HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): a specific and comprehensive pipeline for metagenomic shotgun sequencing data analysis

Background: Next-Generation-Sequencing (NGS) enables detection of microorganisms present in biological and other matrices of various origin and nature, allowing not only the identification of known phyla and strains but also the discovery of novel ones. The large amount of metagenomic shotgun data produced by NGS require comprehensive and user-friendly pipelines for data analysis, that speed up the bioinformatics steps, relieving the users from the need to manually perform complex and time-consuming tasks. Results: We describe here HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities), an exhaustive pipeline for metagenomics data analysis, comprising three independent analytical modules designed for an inclusive analysis of large NGS datasets. Conclusions: HOME-BIO is a powerful and easy-to-use tool that can be run also by users with limited computational expertise. It allows in-depth analyses by removing low-complexity/ problematic reads, integrating the analytical steps that lead to a comprehensive taxonomy profile of each sample by querying different source databases, and it is customizable according to specific users’ needs

an accurate pipeline for analysis of ngs data of small non coding rna

Motivations. The discovery of various families of small non-coding RNAs (sncRNAs) in recent years revealed the complexity of the regulation of gene expression at both transcriptional and post-transcriptional level. Of the numerous sncRNAs, microRNAs (miRNAs) constitute a large family of 19-23 nucleotides long RNAs that participate in a variety of processes, such as cell development and differentiation, apoptosis and stress responses to carcinogenesis. Computational analysis indicates that a unique miRNA can regulate hundreds of genes, underlining the potential influence of miRNAs in almost every cellular pathway. Deep sequencing technologies provides a powerful strategy to explore miRNA populations (miRNA-Seq) with high sensitivity and specificity. Different computational approaches have been developed to analyze miRNA-Seq data, allowing to identify known and novel miRNAs, perform differential expression analysis and predict putative miRNAs targets. We combined these algorithms into an analysis pipeline and tested it on data obtained from our experiments in cancer cell lines. Methods. The data obtained from the sequencer were filtered following several criteria. Since the sequence of the adapter is known, a Perl script was used to trim, from the raw data, the adaptors. The sequence reads were then filtered for quality and clustered to unique sequences to remove redundancy, retaining their individual read count information. Unique sequences 18 nucleotides or more in length were mapped, allowing up to one mismatch, on miRNA annotation according to miRBase version 18 using miRanalyzer. This detects the reads which correspond to known miRNAs, giving an estimation of expression level. miRBase repository is used because it offers information about mature (the mature sequence of known miRNAs), mature-star (the sequence which pairs with the mature miRNA in the miRNA secondary structure) and precursor miRNA sequences (sequence of the hairpin). miRNAs have been considered as expressed if they are detected at least 5 reads/sample. After detecting those that correspond to known miRNAs, the remaining reads were mapped to databases of transcribed sequences as mRNA and non-coding RNA (RFam). This step has two goals: (i) the number of matches can be viewed as a sample quality parameter (contamination of the RNA sample with degradation products and poly A tails) and (ii) it might be interesting to see which other known sncRNAs are in the sample. To predict novel miRNAs we used a probabilistic algorithm, miRDeep2, based on miRNA biogenesis model, to score compatibility of the position and frequency of sequenced RNA with the secondary structure of the miRNA precursor. This tool aligns sequencing reads to potential hairpin structures in a manner consistent with Dicer processing and assigns log-odds scores to measure the probability that hairpins are true miRNA precursors. To detect novel miRNAs by miRDeep2, a score cutoff corresponding to a prediction signal-to-noise ratio >10 was used. Identification of differentially expressed miRNAs was performed with the Bioconductor DESeq package. Starting from the expression values, the first step was to minimize the effect of the systematic technical variations, and then a negative binomial distribution model was used to test differential expression in deep sequencing datasets. Only miRNAs with a p-values less or equal to 0.05 and fold-change less or equal to -1.5 and greater or equal to 1.5 were considered as differentially expressed. Given the critical roles of miRNAs in regulating gene expression and cellular functions, we predicted their putative targets, intersecting results obtained from two resources, TargetScan and microRNA.org. TargetScan provide computationally predicted miRNA gene targets by searching for the presence of 8 and 7 mer sites that match the seed region of each miRNA, while microRNA.org target prediction incorporates current knowledge on target rules and on the use of a compendium of mammalian miRNAs. A further step of the analysis was to investigate nucleotide variations relative to the reference genome. To this purpose, preliminary steps were to reduce alignment artifacts and compute a more accurate quality estimation, removing biases due to sequencing cycle and preceding nucleotide. Further evidences were used to identify new miRNA variation sites: (i) Sequencing depth of variation sites should be equal to or larger than 5 reads per site, (ii) frequency of Single Nucleotide Variant occurrence >5% and (iii) variants not found in previous SNP annotation databases, like dbSNP. Results. We developed an accurate pipeline for integral analysis of next generation sequencing data of small RNA molecules. Based on solid statistical methods, this allows both detection of known miRNAs and prediction of new miRNAs, integrating steps for differential analysis, sequence analysis and target prediction. Acknowledgements Research support by: Fondazione con il Sud; Italian Association for Cancer Research; Italian Ministry for Education, University and Research; Regione Campania; University of Salerno; Fondazione Veronesi. Giorgio Giurato is a student of PhD School in Experimental and Clinic Medicine / Doctorate in Experimental Physiopathology and Neuroscience, Second University of Naples. Maria Ravo is supported by a 'Vladimir Ashkenazy' fellowship of Italian Association for Cancer Research. Concita Cantarella and Giovanni Nassa are fellows of Fondazione con il Sud

Direct regulation of microRNA biogenesis and expression by estrogen receptor beta in hormone-responsive breast cancer.

Estrogen effects on mammary epithelial and breast cancer (BC) cells are mediated by the nuclear receptors ERα and ERβ, transcription factors that display functional antagonism with each other, with ERβ acting as oncosuppressor and interfering with the effects of ERα on cell proliferation, tumor promotion and progression. Indeed, hormone-responsive, ERα+ BC cells often lack ERβ, which when present associates with a less aggressive clinical phenotype of the disease. Recent evidences point to a significant role of microRNAs (miRNAs) in BC, where specific miRNA expression profiles associate with distinct clinical and biological phenotypes of the lesion. Considering the possibility that ERβ might influence BC cell behavior via miRNAs, we compared miRNome expression in ERβ+ vs ERβ- hormone-responsive BC cells and found a widespread effect of this ER subtype on the expression pattern of these non-coding RNAs. More importantly, the expression pattern of 67 miRNAs, including 10 regulated by ERβ in BC cells, clearly distinguishes ERβ+, node-negative, from ERβ-, metastatic, mammary tumors. Molecular dissection of miRNA biogenesis revealed multiple mechanisms for direct regulation of this process by ERβ+ in BC cell nuclei. In particular, ERβ downregulates miR-30a by binding to two specific sites proximal to the gene and thereby inhibiting pri-miR synthesis. On the other hand, the receptor promotes miR-23b, -27b and 24-1 accumulation in the cell by binding in close proximity of the corresponding gene cluster and preventing in situ the inhibitory effects of ERα on pri-miR maturation by the p68/DDX5-Drosha microprocessor complex. These results indicate that cell autonomous regulation of miRNA expression is part of the mechanism of action of ERβ in BC cells and could contribute to establishment or maintenance of a less aggressive tumor phenotype mediated by this nuclear receptor

Effects of Oestrogen on MicroRNA Expression in Hormone-Responsive Breast Cancer Cells

Oestrogen receptor alpha (ERα) is a ligand-dependent transcription factor that mediates oestrogen effects in hormone-responsive cells. Following oestrogenic activation, ERα directly regulates the transcription of target genes via DNA binding. MicroRNAs (miRNAs) represent a class of small noncoding RNAs that function as negative regulators of protein-coding gene expression. They are found aberrantly expressed or mutated in cancer, suggesting their crucial role as either oncogenes or tumour suppressor genes. Here, we analysed changes in miRNA expression in response to oestrogen in hormone-responsive breast cancer MCF-7 and ZR-75.1 cells by microarray-mediated expression profiling. This led to the identification of 172 miRNAs up- or down-regulated by ERα in response to 17β-oestradiol, of which 52 are similarly regulated by the hormone in the two cell models investigated. To identify mechanisms by which ERα exerts its effects on oestrogen-responsive miRNA genes, the oestrogen-dependent miRNA expression profiles were integrated with global in vivo ERα binding site mapping in the genome by ChIP-Seq. In addition, data from miRNA and messenger RNA (mRNA) expression profiles obtained under identical experimental conditions were compared to identify relevant miRNA target transcripts. Results show that miRNAs modulated by ERα represent a novel genomic pathway to impact oestrogen-dependent processes that affect hormone-responsive breast cancer cell behaviour. MiRNome analysis in tumour tissues from breast cancer patients confirmed a strong association between expression of these small RNAs and clinical outcome of the disease, although this appears to involve only marginally the oestrogen-regulated miRNAs identified in this study

Inhibition of histone methyltransferase DOT1L silences ER alpha gene and blocks proliferation of antiestrogen-resistant breast cancer cells

Breast cancer (BC) resistance to endocrine therapy results from constitutively active or aberrant estrogen receptor alpha (ER alpha) signaling, and ways to block ERa pathway in these tumors are sought after. We identified the H3K79 methyltransferase DOT1L as a novel cofactor of ER alpha in BC cell chromatin, where the two proteins colocalize to regulate estrogen target gene transcription. DOT1L blockade reduces proliferation of hormone-responsive BC cells in vivo and in vitro, consequent to cell cycle arrest and apoptotic cell death, with widespread effects on ER-dependent gene transcription, including ER alpha and FOXA1 gene silencing. Antiestrogen-resistant BC cells respond to DOT1L inhibition also in mouse xenografts, with reduction in ER alpha levels, H3K79 methylation, and tumor growth. These results indicate that DOT1L is an exploitable epigenetic target for treatment of endocrine therapy-resistant ER alpha-positive BCs

Laparoscopic versus open colorectal surgery in the acute setting (LaCeS trial): a multicentre randomized feasibility trial

AbstractBackgroundApproximately 30,000 people per annum undergo major, emergency abdominal, gastrointestinal surgery, of which 36% (~10,800) are carried out for emergency colorectal pathology. Approximately 14% of all patients requiring emergency surgery undergo laparoscopic surgery. AimsThe aims of the LaCeS feasibility trial (Laparoscopic versus Open Colorectal Surgery in the Acute Setting) were to assess the feasibility, safety and acceptability of performing a large-scale definitive phase III randomised controlled trial with a comparison of emergency laparoscopic with open surgery for acute colorectal pathology. MethodsLaCeS was designed as a prospective, multicentre, single blind, parallel group, pragmatic, randomised controlled feasibility trial with an integrated qualitative study. Randomisation was performed centrally with patients being randomised on a 1:1 basis between laparoscopic or open surgery. ResultsA total of 64 patients were recruited across 5 centres. The overall average steady state recruitment rate was 1.2 patients/month. Baseline compliance for clinical and HrQoL data was 99.8% and 93.8% respectively. The conversion rate from laparoscopic to open surgery was 39.4% (95% CI 22.9% – 57.9%). The 30 day post-operative complication rate was 27.3% (95% CI 13.3- 45.5) in the laparoscopic arm and 41.9% (95% CI 24.6 – 60.9) in the open arm. DiscussionThe LaCeS feasibility trial has demonstrated that it is possible to evaluate laparoscopic surgery in the emergency colorectal setting within the context of a randomised controlled trial. LaCeS has demonstrated that it is possible to recruit to a surgical trial in the emergency setting, with good compliance to trial procedures and processes, and overall acceptability by patients and clinicians. The safety data obtained for laparoscopic emergency colorectal surgery indicate an acceptable safety profile, particularly when considering it to that observed in the open arm.Trial Registration ISRCTN15681041 https://doi.org/10.1186/ISRCTN15681041.Funding body: National Institute of Health Research – Research for Patient Benefi

Global analysis of estrogen receptor beta binding to breast cancer cell genome reveals an extensive interplay with estrogen receptor alpha for target gene regulation

Background: Estrogen receptors alpha (ERa) and beta (ERb) are transcription factors (TFs) that mediate estrogen signaling and define the hormone-responsive phenotype of breast cancer (BC). The two receptors can be found co-expressed and play specific, often opposite, roles, with ERb being able to modulate the effects of ERa on gene transcription and cell proliferation. ERb is frequently lost in BC, where its presence generally correlates with a better prognosis of the disease. The identification of the genomic targets of ERb in hormone-responsive BC cells is thus a critical step to elucidate the roles of this receptor in estrogen signaling and tumor cell biology. Results: Expression of full-length ERb in hormone-responsive, ERa-positive MCF-7 cells resulted in a marked reduction in cell proliferation in response to estrogen and marked effects on the cell transcriptome. By ChIP-Seq we identified 9702 ERb and 6024 ERa binding sites in estrogen-stimulated cells, comprising sites occupied by either ERb, ERa or both ER subtypes. A search for TF binding matrices revealed that the majority of the binding sites identified comprise one or more Estrogen Response Element and the remaining show binding matrixes for other TFs known to mediate ER interaction with chromatin by tethering, including AP2, E2F and SP1. Of 921 genes differentially regulated by estrogen in ERb+ vs ERb- cells, 424 showed one or more ERb site within 10 kb. These putative primary ERb target genes control cell proliferation, death, differentiation, motility and adhesion, signal transduction and transcription, key cellular processes that might explain the biological and clinical phenotype of tumors expressing this ER subtype. ERb binding in close proximity of several miRNA genes and in the mitochondrial genome, suggests the possible involvement of this receptor in small non-coding RNA biogenesis and mitochondrial genome functions. Conclusions: Results indicate that the vast majority of the genomic targets of ERb can bind also ERa, suggesting that the overall action of ERb on the genome of hormone-responsive BC cells depends mainly on the relative concentration of both ERs in the cell

Mortality and pulmonary complications in patients undergoing surgery with perioperative sars-cov-2 infection: An international cohort study

Background The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on postoperative recovery needs to be understood to inform clinical decision making during and after the COVID-19 pandemic. This study reports 30-day mortality and pulmonary complication rates in patients with perioperative SARS-CoV-2 infection. Methods This international, multicentre, cohort study at 235 hospitals in 24 countries included all patients undergoing surgery who had SARS-CoV-2 infection confirmed within 7 days before or 30 days after surgery. The primary outcome measure was 30-day postoperative mortality and was assessed in all enrolled patients. The main secondary outcome measure was pulmonary complications, defined as pneumonia, acute respiratory distress syndrome, or unexpected postoperative ventilation. Findings This analysis includes 1128 patients who had surgery between Jan 1 and March 31, 2020, of whom 835 (740%) had emergency surgery and 280 (248%) had elective surgery. SARS-CoV-2 infection was confirmed preoperatively in 294 (261%) patients. 30-day mortality was 238% (268 of 1128). Pulmonary complications occurred in 577 (512%) of 1128 patients; 30-day mortality in these patients was 380% (219 of 577), accounting for 817% (219 of 268) of all deaths. In adjusted analyses, 30-day mortality was associated with male sex (odds ratio 175 [95% CI 128-240], p<00001), age 70 years or older versus younger than 70 years (230 [165-322], p<00001), American Society of Anesthesiologists grades 3-5 versus grades 1-2 (235 [157-353], p<00001), malignant versus benign or obstetric diagnosis (155 [101-239], p=0046), emergency versus elective surgery (167 [106-263], p=0026), and major versus minor surgery (152 [101-231], p=0047). Interpretation Postoperative pulmonary complications occur in half of patients with perioperative SARS-CoV-2 infection and are associated with high mortality. Thresholds for surgery during the COVID-19 pandemic should be higher than during normal practice, particularly in men aged 70 years and older. Consideration should be given for postponing non-urgent procedures and promoting non-operative treatment to delay or avoid the need for surgery. Funding National Institute for Health Research (NIHR), Association of Coloproctology of Great Britain and Ireland, Bowel and Cancer Research, Bowel Disease Research Foundation, Association of Upper Gastrointestinal Surgeons, British Association of Surgical Oncology, British Gynaecological Cancer Society, European Society of Coloproctology, NIHR Academy, Sarcoma UK, Vascular Society for Great Britain and Ireland, and Yorkshire Cancer Research