Non-coding RNA and gene expression analyses of papillary renal neoplasm with reverse polarity (PRNRP) reveal distinct pathological mechanisms from other renal neoplasms.

Papillary renal neoplasm with reversed polarity (PRNRP) is a recently described rare renal neoplasm. Traditionally, it was considered a variant of papillary renal cell carcinoma (PRCC). However, several studies reported significant differences between PRNRP and PRCC in terms of clinical, morphological, immunohistochemical and molecular features. Nonetheless, PRNRP remains a poorly understood entity. We used microarray analysis to elucidate the non-coding RNA (ncRNA) and gene expression profiles of 10 PRNRP cases and compared them with other renal neoplasms. Unsupervised cluster analysis showed that PRNRP had distinct expression profiles from either clear cell renal cell carcinoma (ccRCC) or PRCC cases at the level of ncRNA but were less distinct at the level of gene expression. An integrated omic approach determined miRNA:gene interactions that distinguished PRNRP from PRCC and we validated 10 differentially expressed miRNAs and six genes by quantitative RT-PCR. We found that levels of the miRNAs, miR-148a, miR-375 and miR-429, were up-regulated in PRNRP cases compared to ccRCC and PRCC. miRNA target genes, including KRAS and VEGFA oncogenes, and CXCL8, which regulates VEGFA, were also differentially expressed between renal neoplasms. Gene set enrichment analysis (GSEA) determined different activation of metabolic pathways between PRNRP and PRCC cases. Overall, this study is by far the largest molecular study of PRNRP cases and the first to investigate either ncRNA expression or their gene expression by microarray assays.

Neurosarcoidosis: inicio con compromiso de múltiples sitios neurológicos / Neurosarcoidosis: Onset with involvement of multiple neurological sites

Resumen Presentamos el caso de una mujer joven sana, que consultó por parálisis facial periférica izquierda asociada a fiebre, tos seca, disnea y astenia de dos semanas de evolución. Al examen físico se evidenció hipoestesia en dermatomas D6 a D12 izquierdos y galactorrea bi lateral. En el laboratorio presentaba serologías virales negativas, eritrosedimentación, títulos de anticuerpos antinucleares, prolactina y hormona tiroestimulante elevados, con anticuerpos antiperoxidasa positivos. La tomografía computarizada mostró múltiples adenopatías cervicales, mediastinales e hiliares bilaterales, sin com promiso del parénquima pulmonar. El cultivo de líquido cefalorraquídeo fue negativo para gérmenes comunes, micobacterias (Xpert MTB/RIF), y la citología no mostró atipia. Se realizó una resonancia magnética con con traste endovenoso de cerebro sin hallazgos patológicos y de columna con alteración de la señal centromedular de D6 a D9 de casi la totalidad del espesor del cordón, con refuerzo con contraste endovenoso. Durante la in ternación recuperó la sensibilidad en tronco izquierdo y no repitió episodios febriles o tusígenos. Se realizó mediastinoscopía con biopsia ganglionar con anatomía patológica con presencia de numerosos granulomas no caseificantes compatibles con sarcoidosis. Se clasificó como neurosarcoidosis probable e inició tratamiento con corticoides con mejoría de los síntomas neurológi cos restantes, realizándose una resonancia magnética a los tres meses, donde la alteración de la señal se limitaba desde D7 a D8. Nuestro objetivo es destacar la presentación neurológica en múltiples sitios que obligó a descartar otras entidades más frecuentes, así como la evolución favorable incluso previo al inicio de un esquema de tratamiento de primera línea.

Abstract We present the case of a healthy young woman who consulted for left peripheral facial palsy associated with fever, dry cough, dyspnea, and asthenia of two weeks' evolution. Physical examination revealed hypoesthesia in left T6 to T12 dermatomes and bilateral galactorrhea. In the laboratory, she presented negative viral serology, elevated erythrocyte sedimentation rate, antinuclear an tibody titers, prolactin and thyroid-stimulating hormone, with positive antiperoxidase antibodies. Computed to mography showed multiple bilateral cervical, mediastinal, and hilar adenopathies, without involvement of lung parenchyma. Cerebrospinal fluid culture was negative for common germs, mycobacteria, and Xpert MTB/RIF, and cytology did not show atypia. Contrast-enhanced magnetic resonance was performed on the brain without pathological findings and on the spine with alteration of the centromedullary signal from T6 to T9 of almost the entire thickness of the cord, with posterior enhancement with gadolinium. During hospitalization, she recovered sensitivity in the left trunk and did not repeat febrile or cough episodes. She was referred to another center for mediastinoscopy with lymph node biopsy revealing the presence of numerous non-caseating granulomas compatible with sarcoidosis. It was classified as probable neurosarcoidosis and started treatment with corticoste roids with improvement of the remaining neurological symptoms. A magnetic resonance was performed three months later where the signal alteration was limited from T7 to T8. Our objective is to highlight the florid neu rological presentation that made it necessary to rule out other more frequent entities and the favorable evolution even before starting a first-line scheme of treatment.

[Neurosarcoidosis: Onset with involvement of multiple neurological sites]. / Neurosarcoidosis: inicio con compromiso de múltiples sitios neurológicos.

We present the case of a healthy young woman who consulted for left peripheral facial palsy associated with fever, dry cough, dyspnea, and asthenia of two weeks' evolution. Physical examination revealed hypoesthesia in left T6 to T12 dermatomes and bilateral galactorrhea. In the laboratory, she presented negative viral serology, elevated erythrocyte sedimentation rate, antinuclear antibody titers, prolactin and thyroid-stimulating hormone, with positive antiperoxidase antibodies. Computed tomography showed multiple bilateral cervical, mediastinal, and hilar adenopathies, without involvement of lung parenchyma. Cerebrospinal fluid culture was negative for common germs, mycobacteria, and Xpert MTB/RIF, and cytology did not show atypia. Contrast-enhanced magnetic resonance was performed on the brain without pathological findings and on the spine with alteration of the centromedullary signal from T6 to T9 of almost the entire thickness of the cord, with posterior enhancement with gadolinium. During hospitalization, she recovered sensitivity in the left trunk and did not repeat febrile or cough episodes. She was referred to another center for mediastinoscopy with lymph node biopsy revealing the presence of numerous non-caseating granulomas compatible with sarcoidosis. It was classified as probable neurosarcoidosis and started treatment with corticosteroids with improvement of the remaining neurological symptoms. A magnetic resonance was performed three months later where the signal alteration was limited from T7 to T8. Our objective is to highlight the florid neurological presentation that made it necessary to rule out other more frequent entities and the favorable evolution even before starting a first-line scheme of treatment.

Presentamos el caso de una mujer joven sana, que consultó por parálisis facial periférica izquierda asociada a fiebre, tos seca, disnea y astenia de dos semanas de evolución. Al examen físico se evidenció hipoestesia en dermatomas D6 a D12 izquierdos y galactorrea bilateral. En el laboratorio presentaba serologías virales negativas, eritrosedimentación, títulos de anticuerpos antinucleares, prolactina y hormona tiroestimulante elevados, con anticuerpos antiperoxidasa positivos. La tomografía computarizada mostró múltiples adenopatías cervicales, mediastinales e hiliares bilaterales, sin compromiso del parénquima pulmonar. El cultivo de líquido cefalorraquídeo fue negativo para gérmenes comunes, micobacterias (Xpert MTB/RIF), y la citología no mostró atipia. Se realizó una resonancia magnética con contraste endovenoso de cerebro sin hallazgos patológicos y de columna con alteración de la señal centromedular de D6 a D9 de casi la totalidad del espesor del cordón, con refuerzo con contraste endovenoso. Durante la internación recuperó la sensibilidad en tronco izquierdo y no repitió episodios febriles o tusígenos. Se realizó mediastinoscopía con biopsia ganglionar con anatomía patológica con presencia de numerosos granulomas no caseificantes compatibles con sarcoidosis. Se clasificó como neurosarcoidosis probable e inició tratamiento con corticoides con mejoría de los síntomas neurológicos restantes, realizándose una resonancia magnética a los tres meses, donde la alteración de la señal se limitaba desde D7 a D8. Nuestro objetivo es destacar la presentación neurológica en múltiples sitios que obligó a descartar otras entidades más frecuentes, así como la evolución favorable incluso previo al inicio de un esquema de tratamiento de primera línea.

Validation of Rapid and Economic Colorimetric Nanoparticle Assay for SARS-CoV-2 RNA Detection in Saliva and Nasopharyngeal Swabs.

Even with the widespread uptake of vaccines, the SARS-CoV-2-induced COVID-19 pandemic continues to overwhelm many healthcare systems worldwide. Consequently, massive scale molecular diagnostic testing remains a key strategy to control the ongoing pandemic, and the need for instrument-free, economic and easy-to-use molecular diagnostic alternatives to PCR remains a goal of many healthcare providers, including WHO. We developed a test (Repvit) based on gold nanoparticles that can detect SARS-CoV-2 RNA directly from nasopharyngeal swab or saliva samples with a limit of detection (LOD) of 2.1 × 105 copies mL-1 by the naked eye (or 8 × 104 copies mL-1 by spectrophotometer) in less than 20 min, without the need for any instrumentation, and with a manufacturing price of <$1. We tested this technology on 1143 clinical samples from RNA extracted from nasopharyngeal swabs (n = 188), directly from saliva samples (n = 635; assayed by spectrophotometer) and nasopharyngeal swabs (n = 320) from multiple centers and obtained sensitivity values of 92.86%, 93.75% and 94.57% and specificities of 93.22%, 97.96% and 94.76%, respectively. To our knowledge, this is the first description of a colloidal nanoparticle assay that allows for rapid nucleic acid detection at clinically relevant sensitivity without the need for external instrumentation that could be used in resource-limited settings or for self-testing.

Synergistic Antimicrobial Effect of a Lippia citriodora Natural Extract with Vanillin against Verotoxigenic Escherichia coli in Refrigerated Piel de Sapo Melon Juice.

ABSTRACT: The antimicrobial activity of a commercial Lippia citriodora extract (LCE) at 2,500 µg mL-1 (maximum sensory acceptable level) and vanillin (MIC and 2 MIC) alone and in combination were analyzed in four strains of Escherichia coli (two nonverotoxigenic and two verotoxigenic) in cation-adjusted Mueller-Hinton medium and in Piel de Sapo melon juice (MJ) stored under refrigeration (4°C) for 7 days. The bacterial counts of the four strains together in untreated samples were higher (≈4 log CFU/mL) in cation-adjusted Mueller-Hinton medium than in stored MJ. LCE showed higher antimicrobial activity in MJ than in standard culture broth, but vanillin showed a higher effect in broth. The verotoxigenic strain E. coli O146:H stx2 was the most sensitive to LCE in refrigerated MJ. Combinations of vanillin (at MIC and 2 MIC) with LCE were very effective in reducing E. coli counts either in broth or in refrigerated MJ to undetectable levels. Bactericidal effects were observed for the combinations in all strains in broth and in MJ. Also, these combinations showed an antimicrobial synergistic effect after day 3 of storage in MJ in three of the bacterial strains tested. These results indicate that the combination of LCE (at maximum sensory acceptable levels) and vanillin (at low concentrations) could be considered as a promising natural antimicrobial agent to inhibit verotoxigenic E. coli growth in refrigerated MJ and improve its quality.

Identification of Amino Acids within Nonstructural Proteins 10 and 14 of the Avian Coronavirus Infectious Bronchitis Virus That Result in Attenuation In Vivo and In Ovo.

The Gammacoronavirus infectious bronchitis virus (IBV) is a highly contagious global pathogen prevalent in all types of poultry flocks. IBV is responsible for economic losses and welfare issues in domestic poultry, resulting in a significant risk to food security. IBV vaccines are currently generated by serial passage of virulent IBV field isolates through embryonated hens' eggs. The different patterns of genomic variation accumulated during this process means that the exact mechanism of attenuation is unknown and presents a risk of reversion to virulence. Additionally, the passaging process adapts the virus to replicate in chicken embryos, increasing embryo lethality. Vaccines produced in this manner are therefore unsuitable for in ovo application. We have developed a reverse genetics system, based on the pathogenic IBV strain M41, to identify genes which can be targeted for rational attenuation. During the development of this reverse genetics system, we identified four amino acids, located in nonstructural proteins (nsps) 10, 14, 15, and 16, which resulted in attenuation both in vivo and in ovo. Further investigation highlighted a role of amino acid changes, Pro85Leu in nsp 10 and Val393Leu in nsp 14, in the attenuated in vivo phenotype observed. This study provides evidence that mutations in nsps offer a promising mechanism for the development of rationally attenuated live vaccines against IBV, which have the potential for in ovo application. IMPORTANCE The Gammacoronavirus infectious bronchitis virus (IBV) is the etiological agent of infectious bronchitis, an acute, highly contagious, economically important disease of poultry. Vaccination is achieved using a mixture of live attenuated vaccines for young chicks and inactivated vaccines as boosters for laying hens. Live attenuated vaccines are generated through serial passage in embryonated hens' eggs, an empirical process which achieves attenuation but retains immunogenicity. However, these vaccines have a risk of reversion to virulence, and they are lethal to the embryo. In this study, we identified amino acids in the replicase gene which attenuated IBV strain M41, both in vivo and in ovo. Stability assays indicate that the attenuating amino acids are stable and unlikely to revert. The data in this study provide evidence that specific modifications in the replicase gene offer a promising direction for IBV live attenuated vaccine development, with the potential for in ovo application.

Integrated mRNA and miRNA Transcriptomic Analyses Reveals Divergent Mechanisms of Sunitinib Resistance in Clear Cell Renal Cell Carcinoma (ccRCC).

The anti-angiogenic therapy sunitinib remains the standard first-line treatment for meta static clear cell renal cell carcinoma (ccRCC). However, acquired resistance develops in nearly all responsive patients and represents a major source of treatment failure. We used an integrated miRNA and mRNA transcriptomic approach to identify miRNA:target gene interactions involved in sunitinib resistance. Through the generation of stably resistant clones in three ccRCC cell lines (786-O, A498 and Caki-1), we identified non-overlapping miRNA:target gene networks, suggesting divergent mechanisms of sunitinib resistance. Surprisingly, even though the genes involved in these networks were different, they shared targeting by multiple members of the miR-17~92 cluster. In 786-O cells, targeted genes were related to hypoxia/angiogenic pathways, whereas, in Caki-1 cells, they were related to inflammatory/proliferation pathways. The immunotherapy target PD-L1 was consistently up-regulated in resistant cells, and we demonstrated that the silencing of this gene resulted in an increase in sensitivity to sunitinib treatment only in 786-O-resistant cells, suggesting that some ccRCC patients might benefit from combination therapy with PD-L1 checkpoint inhibitors. In summary, we demonstrate that, although there are clearly divergent mechanisms of sunitinib resistance in ccRCC subtypes, the commonality of miRNAs in multiple pathways could be targeted to overcome sunitinib resistance.

Assessment of (-) epicatechin as natural additive for improving safety and functionality in fresh "Piel de Sapo" melon juice.

Epicatechin (EC) is a very abundant flavonoid in vegetable tissues that presents high antioxidant activity in living systems. The minimum inhibitory concentration (MIC) of (-)EC was determined in three species of bacteria commonly associated with foodborne illness of plant origin: Listeria (L.) monocytogenes, Escherichia (E.) coli -serogroups O157: H7 and O111- and Bacillus (B.) cereus; two strains of probiotic-type lactic acid bacteria (PT-LAB) and two control strains. All 10 strains were assayed under three temperature conditions (30º, 10º, and 4ºC) and at each temperature under two pH conditions (6.7 and 5.5). Mean EC MIC values were generally lower at refrigeration (4º and 10ºC) temperatures and at standard pH (6.7). By inoculating with each of the strains separately, both melon juice (MJ) and MJ supplemented with EC (ECSMJ), at the accepted maximum sensorial limit, and storing them at 4ºC for 10 days; the final counts (CFU/mL) were lower for ECSMJ than for plain MJ both for pathogenic bacteria and for PT-LAB. The presence of EC during refrigerated storage counteracted the ability of MJ as a growth medium for all the pathogenic bacteria. ECSMJ increased the antioxidant activity of MJ significantly to levels similar to those of EC alone. (-) Epicathechin would be a promising ingredient for increasing the functional properties of "Piel de Sapo" MJ (phenolic compounds and antioxidant ability) while contributing to improving the safety of this type of juice during prolonged refrigerated storage at 4ºC.

An Integrative Omics Approach Reveals Involvement of BRCA1 in Hepatic Metastatic Progression of Colorectal Cancer.

(1) Background & Aims: The roles of different cells in the tumor microenvironment (TME) are critical to the metastatic process. The phenotypic transformation of the liver cells is one of the most important stages of the hepatic metastasis progression of colorectal cancer (CRC). Our aim was to identify the major molecules (i.e., genes, miRNAs and proteins) involved in this process. (2) Methods: We isolated and performed whole-genome analysis of gene, miRNA, and protein expression in three types of liver cells (Ito cells, Kupffer cells, and liver sinusoidal endothelial cells) from the TME of a murine model of CRC liver metastasis. We selected the statistically significant differentially expressed molecules using the Student's t-test with Benjamini-Hochberg correction and performed functional statistically-significant enrichment analysis of differentially expressed molecules with hypergeometric distribution using the curated collection of molecular signatures, MSigDB. To build a gene-miRNA-protein network centered in Brca1, we developed a software package (miRDiana) that collects miRNA targets from the union of the TargetScan, MicroCosm, mirTarBase, and miRWalk databases. This was used to search for miRNAs targeting Brca1. We validated the most relevant miRNAs with real-time quantitative PCR. To investigate BRCA1 protein expression, we built tissue microarrays (TMAs) from hepatic metastases of 34 CRC patients. (3) Results: Using integrated omics analyses, we observed that the Brca1 gene is among the twenty transcripts simultaneously up-regulated in all three types of TME liver cells during metastasis. Further analysis revealed that Brca1 is the last BRCA1-associated genome surveillance complex (BASC) gene activated in the TME. We confirmed this finding in human reanalyzing transcriptomics datasets from 184 patients from non-tumor colorectal tissue, primary colorectal tumor and colorectal liver metastasis of the GEO database. We found that the most probable sequence of cell activation during metastasis is Endothelial→Ito→Kupffer. Immunohistochemical analysis of human liver metastases showed the BRCA1 protein was co-localized in Ito, Kupffer, and endothelial cells in 81.8% of early or synchronous metastases. However, in the greater part of the metachronous liver metastases, this protein was not expressed in any of these TME cells. (4) Conclusions: These results suggest a possible role of the co-expression of BRCA1 in Ito, Kupffer, and sinusoidal endothelial cells in the early occurrence of CRC liver metastases, and point to BRCA1 as a potential TME biomarker.

The Urinary Transcriptome as a Source of Biomarkers for Prostate Cancer.

Prostate cancer (PCa) is the second most common cancer of men and is typically slow-growing and asymptomatic. The use of blood PSA as a screening method has greatly improved PCa diagnosis, but high levels of false positives has raised much interest in alternative biomarkers. We used next-generation sequencing (NGS) to elucidate the urinary transcriptome of whole urine collected from high-stage and low-stage PCa patients as well as from patients with the confounding diagnosis of benign hyperplasia (BPH). We identified and validated five differentially expressed protein-coding genes (FTH1 BRPF1, OSBP, PHC3, and UACA) in an independent validation cohort of small-volume (1 mL) centrifuged urine (n = 94) and non-centrifuged urine (n = 84) by droplet digital (dd)PCR. These biomarkers were able to discriminate between BPH and PCa patients and healthy controls using either centrifuged or non-centrifuged whole urine samples, suggesting that the urinary transcriptome is a valuable source of non-invasive biomarkers for PCa that warrants further investigation.

Serum levels of hsa-miR-16-5p, hsa-miR-29a-3p, hsa-miR-150-5p, hsa-miR-155-5p and hsa-miR-223-3p and subsequent risk of chronic lymphocytic leukemia in the EPIC study.

Chronic lymphocytic leukemia (CLL) is an incurable disease accounting for almost one-third of leukemias in the Western world. Aberrant expression of microRNAs (miRNAs) is a well-established characteristic of CLL, and the robust nature of miRNAs makes them eminently suitable liquid biopsy biomarkers. Using a nested case-control study within the European Prospective Investigation into Cancer and Nutrition (EPIC), the predictive values of five promising human miRNAs (hsa-miR-16-5p, hsa-miR-29a-3p, hsa-miR-150-5p, hsa-miR-155-5p and hsa-miR-223-3p), identified in a pilot study, were examined in serum of 224 CLL cases (diagnosed 3 months to 18 years after enrollment) and 224 matched controls using Taqman based assays. Conditional logistic regressions were applied to adjust for potential confounders. The median time from blood collection to CLL diagnosis was 10 years (p25-p75: 7-13 years). Overall, the upregulation of hsa-miR-150-5p, hsa-miR-155-5p and hsa-miR-29a-3p was associated with subsequent risk of CLL [OR1∆Ct-unit increase (95%CI) = 1.42 (1.18-1.72), 1.64 (1.31-2.04) and 1.75 (1.31-2.34) for hsa-miR-150-5p, hsa-miR-155-5p and hsa-miR-29a-3p, respectively] and the strongest associations were observed within 10 years of diagnosis. However, the predictive performance of these miRNAs was modest (area under the curve <0.62). hsa-miR-16-5p and hsa-miR-223-3p levels were unrelated to CLL risk. The findings of this first prospective study suggest that hsa-miR-29a, hsa-miR-150-5p and hsa-miR-155-5p were upregulated in early stages of CLL but were modest predictive biomarkers of CLL risk.

Combination of Carvacrol and Thymol: Antimicrobial Activity Against Staphylococcus aureus and Antioxidant Activity.

Plant and essential oil extracts have been used for some time as antimicrobials and antioxidants, although little is known about the interactions between the main components of these plant materials. This knowledge could help to design more potent antimicrobial and antioxidant mixtures. Carvacrol and thymol, the main components of the essential oils of the Lamiaceae family of plants, were assessed in combination to evaluate their antioxidant activity and antimicrobial effect against 19 strains of Staphylococcus aureus (S. aureus) of different origins (clinical, meat, milk, and other) and mostly (12) enterotoxin producers. The microdilution test assay was used to determine the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of the two phenolics alone and in combination. Based on the fractional inhibitory concentration index (FICI), no antimicrobial interaction (0.5 < FICI <4) between carvacrol and thymol was observed against 42% of the S. aureus strains and an antagonistic interaction (FICI >4) was observed in the rest, which indicates different behavior among strains in relation to this antimicrobial combination. Particularly, an antagonistic effect was observed in 29% of the meat origin strains and 57% of the dairy origin strains. Combinations of carvacrol and thymol were bactericidal (differences in MIC and MBC values not more than twofold) for 60% of the tested strains. At low concentrations of both components, the antioxidant effect is additive. However, at high concentrations (2.50 or 2.66 mM) of at least one of the components of the combination, it is antagonistic. The different types of interactions of the components in the combination can depend on many factors (ratio, structural characteristics, and the establishment of intermolecular complexes). The results could be used as reference to apply this combination in foods to control S. aureus, to maintain the organoleptic properties and to extend the shelf-life of them.

The Circulating Transcriptome as a Source of Biomarkers for Melanoma.

The circulating transcriptome is a valuable source of cancer biomarkers, which, with the exception of microRNAs (miRNAs), remains relatively unexplored. To elucidate which RNAs are present in plasma from melanoma patients and which could be used to distinguish cancer patients from healthy individuals, we used next generation sequencing (NGS), and validation was carried out by qPCR and/or ddPCR. We identified 442 different microRNAs in samples, eleven of which were differentially expressed (p < 0.05). Levels of miR-134-5p and miR-320a-3p were significantly down-regulated (p < 0.001) in melanoma samples (n = 96) compared to healthy controls (n = 28). Differentially expressed protein-encoding mRNA 5'-fragments were enriched for the angiopoietin, p21-activated kinase (PAK), and EIF2 pathways. Levels of ATM1, AMFR, SOS1, and CD109 gene fragments were up-regulated (p < 0.001) in melanoma samples (n = 144) compared to healthy controls (n = 41) (AUC = 0.825). Over 40% of mapped reads were YRNAs, a class of non-coding RNAs that to date has been little explored. Expression levels of RNY3P1, RNY4P1, and RNY4P25 were significantly higher in patients with stage 0 disease than either healthy controls or more advanced stage disease (p < 0.001). In conclusion, we have identified a number of novel RNA biomarkers, which, most importantly, we validated in multi-center retrospective and prospective cohorts, suggesting potential diagnostic use of these RNA species.

Antimicrobial efficacy of Lippia citriodora natural extract against Escherichia coli and Enterococcus faecalis in "Piel de Sapo" melon juice.

BACKGROUND: The minimal inhibitory concentration (MIC) of an aqueous extract of Lippia citriodora with reported functional properties (PLX®) was determined on two strains of Escherichia coli (E. coli) belonging to serogroups commonly associated with foodborne illnesses (E. coli O157:H7 ATCC 700728 and E. coli O111 isolate 172) in vegetable products and two control strains for antimicrobial tests assays (E. coli ATCC 25922 and Enterococcus-En. faecalis ATCC 29212). RESULTS: Mean MIC values at standard pH (7.4) in broth for the E. coli strains tested ranged from 4,444 µg/ml (35ºC) to 1,250 µg/ml (10ºC) and to 182 µg/ml (4ºC). At pH 5.5, conditions resembling those of melon juice, MIC was about 2 times higher at 35 and 10ºC compared with 4ºC. The MIC of En. faecalis was similar or slightly lower than those of E. coli at the conditions tested. In melon juice fortified with PLX® (2,500 µg/ml, maximum sensorial acceptable limit), the three strains of E. coli maintained their viability although none showed growth potential after 4 days at 4ºC. CONCLUSIONS: PLX® could be added to melon juice to control E. coli O157:H7 and E. coli O111 during refrigerated storage, reducing the risk of microbiological contamination in this food.

The S2 Subunit of Infectious Bronchitis Virus Beaudette Is a Determinant of Cellular Tropism.

The spike (S) glycoprotein of the avian gammacoronavirus infectious bronchitis virus (IBV) is comprised of two subunits (S1 and S2), has a role in virulence in vivo, and is responsible for cellular tropism in vitro We have previously demonstrated that replacement of the S glycoprotein ectodomain from the avirulent Beaudette strain of IBV with the corresponding region from the virulent M41-CK strain resulted in a recombinant virus, BeauR-M41(S), with the in vitro cell tropism of M41-CK. The IBV Beaudette strain is able to replicate in both primary chick kidney cells and Vero cells, whereas the IBV M41-CK strain replicates in primary cells only. In order to investigate the region of the IBV S responsible for growth in Vero cells, we generated a series of recombinant IBVs expressing chimeric S glycoproteins, consisting of regions from the Beaudette and M41-CK S gene sequences, within the genomic background of Beaudette. The S2, but not the S1, subunit of the Beaudette S was found to confer the ability to grow in Vero cells. Various combinations of Beaudette-specific amino acids were introduced into the S2 subunit of M41 to determine the minimum requirement to confer tropism for growth in Vero cells. The ability of IBV to grow and produce infectious progeny virus in Vero cells was subsequently narrowed down to just 3 amino acids surrounding the S2' cleavage site. Conversely, swapping of the 3 Beaudette-associated amino acids with the corresponding ones from M41 was sufficient to abolish Beaudette growth in Vero cells.IMPORTANCE Infectious bronchitis remains a major problem in the global poultry industry, despite the existence of many different vaccines. IBV vaccines, both live attenuated and inactivated, are currently grown on embryonated hen's eggs, a cumbersome and expensive process due to the fact that most IBV strains do not grow in cultured cells. The reverse genetics system for IBV creates the opportunity for generating rationally designed and more effective vaccines. The observation that IBV Beaudette has the additional tropism for growth on Vero cells also invokes the possibility of generating IBV vaccines produced from cultured cells rather than by the use of embryonated eggs. The regions of the IBV Beaudette S glycoprotein involved in the determination of extended cellular tropism were identified in this study. This information will enable the rational design of a future generation of IBV vaccines that may be grown on Vero cells.

The ADRP domain from a virulent strain of infectious bronchitis virus is not sufficient to confer a pathogenic phenotype to the attenuated Beaudette strain.

The replicase gene of the coronavirus infectious bronchitis virus (IBV) encodes 15 non-structural proteins (nsps). Nsp 3 is a multi-functional protein containing a conserved ADP-ribose-1″-phosphatase (ADRP) domain. The crystal structures of the domain from two strains of IBV, M41 (virulent) and Beaudette (avirulent), identified a key difference; M41 contains a conserved triple-glycine motif, whilst Beaudette contains a glycine-to-serine mutation that is predicted to abolish ADRP activity. Although ADRP activity has not been formally demonstrated for IBV nsp 3, Beaudette fails to bind ADP-ribose. The role of ADRP in virulence was investigated by generating rIBVs, based on Beaudette, containing either a restored triple-glycine motif or the complete M41 ADRP domain. Replication in vitro was unaffected by the ADRP modifications and the in vivo phenotype of the rIBVs was found to be apathogenic, indicating that restoration of the triple-glycine motif is not sufficient to restore virulence to the apathogenic Beaudette strain.

Mutational profiling can identify laryngeal dysplasia at risk of progression to invasive carcinoma.

Early diagnosis of laryngeal squamous cell carcinoma (LSCC) at the stage of dysplasia could greatly improve the outcome of affected patients. For the first time we compared the mutational landscape of non-progressing dysplasia (NPD; n = 42) with progressing dysplasia (PD; n = 24), along with patient-matched LSCC biopsies; a total of 90 samples. Using targeted next-generation sequencing identified non-synonymous mutations in six genes (PIK3CA, FGFR3, TP53, JAK3, MET, FBXW7), and mutations were validated by Sanger sequencing and/or qPCR. Analysis was extended in silico to 530 head and neck (HNSCC) cases using TCGA data. Mutations in PIK3CA and FGFR3 were detected in PD and LSCC cases, as well as other HNSCC cases, but absent in NPD cases. In contrast, mutations in JAK3, MET and FBXW7 were found in NPD cases but not PD, LSCC or other HNSCC cases. TP53 was the most frequently mutated gene in both PD and NPD cases. With the exception of R248W, mutations were mutually exclusive. Moreover, five of seven PD mutations were located in motif H2 of p53, whereas none of the NPD mutations were. In summary, we propose that the mutational profile of laryngeal dysplasia has utility for the early detection of patients at risk of progression.

Noncoding RNA Expression and Targeted Next-Generation Sequencing Distinguish Tubulocystic Renal Cell Carcinoma (TC-RCC) from Other Renal Neoplasms.

Tubulocystic renal cell carcinoma (TC-RCC) is a rare recently described renal neoplasm characterized by gross, microscopic, and immunohistochemical differences from other renal tumor types and was recently classified as a distinct entity. However, this distinction remains controversial particularly because some genetic studies suggest a close relationship with papillary RCC (PRCC). The molecular basis of this disease remains largely unexplored. We therefore performed noncoding (nc) RNA/miRNA expression analysis and targeted next-generation sequencing mutational profiling on 13 TC-RCC cases (11 pure, two mixed TC-RCC/PRCC) and compared with other renal neoplasms. The expression profile of miRNAs and other ncRNAs in TC-RCC was distinct and validated 10 differentially expressed miRNAs by quantitative RT-PCR, including miR-155 and miR-34a, that were significantly down-regulated compared with PRCC cases (n = 22). With the use of targeted next-generation sequencing we identified mutations in 14 different genes, most frequently (>60% of TC-RCC cases) in ABL1 and PDFGRA genes. These mutations were present in <5% of clear cell RCC, PRCC, or chromophobe RCC cases (n > 600) of The Cancer Genome Atlas database. In summary, this study is by far the largest molecular study of TC-RCC cases and the first to investigate either ncRNA expression or their genomic profile. These results add molecular evidence that TC-RCC is indeed a distinct entity from PRCC and other renal neoplasms.

Spatial intratumoural heterogeneity in the expression of GIT1 is associated with poor prognostic outcome in oestrogen receptor positive breast cancer patients with synchronous lymph node metastases.

Background: The outcome for oestrogen receptor positive (ER+) breast cancer patients has improved greatly in recent years largely due to targeted therapy. However, the presence of involved multiple synchronous lymph nodes remains associated with a poor outcome. Consequently, these patients would benefit from the identification of new prognostic biomarkers and therapeutic targets. The expression of G-protein-coupled receptor kinase-interacting protein 1 (GIT1) has recently been shown to be an indicator of advanced stage breast cancer. Therefore, we investigated its expression and prognostic value of GIT1 in a cohort of 140 ER+ breast cancer with synchronous lymph node involvement. Methods: Immunohistochemistry was employed to assess GIT1 expression in a tissue microarray (TMA) containing duplicate non-adjacent cores with matched primary tumour and lymph node tissue (n=140). GIT1 expression in tumour cells was scored and statistical correlation analyses were carried out. Results: The results revealed a sub-group of patients that displayed discordant expression of GIT1 between the primary tumour and the lymph nodes (i.e. spatial intratumoural heterogeneity). We observed that loss of GIT1 expression in the metastasis was associated with a shorter time to recurrence, poorer overall survival, and a shorter median survival time. Moreover, multivariate analysis demonstrated that GIT1 expression was an independent prognostic indicator. Conclusions: GIT1 expression enabled the identification of a sub-class of ER+ patients with lymph node metastasis that have a particularly poor prognostic outcome. We propose that this biomarker could be used to further stratify ER+ breast cancer patients with synchronous lymph node involvement and therefore facilitate adjuvant therapy decision making.

Aberrant expression of MicroRNAs in B-cell lymphomas.

B-cell lymphomas represent a heterogeneous collection of more than twenty-five different malignancies. Classification is often challenging as primarily based upon, sometimes subjective, histopathological criteria and misdiagnosis can result in inappropriate treatment decisions. MicroRNAs (miRNAs) hold great promise as novel biomarkers (diagnostic, prognostic and predictive) of B-cell lymphoma in addition to being potential therapeutic targets. The most promising of these miRNAs more often than not play key regulatory roles in lymphopoiesis (development of lymphocytes) when under physiological conditions, and in the pathology of lymphoid malignancies when aberrantly expressed. In this review we consider the identity and functional role of miRNAs in the most common forms of B-cell lymphomas, their role in lymphopoiesis and their potential as biomarkers for these malignancies.