Emerging roles of gut virome in pediatric diseases

In the last decade, the widespread application of shotgun metagenomics provided extensive characterization of the bacterial “dark matter” of the gut microbiome, propelling the development of dedicated, standardized bioinformatic pipelines and the systematic collection of metagenomic data into comprehensive databases. The advent of next-generation sequencing also unravels a previously underestimated viral population (virome) present in the human gut. Despite extensive efforts to characterize the human gut virome, to date, little is known about the childhood gut virome. However, alterations of the gut virome in children have been linked to pathological conditions such as inflammatory bowel disease, type 1 diabetes, malnutrition, diarrhea and celiac diseas

Comprehensive RNA dataset of AGO2 associated RNAs in Jurkat cells following miR-21 over-expression

AbstractWe set out to identify miR-21 targets in Jurkat cells using a high-throughput biochemical approach (10.1016/j.biochi.2014.09.021 [1]). Using a specific monoclonal antibody raised against AGO2, RISC complexes were immunopurified in Jurkat cells over-expressing miR-21 following lentiviral trasduction as well as in Jurkat control cells lines. A parallel immunoprecipitation using isotype-matched rat IgG was performed as a control. AGO2 associated mRNAs were profiled by microarray (GEO: GSE37212). AGO2 bound miRNAs were profiled by RNA-seq

ARGONAUTE2 cooperates with SWI/SNF complex to determine nucleosome occupancy at human Transcription Start Sites.

Argonaute (AGO) proteins have a well-established role in post-transcriptional regulation of gene expression as key component of the RNA silencing pathways. Recent evidence involves AGO proteins in mammalian nuclear processes such as transcription and splicing, though the mechanistic aspects of AGO nuclear functions remain largely elusive. Here, by SILAC-based interaction proteomics, we identify the chromatin-remodelling complex SWI/SNF as a novel AGO2 interactor in human cells. Moreover, we show that nuclear AGO2 is loaded with a novel class of Dicer-dependent short RNAs (sRNAs), that we called swiRNAs, which map nearby the Transcription Start Sites (TSSs) bound by SWI/SNF. The knock-down of AGO2 decreases nucleosome occupancy at the first nucleosome located downstream of TSSs in a swiRNA-dependent manner. Our findings indicate that in human cells AGO2 binds SWI/SNF and a novel class of sRNAs to establish nucleosome occupancy on target TSSs

Fecal and mucosal microbiota profiling in pediatric inflammatory bowel diseases

An altered gut microbiota profile has been widely documented in inflammatory bowel diseases (IBD). The intestinal microbial community has been more frequently investigated in the stools than at the level of the mucosa, while most of the studies have been performed in adults. We aimed to define the gut microbiota profile either by assessing fecal and colonic mucosa samples (inflamed or not) from pediatric IBD patients

TP53 regulates miRNA association with AGO2 to remodel the miRNA-mRNA interaction network

DNA damage activates TP53-regulated surveillance mechanisms that are crucial in suppressing tumorigenesis. TP53 orchestrates these responses directly by transcriptionally modulating genes, including microRNAs (miRNAs), and by regulating miRNA biogenesis through interacting with the DROSHA complex. However, whether the association between miRNAs and AGO2 is regulated following DNA damage is not yet known. Here, we show that, following DNA damage, TP53 interacts with AGO2 to induce or reduce AGO2's association of a subset of miRNAs, including multiple let-7 family members. Furthermore, we show that specific mutations in TP53 decrease rather than increase the association of let-7 family miRNAs, reducing their activity without preventing TP53 from interacting with AGO2. This is consistent with the oncogenic properties of these mutants. Using AGO2 RIP-seq and PAR-CLIP-seq, we show that the DNA damage–induced increase in binding of let-7 family members to the RISC complex is functional. We unambiguously determine the global miRNA–mRNA interaction networks involved in the DNA damage response, validating them through the identification of miRNA-target chimeras formed by endogenous ligation reactions. We find that the target complementary region of the let-7 seed tends to have highly fixed positions and more variable ones. Additionally, we observe that miRNAs, whose cellular abundance or differential association with AGO2 is regulated by TP53, are involved in an intricate network of regulatory feedback and feedforward circuits. TP53-mediated regulation of AGO2–miRNA interaction represents a new mechanism of miRNA regulation in carcinogenesis

Perfis hematológico e bioquímico de ratos (Rattus norvegicus) mantidos sob sistema de ventilação microambiental

Previous studies reported that rats (Rattus norvegicus) kept under microenvironmental ventilation systems (MEV) present better productive and health parameters when compared to animals kept under general diluting ventilation (GDV). The objective of the present research trial was to evaluate hematological and biochemical profiles of rats kept under MVS. In order to achieve this objective, two different trials were designed: Trail 1 (E1), in which it was evaluated the reproductive performance of males and females submitted to two different air speed limits - FV1, from 0.03 to 0.26 m / sec and FV2, from 0.27 to 0.80 m / sec. In Trial 2 (E2) it was evaluated different bed change intervals (3, 5, 7 and 9 days), for males kept under constant air speed (0.5 m / sec). Values for hemogram and biochemical patterns of these animals were compared to those of rats kept under GDV. Results show statistical differences in some of the studied parameters not only for the comparison between GVD and E1 and GVD and E2, but also between both groups submitted to MEV (E1 and E2). However, values found for all studied parameters are inside the normal range reported for this species, what indicates that MEV does not induce important changes in the physiological parameters evaluated.Em estudos anteriores, demonstrou-se que ratos mantidos em sistema de Ventilação Microambiental (VMA) apresentaram parâmetros de produtividade e padrão sanitário melhores do que aqueles mantidos em sistema de Ventilação Geral Diluidora (VGD). Outra etapa dos experimentos foi determinar os parâmetros fisiológicos destes animais. O presente estudo foi realizado para avaliar os perfis hematológico e bioquímico de ratos mantidos sob o sistema de VMA. Para tanto, foram realizados dois experimentos diferentes, com ratos mantidos em VMA, quais sejam: Experimento 1 (E1), no qual foi avaliado o desempenho reprodutivo de machos e fêmeas, sob duas faixas de velocidade de ar (FV1 - de 0,03 a 0,26 m/s, e FV2 - de 0,27 a 0,80 m/s); Experimento 2 (E2), no qual foram avaliados diferentes intervalos de troca de cama (3, 5, 7 e 9 dias), para ratos machos mantidos a uma velocidade de ar constante de 0,5 m/s. Os valores do hemograma e de parâmetros bioquímicos destes animais foram comparados com os valores encontrados em ratos mantidos sob VGD. Os resultados obtidos demonstraram diferenças estatísticas em alguns dos parâmetros observados, tanto entre os sistemas VGD e VMA, como entre os diferentes grupos de VMA. Contudo, os valores encontrados em todos os parâmetros avaliados encontram-se dentro de faixas de variação normal para a espécie estudada, como é descrito na literatura. Isto indica que o emprego do sistema de VMA não induz alterações relevantes nos parâmetros fisiológicos estudados

Evaluation of equine corneal endothelium after exposure to 0.5% indocyanine green - in vitro study

The purpose of the study was to investigate whether indocyanine green (ICG) dye damages the corneal endothelium of horses. Twenty-four corneas of 12 healthy equines, males or females, of different ages were used in this study. Only eyes with no ocular findings were used. Randomly, one eye was included in the treatment group and one in the control group. The eyes of the treatment group were exposed for 1 minute to dye ICG 0.5%. After that the endothelium of all eyes was stained with trypan blue and alizarin red S and analyzed and photographed under an optical microscope. Areas with damaged endothelial cells were manually measured and quantified using software for morphometric analysis and expressed as a percentage of cell damage. In all eyes examined areas of cell damage were observed in both corneas of the control group and the treatment group. The mean endothelial damage was 0.8 ± 0.37% in the treatment group and 0.97 ± 0.39% in the control. The Qui-square test stated that treatment and control group were not different. The ICG 0.5% did not cause acute damage to equine corneal endothelium

Ribonucleoprotein Assembly Defects Correlate with Spinal Muscular Atrophy Severity and Preferentially Affect a Subset of Spliceosomal snRNPs

Spinal muscular atrophy (SMA) is a motor neuron disease caused by reduced levels of the survival motor neuron (SMN) protein. SMN together with Gemins2-8 and unrip proteins form a macromolecular complex that functions in the assembly of small nuclear ribonucleoproteins (snRNPs) of both the major and the minor splicing pathways. It is not known whether the levels of spliceosomal snRNPs are decreased in SMA. Here we analyzed the consequence of SMN deficiency on snRNP metabolism in the spinal cord of mouse models of SMA with differing phenotypic severities. We demonstrate that the expression of a subset of Gemin proteins and snRNP assembly activity are dramatically reduced in the spinal cord of severe SMA mice. Comparative analysis of different tissues highlights a similar decrease in SMN levels and a strong impairment of snRNP assembly in tissues of severe SMA mice, although the defect appears smaller in kidney than in neural tissue. We further show that the extent of reduction in both Gemin proteins expression and snRNP assembly activity in the spinal cord of SMA mice correlates with disease severity. Remarkably, defective SMN complex function in snRNP assembly causes a significant decrease in the levels of a subset of snRNPs and preferentially affects the accumulation of U11 snRNP—a component of the minor spliceosome—in tissues of severe SMA mice. Thus, impairment of a ubiquitous function of SMN changes the snRNP profile of SMA tissues by unevenly altering the normal proportion of endogenous snRNPs. These findings are consistent with the hypothesis that SMN deficiency affects the splicing machinery and in particular the minor splicing pathway of a rare class of introns in SMA

Colorectal Cancer Stage at Diagnosis Before vs During the COVID-19 Pandemic in Italy

IMPORTANCE Delays in screening programs and the reluctance of patients to seek medical attention because of the outbreak of SARS-CoV-2 could be associated with the risk of more advanced colorectal cancers at diagnosis. OBJECTIVE To evaluate whether the SARS-CoV-2 pandemic was associated with more advanced oncologic stage and change in clinical presentation for patients with colorectal cancer. DESIGN, SETTING, AND PARTICIPANTS This retrospective, multicenter cohort study included all 17 938 adult patients who underwent surgery for colorectal cancer from March 1, 2020, to December 31, 2021 (pandemic period), and from January 1, 2018, to February 29, 2020 (prepandemic period), in 81 participating centers in Italy, including tertiary centers and community hospitals. Follow-up was 30 days from surgery. EXPOSURES Any type of surgical procedure for colorectal cancer, including explorative surgery, palliative procedures, and atypical or segmental resections. MAIN OUTCOMES AND MEASURES The primary outcome was advanced stage of colorectal cancer at diagnosis. Secondary outcomes were distant metastasis, T4 stage, aggressive biology (defined as cancer with at least 1 of the following characteristics: signet ring cells, mucinous tumor, budding, lymphovascular invasion, perineural invasion, and lymphangitis), stenotic lesion, emergency surgery, and palliative surgery. The independent association between the pandemic period and the outcomes was assessed using multivariate random-effects logistic regression, with hospital as the cluster variable. RESULTS A total of 17 938 patients (10 007 men [55.8%]; mean [SD] age, 70.6 [12.2] years) underwent surgery for colorectal cancer: 7796 (43.5%) during the pandemic period and 10 142 (56.5%) during the prepandemic period. Logistic regression indicated that the pandemic period was significantly associated with an increased rate of advanced-stage colorectal cancer (odds ratio [OR], 1.07; 95%CI, 1.01-1.13; P = .03), aggressive biology (OR, 1.32; 95%CI, 1.15-1.53; P < .001), and stenotic lesions (OR, 1.15; 95%CI, 1.01-1.31; P = .03). CONCLUSIONS AND RELEVANCE This cohort study suggests a significant association between the SARS-CoV-2 pandemic and the risk of a more advanced oncologic stage at diagnosis among patients undergoing surgery for colorectal cancer and might indicate a potential reduction of survival for these patients