Supplementary Table 3 from Large-scale Transcriptome Analyses Reveal New Genetic Marker Candidates of Head, Neck, and Thyroid Cancer

Phaseolus vulgaris plants from the Mesoamerican centre of genetic diversification establish a preferential and more efficient root nodule symbiosis with sympatric Rhizobium etli strains. This is mediated by changes in host gene expression, which might occur either at the transcriptional or at the post-transcriptional level. However, the implication of small RNA (sRNA)-mediated control of gene expression in strain selectivity has remained elusive. sRNA sequencing was used to identify host microRNAs (miRNAs) differentially regulated in roots at an early stage of the symbiotic interaction, which were further characterized by applying a reverse genetic approach. In silico analysis identified known and new miRNAs that accumulated to a greater extent in the preferential and more efficient interaction. One of them, designated as Pvu-miR5924, participates in the mechanisms that determine the selection of R. etli strains that will colonize the nodules. In addition, the functional analysis of Pvu-miR390b verified that this miRNA is a negative modulator of nodule formation and bacterial infection. This study not only extended the list of miRNAs identified in P. vulgaris but also enabled the identification of miRNAs that play relevant functions in nodule formation, rhizobial infection and the selection of the rhizobial strains that will occupy the nodule.

Bacteria of the genus Burkholderia are commonly found in diverse ecological niches in nature. We report here the draft genome sequence of Burkholderia cordobensis type strain LMG 27620, isolated from agricultural soil in Córdoba, Argentina. This strain harbors several genes involved in chitin utilization and phenol degradation, which make it an interesting candidate for biocontrol purposes and xenobiotic degradation in polluted environments.

Caveolin-1 (Cav-1) is a structural protein present in invaginations of the cell membrane. In human breast cancer, the cav-1 gene is believed to be a tumor suppressor gene associated with inhibition of tumor metastasis. However, little is known about its expression, regulation and function in canine mammary tumors. Expression levels of cav-1 were investigated using real- time PCR and immunohistochemical detection with an anti-human Cav- 1 antibody. Gene expression stability of different samples was analyzed using the geNorm software. Mammary tumors from 51 female dogs were compared to normal mammary tissue from 10 female dogs. Malignant mammary cells showed a loss of Cav-1 expression by quantitative RTPCR and weak Cav-1 staining by immunohistochemistry compared to normal mammary gland tissue. There was a significant relationship between outcome and immunostaining as well as with tumor size, indicating that caveolin subexpression has a positive predictive value and is related to higher survival and smaller tumor size. Our findings indicate that Cav-1 is a potential prognostic marker for canine mammary tumors.

The use of prognostic markers for mammary cancer is important for routine diagnosis and research. Interleukin-8 (IL-8) is a chemotactic cytokine, produced by several cell types in response to inflammation. The expression, regulation and function of IL-8 in dogs are little known. Recent studies have associated angiogenesis and inflammatory processes with tumor malignancy. We investigated a possible correlation between IL-8 expression and mammary tumor prognosis in female dogs. IL-8 expression was measured in 50 dogs with mammary neoplasia by immunohistochemistry and real-time PCR. Immunohistochemical staining was done with anti-IL-8 antibodies and PCR amplifications were performed in a 7500 Fast Real-Time PCR system. Gene expression stability was analyzed by the geNorm software. Quantitative real-time PCR showed that IL-8 expression decreased in malignant mammary cells compared to normal mammary tissue, while weak immunostaining was associated with a diagnosis of carcinoma. Complementing earlier studies on IL-8 expression in several types of cancer, including mammary cancer, we conclude that IL-8 has potential for use as a prognostic marker for canine mammary neoplasia.

Forty-eight cases of canine mammary cancer were investigated to evaluate the immunohistochemical distribution of the γ2 chain of laminin-332. Tumor cells were compared to a pool of normal mammary tissues using quantitative RT-PCR. The western blot was performed in eight tumor samples as complementary test to evaluate protein integrity. Immunohistochemistry experiments showed negative, focal, and weak expression of laminin-332 γ2 in tumors with the worst prognosis. Quantitative PCR revealed downregulation of the gene in 27 (56.2%) of the animals. Out of the 16 dogs with γ2 chain overexpression, seven were still alive. The western blot results showed bands generation of 36, 50, and 98kDa, suggesting degradation of laminin-332 γ2 in malignant tumors. The results suggest that, in the future, low expression and/or degradation of laminin-332 γ2 chain in canine mammary tumors may be used as an indicator of malignant potential. However, further studies are necessary to corroborate these results

The serpin maspin, a tumor suppressor in breast cancer was described as an inhibitor of cell migration and inducer of cell adhesion between the basement membrane and extracellular matrix resulting in inhibition of tumor metastasis. In contrast, overexpression of maspin is correlated with poor prognosis in other types of cancer. Little is known about expression, regulation and function of maspin in canine mammary tumors. It was demonstrated in this study, a loss of maspin expression in malignant canine mammary cells compared with a pool of normal canine mammary tissue, analyzed by quantitative real-time PCR; weak maspin expression in malignant canine mammary tumors were observed by immunohistochemistry. It was also demonstrated that a correlation with nuclear maspin expression and a good prognosis. It is suggested that maspin could be used as a prognostic marker in canine mammary neoplasia.

The heterogeneous nuclear ribonucleoproteins (hnRNPs) comprise a large family of proteins that play important roles in telomere biogenesis, DNA repair, cellular signaling, and the regulation of expression at both the transcriptional and translational levels. One of the most extensively studied hnRNP family members, hnRNP K, has been implicated in a variety of processes, including chromatin remodeling, transcription, splicing, and translation events. In this study, we analyzed processed HNRPK pseudogenes (HNRPK psi1-psi4) and coding sequences. HNRPK pseudogenes are apparently nonfunctional, and psi1 might correspond to transcripts from an ancestral gene. Phylogenetic and sequence analyses suggest that HNRP genes arose by duplication, and that new structural and sequence features expanded the functions of hnRNPs. The expression analysis of hnRNP K isoforms showed that isoform a is expressed in normal testis and in non-small cell lung cancer (NCI-H1155 NSCLC cell line), although the shorter isoform (isoform b) is expressed in different tumor cell lines (IM9 B-lymphoblastoid, Hs578T human breast cancer epithelial, T98G human glioma cell lines). Using molecular modeling, we obtained KH1 and KH3 models, which pointed to important residues for DNA-protein binding and no structural differences between isoforms a and b. To our knowledge, this is the first phylogenetic study including vertebrate HNRP genes and HNRPK pseudogenes, and the first report comparing the KH1 and KH3 domains of isoforms a and b of the hnRNP K protein. New investigations in tumor samples must be done to validate the differential expression observed here. The results shown are important because the hnRNP K protein might represent a new target for pharmacologic intervention in virus replication and cancer.

Neurofibromatosis type 1 (NF1) is a common autosomal dominant disorder caused by mutations in the NF1 gene. In the present study, a total of 55 unrelated NF1 patients were screened for mutations in the GAP-related domain/GRD (exons 20-27a) by single-strand conformation polymorphism (SSCP). Four different mutations were identified and, taken together, they comprise one nonsense substitution (Q1189X), one deletion (3525-3526delAA), one missense substitution (E1356G) and one mutation in the splice acceptor site (c.4111-1G>A). One novel polymorphism (c.4514+11C>G) and other three putative polymorphisms were also found (c.3315-27G>A, V1146I and V1317A). Genotype-phenotype correlations were investigated, but no particular association was detected.

Squamous cell carcinoma of the head and neck (HNSCC) is one of the most common cancers in Brazil. The most important prognostic factor for this carcinoma is related to complete surgical removal of the neoplasm [ [1] Greenman J. Homer J.J. Stafford N.D. Markers in cancer of the larynx and pharynx. Clin Otolaryngol. 2000; 25: 9-18 Crossref PubMed Scopus (15) Google Scholar ]. When tumor is present at a margin of resection, the rate of local recurrence increases substantially and the survival rate decreases [ [2] Brennan J.A. Mao L. Hruban R.H. Boyle J.O. Eby Y.J. Koch W.M. Goodman S.N. Sidransky D. Molecular assessment of histopathological staging in squamous-cell carcinoma of the head and neck. N Engl J Med. 1995; 332 (16): 429-435 Crossref PubMed Scopus (679) Google Scholar ].