Roberto Romero

Bio: Roberto Romero is an academic researcher from National Institutes of Health. The author has contributed to research in topics: Amniotic fluid & Chorioamnionitis. The author has an hindex of 151, co-authored 1516 publications receiving 108321 citations. Previous affiliations of Roberto Romero include University of Michigan & Weizmann Institute of Science.

Failure of endotoxin to cross the chorioamniotic membranes in vitro

Abstract: We have previously reported the detection of endotoxin in the amniotic fluid of patients with gram-negative intra-amniotic infection. Endotoxin or lipopolysaccharide (LPS) is a potent biologic product capable of inducing prostaglandin release from several cell types, and therefore may be involved in the onset of human parturition in the setting of intra-amniotic infection. The experiments outlined in this report were designed to determine whether endotoxin crosses chorioamniotic membranes in vitro. Chorioamniotic membranes obtained at the time of elective cesarean section were placed in Ussing chambers used for transport experiments. Endotoxin was placed in one chamber, and serial timed samples were taken from both chambers for endotoxin quantification, which was performed with the limulus amebocyte gel clot assay. Blue dextran was used to exclude the presence of large defects. Bromophenol blue was used to demonstrate membrane permeability to low-molecular weight substances. Endotoxin failed to cross the chorioamniotic membranes in all experiments (n = 11).

Are B cells altered in the decidua of women with preterm or term labor

Abstract: Problem The immunophenotype of B cells at the maternal-fetal interface (decidua) in labor at term and preterm labor is poorly understood. Method of study Decidual tissues were obtained from women with preterm or term labor and from non-labor gestational age-matched controls. Immunophenotyping of decidual B cells was performed using multicolor flow cytometry. Results (a) In the absence of acute or chronic chorioamnionitis, total B cells were more abundant in the decidua parietalis of women who delivered preterm than in those who delivered at term, regardless of the presence of labor; (b) decidual transitional and naive B cells were the most abundant B-cell subsets; (c) decidual B1 B cells were increased in women with either labor at term or preterm labor and chronic chorioamnionitis compared to those without this placental lesion; (d) decidual transitional B cells were reduced in women with preterm labor compared to those without labor; (e) naive, class-switched, and non-class-switched B cells in the decidual tissues underwent mild alterations with the process of preterm labor; (f) decidual plasmablasts seemed to increase in women with either labor at term or preterm labor with chronic chorioamnionitis; and (g) decidual B cells expressed high levels of interleukin (IL)-12, IL-6, and/or IL-35. Conclusion Total B cells are not increased with the presence of preterm or term labor; yet, specific subsets (B1 and plasmablasts) undergo alterations in women with chronic chorioamnionitis. Therefore, B cells are solely implicated in the pathological process of preterm labor in a subset of women with chronic inflammation of the placenta. These findings provide insight into the immunology of the maternal-fetal interface in preterm and term labor.

The alarmin interleukin-1α causes preterm birth through the NLRP3 inflammasome

Abstract: Sterile intra-amniotic inflammation is a clinical condition frequently observed in women with preterm labor and birth, the leading cause of neonatal morbidity and mortality worldwide. Growing evidence suggests that alarmins found in amniotic fluid, such as interleukin (IL)-1α, are central initiators of sterile intra-amniotic inflammation. However, the causal link between elevated intra-amniotic concentrations of IL-1α and preterm birth has yet to be established. Herein, using an animal model of ultrasound-guided intra-amniotic injection of IL-1α, we show that elevated concentrations of IL-1α cause preterm birth and neonatal mortality. Additionally, using immunoblotting techniques and a specific immunoassay, we report that the intra-amniotic administration of IL-1α induces activation of the NOD-like receptor family, pyrin domain containing 3 (NLRP3) inflammasome in the fetal membranes, but not in the decidua, as evidenced by a concomitant increase in the protein levels of NLRP3, active caspase-1, and IL-1β. Lastly, using Nlrp3-/- mice, we demonstrate that the deficiency of this inflammasome sensor molecule reduces the rates of preterm birth and neonatal mortality caused by the intra-amniotic injection of IL-1α. Collectively, these results demonstrate a causal link between elevated IL-1α concentrations in the amniotic cavity and preterm birth as well as adverse neonatal outcomes, a pathological process that is mediated by the NLRP3 inflammasome. These findings shed light on the mechanisms underlying sterile intra-amniotic inflammation and provide further evidence that this clinical condition can potentially be treated by targeting the NLRP3 inflammasome.

New Onto-Tools: Promoter-Express, nsSNPCounter and Onto-Translate

Abstract: The Onto-Tools suite is composed of an annotation database and eight complementary, web-accessible data mining tools: Onto-Express, Onto-Compare, Onto-Design, Onto-Translate, Onto-Miner, Pathway-Express, Promoter-Express and nsSNPCounter. Promoter-Express is a new tool added to the Onto-Tools ensemble that facilitates the identification of transcription factor binding sites active in specific conditions. nsSNPCounter is another new tool that allows computation and analysis of synonymous and non-synonymous codon substitutions for studying evolutionary rates of protein coding genes. Onto-Translate has also been enhanced to expand its scope and accuracy by fully utilizing the capabilities of the Onto-Tools database. Currently, Onto-Translate allows arbitrary mappings between 28 types of IDs for 53 organisms. Onto-Tools are freely available at http://vortex.cs.wayne.edu/Projects.html.

A single-cell atlas of the myometrium in human parturition

Abstract: Parturition is a well-orchestrated process characterized by increased uterine contractility, cervical ripening, and activation of the chorioamniotic membranes; yet, the transition from a quiescent to a contractile myometrium heralds the onset of labor. However, the cellular underpinnings of human parturition in the uterine tissues are still poorly understood. Herein, we performed a comprehensive study of the human myometrium during spontaneous term labor using single-cell RNA sequencing (scRNA-Seq). First, we established a single-cell atlas of the human myometrium and unraveled the cell type–specific transcriptomic activity modulated during labor. Major cell types included distinct subsets of smooth muscle cells, monocytes/macrophages, stromal cells, and endothelial cells, all of which communicated and participated in immune (e.g., inflammation) and nonimmune (e.g., contraction) processes associated with labor. Furthermore, integrating scRNA-Seq and microarray data with deconvolution of bulk gene expression highlighted the contribution of smooth muscle cells to labor-associated contractility and inflammatory processes. Last, myometrium-derived single-cell signatures can be quantified in the maternal whole-blood transcriptome throughout pregnancy and are enriched in women in labor, providing a potential means of noninvasively monitoring pregnancy and its complications. Together, our findings provide insights into the contributions of specific myometrial cell types to the biological processes that take place during term parturition.

limma powers differential expression analyses for RNA-sequencing and microarray studies

Abstract: limma is an R/Bioconductor software package that provides an integrated solution for analysing data from gene expression experiments. It contains rich features for handling complex experimental designs and for information borrowing to overcome the problem of small sample sizes. Over the past decade, limma has been a popular choice for gene discovery through differential expression analyses of microarray and high-throughput PCR data. The package contains particularly strong facilities for reading, normalizing and exploring such data. Recently, the capabilities of limma have been significantly expanded in two important directions. First, the package can now perform both differential expression and differential splicing analyses of RNA sequencing (RNA-seq) data. All the downstream analysis tools previously restricted to microarray data are now available for RNA-seq as well. These capabilities allow users to analyse both RNA-seq and microarray data with very similar pipelines. Second, the package is now able to go past the traditional gene-wise expression analyses in a variety of ways, analysing expression profiles in terms of co-regulated sets of genes or in terms of higher-order expression signatures. This provides enhanced possibilities for biological interpretation of gene expression differences. This article reviews the philosophy and design of the limma package, summarizing both new and historical features, with an emphasis on recent enhancements and features that have not been previously described.

STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.

Abstract: Proteins and their functional interactions form the backbone of the cellular machinery. Their connectivity network needs to be considered for the full understanding of biological phenomena, but the available information on protein-protein associations is incomplete and exhibits varying levels of annotation granularity and reliability. The STRING database aims to collect, score and integrate all publicly available sources of protein-protein interaction information, and to complement these with computational predictions. Its goal is to achieve a comprehensive and objective global network, including direct (physical) as well as indirect (functional) interactions. The latest version of STRING (11.0) more than doubles the number of organisms it covers, to 5090. The most important new feature is an option to upload entire, genome-wide datasets as input, allowing users to visualize subsets as interaction networks and to perform gene-set enrichment analysis on the entire input. For the enrichment analysis, STRING implements well-known classification systems such as Gene Ontology and KEGG, but also offers additional, new classification systems based on high-throughput text-mining as well as on a hierarchical clustering of the association network itself. The STRING resource is available online at https://string-db.org/.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

Standards of Medical Care in Diabetes

Abstract: XI. STRATEGIES FOR IMPROVING DIABETES CARE D iabetes is a chronic illness that requires continuing medical care and patient self-management education to prevent acute complications and to reduce the risk of long-term complications. Diabetes care is complex and requires that many issues, beyond glycemic control, be addressed. A large body of evidence exists that supports a range of interventions to improve diabetes outcomes. These standards of care are intended to provide clinicians, patients, researchers, payors, and other interested individuals with the components of diabetes care, treatment goals, and tools to evaluate the quality of care. While individual preferences, comorbidities, and other patient factors may require modification of goals, targets that are desirable for most patients with diabetes are provided. These standards are not intended to preclude more extensive evaluation and management of the patient by other specialists as needed. For more detailed information, refer to Bode (Ed.): Medical Management of Type 1 Diabetes (1), Burant (Ed): Medical Management of Type 2 Diabetes (2), and Klingensmith (Ed): Intensive Diabetes Management (3). The recommendations included are diagnostic and therapeutic actions that are known or believed to favorably affect health outcomes of patients with diabetes. A grading system (Table 1), developed by the American Diabetes Association (ADA) and modeled after existing methods, was utilized to clarify and codify the evidence that forms the basis for the recommendations. The level of evidence that supports each recommendation is listed after each recommendation using the letters A, B, C, or E.