Search tips
Search criteria

Results 1-25 (179)

Clipboard (0)

Select a Filter Below

more »
Year of Publication
more »
1.  Human Gene-Centered Transcription Factor Networks for Enhancers and Disease Variants 
Cell  2015;161(3):661-673.
Gene regulatory networks (GRNs) comprising interactions between transcription factors (TFs) and regulatory loci control development and physiology. Numerous disease-associated mutations have been identified, the vast majority residing in non-coding regions of the genome. As current GRN mapping methods test one TF at a time and require the use of cells harboring the mutation(s) of interest, they are not suitable to identify TFs that bind to wild type and mutant loci. Here, we use gene-centered yeast one-hybrid (eY1H) assays to interrogate binding of 1,086 human TFs to 246 enhancers, as well as to 109 non-coding disease mutations. We detect both loss and gain of TF interactions with mutant loci that are concordant with target gene expression changes. This work establishes eY1H assays as a powerful addition to the toolkit of mapping human GRNs and for the high-throughput characterization of genomic variants that are rapidly being identified by genome-wide association studies.
PMCID: PMC4409666  PMID: 25910213
2.  Widespread Macromolecular Interaction Perturbations in Human Genetic Disorders 
Cell  2015;161(3):647-660.
How disease-associated mutations impair protein activities in the context of biological networks remains mostly undetermined. Although a few renowned alleles are well characterized, functional information is missing for over 100,000 disease-associated variants. Here we functionally profile several thousand missense mutations across a spectrum of Mendelian disorders using various interaction assays. The majority of disease-associated alleles exhibit wild-type chaperone binding profiles, suggesting they preserve protein folding or stability. While common variants from healthy individuals rarely affect interactions, two-thirds of disease-associated alleles perturb protein-protein interactions, with half corresponding to “edgetic” alleles affecting only a subset of interactions while leaving most other interactions unperturbed. With transcription factors, many alleles that leave protein-protein interactions intact affect DNA binding. Different mutations in the same gene leading to different interaction profiles often result in distinct disease phenotypes. Thus disease-associated alleles that perturb distinct protein activities rather than grossly affecting folding and stability are relatively widespread.
PMCID: PMC4441215  PMID: 25910212
3.  Ontology Engineering 
Nature biotechnology  2010;28(2):128-130.
Gene Ontology1 and similar biomedical ontologies are critical tools of today genetic research. These ontologies are crafted through a painstaking process of manual editing, and their organization relies on the intuition of human curators. Here we describe a method that uses information theory to automatically organize the structure of GO and optimize the distribution of the information within it. We used this approach to analyze the evolution of GO, and we identified several areas where the information was suboptimally organized. We optimized the structure of GO and used it to analyze 10,117 gene expression signatures. The use of this new version changed the functional interpretations of 97.5% (p < 10-3) of the signatures by, on average, 14.6%. As a result of this analysis, several changes will be introduced in the next releases of GO. We expect that these formal methods will become the standard to engineer biomedical ontologies.
PMCID: PMC4829499  PMID: 20139945
4.  Spatio-temporal 16p11.2 protein network implicates cortical late mid-fetal brain development and KCTD13-Cul3-RhoA pathway in psychiatric diseases 
Neuron  2015;85(4):742-754.
Psychiatric disorders autism and schizophrenia have a strong genetic component, and copy number variants (CNVs) are firmly implicated. Recurrent deletions and duplications of chromosome 16p11.2 confer high risk for both diseases, but the pathways disrupted by this CNV are poorly defined. Here we investigate the dynamics of 16p11.2 network by integrating physical interactions of 16p11.2 proteins with spatio-temporal gene expression from developing human brain. We observe profound changes in protein interaction networks throughout different stages of brain development and/or in different brain regions. We identify late mid-fetal period of cortical development as most critical for establishing connectivity of 16p11.2 proteins with their co-expressed partners. Furthermore, our results suggest that the regulation of KCTD13-Cul3-RhoA pathway in layer four of inner cortical plate is crucial for controlling brain size and connectivity, and its dysregulation by the de novo mutations may be a potential determinant of 16p11.2 CNV deletion and duplication phenotypes.
PMCID: PMC4335356  PMID: 25695269
5.  Early Detection of Lung Cancer with Meso Tetra (4-Carboxyphenyl) Porphyrin-Labeled Sputum 
Early detection of lung cancer in high-risk individuals reduces mortality. Low-dose spiral computed tomography (LDCT) is the current standard but suffers from an exceedingly high false-positive rate (>96%) leading to unnecessary and potentially dangerous procedures. We, therefore, set out to develop a simple, noninvasive, and quantitative assay to detect lung cancer.
This proof-of-concept study evaluated the sensitivity/specificity of the CyPath Early Lung Cancer Detection Assay to correctly classify LDCT-confirmed cohorts of high-risk control (n = 102) and cancer (n = 26) subjects. Fluorescence intensity parameters of red fluorescent cells (RFCs) from tetra (4-carboxyphe-nyl) porphyrin (TCPP)-labeled lung sputum samples and subjects’ baseline characteristics were assessed for their predictive power by multivariable logistic regression. A receiver operating characteristic curve was constructed to evaluate the sensitivity/specificity of the CyPath assay.
RFCs were detectable in cancer subjects more often than in high-risk ones (p = 0.015), and their characteristics differed between cohorts. Two independent predictors of cancer were the mean of RFC average fluorescence intensity/area per subject (p < 0.001) and years smoked (p = 0.003). The CyPath-based classifier had an overall accuracy of 81% in the test population; false-positive rate of 40% and negative predictive value of 83%.
The tetra (4-carboxyphenyl) porphyrin-based CyPath assay correctly classified study participants into cancer or high-risk cohorts with considerable accuracy. Optimizing sputum collection, sample reading, and refining the classifier should improve sensitivity and specificity. The CyPath assay thus has the potential to complement LDCT screening or serve as a stand-alone approach for early lung cancer detection.
PMCID: PMC4754958  PMID: 26200451
Sputum cytology; Porphyrin; Early detection; Lung cancer
6.  Beliefs, Barriers, and Preferences of European Overweight Women to Adopt a Healthier Lifestyle in Pregnancy to Minimize Risk of Developing Gestational Diabetes Mellitus: An Explorative Study 
Journal of Pregnancy  2016;2016:3435791.
Introduction. We explored beliefs, perceived barriers, and preferences regarding lifestyle changes among overweight European pregnant women to help inform the development of future lifestyle interventions in the prevention of gestational diabetes mellitus. Methods. An explorative mixed methods, two-staged study was conducted to gather information from pregnant European women (BMI ≥ 25 kg/m2). In three European countries 21 interviews were conducted, followed by 71 questionnaires in six other European countries. Content analysis and descriptive and chi-square statistics were applied (p < 0.05). Results. Women preferred to obtain detailed information about their personal risk. The health of their baby was a major motivating factor. Perceived barriers for physical activity included pregnancy-specific issues such as tiredness and experiencing physical complaints. Insufficient time was a barrier more frequently reported by women with children. Abstaining from snacking was identified as a challenge for the majority of women, especially for those without children. Women preferred to obtain support from their partner, as well as health professionals and valued flexible lifestyle programs. Conclusions. Healthcare professionals need to inform overweight pregnant women about their personal risk, discuss lifestyle modification, and assist in weight management. Lifestyle programs should be tailored to the individual, taking into account barriers experienced by overweight first-time mothers and multipara women.
PMCID: PMC4738738  PMID: 26885396
7.  Intrafollicular Cortisol Levels Inversely Correlate with Cumulus Cell (CC) Lipid Content As a Possible Energy Source During Oocyte Meiotic Resumption In Women Undergoing Ovarian Stimulation For In Vitro Fertilization (IVF) 
Fertility and sterility  2014;103(1):249-257.
To determine whether follicular fluid (FF) cortisol levels affect cumulus cell (CC) lipid content during oocyte meiotic resumption and whether CCs express genes for glucocorticoid action.
Prospective cohort study
Academic medical center
Thirty-seven non-obese women underwent ovarian stimulation for IVF
At oocyte retrieval, FF was aspirated from the first follicle (>16 mm in size) of each ovary and pooled CC were collected.
Main Outcome Measure(s)
FF cortisol and cortisone analysis was performed by liquid chromatography-tandem mass spectrometry. CCs were stained with lipid fluorescent dye BODIPY FL C16 to determine lipid content by confocal microscopy. Quantitative real-time PCR was used to detect CC gene expression of 11β-hydroxysteroid dehydrogenase (11βHSD) types 1 and 2, glucocorticoid receptor (NR3C1), lipoprotein lipase (LPL) and hormone sensitive lipase (HSL).
Adjusting for maternal age, FF cortisol levels negatively correlated with CC lipid content and positively correlated with numbers of total and mature oocytes. CCs expressed genes for 11βHSD type 1 as the predominant 11βHSD isoform, NR3C1, LPL and HSL.
FF cortisol levels may regulate CC lipolysis during oocyte meiotic resumption and affect oocyte quality during IVF.
PMCID: PMC4380141  PMID: 25439840
cortisol; cumulus cell lipid; meiosis; oocyte developmental competence; in vitro fertilization
8.  Disruption and eradication of P. aeruginosa biofilms using nitric oxide-releasing chitosan oligosaccharides 
Biofouling  2015;31(0):775-787.
Biofilm disruption and eradication were investigated as a function of nitric oxide- (NO) releasing chitosan oligosaccharide dose with results compared to control (ie non-NO-releasing) chitosan oligosaccharides and tobramycin. Quantification of biofilm expansion/contraction and multiple-particle tracking microrheology were used to assess the structural integrity of the biofilm before and after antibacterial treatment. While tobramycin had no effect on the physical properties of the biofilm, NO-releasing chitosan oligosaccharides exhibited dose-dependent behavior with biofilm degradation. Control chitosan oligosaccharides increased biofilm elasticity, indicating that the scaffold may mitigate the biofilm disrupting power of nitric oxide somewhat. The results from this study indicate that nitric oxide-releasing chitosan oligosaccharides act as dual-action therapeutics capable of eradicating and physically disrupting P. aeruginosa biofilms.
PMCID: PMC4695972  PMID: 26610146
nitric oxide; P. aeruginosa; biofilm; rheology
9.  The Xenopus ORFeome: A resource that enables functional genomics 
Developmental Biology  2015;408(2):345-357.
Functional characterisation of proteins and large-scale, systems-level studies are enabled by extensive sets of cloned open reading frames (ORFs) in an easily-accessible format that enables many different applications. Here we report the release of the first stage of the Xenopus ORFeome, which contains 8673 ORFs from the Xenopus Gene Collection (XGC) for Xenopus laevis, cloned into a Gateway® donor vector enabling rapid in-frame transfer of the ORFs to expression vectors. This resource represents an estimated 7871 unique genes, approximately 40% of the non-redundant X. laevis gene complement, and includes 2724 genes where the human ortholog has an association with disease. Transfer into the Gateway system was validated by 5′ and 3′ end sequencing of the entire collection and protein expression of a set of test clones. In a parallel process, the underlying ORF predictions from the original XGC collection were re-analysed to verify quality and full-length status, identifying those proteins likely to exhibit truncations when translated. These data are integrated into Xenbase, the Xenopus community database, which associates genomic, expression, function and human disease model metadata to each ORF, enabling end-users to search for ORFeome clones with links to commercial distributors of the collection. When coupled with the experimental advantages of Xenopus eggs and embryos, the ORFeome collection represents a valuable resource for functional genomics and disease modelling.
•The Xenopus ORFeome, v1.0, containing 8673 ORFs from the Xenopus Gene Collection.•7871 genes, ∼40% of the X. laevis proteome, 2724 genes with human disease orthologs.•XGC ORFs re-analysed via improved bioinformatics approaches, 85% verified full-length.•Information on ORFeome clones can be found on, with links to distributors.•A valuable resource for accelerating functional genomics and human disease modelling.
PMCID: PMC4684507  PMID: 26391338
Gateway; Recombinational cloning; ORFeome; Xenopus; Open reading frame; Gene annotation
10.  Pulmonary Fluid Flow Challenges for Experimental and Mathematical Modeling 
Integrative and Comparative Biology  2014;54(6):985-1000.
Modeling the flow of fluid in the lungs, even under baseline healthy conditions, presents many challenges. The complex rheology of the fluids, interaction between fluids and structures, and complicated multi-scale geometry all add to the complexity of the problem. We provide a brief overview of approaches used to model three aspects of pulmonary fluid and flow: the surfactant layer in the deep branches of the lung, the mucus layer in the upper airway branches, and closure/reopening of the airway. We discuss models of each aspect, the potential to capture biological and therapeutic information, and open questions worthy of further investigation. We hope to promote multi-disciplinary collaboration by providing insights into mathematical descriptions of fluid-mechanics in the lung and the kinds of predictions these models can make.
PMCID: PMC4296202  PMID: 25096289
11.  A proteome-scale map of the human interactome network 
Cell  2014;159(5):1212-1226.
Just as reference genome sequences revolutionized human genetics, reference maps of interactome networks will be critical to fully understand genotype-phenotype relationships. Here, we describe a systematic map of ~14,000 high-quality human binary protein-protein interactions. At equal quality, this map is ~30% larger than what is available from small-scale studies published in the literature in the last few decades. While currently available information is highly biased and only covers a relatively small portion of the proteome, our systematic map appears strikingly more homogeneous, revealing a “broader” human interactome network than currently appreciated. The map also uncovers significant inter-connectivity between known and candidate cancer gene products, providing unbiased evidence for an expanded functional cancer landscape, while demonstrating how high quality interactome models will help “connect the dots” of the genomic revolution.
PMCID: PMC4266588  PMID: 25416956
12.  Mechanisms by which Synthetic 6,7-Annulated-4-substituted Indole Compounds with Anti-proliferative Activity Disrupt Mitosis and Block Cytokinesis in Human HL-60 Tumor Cells In Vitro 
Anticancer research  2014;34(4):1643-1655.
Synthetic 6,7-annulated-4-substituted indole compounds, which elicit interesting antitumor effects in murine L1210 leukemia cells, were tested for their ability to inhibit human HL-60 tumor cell proliferation, disrupt mitosis and cytokinesis, and interfere with tubulin and actin polymerization in vitro.
Materials and Methods
Various markers of metabolic activity, mitotic disruption and cytokinesis were used to assess the effectiveness of the drugs in the HL-60 tumor cell system. The ability of annulated indoles to alter the polymerizations of purified tubulin and actin were monitored in cell-free assays and were compared to the effects of drugs known to disrupt the dynamic structures of the mitotic spindle and cleavage furrow.
With one exception, annulated indoles inhibited the metabolic activity of HL-60 tumor cells in the low-micromolar range after two and four days in culture but these anti-proliferative effects were weaker than those of jasplakinolide, a known actin binder that blocks cytokinesis. After 24-48 h, antiproliferative concentrations of annulated indoles increased the mitotic index of HL-60 cells similarly to vincristine and stimulated the formation of many bi-nucleated cells, multi-nucleated cells and micronuclei, similarly to taxol and jasplakinolide, suggesting that these antitumor compounds might increase mitotic abnormality, induce chromosomal damage or missegregation, and block cytokinesis. Since annulated indoles mimicked the effect of vincristine on tubulin polymerization, but not that of taxol, these compounds might represent a new class of microtubule de-stabilizing agents that inhibit tubulin polymerization. Moreover, annulated indoles remarkably increased the rate and level of actin polymerization similarly to jasplakinolide, suggesting that they might also stabilize the cleavage furrow to block cytokinesis.
Although novel derivatives with different substitutions must be synthesized to elucidate structure–activity relationships, identify more potent antitumor compounds and investigate different molecular targets, annulated indoles appear to interact with both tubulin to reduce microtubule assembly and actin to block cytokinesis, thereby inducing bi- and multinucleation, resulting in genomic instability and apoptosis.
PMCID: PMC4618554  PMID: 24692693
Annulated indoles; tumor cell proliferation; cells with mitotic figures; several nuclei and micronuclei; cytokinesis; tubulin polymerization; actin polymerization
13.  Micro-heterogeneity metrics for diffusion in soft matter† 
Soft matter  2014;10(39):7781-7796.
Passive particle tracking of diffusive paths in soft matter, coupled with analysis of the path data, is firmly established as a fundamental methodology for characterization of both diffusive transport properties (the focus here) and linear viscoelasticity. For either focus, particle time series are typically analyzed by ensemble averaging over paths, a perfectly natural protocol for homogeneous materials or for applications where mean properties are sufficient. Many biological materials, however, are heterogeneous over length scales above the probe diameter, and the implications of heterogeneity for biologically relevant transport properties (e.g. diffusive passage times through a complex fluid layer) motivate this paper. Our goals are three-fold: first, to detect heterogeneity as reflected by the ensemble path data; second, to further decompose the ensemble of particle paths into statistically distinct clusters; and third, to fit the path data in each cluster to a model for the underlying stochastic process. After reviewing current best practices for detection and assessment of heterogeneity in diffusive processes, we introduce our strategy toward the first two goals with methods from the statistics and machine learning literature that have not found application thus far to passive particle tracking data. We apply an analysis based solely on the path data that detects heterogeneity and yields a decomposition of particle paths into statistically distinct clusters. After these two goals are achieved, one can then pursue model-fitting. We illustrate these heterogeneity metrics on diverse datasets: for numerically generated and experimental particle paths, with tunable and unknown heterogeneity, on numerical models for simple diffusion and anomalous sub-diffusion, and experimentally on sucrose, hyaluronic acid, agarose, and human lung culture mucus solutions.
PMCID: PMC4186960  PMID: 25144347
14.  Physical activity, depressed mood and pregnancy worries in European obese pregnant women: results from the DALI study 
The purpose of this study was to examine the association between mental health status (i.e. depressed mood and pregnancy-related worries) and objectively measured physical activity levels in obese pregnant women from seven European countries.
Baseline data from the vitamin D and lifestyle intervention for the prevention of gestational diabetes mellitus (DALI) study were used. Time spent in moderate-to-vigorous physical activity (MVPA) and sedentary behaviour was measured with accelerometers. Depressed mood was measured with the WHO well-being index (WHO-5) and pregnancy-related worries with the Cambridge Worry Scale (CWS). In addition, socio-demographic characteristics, lifestyle factors, and perceptions and attitude regarding weight management and physical activity were measured. Linear regression analyses were performed to assess the association of mental health status with MVPA and sedentary behaviour.
A total of 98 obese pregnant women from Austria, Belgium, Ireland, Italy, Poland, Spain and the Netherlands were included. Women had a mean age of 31.6 ± 5.8 years, a pre-pregnancy BMI of 34.1 ± 4.3 kg/m2, and were on average 15.4 ± 2.8 weeks pregnant. WHO-5 scores indicative of depressed mood (<50) were reported by 27.1 % of the women and most frequently endorsed pregnancy-related worries pertained to own and the baby’s health. Women with good well-being spent 85 % more time in MVPA compared to women with a depressed mood (P = 0.03). No differences in MVPA levels were found for women with no, some, or many pregnancy worries. Depressed mood and pregnancy-related worries were not associated with sedentary behaviour.
These findings suggest that in pregnant women who are obese, a depressed mood, but not pregnancy-related worries, may be associated with less physical activity. The combined risk of poor mental health and low physical activity levels makes women vulnerable for pregnancy complications. Whether a depressed mood may be a barrier for improving physical activity warrants further study.
PMCID: PMC4521453  PMID: 26228253
Exercise; Mental health; Pregnancy; Obesity
15.  Expanded Terminal Fields of Gustatory Nerves Accompany Embryonic BDNF Overexpression in Mouse Oral Epithelia 
The Journal of Neuroscience  2015;35(1):409-421.
Brain-derived neurotrophic factor (BDNF) is expressed in gustatory epithelia and is required for gustatory neurons to locate and innervate their correct target during development. When BDNF is overexpressed throughout the lingual epithelium, beginning embryonically, chorda tympani fibers are misdirected and innervate inappropriate targets, leading to a loss of taste buds. The remaining taste buds are hyperinnervated, demonstrating a disruption of nerve/target matching in the tongue. We tested the hypothesis here that overexpression of BDNF peripherally leads to a disrupted terminal field organization of nerves that carry taste information to the brainstem. The chorda tympani, greater superficial petrosal, and glossopharyngeal nerves were labeled in adult wild-type (WT) mice and in adult mice in which BDNF was overexpressed (OE) to examine the volume and density of their central projections in the nucleus of the solitary tract. We found that the terminal fields of the chorda tympani and greater superficial petrosal nerves and overlapping fields that included these nerves in OE mice were at least 80% greater than the respective field volumes in WT mice. The shapes of terminal fields were similar between the two groups; however, the density and spread of labels were greater in OE mice. Unexpectedly, there were also group-related differences in chorda tympani nerve function, with OE mice showing a greater relative taste response to a concentration series of sucrose. Overall, our results show that disruption in peripheral innervation patterns of sensory neurons have significant effects on peripheral nerve function and central organization of their terminal fields.
PMCID: PMC4287156  PMID: 25568132
BDNF; chorda tympani; glossopharyngeal; greater superficial petrosal; terminal field
16.  Application of comparative biology in GO functional annotation: the mouse model 
Mammalian Genome  2015;26(9-10):574-583.
The Gene Ontology (GO) is an important component of modern biological knowledge representation with great utility for computational analysis of genomic and genetic data. The Gene Ontology Consortium (GOC) consists of a large team of contributors including curation teams from most model organism database groups as well as curation teams focused on representation of data relevant to specific human diseases. Key to the generation of consistent and comprehensive annotations is the development and use of shared standards and measures of curation quality. The GOC engages all contributors to work to a defined standard of curation that is presented here in the context of annotation of genes in the laboratory mouse. Comprehensive understanding of the origin, epistemology, and coverage of GO annotations is essential for most effective use of GO resources. Here the application of comparative approaches to capturing functional data in the mouse system is described.
PMCID: PMC4602061  PMID: 26141960
17.  Transcriptome-wide Analysis Reveals Hallmarks of Human Intestine Development and Maturation In Vitro and In Vivo 
Stem Cell Reports  2015;4(6):1140-1155.
Human intestinal organoids (HIOs) are a tissue culture model in which small intestine-like tissue is generated from pluripotent stem cells. By carrying out unsupervised hierarchical clustering of RNA-sequencing data, we demonstrate that HIOs most closely resemble human fetal intestine. We observed that genes involved in digestive tract development are enriched in both fetal intestine and HIOs compared to adult tissue, whereas genes related to digestive function and Paneth cell host defense are expressed at higher levels in adult intestine. Our study also revealed that the intestinal stem cell marker OLFM4 is expressed at very low levels in fetal intestine and in HIOs, but is robust in adult crypts. We validated our findings using in vivo transplantation to show that HIOs become more adult-like after transplantation. Our study emphasizes important maturation events that occur in the intestine during human development and demonstrates that HIOs can be used to model fetal-to-adult maturation.
•HIOs derived from hPSCs remain fetal in vitro•HIOs become adult-like when transplanted into mice•Transcriptional profiling across time reveals hallmarks of human gut maturation•The intestinal stem cell protein OLFM4 is a marker of human crypt maturation
Human pluripotent stem cell-derived intestinal organoids (HIOs) are an in vitro model of the small intestine. Spence and colleagues used transcriptional profiling to demonstrate that HIOs remain fetal in vitro and show that they undergo maturation into adult-like tissue when transplanted in vivo. Their results demonstrate that HIOs are a valuable in vitro model to study the fetal intestine.
PMCID: PMC4471827  PMID: 26050928
18.  The Impact of Abnormal Glucose Tolerance and Obesity on Fetal Growth 
Journal of Diabetes Research  2015;2015:847674.
Objective. Factors linked with insulin resistance were examined for their association with large-for-gestational-age (LGA) infant birth weight and gestational diabetes. Study Design. Data came from a longitudinal cohort study of 2,305 subjects without overt diabetes, analyzed using multinomial logistic and linear regression. Results. High maternal BMI (OR = 1.53 (1.11, 2.12)), height (1.98 (1.62, 2.42)), antidepressant use (1.71 (1.20, 2.44)), pregnancy weight-gain exceeding 40 pounds (1.79 (1.25, 2.57)), and high blood sugar (2.68, (1.53, 5.27)) were all positively associated with LGA birth. Strikingly, the difference in risk from diagnosed and treated gestational diabetes compared to women with a single abnormal glucose tolerance test (but no diagnosis of gestational diabetes) was significant (OR = 0.65, p = 0.12 versus OR = 2.84, p < 0.01). When weight/length ratio was used instead, different factors were found to be significant. BMI and pregnancy weight-gain were found to influence the development of gestational diabetes, through an additive interaction. Conclusions. High prepregnancy BM, height, antidepressant use, pregnancy weight-gain exceeding 40 pounds, and high blood sugar were associated with LGA birth, but not necessarily infant weight/length ratio. An additive interaction between BMI and pregnancy weight-gain influenced gestational diabetes development.
PMCID: PMC4421033  PMID: 25977929
19.  In vitro generation of human pluripotent stem cell derived lung organoids 
eLife  null;4:e05098.
Recent breakthroughs in 3-dimensional (3D) organoid cultures for many organ systems have led to new physiologically complex in vitro models to study human development and disease. Here, we report the step-wise differentiation of human pluripotent stem cells (hPSCs) (embryonic and induced) into lung organoids. By manipulating developmental signaling pathways hPSCs generate ventral-anterior foregut spheroids, which are then expanded into human lung organoids (HLOs). HLOs consist of epithelial and mesenchymal compartments of the lung, organized with structural features similar to the native lung. HLOs possess upper airway-like epithelium with basal cells and immature ciliated cells surrounded by smooth muscle and myofibroblasts as well as an alveolar-like domain with appropriate cell types. Using RNA-sequencing, we show that HLOs are remarkably similar to human fetal lung based on global transcriptional profiles, suggesting that HLOs are an excellent model to study human lung development, maturation and disease.
eLife digest
Cell behavior has traditionally been studied in the lab in two-dimensional situations, where cells are grown in thin layers on cell-culture dishes. However, most cells in the body exist in a three-dimensional environment as part of complex tissues and organs, and so researchers have been attempting to re-create these environments in the lab. To date, several such ‘organoids’ have been successfully generated, including models of the human intestine, stomach, brain and liver. These organoids can mimic the responses of real tissues and can be used to investigate how organs form, change with disease, and how they might respond to potential therapies.
Here, Dye et al. developed a new three-dimensional model of the human lung by coaxing human stem cells to become specific types of cells that then formed complex tissues in a petri dish. To make these lung organoids, Dye et al. manipulated several of the signaling pathways that control the formation of organs during the development of animal embryos. First, the stem cells were instructed to form a type of tissue called endoderm, which is found in early embryos and gives rise to the lung, liver and other several other internal organs.
Then, Dye et al. activated two important developmental pathways that are known to make endoderm form three-dimensional intestinal tissue. However, by inhibiting two other key developmental pathways at the same time, the endoderm became tissue that resembles the early lung found in embryos instead.
This early lung-like tissue formed three-dimensional spherical structures as it developed. The next challenge was to make these structures develop into lung tissue. Dye et al. worked out a method to do this, which involved exposing the cells to additional proteins that are involved in lung development. The resulting lung organoids survived in laboratory cultures for over 100 days and developed into well-organized structures that contain many of the types of cells found in the lung.
Further analysis revealed the gene activity in the lung organoids resembles that of the lung of a developing human fetus, suggesting that lung organoids grown in the dish are not fully mature. Dye et al.'s findings provide a new approach for creating human lung organoids in culture that may open up new avenues for investigating lung development and diseases.
PMCID: PMC4370217  PMID: 25803487
pluripotent stem cells; organoids; endoderm; lung; foregut; spheroid; human
20.  Protein Domain-Level Landscape of Cancer-Type-Specific Somatic Mutations 
PLoS Computational Biology  2015;11(3):e1004147.
Identifying driver mutations and their functional consequences is critical to our understanding of cancer. Towards this goal, and because domains are the functional units of a protein, we explored the protein domain-level landscape of cancer-type-specific somatic mutations. Specifically, we systematically examined tumor genomes from 21 cancer types to identify domains with high mutational density in specific tissues, the positions of mutational hotspots within these domains, and the functional and structural context where possible. While hotspots corresponding to specific gain-of-function mutations are expected for oncoproteins, we found that tumor suppressor proteins also exhibit strong biases toward being mutated in particular domains. Within domains, however, we observed the expected patterns of mutation, with recurrently mutated positions for oncogenes and evenly distributed mutations for tumor suppressors. For example, we identified both known and new endometrial cancer hotspots in the tyrosine kinase domain of the FGFR2 protein, one of which is also a hotspot in breast cancer, and found new two hotspots in the Immunoglobulin I-set domain in colon cancer. Thus, to prioritize cancer mutations for further functional studies aimed at more precise cancer treatments, we have systematically correlated mutations and cancer types at the protein domain level.
Author Summary
Extensive tumor genome sequencing has provided raw material to understand mutational processes and identify cancer-associated somatic variants. However, fundamental problems remain to: i) separate ‘driver’ from ‘passenger’ mutations, ii) further understand the functional mechanisms and consequences of driver mutations, and iii) identify the cancer types in which each driver mutation is relevant. Here we analyze whole-genome and exome tumor sequencing data from the perspective of protein domains—the basic structural and functional units of proteins. Exploring the cancer-type-specific landscape of domain mutations across 21 cancer types, we identify both cancer-type-specific mutated domains and mutational hotspots. Frequently-mutated domains were identified for oncoproteins for which the ‘mutational hotspot’ phenomenon owing to the relative rarity of gain-of-function mutations is well known, and also for tumor suppressor proteins, for which more uniformly distributed loss-of-function driver mutations are expected. A given gene product may be perturbed differently in different cancers. Indeed, we observed systematic shifts between cancer types of the positions at which mutations occur within a given protein. Both known and novel candidate driver mutations were retrieved. Novel cancer gene candidates significantly overlapped with orthogonal systematic cancer screen hits, supporting the power of this approach to identify cancer genes.
PMCID: PMC4368709  PMID: 25794154
21.  Multiplex single-molecule interaction profiling of DNA barcoded proteins 
Nature  2014;515(7528):554-557.
In contrast with advances in massively parallel DNA sequencing1, high-throughput protein analyses2-4 are often limited by ensemble measurements, individual analyte purification and hence compromised quality and cost-effectiveness. Single-molecule (SM) protein detection achieved using optical methods5 is limited by the number of spectrally nonoverlapping chromophores. Here, we introduce a single molecular interaction-sequencing (SMI-Seq) technology for parallel protein interaction profiling leveraging SM advantages. DNA barcodes are attached to proteins collectively via ribosome display6 or individually via enzymatic conjugation. Barcoded proteins are assayed en masse in aqueous solution and subsequently immobilized in a polyacrylamide (PAA) thin film to construct a random SM array, where barcoding DNAs are amplified into in situ polymerase colonies (polonies)7 and analyzed by DNA sequencing. This method allows precise quantification of various proteins with a theoretical maximum array density of over one million polonies per square millimeter. Furthermore, protein interactions can be measured based on the statistics of colocalized polonies arising from barcoding DNAs of interacting proteins. Two demanding applications, G-protein coupled receptor (GPCR) and antibody binding profiling, were demonstrated. SMI-Seq enables “library vs. library” screening in a one-pot assay, simultaneously interrogating molecular binding affinity and specificity.
PMCID: PMC4246050  PMID: 25252978
22.  Mutations that disrupt PHOXB interaction with the neuronal calcium sensor HPCAL1 impede cellular differentiation in neuroblastoma 
Oncogene  2013;33(25):3316-3324.
Heterozygous germline mutations in PHOX2B, a transcriptional regulator of sympathetic neuronal differentiation, predispose to diseases of the sympathetic nervous system, including neuroblastoma and congenital central hypoventilation syndrome (CCHS). Whereas the PHOX2B variants in CCHS largely involve expansions of the second polyalanine repeat within the C-terminus of the protein, those associated with neuroblastic tumors are nearly always frameshift and truncation mutations. To test the hypothesis that the neuroblastoma-associated variants exert their effects through loss or gain of protein-protein interactions, we performed a large-scale yeast two-hybrid screen using both wild-type (WT) and six different mutant PHOX2B proteins against over 10,000 human genes. The neuronal calcium sensor protein HPCAL1 (VILIP-3) exhibited strong binding to WT PHOX2B and a CCHS-associated polyalanine expansion mutant, but only weakly or not at all to neuroblastoma-associated frameshift and truncation variants. We demonstrate that both WT PHOX2B, the neuroblastoma-associated R100L missense and the CCHS-associated alanine expansion variants induce nuclear translocation of HPCAL1 in a Ca2+-independent manner, while the neuroblastoma-associated 676delG frameshift and K155X truncation mutants impair subcellular localization of HPCAL1, causing it to remain in the cytoplasm. HPCAL1 did not appreciably influence the ability of WT PHOX2B to transactivate the DBH promoter, nor did it alter the decreased transactivation potential of PHOX2B variants in 293T cells. Abrogation of the PHOX2B-HPCAL1 interaction by shRNA knockdown of HPCAL1 in neuroblastoma cells expressing PHOX2B led to impaired neurite outgrowth with transcriptional profiles indicative of inhibited sympathetic neuronal differentiation. Our results suggest that certain PHOX2B variants associated with neuroblastoma pathogenesis, because of their inability to bind to key interacting proteins such as HPCAL1, may predispose to this malignancy by impeding the differentiation of immature sympathetic neurons.
PMCID: PMC4040330  PMID: 23873030
PHOX2B; HPCAL1; neuroblastoma; neuronal calcium sensor; differentiation; network perturbation
23.  Methodology for the inference of gene function from phenotype data 
BMC Bioinformatics  2014;15(1):405.
Biomedical ontologies are increasingly instrumental in the advancement of biological research primarily through their use to efficiently consolidate large amounts of data into structured, accessible sets. However, ontology development and usage can be hampered by the segregation of knowledge by domain that occurs due to independent development and use of the ontologies. The ability to infer data associated with one ontology to data associated with another ontology would prove useful in expanding information content and scope. We here focus on relating two ontologies: the Gene Ontology (GO), which encodes canonical gene function, and the Mammalian Phenotype Ontology (MP), which describes non-canonical phenotypes, using statistical methods to suggest GO functional annotations from existing MP phenotype annotations. This work is in contrast to previous studies that have focused on inferring gene function from phenotype primarily through lexical or semantic similarity measures.
We have designed and tested a set of algorithms that represents a novel methodology to define rules for predicting gene function by examining the emergent structure and relationships between the gene functions and phenotypes rather than inspecting the terms semantically. The algorithms inspect relationships among multiple phenotype terms to deduce if there are cases where they all arise from a single gene function.
We apply this methodology to data about genes in the laboratory mouse that are formally represented in the Mouse Genome Informatics (MGI) resource. From the data, 7444 rule instances were generated from five generalized rules, resulting in 4818 unique GO functional predictions for 1796 genes.
We show that our method is capable of inferring high-quality functional annotations from curated phenotype data. As well as creating inferred annotations, our method has the potential to allow for the elucidation of unforeseen, biologically significant associations between gene function and phenotypes that would be overlooked by a semantics-based approach. Future work will include the implementation of the described algorithms for a variety of other model organism databases, taking full advantage of the abundance of available high quality curated data.
Electronic supplementary material
The online version of this article (doi:10.1186/s12859-014-0405-z) contains supplementary material, which is available to authorized users.
PMCID: PMC4302099  PMID: 25495798
Gene ontology; Mammalian phenotype ontology; Function prediction; Ontology development
24.  TermGenie – a web-application for pattern-based ontology class generation 
Biological ontologies are continually growing and improving from requests for new classes (terms) by biocurators. These ontology requests can frequently create bottlenecks in the biocuration process, as ontology developers struggle to keep up, while manually processing these requests and create classes.
TermGenie allows biocurators to generate new classes based on formally specified design patterns or templates. The system is web-based and can be accessed by any authorized curator through a web browser. Automated rules and reasoning engines are used to ensure validity, uniqueness and relationship to pre-existing classes. In the last 4 years the Gene Ontology TermGenie generated 4715 new classes, about 51.4% of all new classes created. The immediate generation of permanent identifiers proved not to be an issue with only 70 (1.4%) obsoleted classes.
TermGenie is a web-based class-generation system that complements traditional ontology development tools. All classes added through pre-defined templates are guaranteed to have OWL equivalence axioms that are used for automatic classification and in some cases inter-ontology linkage. At the same time, the system is simple and intuitive and can be used by most biocurators without extensive training.
PMCID: PMC4417543  PMID: 25937883
Ontology; Class generation
25.  Temporal Signatures of Taste Quality Driven by Active Sensing 
The Journal of Neuroscience  2014;34(22):7398-7411.
Animals actively acquire sensory information from the outside world, with rodents sniffing to smell and whisking to feel. Licking, a rapid motor sequence used for gustation, serves as the primary means of controlling stimulus access to taste receptors in the mouth. Using a novel taste-quality discrimination task in head-restrained mice, we measured and compared reaction times to four basic taste qualities (salt, sour, sweet, and bitter) and found that certain taste qualities are perceived inherently faster than others, driven by the precise biomechanics of licking and functional organization of the peripheral gustatory system. The minimum time required for accurate perception was strongly dependent on taste quality, ranging from the sensory-motor limits of a single lick (salt, ∼100 ms) to several sampling cycles (bitter, >500 ms). Further, disruption of sensory input from the anterior tongue significantly impaired the speed of perception of some taste qualities, with little effect on others. Overall, our results show that active sensing may play an important role in shaping the timing of taste-quality representations and perception in the gustatory system.
PMCID: PMC4035510  PMID: 24872546

Results 1-25 (179)