generated over-expressing wild-type and mutant protein harbouring the same missense variation identified in the patients. ROS levels were measured by flow cytometry and production by electron spin resonance (ESR). Co-localisation studies were conducted in HEK-293T cells and peripheral blood mononuclear cells using confocal microscopy.Within the 5Mb region identified from the homozygosity mapping; a missense variant of interest in a mitochondrial chaperone-like protein was discovered. This segregated with disease in the family. This variant was rare or absent in ethnically matched and other healthy controls. Knockdown of this gene in macrophage-like THP1 cells led to increased mitochondrial ROS production; whilst wild-type protein overexpression led to reduced levels of mitochondrial ROS, which was not observed with mutant protein overexpression.We describe a novel monogenic autoinflammatory disease caused by a loss-of-function mutation in a mitochondrial chaperone protein, leading to dysregulated mitochondrial ROS production and severe autoinflammatory phenotype, and cured with allogeneic HSCT.


Skeletal muscle is not only translating chemical energy into mechanical work, it is also a highly adaptive and regenerative tissue whose architecture and functionality is determined by its mechanical and physical environment. Processing intra- and extracellular mechanical signaling cues contributes to the regulation of cell growth, survival, migration and differentiation. Yes-associated Protein (YAP), a transcriptional coactivator downstream of the Hippo pathway and its paralog, the transcriptional co-activator with PDZ-binding motif (TAZ), were recently found to play a key role in mechanotransduction in various tissues including skeletal muscle. Furthermore, YAP/TAZ modulate myogenesis and muscle regeneration and abnormal YAP activity has been reported in muscular dystrophy and rhabdomyosarcoma. Here, we summarize the current knowledge of mechanosensing and -signaling in striated muscle. We highlight the role of YAP signaling and discuss the different routes and hypotheses of its regulation in the context of mechanotransduction. Mechanotransduction refers to the conversion of mechanical inputs to intracellular biochemical and biophysical signals  or neighboring cells. These mechanical stimulations are then integrated into signaling pathways induced by soluble factors and consequently regulate transcriptional changes. In an alternative model, the cell itself is considered a compartmentalized mechanical body with given physical properties such as its viscosity, elasticity or stiffness. Here, the cellular mechanics are mainly defined through the actin, tubulin or septin cytoskeleton, intermediate filaments and the nuclear envelope and nuclear skeleton. These intracellular networks are connected to the ECM through adhesion complexes so that the cellular mechanics are in a permanent coordination with the extracellular constraints. According to this model, mechanical changes are not translated into one specialized mechanosensing pathway but into a simultaneous change in various cell processes, which are regulated by cytoskeletal dynamics, including the activation of signaling pathways.The IGF-1-Akt-mTOR  pathway has emerged to be the main positive regulator of muscle mass Sandri,  and MyosThe transcriptional co-activator YAP was first described in 1994 as a 65 kDa binding partner of the Yes protein-tyrosine kinase , YAP controls a wide range of cellular functions. During embryogenesis in mice YAP is expressed at all stages from blastocyst to perinatal stage. Homozygous disruption of the YAP allele in mice results in embryonic lethality and causes developmental arrest at E8.5. In contrast, TAZ shows a later onset and is not yet expressed at blastocyst stage , leading to phosphorylation and inactivation of YAP . Cells grown at low density show nuclear YAP and an inactive Hippo cascade, while at high cell density, the Hippo pathway is switched on and YAP is inactivated via LATS1/2 mediated phosphorylation , sphingosine-1-phosphate (S1P)) activate YAP/TAZ while Epinephrine and Glucagon inhibit YAP/TAZ via Gs-coupled GPCR signaling  and serum starvation inhibits YAP activity via reduced GPCR signaling. GThere is increasing evidence that YAP is a key regulator of mechanotransduction. Pioneering work of Piccolo and co-workers showed that mechanical forces can serve as inputs for the regulation of YAP. By analyzing YAP localization and transcriptional response, they showed YAP activity to be regulated by ECM stiffness, cell-spreading or substrate rigidity , consisting of Nesprin and SUN proteins, thereby connects actin stress fibers to the nucleoskeleton  binds to G-actin and is released when G-actin polymerizes to form F-actin  is released by the muscles and acts as an autocrine muscle hormone leading to muscle growth. The importance of the IGF-I-PI3K-Akt-mTOR pathway signaling has been largely confirmed and the multi-protein complex mTORC1 emerged to play a fundamental role in the regulation of skeletal muscle mass by regulating protein synthesis and cell size Sandri, . The actSince mTOR regulates organ size through cell growth by regulating protein synthesis and the Hippo pathway regulates organ size by regulating proliferation it seems apparent that these pathways are coordinately regulated , the YAP ortholog, most likely via activation of the MST1/2 ortholog hippo (hpo) or even upstream of hpo  and alveolar rhabdomyosarcoma (aRMS). Levels of YAP phosphorylation show high variability between different RMS cell lines. Total YAP protein levels, however, are elevated in RMS cells and histological RMS tumor sections show increased nuclear YAP stainings (Crose et al., Furthermore, muscles of mdx mice show elevated levels of phosphorylated and total YAP protein (Judson et al., YAP has emerged as an important player in mechanotransduction, transmitting mechanical cues into a transcriptional cell response. At the same time, YAP has been shown to be involved in skeletal muscle development and regeneration, as YAP contributes to the regulation of activation, proliferation and differentiation of satellite cells. Beyond that, YAP signaling is also important in adult skeletal muscle homeostasis as misregulation can lead to atrophy or hypertrophy and aberrant YAP activities have been observed in disease states, including skeletal muscle dystrophies. Adult muscle homeostasis again is mainly regulated by muscle activity, which is a mechanical cue itself. Akt-mTOR signaling is widely accepted as the main regulatory pathway defining muscle mass, but the autocrine activation of this pathway by IGF-1 is controversial and several crosstalks to YAP have been identified. Precise mechanisms by which YAP is regulated by mechanical cues are still unknown. Cytoskeletal and presumably also nucleoskeletal tension, in particular actin dynamics and Rho signaling, have been identified as important players of mechanotransduction on YAP, but the detailed mechanism still remains to be elucidated. Uncovering this mechanism, also in regard to the specially organized cytoskeleton of postmitotic myofibers, could reveal important insights into our understanding of muscle homeostasis and subsequently into the physiopathology of muscle diseases.MF conceived and wrote the article, PR contributed to the writing and designed the figures. PK and CC revised the article. All authors approved the work 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.


MicroRNAs (miRNAs) are a group of small noncoding RNAs (ncRNAs) that posttranscriptionally regulate gene expression by targeting their corresponding messenger RNAs (mRNAs). Dysregulated miRNAs have been considered as a new type of ‘‘oncomiRs” or ‘‘tumor suppressors,” playing essential roles in cancer initiation and progression. Using genome-wide detection methods, ubiquitously aberrant expression profiles of miRNAs have been identified in a broad array of human cancers, showing great potential as novel diagnostic and prognostic biomarkers of cancer with high specificity and sensitivity. The detectable miRNAs in tissue, blood, and other body fluids with high stability provide an abundant source for miRNA-based biomarkers in human cancers. Despite the fact that an increasing number of potential miRNA biomarkers have been reported, the transition of miRNAs-based biomarkers from bench to bedside still necessitates addressing several challenges. In this review, we will summarize our current understanding of miRNAs as potential biomarkers in human cancers. According to NIH , a biomarker is described with a characteristic that it is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention . Useful  C. elegans, known as the first member of miRNAs, discovered in 1993 [The discovery of miRNAs has captured increased attention of researchers recently. Following the Lin-4 in in 1993 . Strikin in 1993 , transla in 1993 . Among tIn this review, we will overview recent advances in the dysregulation of tumor-associated miRNAs in both biopsies and circulation and highlight some critical challenges for the transition of miRNAs as cancer biomarkers from a research setting into clinical application.http://www.mirbase.org/), there are 28645 entries representing hairpin precursor miRNAs from 223 species, expressing 35828 mature miRNA products. MiRNA genes are located either in independent noncoding DNA loci or in the introns of protein-coding genes [miRNAs belong to the heterogeneous class of ncRNAs, of 22–24 nt RNAs that play important regulatory roles by targeting mRNAs for cleavage or translational repression . By defing genes . Furtherng genes  and cotrng genes .It is well established that miRNA biogenesis is a complex process which generally includes three main steps as follows. (i) In the nucleus, miRNA genes are transcripted by RNA polymerase II to form primary miRNA transcripts (pri-miRNAs) . (ii) SuAfter being incorporated into the RISC, the mature miRNA induces posttranscriptional gene silencing by tethering RISC to be partially complementary to the target mRNA predominantly found within the 3′-untranslated region (UTR) . InspiriAberrant expression of miRNAs in cancer is characterized by abnormal expression levels of mature or precursor miRNA transcripts in comparison with those in the corresponding normal tissues. A steadily growing number of reports have proven that human cancers frequently show an aberrant expression profile of miRNAs as well as pre-miRNAs. With various kinds of high-throughput sequencing platforms applied to analyze the genome-wide expression of miRNA genes these years, aberrant expression profiles of miRNAs either downregulated or upregulated have been discovered in a broad variety of human malignant cancers, including lymphoma , breast Although the causes of aberrant miRNAs expression in cancer have not yet been fully elucidated, several defined mechanisms can be possible, including chromosomal abnormalities, genomic mutations, epigenetic changes, and alterations in miRNA biogenesis. Notably, some miRNA genes are frequently located at fragile sites and genomic regions related to cancer . In otheGiven those circumstances above, alterations of miRNAs expression in different types of neoplasia constitute specific patterns of miRNA signature for certain types of cancer. Logically, these specific miRNA signatures would be attractively conducive to early diagnosis, signifying the prognosis and predicting the response of cancer therapy.(i) Diagnosis and Classification. It was observed that, with cancers derived from different epithelial and hematopoietic lineage having distinct miRNA profiles, miRNA signatures were able to discriminate them according to their developmental origins. For example, in a research trying to identify cancers with unknown primary tissue of origin by using microarray platform to evaluate the expressions of 47 miRNAs in 101 FFPE  samples from primary or metastatic cancers, overall, the accuracy reached 100% for primary cancers and 78% for metastatic cancers. When the signature was applied to an independent published dataset of 170 samples, correct prediction was further verified in 86% of the metastasis cases [is cases .For patients with malignant cancers, precise determination of tumor subtype significantly influences the decision-making of treatments. For example, In renal cell carcinoma (RCC), a research team developed a classification system applying method of decision trees that can distinguish different RCC subtypes in 94 different subtype cases using unique miRNA signatures analysis . This syMoreover, the need of biomarkers for cancer early diagnosis is extremely important because of the fact that survival and prognosis of patients extensively depend on the stage of tumor at the time of detection, with an early diagnosis generally associated with a better prognosis. Promisingly, miRNA signatures have been identified to possess a robust potential as early diagnosis biomarkers. For example, overexpression of miR-205 and miR-21 in ductal adenocarcinoma has been reported to precede phenotypic changes in the ducts , suggest(ii) Prognostic Values. In addition to cancer diagnosis including distinguishing tissue of origin, subtypes, and early detection of cancer, miRNA signatures can be also valuable for cancer prognosis prediction, which has been vilified by a number of studies recently. The first evidence was proposed by Calin et al. in chronic lymphocytic leukemia (CLL), where a unique miRNA signature composed of 13 genes can differentiate CLL patients with abnormal expression of prognostic factors (ZAP-70 and IgV(H)) from normal cases. Besides, the same miRNA signature was associated with the presence or absence of disease progression [gression . Moreovegression . Likewisgression . In addigression . It is wgression . In prosgression . Besidesgression . Remarkagression , and, ingression .(iii) Predictive Values for Response to Therapy. Apart from their use as prognostic biomarkers, miRNA signatures could also predict the responses to various cancer managements. The correlation between miRNA signatures and the responses of specific therapies is of great clinical value because of the involvement of miRNAs in chemoresistance identified in many studies [ studies , 50. For studies . Subsequ studies . Likewis studies . In colo studies . Additio studies . In glio studies . Remarka studies . In beli studies .In summary, based on the aberrant miRNA expression profiles identified in human cancers, miRNAs give us a totally new horizon in understanding the development management of cancer. Despite of some certain miRNAs commonly exhibiting altered expression across various kinds of tumors, particular types of cancers often express their exclusive patterns of miRNAs referring to their tissues of origin . Such spIn addition to the high specificity and sensitivity of miRNA biomarkers in cancer diagnosis as previously described, miRNAs are characterized by robust stability as well in stored RNA samples, including fixed tissue, blood, and other body fluids, which further supports their potential as biomarkers. Recent studies have systematically investigated the stability of miRNAs even after being subjected to severe conditions that would normally degrade mRNA or other types of larger RNAs. For example, in two similar studies, miRNA expression profiles in FFPE from colorectal cancer (CRC) samples dating back up to 10 year were assessed and compared with fresh frozen CRC samples; a high similarity of miRNAs profiles was observed. Moreover, differing formalin fixation times did not significantly influence miRNAs profiles in FFPE specimens in light of quantitative real-time polymerase chain reaction (qRT-PCR) , 59. ForGenerally, there are mainly three explanations for miRNAs' stability. Firstly, as a class of small molecules with a short length of only 20–24 nt, miRNAs tend to be less subjected to degradation during FFPE sample processing. Secondly, these small RNAs are taken into encapsulation by cell-derived lipid vesicles such as exosomes , micropaTissue biopsy specimen in the form of FFPET (FFPE tissue) is commonly used for tissue storage, which preserves good tissue integrity so as to provide excellent resources for discovery of disease-detecting biomarkers, not excepting the miRNAs-based biomarkers of cancer certainly. Better than mRNAs which are too unstable to be suitable for qRT-PCR, miRNAs are stable enough to be well preserved even over prolonged FFPE block storage and quantified from FFPET by qRT-PCR. In a word, miRNAs from substantial FFPET can provide tremendous source for cancer-related biomarkers.Numerous studies have discovered and evaluated a broad variety of potential miRNAs biomarker candidates in FFPET which provide valuable information for cancer diagnosis and prognosis. A recent study used bioinformatics to screen miRNAs classifiers in 69 FFPE pancreatic specimens including benign, premalignant, and malignant. Different miRNA panels mapped to these lesions above, separate anyone from the two others with sensitivity and specificity up to 85%–100% . FurtherIn addition, other miRNAs identified as potential biomarkers in FFPET for various types of malignancies are summarized in Apart from the diagnostic miRNA signatures identified in specimens from tumor tissues, studies have also shown the diagnostic and prognostic usefulness of miRNAs in circulation. In fact, except for miRNAs in the biopsies and tumor samples, a substantial number of cancer-related miRNAs can be also detected in blood including total blood, serum, and plasma, as well as other body fluids such as saliva, urine, breast milk, seminal fluid, and tears .In fact, the intriguing phenomenon of cancer-associated nucleic acids in circulation has been identified for decades. Generally, from their intracellular origin, miRNAs can be secreted extracellularly in cell-derived extracellular vesicles such as exosomes or bound to other lipoproteins as mentioned above, although the concrete mechanisms for the origin of such miRNAs released by tumor cells have not yet been clarified and little is known about the mechanisms of how to specifically direct miRNAs into multivesicular bodies or exosomes.κB activation and secretion of prometastatic inflammatory cytokines that may ultimately lead to tumor growth and metastasis [However, what we know at present is that miRNAs in blood released by tumor cells may not simply act as a set of bystander product of tumor cells. It has been widely identified that tumor-released (TR) exosomes could act as intercellular mediators transporting diverse types of proteins, mRNA, and miRNAs that can promote angiogenesis, cell proliferation, and cell survival, resulting in establishing an oncogenic niche systemically . Recentltastasis . These oAdditionally, Pigati and colleagues verified the fact that the cancer-related miRNAs are specific to the cancer cells, which is a further consideration supporting detection of the circulating miRNAs to serve as molecular tumor markers. They found that the bulk of miR-451 and miR-1246 produced by malignant cells was selectively released into blood particularly, but the majority of these miRNAs produced by normal cells were retained intracellularly . Their fTherefore, with a stable form and extensively hormone-like effects, the noninvasively detectable cancer-specific miRNAs in circulation have been widely investigated and demonstrated to efficiently discriminate cancer patients from healthy people, predict the prognosis, and monitor the therapeutic response. Comprehensively, recent studies for discovery of potential miRNAs biomarkers for types of cancers in blood and other body fluids have been listed in β signaling pathway for their associations with survival among 141 highly expressed serum miRNAs collected from 391 patients with advanced NSCLC. They concluded that 17 miRNAs were significantly associated with 2-year patient survival using Cox regression model. Of these 17 miRNAs, miR-16 exhibited the most statistical significance, whose high expression was associated with an obviously better survival [In serum, following the first paradigm showed that the diagnostic and prognostic potential of miR-21 that was associated with increased relapse-free survival of diffuse large B-cell lymphoma (DLBCL) patients by Lawrie et al.  and lotssurvival . Findingsurvival  and gliosurvival .In plasma, Mitchell et al. firstly proved that miRNAs are readily measurable by direct cloning and sequencing from a plasma small RNA library. To further determine whether tumor-derived miRNAs enter the circulation at levels sufficient to be measurable as biomarkers, they established a mouse prostate cancer xenograft model system, collected the plasma, and isolated miRNAs for analyzing the different expression of miRNAs compared to the control. They found that levels of miR-629 and miR-660 were able to independently differentiate xenografted mice from controls with 100% sensitivity and 100% specificity . Such coExosomes are a class of small (50–90 nm) membrane vesicles formed in the plasma membrane by the fusion of endocytic vesicles and extracellularly released into surrounding body fluids . As is m*, miR-25, miR-142-3p, miR-140-5p, and miR-204) was capable of correctly classifying bladder urothelial cell carcinoma (UCC) patients with an overall sensitivity of 84.8% and specificity of 86.5% [Although the majority of studies identified circulating miRNAs in serum and plasma, miRNAs have also been detected in other body fluids such as urine, tears, breast milk, and seminal, amniotic, bronchial, lavage as well as pleural, peritoneal, and cerebrospinal fluids , 86. Recof 86.5% . In combof 86.5% . What isof 86.5% . Presencof 86.5% .However, as a matter of fact, miRNAs, no matter in serum, plasma, exosomes, or other body fluids, may not be absolutely specific to a certain cancer type. MiR-21 in serum is exactly a representative example for this. From a serial of investigations, it is found that high expression of serum miR-21 in lung cancer associated with poor prognosis  and the Though miRNAs show striking potential as new biomarkers of human cancers in clinic settings and maintain high stability in both FFPET and body fluids, the methods for miRNAs' detection are still challenging yet for the intrinsic characterisitic of miRNAs such as small size, low level, a high degree of sequence similarity among various members, and tissue-specific or stage-specific expressions. Currently, there are various strategies for the detection of miRNAs, including qRT-PCR, in situ hybridization (ISH), enzymatic luminescence miRNA assay and northern blotting, microarrays, deep sequencing or next-generation sequencing (NGS), and nanopore technology et al. . Herein,Microarray is another technique for miRNAs profiling based on nucleic acid hybridization between target molecules and their corresponding complementary probes. The miRNAs oligonucleotide probes are immobilized to glass slides through covalent crosslinking between the amino groups and the SAM (self-assembling monolayer), forming a ready-to-use miRNA microarray. When hybridized with the miRNA microarray, the isolated miRNAs labeled with fluorescent dye can emit fluorescence after being specifically bound to the corresponding probes. Through detecting the fluorescence signal intensity at different positions on the slides, relative quantities of the corresponding miRNAs can be evaluated consequently . FurtherDeep sequencing relying on next-generation sequencing machines appears to be another promising quantitative technology for miRNAs profiling, because it provides high-throughput sequencing enabling processing up to millions of sequence reads in parallel simultaneous with high speed . In thisNanopore single-molecule technology, a novel method recently reported by several studies to electrically detect miRNAs in tissue or biofluids, requires no labeling, enzyme reactions, or amplification , 111. WaYears of research work have indicated that miRNAs play important regulatory roles in translational repression, eventually contributing to the cancer development. Indeed, gene profiling studies have identified a number of significant dysregulated miRNAs as “oncomiRs” or “tumor suppressors” in a variety of human cancers, and overwhelming amounts of data have strongly validated that the ubiquitously aberrant expressions of miRNAs were closely associated with the pathogenesis and progression of human malignancies. These dysregulated miRNAs constitute unique patterns of miRNome in different categories of cancers, which provide accurate fingerprints to detect and classify various cancers. Particularly, as circulating miRNAs in blood and other body fluids are readily detected by various techniques in a relatively noninvasive manner, the clinical application of miRNAs as a new generation of cancer biomarker is considered to be prospecting.Despite the encouraging results, we are still confronted with many difficulties on the long way of transiting miRNAs as biomarker from bench to bedside. First, exactly as the proposing of the misconceptions that the 98% in human genome is noncoding and thus junk DNA, miRNAs are probably only the tip of the iceberg of noncoding genes in our complex genome. More miRNA transcripts remain to be excavated extensively. Second, more fundamental investigations are needed to further elucidate the exact miRNAs' functional roles in cancer biology. Apart from the pathway by targeting mRNAs for cleavage or translational repression, if there are any other unrevealed mechanisms led to the translational repression, or even any other undiscovered regulation functions more than posttranscriptional regulation. Third, it is needed to further clarify the potential biological functions of circulating miRNAs, particularly the mechanisms of MVBs-contained miRNAs for cell-cell communication, tumor immune evasion, and tumor microenvironment. After all, the underlying mechanism of miRNAs secretion or the mechanisms of the selectivity of miRNAs packaging are still elusive. Fourth, more consistent and reliable miRNA signatures or miRNome in both FFPET and circulation are urgent to be established by adequately large sample size of cohort studies on multiple, independent populations. Fifth, methods for the detection and analysis of miRNAs should be further optimized. To ensure the miRNAs' detection results are as consistent as possible, a set of technical methods both miRNA extraction procedures and technology platforms should be compared with each other or optimized for different types of cancer patients. In addition, it is worth noting that further studies are needed to develop a set of stable inner reference genes to accurately quantify miRNAs even for each type of human cancers.Despite such challenges that are a lot, the potential of miRNAs as a new class of cancer biomarkers is attractive and cannot be underestimated. MiRNAs are being expected to bring an exciting new dimension to the field of clinical management for human cancers in the near future.