Molecular mechanisms reconstruction from single-cell multi-omics data with HuMMuS.

MOTIVATION: The molecular identity of a cell results from a complex interplay between heterogeneous molecular layers. Recent advances in single-cell sequencing technologies have opened the possibility to measure such molecular layers of regulation. RESULTS: Here, we present HuMMuS, a new method for inferring regulatory mechanisms from single-cell multi-omics data. Differently from the state-of-the-art, HuMMuS captures cooperation between biological macromolecules and can easily include additional layers of molecular regulation. We benchmarked HuMMuS with respect to the state-of-the-art on both paired and unpaired multi-omics datasets. Our results proved the improvements provided by HuMMuS in terms of transcription factor (TF) targets, TF binding motifs and regulatory regions prediction. Finally, once applied to snmC-seq, scATAC-seq and scRNA-seq data from mouse brain cortex, HuMMuS enabled to accurately cluster scRNA profiles and to identify potential driver TFs. AVAILABILITY AND IMPLEMENTATION: HuMMuS is available at https://github.com/cantinilab/HuMMuS.

Microglia maintain structural integrity during fetal brain morphogenesis.

Microglia (MG), the brain-resident macrophages, play major roles in health and disease via a diversity of cellular states. While embryonic MG display a large heterogeneity of cellular distribution and transcriptomic states, their functions remain poorly characterized. Here, we uncovered a role for MG in the maintenance of structural integrity at two fetal cortical boundaries. At these boundaries between structures that grow in distinct directions, embryonic MG accumulate, display a state resembling post-natal axon-tract-associated microglia (ATM) and prevent the progression of microcavities into large cavitary lesions, in part via a mechanism involving the ATM-factor Spp1. MG and Spp1 furthermore contribute to the rapid repair of lesions, collectively highlighting protective functions that preserve the fetal brain from physiological morphogenetic stress and injury. Our study thus highlights key major roles for embryonic MG and Spp1 in maintaining structural integrity during morphogenesis, with major implications for our understanding of MG functions and brain development.

Paired single-cell multi-omics data integration with Mowgli.

The profiling of multiple molecular layers from the same set of cells has recently become possible. There is thus a growing need for multi-view learning methods able to jointly analyze these data. We here present Multi-Omics Wasserstein inteGrative anaLysIs (Mowgli), a novel method for the integration of paired multi-omics data with any type and number of omics. Of note, Mowgli combines integrative Nonnegative Matrix Factorization and Optimal Transport, enhancing at the same time the clustering performance and interpretability of integrative Nonnegative Matrix Factorization. We apply Mowgli to multiple paired single-cell multi-omics data profiled with 10X Multiome, CITE-seq, and TEA-seq. Our in-depth benchmark demonstrates that Mowgli's performance is competitive with the state-of-the-art in cell clustering and superior to the state-of-the-art once considering biological interpretability. Mowgli is implemented as a Python package seamlessly integrated within the scverse ecosystem and it is available at http://github.com/cantinilab/mowgli .

Identification and economic burden of main adverse events of nerve injuries caused by regional anesthesia: a systematic review

Abstract Background and objectives: Anesthesiologists and hospitals are increasingly confronted with costs associated with the complications of Peripheral Nerve Blocks (PNB) procedures. The objective of our study was to identify the incidence of the main adverse events associated with regional anesthesia, particularly during anesthetic PNB, and to evaluate the associated healthcare and social costs. Methods: According to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, we conducted a systematic search on EMBASE and PubMed with the following search strategy: (‟regional anesthesia" OR ‟nerve block") AND (‟complications" OR ‟nerve lesion" OR ‟nerve damage" OR ‟nerve injury"). Studies on patients undergoing a regional anesthesia procedure other than spinal or epidural were included. Targeted data of the selected studies were extracted and further analyzed. Results: Literature search revealed 487 articles, 21 of which met the criteria to be included in our analysis. Ten of them were included in the qualitative and 11 articles in the quantitative synthesis. The analysis of costs included data from four studies and 2,034 claims over 51,242 cases. The median claim consisted in 39,524 dollars in the United States and 22,750 pounds in the United Kingdom. The analysis of incidence included data from seven studies involving 424,169 patients with an overall estimated incidence of 137/10,000. Conclusion: Despite limitations, we proposed a simple model of cost calculation. We found that, despite the relatively low incidence of adverse events following PNB, their associated costs were relevant and should be carefully considered by healthcare managers and decision makers.

Identification and economic burden of main adverse events of nerve injuries caused by regional anesthesia: a systematic review.

BACKGROUND AND OBJECTIVES: Anesthesiologists and hospitals are increasingly confronted with costs associated with the complications of Peripheral Nerve Blocks (PNB) procedures. The objective of our study was to identify the incidence of the main adverse events associated with regional anesthesia, particularly during anesthetic PNB, and to evaluate the associated healthcare and social costs. METHODS: According to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, we conducted a systematic search on EMBASE and PubMed with the following search strategy: ("regional anesthesia" OR "nerve block") AND ("complications" OR "nerve lesion" OR "nerve damage" OR "nerve injury"). Studies on patients undergoing a regional anesthesia procedure other than spinal or epidural were included. Targeted data of the selected studies were extracted and further analyzed. RESULTS: Literature search revealed 487 articles, 21 of which met the criteria to be included in our analysis. Ten of them were included in the qualitative and 11 articles in the quantitative synthesis. The analysis of costs included data from four studies and 2,034 claims over 51,242 cases. The median claim consisted in 39,524 dollars in the United States and 22,750 pounds in the United Kingdom. The analysis of incidence included data from seven studies involving 424,169 patients with an overall estimated incidence of 137/10,000. CONCLUSIONS: Despite limitations, we proposed a simple model of cost calculation. We found that, despite the relatively low incidence of adverse events following PNB, their associated costs were relevant and should be carefully considered by healthcare managers and decision makers.

Optimal transport improves cell-cell similarity inference in single-cell omics data.

MOTIVATION: High-throughput single-cell molecular profiling is revolutionizing biology and medicine by unveiling the diversity of cell types and states contributing to development and disease. The identification and characterization of cellular heterogeneity are typically achieved through unsupervised clustering, which crucially relies on a similarity metric. RESULTS: We here propose the use of Optimal Transport (OT) as a cell-cell similarity metric for single-cell omics data. OT defines distances to compare high-dimensional data represented as probability distributions. To speed up computations and cope with the high dimensionality of single-cell data, we consider the entropic regularization of the classical OT distance. We then extensively benchmark OT against state-of-the-art metrics over 13 independent datasets, including simulated, scRNA-seq, scATAC-seq and single-cell DNA methylation data. First, we test the ability of the metrics to detect the similarity between cells belonging to the same groups (e.g. cell types, cell lines of origin). Then, we apply unsupervised clustering and test the quality of the resulting clusters. OT is found to improve cell-cell similarity inference and cell clustering in all simulated and real scRNA-seq data, as well as in scATAC-seq and single-cell DNA methylation data. AVAILABILITY AND IMPLEMENTATION: All our analyses are reproducible through the OT-scOmics Jupyter notebook available at https://github.com/ComputationalSystemsBiology/OT-scOmics. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Can a Glove-Coach Technology Significantly Increase the Efficacy of Cardiopulmonary Resuscitation on Non-healthcare Professionals? A Controlled Trial.

Introduction: Cardiovascular accidents are the world's leading cause of death. A good quality cardiopulmonary resuscitation (CPR) can reduce cardiac arrest-associated mortality. This study aims to test the coaching system of a wearable glove, providing instructions during out-of-hospital CPR. Materials and Methods: We performed a single-blind, controlled trial to test non-healthcare professionals during a simulated CPR performed on an electronic mannequin. The no-glove group was the control. The primary outcome was to compare the accuracy of depth and frequency of two simulated CPR sessions. Secondary outcomes were to compare the decay of CPR performance and the percentage of the duration of accurate CPR. Results: About 130 volunteers were allocated to 1:1 ratio in both groups; mean age was 36 ± 15 years (min-max 21-64) and 62 (48%) were men; 600 chest compressions were performed, and 571 chest compressions were analyzed. The mean frequency in the glove group was 117.67 vs. 103.02 rpm in the control group (p < 0.001). The appropriate rate cycle was 92.4% in the glove group vs. 71% in the control group, with a difference of 21.4% (p < 0.001). Mean compression depth in the glove group was 52.11 vs. 55.17 mm in the control group (p < 0.001). A mean reduction of compression depth over time of 5.3 mm/min was observed in the control group vs. 0.83 mm/min of reduction in the glove group. Conclusion: Visual and acoustic feedbacks provided through the utilization of the glove's coaching system were useful for non-healthcare professionals' CPR performance.

Evaluating the Reproducibility of Single-Cell Gene Regulatory Network Inference Algorithms.

Networks are powerful tools to represent and investigate biological systems. The development of algorithms inferring regulatory interactions from functional genomics data has been an active area of research. With the advent of single-cell RNA-seq data (scRNA-seq), numerous methods specifically designed to take advantage of single-cell datasets have been proposed. However, published benchmarks on single-cell network inference are mostly based on simulated data. Once applied to real data, these benchmarks take into account only a small set of genes and only compare the inferred networks with an imposed ground-truth. Here, we benchmark six single-cell network inference methods based on their reproducibility, i.e., their ability to infer similar networks when applied to two independent datasets for the same biological condition. We tested each of these methods on real data from three biological conditions: human retina, T-cells in colorectal cancer, and human hematopoiesis. Once taking into account networks with up to 100,000 links, GENIE3 results to be the most reproducible algorithm and, together with GRNBoost2, show higher intersection with ground-truth biological interactions. These results are independent from the single-cell sequencing platform, the cell type annotation system and the number of cells constituting the dataset. Finally, GRNBoost2 and CLR show more reproducible performance once a more stringent thresholding is applied to the networks (1,000-100 links). In order to ensure the reproducibility and ease extensions of this benchmark study, we implemented all the analyses in scNET, a Jupyter notebook available at https://github.com/ComputationalSystemsBiology/scNET.

Benchmarking joint multi-omics dimensionality reduction approaches for the study of cancer.

High-dimensional multi-omics data are now standard in biology. They can greatly enhance our understanding of biological systems when effectively integrated. To achieve proper integration, joint Dimensionality Reduction (jDR) methods are among the most efficient approaches. However, several jDR methods are available, urging the need for a comprehensive benchmark with practical guidelines. We perform a systematic evaluation of nine representative jDR methods using three complementary benchmarks. First, we evaluate their performances in retrieving ground-truth sample clustering from simulated multi-omics datasets. Second, we use TCGA cancer data to assess their strengths in predicting survival, clinical annotations and known pathways/biological processes. Finally, we assess their classification of multi-omics single-cell data. From these in-depth comparisons, we observe that intNMF performs best in clustering, while MCIA offers an effective behavior across many contexts. The code developed for this benchmark study is implemented in a Jupyter notebook-multi-omics mix (momix)-to foster reproducibility, and support users and future developers.

An Integrated Analysis of miRNA and Gene Expression Changes in Response to an Obesogenic Diet to Explore the Impact of Transgenerational Supplementation with Omega 3 Fatty Acids.

Insulin resistance decreases the ability of insulin to inhibit hepatic gluconeogenesis, a key step in the development of metabolic syndrome. Metabolic alterations, fat accumulation, and fibrosis in the liver are closely related and contribute to the progression of comorbidities, such as hypertension, type 2 diabetes, or cancer. Omega 3 (n-3) polyunsaturated fatty acids, such as eicosapentaenoic acid (EPA), were identified as potent positive regulators of insulin sensitivity in vitro and in animal models. In the current study, we explored the effects of a transgenerational supplementation with EPA in mice exposed to an obesogenic diet on the regulation of microRNAs (miRNAs) and gene expression in the liver using high-throughput techniques. We implemented a comprehensive molecular systems biology approach, combining statistical tools, such as MicroRNA Master Regulator Analysis pipeline and Boolean modeling to integrate these biochemical processes. We demonstrated that EPA mediated molecular adaptations, leading to the inhibition of miR-34a-5p, a negative regulator of Irs2 as a master regulatory event leading to the inhibition of gluconeogenesis by insulin during the fasting-feeding transition. Omics data integration provided greater biological insight and a better understanding of the relationships between biological variables. Such an approach may be useful for deriving innovative data-driven hypotheses and for the discovery of molecular-biochemical mechanistic links.

Prevalence of microhematuria in renal colic and urolithiasis: a systematic review and meta-analysis.

BACKGROUND: This systematic review and meta-analysis aims to investigate the prevalence of microhematuria in patients presenting with suspected acute renal colic and/or confirmed urolithiasis at the emergency department. METHODS: A comprehensive literature search was conducted to find relevant data on prevalence of microhematuria in patients with suspected acute renal colic and/or confirmed urolithiasis. Data from each study regarding study design, patient characteristics and prevalence of microhematuria were retrieved. A random effect-model was used for the pooled analyses. RESULTS: Forty-nine articles including 15'860 patients were selected through the literature search. The pooled microhematuria prevalence was 77% (95%CI: 73-80%) and 84% (95%CI: 80-87%) for suspected acute renal colic and confirmed urolithiasis, respectively. This proportion was much higher when the dipstick was used as diagnostic test (80 and 90% for acute renal colic and urolithiasis, respectively) compared to the microscopic urinalysis (74 and 78% for acute renal colic and urolithiasis, respectively). CONCLUSIONS: This meta-analysis revealed a high prevalence of microhematuria in patients with acute renal colic (77%), including those with confirmed urolithiasis (84%). Intending this prevalence as sensitivity, we reached moderate values, which make microhematuria alone a poor diagnostic test for acute renal colic or urolithiasis. Microhematuria could possibly still important to assess the risk in patients with renal colic.

Real-time continuous monitoring of injection pressure during peripheral nerve blocks in fresh cadavers.

BACKGROUND: The incidence of unintentional intraneural injection while performing peripheral nerve block has been estimated to be 15% under real-time ultrasound guidance. Injection pressure increase may detect an intraneural injection. Real-time injection pressure changes throughout an entire nerve block procedure in relationship with needle tip location have never been reported. METHODS: A new method was developed to precisely monitor the injection pressure curve during nerve blocks, based on a miniaturised Fabbri-Perrot pressure sensor. We tested in three fresh cadavers the ability of continuous pressure monitoring to discriminate between different tissues, as the injection pressure curve ascending slope, shape and plateau pressure value depend on tissue compliance. Injections of saline were performed by an electronic syringe pump with three different constant flow rates. Pressure was measured simultaneously at the tip and in the tubing of the needle. RESULTS: At 10 mL/min injection flow, median peak injection pressure in the intraneural group at the needle tip was 315 mmHg, while at the perineural location it was 100 mmHg (p < 0.05). Median injection pressure was 95 mmHg in the intramuscular locations group, and 819 mmHg when a muscular fascia was indented (p < 0.05). A significant difference was noted for pressure measurements between the proximal port of the needle and the tip, 625 and 417 respectively. CONCLUSIONS: Based on significant differences in injection pressure values and curve shapes, the system was able to discriminate between four needle tip locations. This may help with needle tracking while performing a peripheral nerve block.

Collective intelligence defines biological functions in Wikipedia as communities in the hidden protein connection network.

English Wikipedia, containing more than five millions articles, has approximately eleven thousands web pages devoted to proteins or genes most of which were generated by the Gene Wiki project. These pages contain information about interactions between proteins and their functional relationships. At the same time, they are interconnected with other Wikipedia pages describing biological functions, diseases, drugs and other topics curated by independent, not coordinated collective efforts. Therefore, Wikipedia contains a directed network of protein functional relations or physical interactions embedded into the global network of the encyclopedia terms, which defines hidden (indirect) functional proximity between proteins. We applied the recently developed reduced Google Matrix (REGOMAX) algorithm in order to extract the network of hidden functional connections between proteins in Wikipedia. In this network we discovered tight communities which reflect areas of interest in molecular biology or medicine and can be considered as definitions of biological functions shaped by collective intelligence. Moreover, by comparing two snapshots of Wikipedia graph (from years 2013 and 2017), we studied the evolution of the network of direct and hidden protein connections. We concluded that the hidden connections are more dynamic compared to the direct ones and that the size of the hidden interaction communities grows with time. We recapitulate the results of Wikipedia protein community analysis and annotation in the form of an interactive online map, which can serve as a portal to the Gene Wiki project.

Interpreting pathways to discover cancer driver genes with Moonlight.

Cancer driver gene alterations influence cancer development, occurring in oncogenes, tumor suppressors, and dual role genes. Discovering dual role cancer genes is difficult because of their elusive context-dependent behavior. We define oncogenic mediators as genes controlling biological processes. With them, we classify cancer driver genes, unveiling their roles in cancer mechanisms. To this end, we present Moonlight, a tool that incorporates multiple -omics data to identify critical cancer driver genes. With Moonlight, we analyze 8000+ tumor samples from 18 cancer types, discovering 3310 oncogenic mediators, 151 having dual roles. By incorporating additional data (amplification, mutation, DNA methylation, chromatin accessibility), we reveal 1000+ cancer driver genes, corroborating known molecular mechanisms. Additionally, we confirm critical cancer driver genes by analysing cell-line datasets. We discover inactivation of tumor suppressors in intron regions and that tissue type and subtype indicate dual role status. These findings help explain tumor heterogeneity and could guide therapeutic decisions.

Early detection of intraneural and intravascular injections with real-time injection pressure monitoring in cadavers.

BACKGROUND AND OBJECTIVES: Injection pressure monitoring can help detecting the needle tip position and avoid intraneural injection. However, it shall be measured at the needle tip in order to be accurate and reproducible with any injection system and non operator-dependent. With an innovative system monitoring the injection pressure right at the needle tip we show that it is possible to early detect an intraneural and also an intravascular injection. METHODS: We performed supraclavicular block-like procedures under real-time ultrasound guidance on two fresh cadaver torsos using a sensing needle with an optical fiber pressure sensor within the shaft continuously measuring injection pressure at the needle tip. A total of 45 ultrasound-guided injections were performed (15 perineural, 15 intraneural and 15 intravenous injections). RESULTS: Mean (SD) injection pressure after only 1 mL injected volume was already significantly higher for the intraneural compared to the perineural injections: 70.46 kPa (11.72) vs 8.34 (4.68) kPa; P < .001. Mean (SD) injection pressure at 1 mL injected volume was significantly lower for the intravascular compared to the perineural injections: 1.51 (0.48) vs 8.34 (4.68) kPa; P < .001. CONCLUSIONS: Our results show that injection pressure monitoring at the needle tip has the potential to help identifying an accidental intraneural or intravascular injection at a very early stage.

Investigating the epi-miRNome: identification of epi-miRNAs using transfection experiments.

Aim: Growing evidence shows a strong interplay between post-transcriptional regulation, mediated by miRNAs (miRs) and epigenetic regulation. Nevertheless, the number of experimentally validated miRs (called epi-miRs) involved in these regulatory circuitries is still very small. Material & methods: We propose a pipeline to prioritize candidate epi-miRs and to identify potential epigenetic interactors of any given miR starting from miR transfection experiment datasets. Results & conclusion: We identified 34 candidate epi-miRs: 19 of them are known epi-miRs, while 15 are new. Moreover, using an in-house generated gene expression dataset, we experimentally proved that a component of the polycomb-repressive complex 2, the histone methyltransferase enhancer of zeste homolog 2 (EZH2), interacts with miR-214, a well-known prometastatic miR in melanoma and breast cancer, highlighting a miR-214-EZH2 regulatory axis potentially relevant in tumor progression.

Independent Component Analysis for Unraveling the Complexity of Cancer Omics Datasets.

Independent component analysis (ICA) is a matrix factorization approach where the signals captured by each individual matrix factors are optimized to become as mutually independent as possible. Initially suggested for solving source blind separation problems in various fields, ICA was shown to be successful in analyzing functional magnetic resonance imaging (fMRI) and other types of biomedical data. In the last twenty years, ICA became a part of the standard machine learning toolbox, together with other matrix factorization methods such as principal component analysis (PCA) and non-negative matrix factorization (NMF). Here, we review a number of recent works where ICA was shown to be a useful tool for unraveling the complexity of cancer biology from the analysis of different types of omics data, mainly collected for tumoral samples. Such works highlight the use of ICA in dimensionality reduction, deconvolution, data pre-processing, meta-analysis, and others applied to different data types (transcriptome, methylome, proteome, single-cell data). We particularly focus on the technical aspects of ICA application in omics studies such as using different protocols, determining the optimal number of components, assessing and improving reproducibility of the ICA results, and comparison with other popular matrix factorization techniques. We discuss the emerging ICA applications to the integrative analysis of multi-level omics datasets and introduce a conceptual view on ICA as a tool for defining functional subsystems of a complex biological system and their interactions under various conditions. Our review is accompanied by a Jupyter notebook which illustrates the discussed concepts and provides a practical tool for applying ICA to the analysis of cancer omics datasets.

Molecular Inverse Comorbidity between Alzheimer's Disease and Lung Cancer: New Insights from Matrix Factorization.

Matrix factorization (MF) is an established paradigm for large-scale biological data analysis with tremendous potential in computational biology. Here, we challenge MF in depicting the molecular bases of epidemiologically described disease-disease (DD) relationships. As a use case, we focus on the inverse comorbidity association between Alzheimer's disease (AD) and lung cancer (LC), described as a lower than expected probability of developing LC in AD patients. To this day, the molecular mechanisms underlying DD relationships remain poorly explained and their better characterization might offer unprecedented clinical opportunities. To this goal, we extend our previously designed MF-based framework for the molecular characterization of DD relationships. Considering AD-LC inverse comorbidity as a case study, we highlight multiple molecular mechanisms, among which we confirm the involvement of processes related to the immune system and mitochondrial metabolism. We then distinguish mechanisms specific to LC from those shared with other cancers through a pan-cancer analysis. Additionally, new candidate molecular players, such as estrogen receptor (ER), cadherin 1 (CDH1) and histone deacetylase (HDAC), are pinpointed as factors that might underlie the inverse relationship, opening the way to new investigations. Finally, some lung cancer subtype-specific factors are also detected, also suggesting the existence of heterogeneity across patients in the context of inverse comorbidity.

Assessing reproducibility of matrix factorization methods in independent transcriptomes.

MOTIVATION: Matrix factorization (MF) methods are widely used in order to reduce dimensionality of transcriptomic datasets to the action of few hidden factors (metagenes). MF algorithms have never been compared based on the between-datasets reproducibility of their outputs in similar independent datasets. Lack of this knowledge might have a crucial impact when generalizing the predictions made in a study to others. RESULTS: We systematically test widely used MF methods on several transcriptomic datasets collected from the same cancer type (14 colorectal, 8 breast and 4 ovarian cancer transcriptomic datasets). Inspired by concepts of evolutionary bioinformatics, we design a novel framework based on Reciprocally Best Hit (RBH) graphs in order to benchmark the MF methods for their ability to produce generalizable components. We show that a particular protocol of application of independent component analysis (ICA), accompanied by a stabilization procedure, leads to a significant increase in the between-datasets reproducibility. Moreover, we show that the signals detected through this method are systematically more interpretable than those of other standard methods. We developed a user-friendly tool for performing the Stabilized ICA-based RBH meta-analysis. We apply this methodology to the study of colorectal cancer (CRC) for which 14 independent transcriptomic datasets can be collected. The resulting RBH graph maps the landscape of interconnected factors associated to biological processes or to technological artifacts. These factors can be used as clinical biomarkers or robust and tumor-type specific transcriptomic signatures of tumoral cells or tumoral microenvironment. Their intensities in different samples shed light on the mechanistic basis of CRC molecular subtyping. AVAILABILITY AND IMPLEMENTATION: The RBH construction tool is available from http://goo.gl/DzpwYp. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Hope4Genes: a Hopfield-like class prediction algorithm for transcriptomic data.

After its introduction in 1982, the Hopfield model has been extensively applied for classification and pattern recognition. Recently, its great potential in gene expression patterns retrieval has also been shown. Following this line, we develop Hope4Genes a single-sample class prediction algorithm based on a Hopfield-like model. Differently from previous works, we here tested the performances of the algorithm for class prediction, a task of fundamental importance for precision medicine and therapeutic decision-making. Hope4Genes proved better performances than the state-of-art methodologies in the field independently of the size of the input dataset, its profiling platform, the number of classes and the typical class-imbalance present in biological data. Our results provide encoraging evidence that the Hopfield model, together with the use of its energy for the estimation of the false discoveries, is a particularly promising tool for precision medicine.