RESUMO
Formalin-fixed, paraffin-embedded (FFPE) tissues represent the most widely available clinical material to study colorectal cancer (CRC). However, the accuracy and clinical validity of FFPE microbiome profiling in CRC is uncertain. Here, we compared the microbial composition of 10 paired fresh-frozen (FF) and FFPE CRC tissues using 16S rRNA sequencing and RNA-ISH. Both sample types showed different microbial diversity and composition. FF samples were enriched in archaea and representative CRC-associated bacteria, such as Firmicutes, Bacteroidetes and Fusobacteria. Conversely, FFPE samples were mainly enriched in typical contaminants, such as Sphingomonadales and Rhodobacterales. RNA-ISH in FFPE tissues confirmed the presence of CRC-associated bacteria, such as Fusobacterium and Bacteroides, as well as Propionibacterium allowing discrimination between tumor-associated and contaminant taxa. An internal quality index showed that the degree of similarity within sample pairs inversely correlated with the dominance of contaminant taxa. Given the importance of FFPE specimens for larger studies in human cancer genomics, our findings may provide useful indications on potential confounding factors to consider for accurate and reproducible metagenomics analyses.
RESUMO
The effect of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection on the pathophysiology of the placenta and its impact on pregnancy outcome has not yet been fully elucidated. Here, we present a comprehensive clinical, morphological, and molecular analysis of placental tissues from pregnant women with and without SARS-CoV-2 infection. SARS-CoV-2 could be detected in half of placental tissues from SARS-CoV-2-positive women. The presence of the virus was not associated with any distinctive pathological, maternal, or neonatal outcome features. SARS-CoV-2 tissue load was low in all but one patient who exhibited severe placental damage leading to neonatal neurological manifestations. The placental transcriptional response induced by high viral load of SARS-CoV-2 showed an immunopathology phenotype similar to autopsy lung tissues from patients with severe coronavirus disease 2019. This finding contrasted with the lack of inflammatory response in placental tissues from SARS-CoV-2-positive women with low viral tissue load and from SARS-CoV-2-negative women. Importantly, no evidence of vertical transmission of SARS-CoV-2 was found in any newborns, suggesting that the placenta may be an effective maternal-neonatal barrier against the virus even in the presence of severe infection. Our observations suggest that severe placental damage induced by the virus may be detrimental for the neonate independently of vertical transmission.
Assuntos
COVID-19/complicações , COVID-19/virologia , Doenças Placentárias/virologia , Complicações Infecciosas na Gravidez/virologia , Adulto , COVID-19/transmissão , Estudos de Coortes , Feminino , Perfilação da Expressão Gênica , Humanos , Recém-Nascido , Transmissão Vertical de Doenças Infecciosas , Pandemias , Placenta/patologia , Placenta/virologia , Doenças Placentárias/genética , Doenças Placentárias/patologia , Gravidez , Complicações Infecciosas na Gravidez/genética , Complicações Infecciosas na Gravidez/patologia , Resultado da Gravidez , RNA Viral/genética , RNA Viral/isolamento & purificação , SARS-CoV-2/genética , SARS-CoV-2/isolamento & purificação , SARS-CoV-2/patogenicidade , Adulto JovemRESUMO
BACKGROUND: In a significant percentage of advanced non-small cell lung cancer (NSCLC) patients, tumor tissue is unavailable or insufficient for genetic analyses at time to progression. We prospectively analyzed the appearance of genetic alterations associated with resistance in liquid biopsies of advanced NSCLC patients progressing to targeted therapies using the NGS platform. METHODS: A total of 24 NSCLC patients were included in the study, 22 progressing to tyrosine kinase inhibitors and two to other treatments. Liquid biopsies samples were obtained and analyzed using the GeneReadTM QIAact Lung DNA UMI Panel, designed to enrich specific target regions and containing 550 variant positions in 19 selected genes frequently altered in lung cancer tumors. Previously, a retrospective validation of the panel was performed in clinical samples. RESULTS: Of the 21 patients progressing to tyrosine kinase inhibitors with valid results in liquid biopsy, NGS analysis identified a potential mechanism of resistance in 12 (57%). The most common were acquired mutations in ALK and EGFR, which appeared in 8/21 patients (38%), followed by amplifications in 5/21 patients (24%), and KRAS mutations in one patient (5%). Loss of the p.T790M was also identified in two patients progressing to osimertinib. Three of the 21 (14%) patients presented two or more concomitant alterations associated with resistance. Finally, an EGFR amplification was found in the only patient progressing to immunotherapy included in the study. CONCLUSIONS: NGS analysis in liquid biopsies of patients progressing to targeted therapies using the GeneReader platform is feasible and can help the oncologist to make treatment decisions.
RESUMO
RESUMEN Introducción: un evento adverso es un incidente que ha producido daño en un paciente y que puede o no estar asociado a un error clínico. Un porcentaje elevado de profesionales de la salud se encuentran implicados en este tipo de eventos anualmente. Gran parte de los profesionales desconocen la existencia de los sistemas implantados en sus centros de trabajo para una comunicación correcta de los eventos adversos. Objetivos: identificar las características de los profesionales hospitalarios afectados por algún evento adverso y evaluar su conocimiento de los sistemas de notificación. Metodología: estudio observacional descriptivo transversal. Se evaluaron variables demográficas, laborales y relacionadas con los eventos adversos y los sistemas de notificación. Resultados: participaron 207, 45,4 % enfermeros y 54,6 % médicos, de 39,24 ± 10,07 años y con una experiencia de 14,43 ± 9,9 años. El 71,8 % resultaron afectados por algún evento adverso. El primer evento adverso ocurrió a los 6,45 ± 6,18 años. El 42,1 % conocía algún sistema de notificación; pero sólo el 24,61% de éstos, afectados por un evento adverso, lo notificaron. Los médicos fueron más afectados por un evento adverso, además, más precozmente (p < 0,001); y también conocían los sistemas de notificación (p= 0,001). Conclusión: muchos sanitarios, con escasa experiencia, fueron afectados por eventos adversos. Pocos conocían los sistemas de notificación y muchos menos los utilizaban. Los médicos resultaron más afectados, y más precozmente, por los eventos adversos y conocían mejor los sistemas de notificación.
ABSTRACT Introduction: an adverse event is an incident that has caused harm to a patient and that may or may not be associated with a clinical error. A high percentage of health professionals are involved in this type of event annually. A large part of the professionals are unaware of the existence of the systems implemented in their work centers for a correct communication of adverse events. Objective: to identify the characteristics of hospital professionals affected by an adverse event and to evaluate their knowledge of the notification systems. Methods: cross-sectional descriptive observation-al study. Demographic, labor and related variables with adverse events and notification systems were evaluated. Results: 207, 45.4% nurses and 54.6% doctors, participated, 39.24 ± 10.07 years and with an experience of 14.43 ± 9.9 years. 71.8% were affected by some adverse event. The first adverse event occurred at 6.45 ± 6.18 years. 42.1% knew of some notification system; but only 24.61% of these, affected by an adverse event, report-ed it. Physicians were more affected by an adverse event, moreover earlier (p <0.001) and they were also more aware of notification systems (p = 0.001). Conclusions: many health workers, with little experience, were affected by adverse events. Few knew notification systems and far fewer used them. Doctors were more affected, and earlier, by adverse events and were better acquainted with notification systems.