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101.
Valeria Musella Maurizio Callari Eleonora Di Buduo Manuela Scuro Matteo Dugo Patrizia Miodini Giampaolo Bianchini Biagio Paolini Luca Gianni Maria Grazia Daidone Vera Cappelletti 《PloS one》2015,10(4)
To obtain gene expression profiles from samples collected in clinical trials, we conducted a pilot study to assess feasibility and estimate sample attrition rates when profiling formalin-fixed, paraffin-embedded specimens. Ten matched fresh-frozen and fixed breast cancer samples were profiled using the Illumina HT-12 and Ref-8 chips, respectively. The profiles obtained with Ref 8, were neither technically nor biologically reliable since they failed to yield the expected separation between estrogen receptor positive and negative samples. With the use of Affymetrix HG-U133 2.0 Plus chips on fixed samples and a quantitative polymerase chain reaction -based sample pre-assessment step, results were satisfactory in terms of biological reliability, despite the low number of present calls (M = 21%±5). Compared with the Illumina DASL WG platform, Affymetrix data showed a wider interquartile range (1.32 vs 0.57, P<2.2 E-16,) and larger fold changes. The Affymetrix chips were used to run a pilot study on 60 fixed breast cancers. By including in the workflow the sample pre-assessment steps, 96% of the samples predicted to give good results (44/46), were in fact rated as satisfactory from the point of view of technical and biological meaningfulness. Our gene expression profiles showed strong agreement with immunohistochemistry data, were able to reproduce breast cancer molecular subtypes, and allowed the validation of an estrogen receptor status classifier derived in frozen samples. The approach is therefore suitable to profile formalin-fixed paraffin-embedded samples collected in clinical trials, provided that quality controls are run both before (sample pre-assessment) and after hybridization on the array. 相似文献
102.
In advanced HIV infection, the homeostatic balance between gastrointestinal indigenous bacteria and gut immunity fails and microbes are able to overcome the intestinal barrier and gain the systemic circulation. Because microbial translocation is not fully controlled by antiviral therapy and is associated with inefficient CD4+ reconstitution, we investigated the profile of translocating bacteria in peripheral blood of 44 HIV-infected patients starting therapy with advanced CD4+ T-lymphopenia and displaying poor CD4+ recovery on virologically suppressive HAART. According to CD4+ reconstitution at 12-months HAART, patients were considered Partial Immunological Responders, PIRs (CD4+≥250/µl, n = 29) and Immunological non Responders, INRs (CD4+<200/µl, n = 15)). We show that PIRs and INRs present similarly elevated plasma levels of lipopolysaccharide (LPS) and its ligand sCD14 that were not lowered by virologically suppressive therapy. Bacterial 16S rRNA gene amplification and sequencing resulted in a highly polymicrobic peripheral blood microbiota both prior and after 12-month HAART. Several differences in bacterial composition were shown between patients'' groups, mainly the lack of probiotic Lactobacillaceae both prior and after therapy in INRs. Failure to control microbial translocation on HAART is associated with a polymicrobic flora circulating in peripheral blood that is not substantially modified by therapy. 相似文献
103.
Cananzi S Merlini L Artali R Beretta GL Zaffaroni N Dallavalle S 《Bioorganic & medicinal chemistry》2011,19(16):4971-4984
A novel 5-oxa-6a,8-diazaindeno[2,1-b]phenanthren-7-one scaffold was designed and synthesized as an active analogue of the cytotoxic marine alkaloid Lamellarin D. The design was based on molecular modeling of the site of interaction of Lamellarin D with DNA-topoisomerase I cleavable complex, whereas the synthesis capitalized on a simple Friedel-Crafts cyclization of indole to a β-carbolinone nucleus. The product exhibited topoisomerase I poisoning activity and submicromolar cytotoxicity on human non-small cell lung cancer H460 cell line. 相似文献
104.
Giorgetti S Rossi A Mangione P Raimondi S Marini S Stoppini M Corazza A Viglino P Esposito G Cetta G Merlini G Bellotti V 《Protein science : a publication of the Protein Society》2005,14(3):696-702
It has been claimed that beta2-microglobulin (beta2-m) interacts with type I and type II collagen, and this property has been linked to the tissue specificity of the beta2-m amyloid deposits that target the osteo-articular system. The binding parameters of the interaction between collagen and beta2-m were determined by band shift electrophoresis and surface plasma resonance by using bovine collagen of type I and type II and various isoforms of beta2-m. Wild-type beta2-m binds collagen type I with a Kd of 4.1 x 10(-4) M and type II with 2.3 x 10(-3) M. By the BIAcore system we monitored the binding properties of the conformers of the slow phase of folding of beta2-m. The folding intermediates during the slow phase of folding do not display any significant difference with respect to the binding properties of the fully folded molecule. The affinity of beta2-m truncated at the third N-terminal residue does not differ from that reported for the wild-type protein. Increased affinity for collagen type I is found in the case of N-terminal truncated species lacking of six residues. The Kd of this species is 3.4 x 10 (-5) M at pH 7.4 and its affinity increases to 4.9 x 10(-6) M at pH 6.4. Fluctuations of the affinity caused by beta2-m truncation and pH change can cause modifications of protein concentration in the solvent that surrounds the collagen, and could contribute to generate locally a critical protein concentration able to prime the protein aggregation. 相似文献
105.
Analysis of hepatitis C virus hypervariable region 1 sequence from cryoglobulinemic patients and associated controls 下载免费PDF全文
Bianchettin G Bonaccini C Oliva R Tramontano A Cividini A Casato M Merlini G Silini E Mondelli MU 《Journal of virology》2007,81(9):4564-4571
Chronic hepatitis C virus (HCV) infection is frequently associated with extrahepatic manifestations, including nonmalignant and malignant B-cell lymphoproliferative disorders. It has been reported that specific changes or recurring motifs in the amino acid sequence of the HCV hypervariable region 1 (HVR1) may be associated with cryoglobulinemia. We searched for specific insertions/deletions and/or amino acid motifs within HVR1 in samples from 80 symptomatic and asymptomatic patients with and 33 patients without detectable cryoglobulins, all with chronic HCV infection. At variance with the results of a previous study which reported a high frequency of insertions at position 385 of HVR1 from cryoglobulinemic patients, we found a 6.2% prevalence of insertions in samples from patients with and a 9.1% prevalence in those without cryoglobulinemia. Moreover, statistical and bioinformatics approaches including Fisher's exact test, k-means clustering, Tree determinant-residue identification, correlation of mutations, principal component analysis, and phylogenetic analysis failed to show statistically significant differences between sequences from cryoglobulin-negative and -positive patients. Our findings suggest that cryoglobulinemia may arise by virtue of as-yet-unidentified host- rather than virus-specific factors. Specific changes in HCV envelope sequence distribution are unlikely to be directly involved in the establishment of pathological B-cell monoclonal proliferation. 相似文献
106.
Valentina Pieri Claudia Caserini Stefano Gomarasca Koen Martens Giampaolo Rossetti 《Hydrobiologia》2007,585(1):79-87
Sedimentary records provide important information for understanding changes in the history of eutrophication in Lake Taihu.
In addition, the catchment nutrient model SWAT provides a powerful tool to examine eutrophic changes in a long-term context.
Since it is difficult to evaluate impacts of natural eutrophic development and anthropogenic changes in catchment discharge
and land use, simulation of past changes provides a mirror on processes and dynamics. Boundaries in the simulations are set
to a pre-industrial time to evaluate natural-agricultural nutrient changes in Taihu Basin a 100 years ago. Total nitrogen
(TN) and total phosphorus (TP) in the main channel flowing into the lake are simulated in four sub-basins for 200 model years.
Results show that modeling can capture basic features of basin nutrient development, where mean TN concentration (0.12 mg l−1) can be compared in broad scale to mean TN concentration (0.17 mg kg−1) from Lake Taihu sedimentary cores dating back about 100 years. Spatial nutrient simulations suggest that the two major nutrient
sources are from the southwestern sub-basin (48% TN and 68% TP of the basin total) and the northwestern sub-basin (18% TN
and 17% TP). There are differences of +7.3 × 104 kg TN and +2.0 × 105 kg TP between total input and output values, simulating mean annual amounts of nutrient deposited into the lake. TN and TP
concentration differences between input and output sub-basins become smaller in the second 100 years than the first 100 years,
suggesting a 100 year period to reach a balance of net nutrients. Catchment nutrient modeling provides a basis to evaluate
how nutrient production and balance responded to environmental changes over 200 years in Taihu Basin. 相似文献
107.
Salvati A Ristori S Pietrangeli D Oberdisse J Calamai L Martini G Ricciardi G 《Biophysical chemistry》2007,131(1-3):43-51
The synthesis, characterization and liposome insertion of a novel magnesium(II) carboranyl-porphyrazine, i.e. [2,3,7,8,12,13,17,18-octakis-(1,2-dicarba-closo-dodecaboranyl)-hexylthio-5,10,15,20-porphyrazine]magnesium(II) complex, MgHECSPz, are described. MgHECSPz was designed to improve the potentiality in multiple approach anticancer therapy. Liposomal formulations with different surface charge were prepared as delivering agents. The obtained loaded vectors were characterized by DLS, SAXS, SANS and zeta potential measurements in order to define the overall properties and structural details of loaded liposomes. 相似文献
108.
109.
Antonio Marchetti Maela Del Grammastro Lara Felicioni Sara Malatesta Giampaolo Filice Irene Centi Tommaso De Pas Armando Santoro Antonio Chella Alba Ariela Brandes Paola Venturino Franco Cuccurullo Lucio Crinò Fiamma Buttitta 《PloS one》2014,9(8)
Introduction
Assessment of EGFR mutation in non-small cell lung cancer (NSCLC) patients is mandatory for optimization of pharmacologic treatment. In this respect, mutation analysis of circulating tumor cells (CTCs) may be desirable since they may provide real-time information on patient''s disease status.Experimental Design
Blood samples were collected from 37 patients enrolled in the TRIGGER study, a prospective phase II multi-center trial of erlotinib treatment in advanced NSCLC patients with activating EGFR mutations in tumor tissue. 10 CTC preparations from breast cancer patients without EGFR mutations in their primary tumors and 12 blood samples from healthy subjects were analyzed as negative controls. CTC preparations, obtained by the Veridex CellSearch System, were subjected to ultra-deep next generation sequencing (NGS) on the Roche 454 GS junior platform.Results
CTCs fulfilling all Veridex criteria were present in 41% of the patients examined, ranging in number between 1 and 29. In addition to validated CTCs, potential neoplastic elements were seen in 33 cases. These included cells not fulfilling all Veridex criteria (also known as “suspicious objects”) found in 5 (13%) of 37 cases, and isolated or clustered large naked nuclei with irregular shape observed in 33 (89%) cases. EGFR mutations were identified by NGS in CTC preparations of 31 (84%) patients, corresponding to those present in matching tumor tissue. Twenty-five (96%) of 26 deletions at exon 19 and 6 (55%) of 11 mutations at exon 21 were detectable (P = 0.005). In 4 (13%) cases, multiple EGFR mutations, suggesting CTC heterogeneity, were documented. No mutations were found in control samples.Conclusions
We report for the first time that the CellSearch System coupled with NGS is a very sensitive and specific diagnostic tool for EGFR mutation analysis in CTC preparations with potential clinical impact. 相似文献110.
Andrea Mafficini Eliana Amato Matteo Fassan Michele Simbolo Davide Antonello Caterina Vicentini Maria Scardoni Samantha Bersani Marisa Gottardi Borislav Rusev Giorgio Malpeli Vincenzo Corbo Stefano Barbi Katarzyna O. Sikora Rita T. Lawlor Giampaolo Tortora Aldo Scarpa 《PloS one》2014,9(8)