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Oat kernels exhibit an extra-soft texture, a trait recently demonstrated to be largely modulated by starch-bound tryptophan-rich 2S proteins, the vromindolines. In this study, fractionation by two-dimensional electrophoresis of starch-bound proteins in 25 oat (Avena sativa) cultivars and 11 diploid or tetraploid Avena species revealed novel 2S proteins called Avena α-amylase/trypsin-inhibitors (AATI) because of their sequence similarity with wheat α-amylase/trypsin inhibitors. Thirty-seven AATI polypeptides, about 14 kDa in size, were split into three families named AATI-1, AATI-2, and AATI-3 with different primary structures and isoelectric points. AATI-1 and AATI-2 proteins showed 55.5-60.0 % sequence similarity with wheat α-amylase inhibitors CM1, CM2, and CM16, which have been found to cause innate immunity responses in celiac disease and non-celiac gluten sensitivity. Diploid A-genome and tetraploid AC-genome oat species possess three and five genes encoding for the AATI proteins, respectively, whereas hexaploid A. sativa exhibits 12 genes dispersed over the A-, C-, and D-genomes. Some AATI proteins expressed in hexaploid oats were assigned to the A-genome based on similarity to their counterparts in diploid species, contributing to further clarify the genetic origin of hexaploid oats. Moreover, AATI may interact with starch-bound vromindolines in determining the extra-soft texture of oat kernels and, due to their balanced amino acid compositions, may contribute to the biological value of oat proteins in a positive manner.

Thymic epithelial tumors (TETs) are rare tumors of the mediastinum, with an estimated incidence of about 3 cases per 100,000 inhabitants. Although anthracycline- and platinum-based chemotherapy is an active treatment for TETs, novel systemic therapeutic options are especially needed for metastatic disease, which is virtually incurable. On the basis of the radiographic response obtained with imatinib (Novartis Pharma, Basel, Switzerland) in a patient with thymic carcinoma harboring the V560del c-KIT mutation, a phase II trial was initiated at the Department of Molecular and Clinical Oncology and Endocrinology of University “Federico II of Naples” with the purpose to test imatinib in TETs. Imatinib was daily delivered at the dose of 400 mg to patients affected by TETs, who had progressed after at least one chemotherapy regimen. Positivity of c-KIT on immunohistochemistry was not mandatory for study entry. Radiographic responses were measured by CT scans performed every 3 months, according to the RECIST criteria. Toxicity was graded according to the Common Toxicity Criteria of the National Cancer Institute, version 3.0. Fifteen patients with advanced TETs were enrolled from March 2008 to May 2010. Three patients presented with thymic carcinomas. Two of these three patients presented c-kit expression on immunohistochemistry. No patient harbored a known c-kit activating mutation. Imatinib was very well tolerated, with no toxicity-related death. Diarrhea and migraine were the most frequent events, occurring both in 20% of patients, but were manageable and mild. No radiographic responses were recorded. Median progression-free survival was 3 months (interquartile range, 2.5–4). Median overall survival was not reached. The study was terminated before it reached its target accrual of 42 patients, because of the lack of responses and low accrual rate. This trial indicates the lack of effectiveness of imatinib in unselected patients with thymic epithelial tumors. Nevertheless, imatinib may represent a valuable option in selected patients with TETs, such as those harboring the V560del c-KIT mutation.

Background: Breast cancer (BC) is currently regarded as a heterogeneous disease classified, through gene expression analysis, into various molecular subtypes with different biological characteristics and clinical behaviour. Using a few protein biomarkers as estrogen, progesterone and HER2 receptors, BC subtypes can be divided in four main groups: luminal A, luminal B, HER2 and triple negative (TN). Triple negative BC are a heterogeneous subset of tumors grouped together on the basis of their lack of hormone receptor and HER2 expression. Although they demonstrate similarities in terms of pathological and molecular characteristics, they do not represent a uniform clinical entity since the expression of the basal cytokeratin (CK5) and EGFR may identify a subgroup, called basal-like, of very aggressive tumors encompassing about 10% of BC that display a particularly poor prognosis. Recently, in vitro and in vivo studies reported that the length of a CA Simple Sequence Repeat 1 (CASSRI) dinucleotides in the intron 1 of egfr was associated with the expression of EGFR. In addition, the loss of heterozigosity (LOH) within this region would also lead to altered receptor expression. In this study we aimed to determine the association between LOH and overexpression of EGFR in a series of basal-like BC and their in autologous uninvolved peritumoral tissues (PTT) in comparison to normal tissues (NT). Material and Methods: 35 TN BC, the correspondent PTT and the autologous NT were analyzed for EGFR, CK5 expression by immunohistochemistry (IHC) and for LOH using a fragment separation performed by capillary electrophoresis (ABI 3130 Applied Biosystem). The assessment of LOH on the three tissue substrates were evaluated comparing the peak area of the two alleles using the following equation: LOH score=T1XN2/T2XN1, where T is BC or PTT, N is normal tissue, 1 is the area under the peak corresponding to the shorter allele, and 2 to the longer allele. The result was significantly different from the ratio of the normal allele peak areas when the LOH score was < 0.79 (loss of the longer allele) or >1.27 (loss of the shorter allele). Results: Of the 35 TN BC, 29 (83%) expressed EGFR and/or CK5 and were defined basal-like BC. The remaining 6 (17%) cases, negative both for EGFR and CK5, were excluded from the study. Of the 16 EGFR positive basal-like BC, 10 (63%) showed LOH whereas of the 13 EGFR negative basal-like BC, only 3 (23%) showed LOH (p=0.03). Although in the majority basal-like BC with LOH (8/10; 80%) PTT displayed a genetic profile similar to NT and did not show LOH, interestingly, in 2 cases (20%) PTT is different from NT presenting LOH and expressing EGFR as the autologous BC. Conclusions: Our data indicate that LOH of CASSRI in the intron 1 of egfr is related to EGFR expression in basal-like BC. In addition, the evidence of LOH in PTT, denoting the occurrence of early molecular alterations in histologically normal tissues, could represent a potential biomarker with diagnostic/prognostic implications. Supported by AIRC Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P2-06-10.

The starch granule proteins from 113 einkorn wheat (Triticum monococcum ssp monococcum) accessions were analyzed by acidic, polyacrylamide gel electrophoresis (A-PAGE), and two-dimensional A-PAGE x SDS-PAGE. All accessions were confirmed to contain equal amounts of two polypeptide chains corresponding to puroindoline B (Pin-B), as well as a prominent component plus a faint band corresponding to puroindoline A (Pin-A). When compared with soft-textured common wheat, “monococcum” accessions showed an increase of 3.2- and 2.7-fold in Pin-A and Pin-B levels on the starch granules, respectively. In addition, all accessions contained a novel component of the 2S super-family of seed proteins named Einkorn Trypsin Inhibitor (ETI), which was found to be encoded as a pre-protein 148 residues long. Wild-type ETI encoded by allele Eti-A m 1a and “valine-type” ETI encoded by allele Eti-A m 1b, which occurred in 107 and six einkorn accessions, respectively, were found to accumulate on starch granules as a mature protein of 121 amino acids with a hydrophobic central domain. The einkorn accessions exhibited an average SKCS index as low as −2.05 ± 11.4, which is typical of extra-soft kernels. The total surface area of starch granules in “monococcum” wheat, as determined by visual assessments in counting chambers, was estimated at 764 mm2/mg of starch, and was about 1.5 times higher than that for common wheat. The results are discussed in relation to the identification of factors that cause the extra-soft texture of einkorn kernels.

Puroindolines, the tryptophan-rich proteins controlling grain hardness in wheat, appeared as two pairs of 13 kDa polypeptides in the Acid-PAGE (A-PAGE) and two-dimensional A-PAGE×SDS-PAGE patterns of starch-granule proteins from wild allotetraploid wheat Aegilops ventricosa Tausch. (2n = 4x = 28, genomes DvDvNvNv). Puroindoline pair a1 + a2 reacted strongly with an antiserum specific for puroindoline-a from common wheat (Triticum aestivum L.), whereas puroindoline pair b1 + b2 exhibited A-PAGE relative mobilities similar to that of puroindoline-b in Aegilops tauschii (Coss.), the D-genome donor to both common wheat and Ae. ventricosa. Puroindolines a2 and b1 were found to be encoded by alleles Pina-D1a and Pinb-D1h on chromosome 5Dv, respectively, whereas puroindolines a1 and b2 were assumed to be under the genetic control of chromosome 5Nv. Puroindoline a1 encoded by the novel Pina-N1a allele exhibited a high level of amino acid variation with respect to puroindoline-a. On the other hand, the tryptophan-rich region of puroindoline b2 encoded by allele Pinb-N1a showed a sequence change from lysine-42 to arginine, with no effect on the amount of protein b2 accumulated on the starch granules. A partial duplication of the pin-B gene (Pinb-relic) was identified about 1100 bp downstream from Pinb-D1 on chromosome 5Dv. The present findings are the first evidence of a tetraploid wheat species in which four puroindoline genes are expressed. The potential of Ae. ventricosa as a source of genes that may be used to modulate endosperm texture and other valuable traits in cultivated wheat species is discussed.

The next-generation sequencing (NGS) technologies are revolutionary tools which have made possible achieving remarkable advances in genetics since the beginning of the twenty-first century. Thanks to the possibility to produce large amount of sequence data, these tools are going to completely substitute other high-throughput technologies. Moreover, the large applications of NGS protocols are increasing the genetic decoding of biological systems through studies of genome anatomy and gene mapping, coupled to the transcriptome pictures. The application of NGS pipelines such as (1) de-novo genomic sequencing by mate-paired and whole-genome shotgun strategies; (2) specific gene sequencing on large bacterial communities; and (3) RNA-seq methods including whole transcriptome sequencing and Serial Analysis of Gene Expression (Sage-analysis) are fundamental in the genome-wide fields like metagenomics. Recently, the availability of these advanced protocols has allowed to overcome the usual sequencing technical issues related to the mapping specificity over standard shotgun library sequencing, the detection of large structural genomes variations and bridging sequencing gaps, as well as more precise gene annotation. In this chapter we will discuss how to manage a successful NGS pipeline from the planning of sequencing projects through the choice of the platforms up to the data analysis management.

The next-generation sequencing (NGS) technologies are revolutionary tools which have made possible achieving remarkable advances in genetics since the beginning of the twenty-first century. Thanks to the possibility to produce large amount of sequence data, these tools are going to completely substitute other high-throughput technologies. Moreover, the large applications of NGS protocols are increasing the genetic decoding of biological systems through studies of genome anatomy and gene mapping, coupled to the transcriptome pictures. The application of NGS pipelines such as (1) de-novo genomic sequencing by mate-paired and whole-genome shotgun strategies; (2) specific gene sequencing on large bacterial communities; and (3) RNA-seq methods including whole transcriptome sequencing and Serial Analysis of Gene Expression (Sage-analysis) are fundamental in the genome-wide fields like metagenomics. Recently, the availability of these advanced protocols has allowed to overcome the usual sequencing technical issues related to the mapping specificity over standard shotgun library sequencing, the detection of large structural genomes variations and bridging sequencing gaps, as well as more precise gene annotation. In this chapter we will discuss how to manage a successful NGS pipeline from the planning of sequencing projects through the choice of the platforms up to the data analysis management.

Among cereals, Avena sativa is characterized by an extremely soft endosperm texture, which leads to some negative agronomic and technological traits. On the basis of the well-known softening effect of puroindolines in wheat kernel texture, in this study, indolines and their encoding genes are investigated in Avena species at different ploidy levels. Three novel 14 kDa proteins, showing a central hydrophobic domain with four tryptophan residues and here named vromindoline (VIN)-1,2 and 3, were identified. Each VIN protein in diploid oat species was found to be synthesized by a single Vin gene whereas, in hexaploid A. sativa, three Vin-1, three Vin-2 and two Vin-3 genes coding for VIN-1, VIN-2 and VIN-3, respectively, were described and assigned to the A, C or D genomes based on similarity to their counterparts in diploid species. Expression of oat vromindoline transgenes in the extra-hard durum wheat led to accumulation of vromindolines in the endosperm and caused an approximate 50 % reduction of grain hardness, suggesting a central role for vromindolines in causing the extra-soft texture of oat grain. Further, hexaploid oats showed three orthologous genes coding for avenoindolines A and B, with five or three tryptophan residues, respectively, but very low amounts of avenoindolines were found in mature kernels. The present results identify a novel protein family affecting cereal kernel texture and would further elucidate the phylogenetic evolution of Avena genus. © 2014 Springer-Verlag Berlin Heidelberg.

TP53 is the most widely mutated gene across all cancer types. In head and neck cancer, approximately half of the tumors are found to contain TP53 mutations, which are correlated to an increased risk for locoregional recurrence and poor outcomes. In this study a mutational profiling of TP53 exons 5-8 was performed on tumor, peritumor and normal tissues from 57 HNSCC patients by direct sequencing of genomic DNA and cDNA. Cloning/sequencing in tumors carrying multiple TP53 mutations and semiquantitative SNaPShot mutation assay was performed in order to assess eventual allelic expression imbalances (AEI). We identified 24 out of 57 HNSCC patients (42%) carrying TP53 mutations and 5 patients carrying the R213R polymorphism. Cloning of the genomic DNA encompassing TP53 exons 5-8 from tumors with multiple TP53 mutations revealed that alleles carrying different types of TP53 mutations are present in these tumors. TP53 missense and nonsense mutations exhibit higher and lower TP53 transcript abundance compared to wild-type TP53 allele, respectively. Interestingly, three out of four patients with the R213R polymorphism analyzed were found positive for TP53 loss of heterozygosity (LOH) and also presented higher transcript abundance than the wild-type counterpart, specifically, in the tumor tissue and not in peritumor or normal tissues. HNSCC tumors present heterogenic cell populations carrying different TP53 mutations. All HNSCC samples analyzed show an alteration in the expression of mutated TP53 mRNA compared to the wild-type allele, most likely independently from the TP53 hemizygous status. The higher expression of R213R TP53 polymorphic allele in cancer tissue compared to normal tissue demonstrates a noninherited variation in allelic expression, independently from its mutation status for exons 5-8, suggesting a potential contribution to TP53 expression in HNSCC disease.

Background: The key role of egfr in thymoma pathogenesis has been questioned following the failure in identifying recurrent genetic alterations of egfr coding sequences and relevant egfr amplification rate. We investigated the role of the non-coding egfr CA simple sequence repeat 1 (CA-SSR-1) in a thymoma case series. Methods: We used sequencing and egfr-fluorescence in situ hybridization (FISH) to genotype 43 thymomas; (I) for polymorphisms and somatic loss of heterozygosity of the non-coding egfr CA-SSR-1 microsatellite and (II) for egfr gene copy number changes. Results: We found two prevalent CA-SSR-1 genotypes: A homozygous 16 CA repeat and a heterozygous genotype, bearing alleles with 16 and 20 CA repeats. The average combined allele length was correlated with tumor subtype: Shorter sequences were significantly associated with the more aggressive WHO thymoma subtype group including B2/B3, B3 and B3/C histotypes. Four out of 29 informative cases analysed for somatic CA-SSR-1 loss of heterozygosity showed allelic imbalance (AI), 3/4 with loss of the longer allele. By egfr-FISH analysis, 9 out of 33 cases were FISH positive. Moreover, the two integrated techniques demonstrated that 3 out of 4 CA-SSR-1-AI positive cases with short allele relative prevalence showed significantly low or high chromosome 7 "polysomy"/increased gene copy number by egfr-FISH. Conclusions: Our molecular and genetic and follow up data indicated that CA-SSR-1-allelic imbalance with short allele relative prevalence significantly correlated with EGFR 3+ immunohistochemical score, increased egfr Gene Copy Number, advanced stage and with relapsing/metastatic behaviour in thymomas. © Journal of Thoracic Disease.

Background Mutations in the TP53 (Tumour Protein 53) gene can lead to expression of mutant p53 proteins that accumulate in cancer cells and can induce circulating p53 antibodies in cancer patients. Our aim was to evaluate the presence and prognostic role of these antibodies in lung cancer patients and to investigate whether they were related to p53 expression or TP53 mutations in tumour tissues. Methods A total of 201 lung cancer patients were evaluated for p53 antibodies by ELISA (Enzyme-Linked Immunosorbent Assay) and control was obtained from 54 patients with non-malignant disorders; p53 expression was evaluated in 131 of the lung cancer patients by immunohistochemistry and TP53 mutations were then investigated in 53 tumours positively staining for p53 and in 12 tumours without p53 overexpression, whose DNA was available for direct sequencing. Results Our results show that 20.4% of cancer patients have positive levels of p53 antibodies, while none of the controls resulted positive. High levels of p53 expression are detected in 57.3% of cases and a significant correlation between serum p53 antibodies and high levels of p53 expression in the corresponding tumours is observed. In non-small cell lung cancer, p53 antibodies are significantly associated with poorly differentiated tumours; furthermore, high levels of p53 expression significantly correlated with squamous cell carcinoma and tumours with highest grade. Survival time of non-small cell lung cancer patients low/negative for serum p53 antibodies was significantly longer compared to patients with positive levels (p = 0.049); in particular, patients with squamous cell carcinoma, but not adenocarcinoma, low/negative for these antibodies show a significant better survival compared to serum-positive patients (p = 0.044). Conclusions In our study, detection of serum p53 antibodies in non-small cell lung cancer patients has been shown to be useful in identifying subsets of patients with poor prognosis. A significant correlation between the presence of serum p53 antibodies in lung cancer patients and p53 overexpression in the corresponding tumours was also observed. We did not find a significant correlation between levels of serum p53 antibodies and TP53 mutations in the corresponding tumours.

Background Responsiveness to Cetuximab alone can be mediated by an increase of Epidermal Growth factor Receptor (EGFR) Gene Copy Number (GCN). Aim of this study was to assess the role of EGFR-GCN in advanced colorectal cancer (CRC) patients receiving chemotherapy plus Cetuximab. Methods One hundred and one advanced CRC patients (43 untreated- and 58 pre-treated) were retrospectively studied by fluorescence in situ hybridization (FISH) to assess EGFR-GCN and by immunohistochemistry (IHC) to determine EGFR expression. Sixty-one out of 101 patients were evaluated also for k-ras status by direct sequencing. Clinical end-points were response rate (RR), progression-free survival (PFS) and overall survival (OS). Results Increased EGFR-GCN was found in 60/101 (59%) tumor samples. There was no correlation between intensity of EGFR-IHC and EGFR-GCN (p = 0.43). Patients receiving chemotherapy plus Cetuximab as first line treatment had a RR of 70% (30/43) while it was 18% (10/56) in the group with previous lines of therapy (p < 0.0001). RR was observed in 29/60 (48%) of patients with increased EGFR-GCN and in 6/28 (21%) in those without (p = 0.02). At multivariate analyses, number of chemotherapy lines and increased EGFR-GCN were predictive of response; EGFR-IHC score, increased EGFR-GCN and number of chemotherapy lines were significantly associated with a significant better PFS. Response to therapy was the only prognostic predictive factor for OS. In the 60 patients analyzed for k-ras mutations, number of chemotherapy lines, increased EGFR-GCN and k-ras wild type status predicted a better PFS. Conclusion In metastatic CRC patients treated with chemotherapy plus Cetuximab number of chemotherapy lines and increased EGFR-GCN were significantly associated with a better clinical outcome, independent of k-ras status.