Ovarian cancer pathology characteristics as predictors of variant pathogenicity in BRCA1 and BRCA2.

BACKGROUND: The distribution of ovarian tumour characteristics differs between germline BRCA1 and BRCA2 pathogenic variant carriers and non-carriers. In this study, we assessed the utility of ovarian tumour characteristics as predictors of BRCA1 and BRCA2 variant pathogenicity, for application using the American College of Medical Genetics and the Association for Molecular Pathology (ACMG/AMP) variant classification system. METHODS: Data for 10,373 ovarian cancer cases, including carriers and non-carriers of BRCA1 or BRCA2 pathogenic variants, were collected from unpublished international cohorts and consortia and published studies. Likelihood ratios (LR) were calculated for the association of ovarian cancer histology and other characteristics, with BRCA1 and BRCA2 variant pathogenicity. Estimates were aligned to ACMG/AMP code strengths (supporting, moderate, strong). RESULTS: No histological subtype provided informative ACMG/AMP evidence in favour of BRCA1 and BRCA2 variant pathogenicity. Evidence against variant pathogenicity was estimated for the mucinous and clear cell histologies (supporting) and borderline cases (moderate). Refined associations are provided according to tumour grade, invasion and age at diagnosis. CONCLUSIONS: We provide detailed estimates for predicting BRCA1 and BRCA2 variant pathogenicity based on ovarian tumour characteristics. This evidence can be combined with other variant information under the ACMG/AMP classification system, to improve classification and carrier clinical management.

Predictors of outcomes in emergency department patients with suspected infections and without fulfillment of the sepsis criteria.

BACKGROUND: Data on patient characteristics and determinants of serious outcomes for acutely admitted patients with infections who do not fulfill the sepsis criteria are sparse. The study aimed to characterize acutely admitted emergency department (ED) patients with infections and a composite outcome of in-hospital mortality or transfer to the intensive care unit without fulfilling the criteria for sepsis and to examine predictors of the composite outcome. METHODS: This was a secondary analysis of data from a prospective observational study of patients with suspected bacterial infection admitted to the ED between October 1, 2017 and March 31, 2018. A National Early Warning Score 2 (NEWS2) ≥ 5 within the first 4 h in the ED was assumed to represent a sepsis-like condition with a high risk for the composite endpoint. Patients who achieved the composite outcome were grouped according to fulfillment of the NEWS2 ≥ 5 criteria. We used logistic regression analysis to estimate the unadjusted and adjusted odds ratio (OR) for the composite endpoint among patients with either NEWS2  < 5 (NEWS2-) or NEWS2  ≥ 5 (NEWS2+). RESULTS: A total of 2055 patients with a median age of 73 years were included. Of these, 198 (9.6%) achieved the composite endpoint, including 59 (29.8%) NEWS2- and 139 (70.2%) NEWS2+ patients, respectively. Diabetes (OR 2.23;1.23-4.0), a Sequential Organ Failure Assessment (SOFA) score ≥ 2 (OR 2.57;1.37-4.79), and a Do-not-attempt-cardiopulmonary-resuscitation order (DNACPR) on admission (OR 3.70;1.75-7.79) were independent predictive variables for the composite endpoint in NEWS2- patients (goodness-of-fit test P = 0.291; area under the receiver operating characteristic curve for the model (AUROC) = 0.72). The regression model for NEWS2+ patients revealed that a SOFA score ≥ 2 (OR 2.79; 1.59-4.91), hypothermia (OR 2.48;1.30-4.75), and DNACPR order on admission were predictive variables for the composite endpoint (goodness-of-fit test P = 0.62; AUROC for the model = 0.70). CONCLUSION: Approximately one-third of the patients with infections and serious outcomes during hospitalization did not meet the NEWS2 threshold for likely sepsis. Our study identified factors with independent predictive values for the development of serious outcomes that should be tested in future prediction models.

Unveiling mRNP composition by fluorescence correlation and cross-correlation spectroscopy using cell lysates.

Understanding the mRNA life cycle requires information about the dynamics and macromolecular composition and stoichiometry of mRNPs. Fluorescence correlation and cross-correlation spectroscopy (FCS and FCCS) are appealing technologies to study these macromolecular structures because they have single molecule sensitivity and readily provide information about their molecular composition and dynamics. Here, we demonstrate how FCS can be exploited to study cytoplasmic mRNPs with high accuracy and reproducibility in cell lysates. Cellular lysates not only recapitulate data from live cells but provide improved readings and allow investigation of single mRNP analysis under particular conditions or following enzymatic treatments. Moreover, FCCS employing minute amounts of cells closely corroborated previously reported RNA dependent interactions and provided estimates of the relative overlap between factors in the mRNPs, thus depicting their heterogeneity. The described lysate-based FCS and FCCS analysis may not only complement current biochemical approaches but also provide novel opportunities for the quantitative analysis of the molecular composition and dynamics of single mRNPs.

Benchmarking full-length transcript single cell mRNA sequencing protocols.

BACKGROUND: Single cell mRNA sequencing technologies have transformed our understanding of cellular heterogeneity and identity. For sensitive discovery or clinical marker estimation where high transcript capture per cell is needed only plate-based techniques currently offer sufficient resolution. RESULTS: Here, we present a performance evaluation of four different plate-based scRNA-seq protocols. Our evaluation is aimed towards applications taxing high gene detection sensitivity, reproducibility between samples, and minimum hands-on time, as is required, for example, in clinical use. We included two commercial kits, NEBNext® Single Cell/ Low Input RNA Library Prep Kit (NEB®), SMART-seq® HT kit (Takara®), and the non-commercial protocols Genome & Transcriptome sequencing (G&T) and SMART-seq3 (SS3). G&T delivered the highest detection of genes per single cell. SS3 presented the highest gene detection per single cell at the lowest price. Takara® kit presented similar high gene detection per single cell, and high reproducibility between samples, but at the absolute highest price. NEB® delivered a lower detection of genes but remains an alternative to more expensive commercial kits. CONCLUSION: For the tested kits we found that ease-of-use came at higher prices. Takara can be selected for its ease-of-use to analyse a few samples, but we recommend the cheaper G&T-seq or SS3 for laboratories where a substantial sample flow can be expected.

Impact of specific high-risk human papillomavirus genotypes on survival in oropharyngeal cancer.

The increases observed in incidence and survival of oropharyngeal squamous cell carcinoma (OPSCC) have been attributed to human papillomavirus (HPV) infection, but the survival-impact of specific genotypes is poorly understood. We investigated the potential influence of HPV genotypes on survival in HPV-positive (HPV+) OPSCC. All patients with HPV+/p16+ OPSCC and available genotype data within the period 2011 to 2017 in Eastern Denmark were included. Descriptive statistics on clinical and tumor data, as well as overall survival (OS) and recurrence-free survival (RFS) with Cox hazard models and Kaplan-Meier plots were performed. Overall, 769 HPV+/p16+ OPSCC patients were included of which genotype HPV16 accounted for 86% (n = 662). Compared to high-risk non-HPV16 genotypes (HR non-HPV16), HPV16 patients were younger at diagnosis (median years, 60 vs 64), had a higher male to female ratio (3.7:1 vs 2.1:1), and lower performance scores of ≤1 (90%, n = 559, vs 81%, n = 74). Regarding 5-year OS and RFS, no difference was observed between HPV16 and HR non-HPV16 patients. Subgrouping the HR non-HPV16 group into HPV33 (n = 57), HPV35 (n = 26) and "other genotypes" (n = 24) a significantly worse OS in the "other genotypes" group (hazard rate: 2.33, P = .027) was shown. With similar survival results between HPV16 and non-HPV16 genotypes, genotyping in OPSCC is interesting from an epidemiological point of view as well as in vaccination programs, but not a necessary addition in prognostication of HPV+/p16+ OPSCC.

A catalog of curated breast cancer genes.

PURPOSE: Decades of research have identified multiple genetic variants associated with breast cancer etiology. However, there is no database that archives breast cancer genes and variants responsible for predisposition. We set out to build a dynamic repository of curated breast cancer genes. METHODS: A comprehensive literature search was performed in PubMed and Google Scholar, followed by data extraction and harmonization for downstream analysis. RESULTS: Using a subset of 345 studies, we cataloged 652 breast cancer-associated loci across the genome. A majority of these were present in the non-coding region (i.e., intergenic (101) and intronic (345)), whereas only 158 were located within an exon. Using the odds ratio, we identified 429 loci to increase the disease risk and 198 to confer protection against breast cancer, whereas 25 were identified to both increase disease risk and confer protection against breast cancer. Chromosomal ideogram analysis indicated that chromosomes 17 and 19 have the highest density of breast cancer loci. We manually annotated and collated breast cancer genes in which a previous association between rare-monogenic variant and breast cancer has been documented. Finally, network and functional enrichment analysis revealed that steroid metabolism and DNA repair pathways were predominant among breast cancer genes and variants. CONCLUSIONS: We have built an online interactive catalog of curated breast cancer genes ( https://cbcg.dk ). This will expedite clinical diagnostics and support the ongoing efforts in managing breast cancer etiology. Moreover, the database will serve as an essential repository when designing new breast cancer multigene panels.

Extensive genomic analysis in patients with KRAS-mutated solid tumors shows high frequencies of concurrent alterations and potential targets but has limited clinical impact.

BACKGROUND: This study aimed to investigate the distribution and frequency of concurrent alterations in different cancers across KRAS subtypes and in different KRAS subtypes across cancers, and to identify potentially actionable targets and patients who received targeted treatment matched to their genomic profile (GP). MATERIALS AND METHODS: In this descriptive and single-center study, we included 188 patients with solid tumors harboring KRAS mutations in codon 12, 13, 61, 117, or 146, referred to the Phase 1 Unit, Rigshospitalet, Copenhagen, Denmark from mid-2016 to 2020. Genomic co-alterations were detected with whole-exome sequencing, RNA sequencing, SNP array, and mRNA expression array on fresh biopsies. The study is part of the Copenhagen Prospective Personalized Oncology study (NCT02290522). RESULTS: The majority of patients had colorectal cancer (60.1%), non-small cell lung cancer (11.2%), or pancreatic cancer (10.6%). Most tumors were KRAS-mutated in codon 12 or 13 (93.7%) including G12D (27.1%), G12V (26.6%), G12C (11.7%), and G13D (11.2%). A total of 175 different co-alterations were found, most frequently pathogenic APC and TP53 mutations (55.9% and 46.4%, respectively) and high expression of CEACAM5 (73.4%). Different cancers and KRAS subtypes showed different patterns of co-alterations, and 157 tumors (83.5%) had potentially actionable targets with varying evidence of targetability (assessed using ESMO Scale for Clinical Actionability of molecular Targets). Of the 188 patients included in the study, 15 (7.4%) received treatment matched to their GP (e.g., immunotherapy and synthetic lethality drugs), of whom one had objective partial response according to Response Evaluation Criteria in Solid Tumors (RECIST) version 1.1. CONCLUSION: Performing extensive genomic analysis in patients with known KRAS-mutated solid tumors may contribute with information to the genomic landscape of cancers and identify targets for immunotherapy or synthetic lethality drugs, but currently appears to have overall limited clinical impact, as few patients received targeted therapy matched to their GP.

Cytoplasmic mRNPs revisited: Singletons and condensates.

Cytoplasmic messenger ribonucleoprotein particles (mRNPs) represent the cellular transcriptome, and recent data have challenged our current understanding of their architecture, transport, and complexity before translation. Pre-translational mRNPs are composed of a single transcript, whereas P-bodies and stress granules are condensates. Both pre-translational mRNPs and actively translating mRNPs seem to adopt a linear rather than a closed-loop configuration. Moreover, assembly of pre-translational mRNPs in physical RNA regulons is an unlikely event, and co-regulated translation may occur locally following extracellular cues. We envisage a stochastic mRNP transport mechanism where translational repression of single mRNPs-in combination with microtubule-mediated cytoplasmic streaming and docking events-are prerequisites for local translation, rather than direct transport.

Predictors for mortality in patients admitted with suspected bacterial infections - A prospective long-term follow-up study.

OBJECTIVE: The aim was to examine predictors for all-cause mortality in a long-term follow-up study of adult patients with infectious diseases of suspected bacterial origin. METHODS: A prospective observational study of patients admitted to the emergency department during 1.10.2017-31.03.2018. We used Cox regression to estimate adjusted hazard ratios (aHR) with 95% confidence intervals for mortality. RESULTS: A total of 2110 patients were included (median age 73 years). After a median follow-up of 2.1 years 758 (35.9%, 95% CI 33.9-38.0%) patients had died. Age (aHR1.05; 1.04-1.05), male gender (aHR 1.21; 1.17-1.25), cancer (aHR 1.80; 1.73-1.87), misuse of alcohol (aHR 1.30; 1.22-1.38), if admitted with sepsis within the last year before index admission (aHR 1.56;1.50-1.61), a Sequential Organ Failure Assessment (SOFA) score ≥2 (aHR 1.90; 1.83-1.98), SIRS criteria ≥2 (aHR 1.23;1.18-1.28) at admission to the ED, length of stay (aHR 1.05; 1.04-1.05) and devices and implants as sources of infection (aHR 7.0; 5.61-8.73) were independently associated with mortality. Skin infections and increasing haemoblobin values reduced the risk of death. CONCLUSIONS: More than one-third of a population of patients admitted to the emergency department with infectious diseases of suspected bacterial origin had died during a median follow up of 2.1 years. The study identified several independent predictors for mortality.

Transmission and Antibiotic Resistance of Achromobacter in Cystic Fibrosis.

Achromobacter species are increasingly being detected in patients with cystic fibrosis (CF), and this emerging pathogen is associated with antibiotic resistance and more-severe disease outcomes. Nonetheless, little is known about the extent of transmission and antibiotic resistance development in Achromobacter infections. We sequenced the genomes of 101 Achromobacter clinical isolates (identified as Achromobacter xylosoxidans based on matrix-assister laser desorption ionization-time of flight [MALDI-TOF] or API N20 typing) collected from 51 patients with CF-the largest longitudinal data set to date. We performed phylogenetic analysis on the genomes and combined this with epidemiological and antibiotic resistance data to identify patient-to-patient transmission and the development of antibiotic resistance. We confirmed that the MALDI-TOF or API N20 method was not sufficient for Achromobacter species-level typing and that the population of Achromobacter isolates was composed of five different species, among which A. xylosoxidans accounted for 52% of infections. Most patients were infected by unique Achromobacter clone types; nonetheless, suspected patient-to-patient transmission cases identified by shared clone types were observed in 35% (n = 18) of patients. In 15 of 16 cases, the suspected transmissions were further supported by genome- or clinic visit-based epidemiological analysis. Finally, we found that resistance developed over time. We show that whole-genome sequencing (WGS) is essential for Achromobacter species typing and identification of patient-to-patient transmission, which was revealed for Achromobacter ruhlandii, A. xylosoxidans, and, for the first time, Achromobacter insuavis Furthermore, we show that the development of antibiotic resistance is associated with chronic Achromobacter infections. Our findings emphasize that transmission and antibiotic resistance should be considered in future treatment strategies.

Independent predictors for 90-day readmission of emergency department patients admitted with sepsis: a prospective cohort study.

BACKGROUND: The primary objective of our study was to examine predictors for readmission in a prospective cohort of sepsis patients admitted to an emergency department (ED) and identified by the new Sepsis-3 criteria. METHOD: A single-center observational population-based cohort study among all adult (≥18 years) patients with sepsis admitted to the emergency department of Slagelse Hospital during 1.10.2017-31.03.2018. Sepsis was defined as an increase in the sequential organ failure assessment (SOFA) score of ≥2. The primary outcome was 90-day readmission. We followed patients from the date of discharge from the index admission until the end of the follow-up period or until the time of readmission to hospital, emigration or death, whichever came first. We used competing-risks regression to estimate adjusted subhazard ratios (aSHRs) with 95% confidence intervals (CI) for covariates in the regression models. RESULTS: A total of 2110 patients were admitted with infections, whereas 714 (33.8%) suffered sepsis. A total of 52 patients had died during admission and were excluded leaving 662 patients (44.1% female) with a median age of 74.8 (interquartile range: 66.0-84.2) years for further analysis. A total of 237 (35,8%; 95% CI 32.1-39.6) patients were readmitted within 90 days, and 54(8.2%) had died after discharge without being readmitted. We found that a history of malignant disease (aSHR 1,61; 1.16-2.23), if previously admitted with sepsis within 1 year before the index admission (aSHR; 1.41; 1.08-1.84), and treatment with diuretics (aSHR 1.51; 1.17-1.94) were independent predictors for readmission. aSHR (1.49, 1.13-1.96) for diuretic treatment was almost unchanged after exclusion of patients with heart failure, while aSHR (1.47, 0.96-2.25) for malignant disease was slightly attenuated after exclusion of patients with metastatic tumors. CONCLUSIONS: More than one third of patients admitted with sepsis, and discharged alive, were readmitted within 90 days. A history of malignant disease, if previously admitted with sepsis, and diuretic treatment were independent predictors for 90-day readmission.

Mortality of older acutely admitted medical patients after early discharge from emergency departments: a nationwide cohort study.

BACKGROUND: The mortality of older patients after early discharge from hospitals is sparsely described. Information on factors associated with mortality can help identify high-risk patients who may benefit from preventive interventions. The aim of this study was to examine whether demographic factors, comorbidity and admission diagnoses are predictors of 30-day mortality among acutely admitted older patients discharged within 24 h after admission. METHODS: All medical patients aged ≥65 years admitted acutely to Danish hospitals between 1 January 2013 and 30 June 2014 surviving a hospital stay of ≤24 h were included. Demographic factors, comorbidity, discharge diagnoses and mortality within 30 days were described using data from the Danish National Patient Registry and the Civil Registration System. Cox regression was used to estimate adjusted hazard ratios (aHR) with 95% confidence intervals (CI) for all-cause mortality. RESULTS: A total of 93,295 patients (49.4% men) with a median age of 75 years (interquartile range: 69-82 years), were included. Out of these, 2775 patients (3.0%; 95% CI 2.9-3.1%) died within 30 days after discharge. The 30-day mortality was increased in patients with age 76-85 years (aHR 1.59; 1.45-1.75) and 86+ years (aHR 3.35; 3.04-3.70), male gender (aHR 1.22; 1.11-1.33), a Charlson Comorbidity Index of 1-2 (aHR 2.15; 1.92-2.40) and 3+ (aHR 4.07; 3.65-4.54), and unmarried status (aHR 1.17; 1.08-1.27). Discharge diagnoses associated with 30-day mortality were heart failure (aHR 1.52; 1.17-1.95), respiratory failure (aHR 3.18; 2.46-4.11), dehydration (aHR 2.87; 2.51-3.29), constipation (aHR 1.31; 1.02-1.67), anemia (aHR 1.45; 1.27-1.66), pneumonia (aHR 2.24; 1.94-2.59), urinary tract infection (aHR 1.33; 1.14-1.55), dyspnea (aHR 1.57; 1.32-1.87) and suspicion of malignancy (aHR 2.06; 1.64-2.59). CONCLUSIONS: Three percent had died within 30 days. High age, male gender, the comorbidity burden, unmarried status and several primary discharge diagnoses were identified as independent prognostic factors of 30-day all-cause mortality.

Epidemiological characterisation of the first 785 SARS-CoV-2 Omicron variant cases in Denmark, December 2021.

By 9 December 2021, 785 SARS-CoV-2 Omicron variant cases have been identified in Denmark. Most cases were fully (76%) or booster-vaccinated (7.1%); 34 (4.3%) had a previous SARS-CoV-2 infection. The majority of cases with available information reported symptoms (509/666; 76%) and most were infected in Denmark (588/644; 91%). One in five cases cannot be linked to previous cases, indicating widespread community transmission. Nine cases have been hospitalised, one required intensive care and no deaths have been registered.

mTOR complex 2 phosphorylates IMP1 cotranslationally to promote IGF2 production and the proliferation of mouse embryonic fibroblasts.

Lack of IGF2 in mice results in diminished embryonic growth due to diminished cell proliferation. Here we show that mouse embryonic fibroblasts lacking the RNA-binding protein IMP1 (IGF2 mRNA-binding protein 1) have defective splicing and translation of IGF2 mRNAs, markedly reduced IGF2 polypeptide production, and diminished proliferation. The proliferation of the IMP1-null fibroblasts can be restored to wild-type levels by IGF2 in vitro or by re-expression of IMP1, which corrects the defects in IGF2 RNA splicing and translation. The ability of IMP1 to correct these defects is dependent on IMP1 phosphorylation at Ser181, which is catalyzed cotranslationally by mTOR complex 2 (mTORC2). Phosphorylation strongly enhances IMP1 binding to the IGF2-leader 3 5' untranslated region, which is absolutely required to enable IGF2-leader 3 mRNA translational initiation by internal ribosomal entry. These findings uncover a new mechanism by which mTOR regulates organismal growth by promoting IGF2 production in the mouse embryo through mTORC2-catalyzed cotranslational IMP1/IMP3 phosphorylation. Inasmuch as TORC2 is activated by association with ribosomes, the present results indicate that mTORC2-catalyzed cotranslational protein phosphorylation is a core function of this complex.

Variant in ERAP1 promoter region is associated with low expression in a patient with a Behçet-like MHC-I-opathy.

Behçet disease (BD) is an immune-mediated disease. The cause of BD remains unknown, but the existence of multiple pathological pathways is suspected, including different genetic factors. Polymorphisms in ERAP1 gene have been associated with an increased risk of BD. However, while current BD-associated ERAP1 variants are suggested to contribute to disease by altering the activity of the encoded protein, there is no knowledge of variants that alter the expression level of ERAP1, despite previous associations between ERAP1 expression and BD. Here, we used whole-exome sequencing of a patient with a Behçet-like MHC-I-opathy to identify that the patient, unlike its healthy parents, was homozygous for a rare 1-bp deletion, rs140416843, in the promoter region of ERAP1. rs140416843 has not previously been associated with disease, but is linked to ERAP1 haplotype Hap10 which is associated with BD. The expression of ERAP1 by both RT-qPCR and RNA sequencing showed that ERAP1 mRNA expression correlated with the zygosity for the identified deletion and was decreased in comparison to a healthy cohort. In conclusion, we diagnosed the patient as having BD, and hypothesize that rs140416843-mediated changes in ERAP1 expression play a causative role in BD and that this risk factor is contributing to the association between Hap10 and BD. This is the first report to identify a variant that may cause BD by altering the expression of ERAP1, and our findings suggest that downregulation of ERAP1 expression can serve as a diagnostic marker for BD.

Ultra-fast detection and quantification of nucleic acids by amplification-free fluorescence assay.

Two types of clinically important nucleic acid biomarkers, microRNA (miRNA) and circulating tumor DNA (ctDNA) were detected and quantified from human serum using an amplification-free fluorescence hybridization assay. Specifically, miRNAs hsa-miR-223-3p and hsa-miR-486-5p with relevance for rheumatoid arthritis and cancer related mutations BRAF and KRAS of ctDNA were directly measured. The required oligonucleotide probes for the assay were rationally designed and synthesized through a novel "clickable" approach which is time and cost-effective. With no need for isolating nucleic acid components from serum, the fluoresence-based assay took only 1 hour. Detection and absolute quantification of targets was successfully achieved despite their notoriously low abundance, with a precision down to individual nucleotides. Obtained miRNA and ctDNA amounts showed overall a good correlation with current techniques. With appropriate probes, our novel assay and signal boosting approach could become a useful tool for point-of-care measuring other low abundance nucleic acid biomarkers.

qSOFA is a useful prognostic factor for 30-day mortality in infected patients fulfilling the SIRS criteria for sepsis.

INTRODUCTION: The "quick Sequential Organ Failure Assessment" (qSOFA) score is a bedside risk-stratification tool to predict the likelihood of organ dysfunction. This study evaluated the qSOFA score as a prognostic factor for 30-day mortality in emergency department (ED) patients with sepsis identified by the Systemic Inflammatory Response Syndrome (SIRS) criteria. METHODS: A historical cohort study was conducted reviewing patients admitted to a single-center ED from November 1, 2013, to October 31, 2014. All patients with suspected or proven infections who fulfilled two or more SIRS criteria were included. Data of SIRS, qSOFA and baseline clinical data were obtained from triage forms and patient records. RESULTS: A total of 434 patients with sepsis of any severity were included. A total of 73 (16.8%) had a qSOFA score of ≥2 and were more frequently transferred to the intensive care unit (ICU) (26.0 vs. 6.7%; 95% confidence interval (CI) of the difference 8.9-29.7%) and had increased 30-day mortality (32.9 vs. 9.1%, 95% CI of the difference 12.6-35.0%) compared to patients with a qSOFA score of <2. In an adjusted logistic regression model, a qSOFA score of ≥2 was independently associated with 30-day mortality (odds ratio 4.83; 95% CI 2.11-11.02). CONCLUSION: Almost one third of the patients with a qSOFA score of ≥2 had died within 30 days and a qSOFA score of ≥2 was independently associated with mortality. This study indicated that qSOFA score of at least two could provide useful prognostic information for septic patients defined by the SIRS criteria.

Tumor miRNA expression profile is related to vestibular schwannoma growth rate.

OBJECTIVE: Our objective was to investigate if the tumor microRNA (miRNA) expression profile was related to tumor growth rate. Growth-related miRNAs might be potential targets for future therapeutic intervention. MATERIAL AND METHODS: Tumor tissue was sampled during surgery of patients with a sporadic vestibular schwannoma. Tumor growth rate was determined by tumor measurement on the two latest pre-operative MRI scans. Tumor miRNA expression was analyzed using the Affymetrix Gene Chip® protocol, and CEL files were generated using GeneChip® Command Console® Software and normalized using Partek Genomics Suite 6.5. The CEL files were analyzed using the statistical software program R. Principal component analysis, affected gene ontology analysis, and analysis of miRNA expression fold changes were used for analysis of potential relations between miRNA expression profile and tumor growth rate. RESULTS AND CONCLUSION: Tumor miRNA expression is related to the growth rate of sporadic vestibular schwannomas. Rapid tumor growth is associated with deregulation of several miRNAs, including upregulation of miR-29abc, miR-19, miR-340-5p, miR-21, and miR-221 and downregulation of miR-744 and let-7b. Gene ontologies affected by the deregulated miRNAs included neuron development and differentiation, gene silencing, and negative regulation of various biological processes, including cellular and intracellular signaling and metabolism.

Deconvolution of autoencoders to learn biological regulatory modules from single cell mRNA sequencing data.

BACKGROUND: Unsupervised machine learning methods (deep learning) have shown their usefulness with noisy single cell mRNA-sequencing data (scRNA-seq), where the models generalize well, despite the zero-inflation of the data. A class of neural networks, namely autoencoders, has been useful for denoising of single cell data, imputation of missing values and dimensionality reduction. RESULTS: Here, we present a striking feature with the potential to greatly increase the usability of autoencoders: With specialized training, the autoencoder is not only able to generalize over the data, but also to tease apart biologically meaningful modules, which we found encoded in the representation layer of the network. Our model can, from scRNA-seq data, delineate biological meaningful modules that govern a dataset, as well as give information as to which modules are active in each single cell. Importantly, most of these modules can be explained by known biological functions, as provided by the Hallmark gene sets. CONCLUSIONS: We discover that tailored training of an autoencoder makes it possible to deconvolute biological modules inherent in the data, without any assumptions. By comparisons with gene signatures of canonical pathways we see that the modules are directly interpretable. The scope of this discovery has important implications, as it makes it possible to outline the drivers behind a given effect of a cell. In comparison with other dimensionality reduction methods, or supervised models for classification, our approach has the benefit of both handling well the zero-inflated nature of scRNA-seq, and validating that the model captures relevant information, by establishing a link between input and decoded data. In perspective, our model in combination with clustering methods is able to provide information about which subtype a given single cell belongs to, as well as which biological functions determine that membership.

Plasma total cell-free DNA is a prognostic biomarker of overall survival in metastatic solid tumour patients.

BACKGROUND: Selecting patients for early clinical trials is a challenging process and clinicians lack sufficient tools to predict overall survival (OS). Circulating cell-free DNA (cfDNA) has recently been shown to be a promising prognostic biomarker. The aim of this study was to investigate whether baseline cfDNA measurement could improve the prognostic information of the Royal Marsden Hospital (RMH) score. METHODS: Solid tumour patients referred for phase I trials were included in the Copenhagen Personalized Oncology (CoPPO) programme. Baseline characteristics were collected prospectively, including the RMH prognostic score, Eastern Cooperative Oncology Group (ECOG) performance status and concentration of cfDNA per millilitre plasma. Cox proportional hazards model was used to assess the prognostic value of baseline variables. RESULTS: Plasma cfDNA concentration was quantifiable in 302 patients out of a total of 419 included in the study period of 2 years and 5 months. The RMH score was confirmed to be associated with OS. Cell-free DNA was shown to be an independent prognostic marker of OS and improved the risk model, including RMH, performance status and age. Furthermore, both plasma cfDNA concentration and RMH score were associated with treatment allocation (p < 0.00001). CONCLUSION: Our model based on RMH score, age, ECOG performance status and cfDNA improved prediction of OS and constitutes a clinically valuable tool when selecting patients for early clinical trials. An interactive version of the prognostic model is published on http://bit.ly/phase1survival .