Identification of a minimum number of genes to predict triple-negative breast cancer subgroups from gene expression profiles

Background: Triple-negative breast cancer (TNBC) is a very heterogeneous disease. Several gene expression and mutation profiling approaches were used to classify it, and all converged to the identification of distinct molecular subtypes, with some overlapping across different approaches. However, a standardised tool to routinely classify TNBC in the clinics and guide personalised treatment is lacking. We aimed at defining a specific gene signature for each of the six TNBC subtypes proposed by Lehman et al. in 2011 (basal-like 1 (BL1); basal-like 2 (BL2); mesenchymal (M); immunomodulatory (IM); mesenchymal stem-like (MSL); and luminal androgen receptor (LAR)), to be able to accurately predict them. Methods: Lehman’s TNBCtype subtyping tool was applied to RNA-sequencing data from 482 TNBC (GSE164458), and a minimal subtype-specific gene signature was defined by combining two class comparison techniques with seven attribute selection methods. Several machine learning algorithms for subtype prediction were used, and the best classifier was applied on microarray data from 72 Italian TNBC and on the TNBC subset of the BRCA-TCGA data set. Results: We identified two signatures with the 120 and 81 top up- and downregulated genes that define the six TNBC subtypes, with prediction accuracy ranging from 88.6 to 89.4%, and even improving after removal of the least important genes. Network analysis was used to identify highly interconnected genes within each subgroup. Two druggable matrix metalloproteinases were found in the BL1 and BL2 subsets, and several druggable targets were complementary to androgen receptor or aromatase in the LAR subset. Several secondary drug–target interactions were found among the upregulated genes in the M, IM and MSL subsets. Conclusions: Our study took full advantage of available TNBC data sets to stratify samples and genes into distinct subtypes, according to gene expression profiles. The development of a data mining approach to acquire a large amount of information from several data sets has allowed us to identify a well-determined minimal number of genes that may help in the recognition of TNBC subtypes. These genes, most of which have been previously found to be associated with breast cancer, have the potential to become novel diagnostic markers and/or therapeutic targets for specific TNBC subsets

Cyclooxygenase-2 overexpression abrogates the antiproliferative effects of TGF-β

The influence of cyclooxygenase-2 (COX-2) overexpression on the development of tumours has been well documented. The underlying mechanism however has still not been completely elucidated. An escape of proliferating cells from the regulatory influence of TGF-β for example in the intestine has been discussed as well as a preponderance or prolongation of growth factor stimulation. The experiments presented here demonstrated that COX-2 transfection of a TGF-β-sensitive cell line abrogates the growth inhibitory effects of TGF-β. However, analysis of the TGF-β/Smad-signalling pathway clearly revealed that COX-2 overexpression did not interfere with that. Neither TGF-receptor expression nor Smad phosphorylation and signal transfer into the nucleus were influenced by COX-2 overexpression. In addition, a TGF-β reporter assay revealed no difference between controls and COX-2-transfected cells. Thus, the proliferation inhibiting effects must have been well compensated by growth-inducing stimuli. Indications for this came from experiments showing an induction of TGF-α expression and secretion with a higher and prolonged stimulation of the ERK 1/2 (p42/44) pathway in COX-2 transfectants. This effect could have been triggered by direct prostaglandin receptor stimulation or changes in intracellular lipid mediators. An increase in PPAR signalling as proven by a reporter assay is indication for the latter. Therefore, inhibiting both COX-2 as well as the PPAR and TGF/EGF pathway could be effective in the inhibition of adenoma or even carcinoma development in the intestine

DNA damage by lipid peroxidation products: implications in cancer, inflammation and autoimmunity

Oxidative stress and lipid peroxidation (LPO) induced by inflammation, excess metal storage and excess caloric intake cause generalized DNA damage, producing genotoxic and mutagenic effects. The consequent deregulation of cell homeostasis is implicated in the pathogenesis of a number of malignancies and degenerative diseases. Reactive aldehydes produced by LPO, such as malondialdehyde, acrolein, crotonaldehyde and 4-hydroxy-2-nonenal, react with DNA bases, generating promutagenic exocyclic DNA adducts, which likely contribute to the mutagenic and carcinogenic effects associated with oxidative stress-induced LPO. However, reactive aldehydes, when added to tumor cells, can exert an anticancerous effect. They act, analogously to other chemotherapeutic drugs, by forming DNA adducts and, in this way, they drive the tumor cells toward apoptosis. The aldehyde-DNA adducts, which can be observed during inflammation, play an important role by inducing epigenetic changes which, in turn, can modulate the inflammatory process. The pathogenic role of the adducts formed by the products of LPO with biological macromolecules in the breaking of immunological tolerance to self antigens and in the development of autoimmunity has been supported by a wealth of evidence. The instrumental role of the adducts of reactive LPO products with self protein antigens in the sensitization of autoreactive cells to the respective unmodified proteins and in the intermolecular spreading of the autoimmune responses to aldehyde-modified and native DNA is well documented. In contrast, further investigation is required in order to establish whether the formation of adducts of LPO products with DNA might incite substantial immune responsivity and might be instrumental for the spreading of the immunological responses from aldehyde-modified DNA to native DNA and similarly modified, unmodified and/or structurally analogous self protein antigens, thus leading to autoimmunity

Textural study of metamorphic rocks by means of a conventional X-ray source

The aim of this study is the textural characterization of very low togreenschist facies metamorphic rocks by means of a conventional X-ray source, possibly establishing a relationship between the extent of morphological orientation of mineral grains and metamorphic degree.For a long time geologists investigated the morphological orientation of mineral grains in polycrystalline rocks by means of petrographic microscope equipped with a Universal stage. More recently diffraction of conventional X-ray sources as well as diffraction (or transmission) of hard X-rays, electrons and neutrons has been applied to these kind of study.However, whereas X-ray conventional sources can be regarded as a routine technology, hard X-ray, electron and neutron sources are only available in a few facilities around the world.Phyllosilicates such as smectite, illite, muscovite, chlorite and biotite play a key role in the textural characteristics of the mineral assemblages of rocks characterized by increasing metamorphic degree. The present study is focused on the variation of the X-ray intensities of selected reflections of these phases. In short, if a morphologic orientation of the grains of a certain phyllosilicate is present, a variation of the intensity of these reflections will be measured when the rock sample is rotated in a goniometer keeping constant both the incident beam angle and the position of the detector.The samples selected for the study are the following: 1) a Ms, Chl, Qtz, Pl fine grained metapelite from Frassenetto (UD, Italy) (very low grade metamorphism, Anchizone) with some detrital muscovite flakes recognizable by their coarser grain size; 2) Ms, Chl, Qtz, Pl fine grained metapelite from Chiadenis (UD, Italy) (low grade metamorphism, Epizone) with some detrital muscovite flakes recognizable by their coarser grain size; 3) a Ms, Chl, Ilm, Qtz, Pl layered phyllite from Villabassa (BZ, Italy) (Greenschist facies metamorphism, Ms-Chl-Bt), with crenulated main foliation and axial planes defining a second spaced foliation; 4) a Ms, Bt, Grt, Ilm, Qtz, Pl layered phyllite from Luson (BZ, Italy) (Greenschist facies metamorphism, Ms-Bt-Grt), with crenulated main foliation and axial planes defining a second spaced foliation

Crystal chemistry of trioctahedral micas in the top sequences of the Colli Albani volcano, Roman Region, central Italy

Trioctahedral mica crystals are frequently found in the volcanoclastic products emplaced during the final stages of the activity of the Colli Albani volcano (Roman Region, central Italy). In the youngest phreatomagmatic deposits, mica is found either as a minor mineral phase in holocrystalline ejecta, scoriae, and coherent pyroclastics, or as loose phenocryst in incoherent pyroclastics. Based on optical and electron microscope investigations, as well as crystal chemical and structural data, the micas selected for this study were divided into two groups, the first one encompassing brownish, Fe-rich crystals (type-A phlogopites, hereafter referred as t-A) with 0.68 < Mg/(Mg + Fetotal) < 0.85 and 0.062 < Tiapfu < 0.199, and the other one encompassing colorless, Mg-rich crystals (type-B phlogopites, hereafter referred as t-B) with Mg/(Mg + Fetotal) in excess of 0.85 and 0.007 < Tiapfu < 0.052. t-A phlogopites also show a tetrahedral ring cavity, overlapped tetrahedral hexagon area, and basal tetrahedron area greater than in the t-B phlogopites. From a petrological point of view, the textural and chemical variations of t-A phlogopites are compatible with fractional crystallization processes taking place within the magma chamber. t-B phlogopites show evidence of a Ti-oxy substitution mechanism, thus suggesting high fO2 conditions. Textural and paragenetic features observed in t-B phlogopite-bearing rock samples, indicate a genesis by thermal metamorphism of a siliceous dolomitic limestone with the input of a variable amount of a potassic magma, possibly the same from which the t-A phlogopites formed, with the exception of one sample, for which a different parental magma is suggested. Indeed, there is an almost continuous spectrum of crystal-chemical and structural parameters starting from t-B and evolving towards t-A phlogopites. The t-A phlogopites displays complex, apparently meaningless relationships in their crystal-chemical parameters, thus indicating interplay of several substitution mechanisms. They possibly formed in polybaric conditions, since their cell volumes differ, but the total size of the cations hosted in the octahedral sheet is the same

Crystal chemistry of trioctahedral micas in the top sequences of the Colli Albani volcano, Roman Region, central Italy

Trioctahedral mica crystals are frequently found in the volcanoclastic products emplaced during the final stages of the activity of the Colli Albani volcano (Roman Region, central Italy). In the youngest phreatomagmatic deposits, mica is found either as a minor mineral phase in holocrystalline ejecta, scoriae, and coherent pyroclastics, or as loose mica phenocrysts in incoherent pyroclastics. Based on optical and electron microscope investigations, as well as crystal chemical and structural data, the micas selected for this study were divided into two groups, the first one encompassing brownish, Fe-rich crystals (type-A phlogopites, hereafter referred as t-A) with 0.68 &lt; Mg/(Mg+Fetotal) &lt; 0.85 and 0.062 &lt; Tiapfu &lt; 0.199, and the other one encompassing colorless, Mg-rich crystals (type-B phlogopites, hereafter referred as t-B) with Mg/(Mg+Fetotal) in excess of 0.85 and 0.007 &lt; Tiapfu &lt; 0.052. t-A phlogopites also show a tetrahedral ring cavity, overlapped tetrahedral hexagon area, and basal tetrahedron area greater than in the t-B phlogopites.From a petrological point of view, the textural and chemical variations of t-A phlogopites are compatible with fractional crystallization processes taking place within the magma chamber. t-B phlogopites show evidence of a Ti-oxy substitution mechanism, thus suggesting high fO2 conditions. Textural and paragenetic features observed in t-B phlogopite-bearing rock samples, indicate a genesis by thermal metamorphism of a siliceous dolomitic limestone with the input of a variable amount of a potassic magma, possibly the same from which the t-A phlogopites formed, with the exception of one sample, for which a different parental magma is suggested. Indeed, there is an almost continuous spectrum of crystal-chemical and structural parameters starting from t-B and evolving towards t-A phlogopites. The t-A phlogopites displays complex, apparently meaningless relationships in their crystal-chemical parameters, thus indicating interplay of several substitution mechanisms. They possibly formed in polybaric conditions, since their cell volumes differ, but the total size of the cations hosted in the octahedral sheet is the same

Carbonated peridotite xenoliths from the mantle wedge: The Patagonia case

Carbonated mantle xenoliths are mainly documented in intraplate environments. Here we provide evidence that carbonated mantle also occurs in the wedge of the back-arc region related with the Andean subduction. Along the whole length of the Argentinean Andes, this region is characterised by alkali basalt volcanic centres containing abundant mantle xenoliths. The xenoliths of the easternmost volcanoes bear evidence of mantle interaction with a CO2-rich component. In the volcanic centre of Gobernador Gregores (Santa Cruz Province, Southern Patagonia) this interaction produces abundant carbonates. Here a large diatreme constituted by pyroclastic deposits contains mantle xenoliths up to 60 cm. The peridotites are dominantly lherzolites and subordinate harzburgites, wherlites and dunites, whose texture varies from secondary-protogranular (recrystallized) to weakly foliated. The relationships between the forming phases indicate the following events: an original mineral assemblage of olivine (ol1), clinopyroxene (cpx1), orthopyroxene and spinel (spl1) is overprinted by a subsequent mineral assemblage, constituted by new clinopyroxene (cpx2), pargasite and sometimes phlogopite; in turn, this mineral assemblage reacts with a further metasomatic agent which causes instability of cpx2 and of the hydrous phases. As an effect of the latter episode, cpx2 and hydrous phases are surrounded by pockets of carbonate plus silicate glass. Carbonate also occurs in veins at the crystal boundaries, as blebs in the silicate glass. Euhedral olivine (ol2), clinopyroxene (cpx3), spinel (spl2) and rarely rutile crystallise from the silicate glass. Apatite occurs both in the silicate glass and in the carbonates. Forsterite concentration in olivine varies from 87/91 in ol1 to 89/93 in ol2, which also contains high CaO (0.15/0.80 wt%). Cpx3 is characterised by higher Al2O3, CaO, TiO2 and lower Na2O with respect to cpx2. Spl2 contains higher Al2O3 and TiO2 with respect to spl1. Carbonate is calcite with MgCO3 concentrations up to 4%. Glass composition varies from trachiandesitic to tefriphonolitic. Trace element characteristics of clinopyroxenes vary markedly from cpx1 to cpx3 (Figs. 1a, b, c). Cpx1 is LREE depleted, whereas cpx2 is the richest in REE and has a fractionated REE pattern (La(N)/Yb(N) = 9.6/14.8) with a maximum at Ce. Cpx3 has a lower REE concentration with respect to cpx2; its REE pattern (La(N)/Yb(N) = 1.8/2.9) shows a maximum at MREE. HFSE anomaly are negative and variable in cpx2 and cpx3 (La(N)/Nb(N), Ti/Ti(*) and Zr/Zr(*) range 6.77/52.13, 0.02/0.24, 0.08/0.34 respectively in cpx2 and 0.76/0.88, 0.10/0.16, 0.14/0.22 respectively in cpx3). Amphibole has REE patterns (Fig. 1d) similar to cpx2 ((parg/cpx2)D(REE) ~1), but with marked positive Nb spikes ((parg/cpx2)D(Nb) = 42.3/148.4) and positive Ti and Sr anomalies ((parg/cpx2)D(Ti) = 5.4/8.2; (parg/cpx2)D(Sr) = 1.7/1.9). Zr is preferentially partitioned into amphibole ((parg/cpx2)D(Zr) = 1/1.5). Glass is LREE enriched and has smoothly fractionated patterns from La to Yb (La(N)/Yb(N) = 10.0/29.6). It has remarkable positive Nb anomalies (La(N)/Nb(N) = 0.1/0.6) - much higher respect to the associated amphibole ((parg/glass)D(Nb) = 0.4/0.7) - and generally negative Zr and Ti spikes (Fig. 1e). Apatite has a very high LREE concentration (La(N) ~ 4300) and La(N)/Yb(N) ~3500 (Fig. 1f). The last metasomatic episode is mass balanced by the following reaction: 1.00anf + 0.26opx + 0.02carb = 0.41cpx3 + 0.05spl2 + 0.36ol2 + 0.46glass. The relationships above described indicate that litospheric spinel facies mantle was affected by metasomatic episodes consistent with the former addition of a hydrous component followed by a CO2-rich component. The P-T range of these metasomatic events is 8.3 - 22.4 kbar and 890 - 1230°C (Fig. 2). Amphibole and cpx2 instability increases with increasing T and P, so that the more marked carbonatation occurs in the higher T-P range. Although the metasomatic agents, including the CO2-rich one, are possibly related with dehydration and decarbonation of the slab, their provenience needs to be isotopically constrained, since Gorring et al. (1997) propose that at this latitude the slab had windows through which the mantle underlying the slab interacted with the wedge

II Italian intersociety consensus statement on antithrombotic prophylaxis in orthopaedics and traumatology

Pharmacological prophylaxis for preventing venous thromboembolism (VTE) is a worldwide established procedure in hip and knee replacement surgery, as well as in the treatment of femoral neck fractures, but few data exist in other fields of orthopaedics and traumatology. Thus, no guidelines or recommendations are available in the literature except for a limited number of weak statements about knee arthroscopy and lower limb fractures. In any case, none of them are a multidisciplinary effort as the one here presented. The Italian Society for Studies on Haemostasis and Thrombosis (SISET), the Italian Society of Orthopaedics and Traumatology (SIOT), the Association of Orthopaedic Traumatology of Italian Hospitals (OTODI), together with the Italian Society of Anesthesia, Analgesia, Resuscitation and Intensive Care (SIAARTI) and the Italian Society of General Medicine (SIMG) have set down easy and quick suggestions for VTE prophylaxis in a number of surgical conditions for which only scarce evidence is available. This inter-society consensus statement aims at simplifying the approach to VTE prophylaxis in the single patient with the goal to improve its clinical application