ABSTRACT
All implanted biomaterials are targets of the host's immune system. While the host inflammatory response was once considered a detrimental force to be blunted or avoided, in recent years, it has become a powerful force to be leveraged to augment biomaterial-tissue integration and tissue repair. In this review, we will discuss the major immune cells that mediate the inflammatory response to biomaterials, with a focus on how biomaterials can be designed to modulate immune cell behavior to promote biomaterial-tissue integration. In particular, the intentional activation of monocytes and macrophages with controlled timing, and modulation of their interactions with other cell types involved in wound healing, have emerged as key strategies to improve biomaterial efficacy. To this end, careful design of biomaterial structure and controlled release of immunomodulators can be employed to manipulate macrophage phenotype for the maximization of the wound healing response with enhanced tissue integration and repair, as opposed to a typical foreign body response characterized by fibrous encapsulation and implant isolation. We discuss current challenges in the clinical translation of immunomodulatory biomaterials, such as limitations in the use of in vitro studies and animal models to model the human immune response. Finally, we describe future directions and opportunities for understanding and controlling the biomaterial-immune system interface, including the application of new imaging tools, new animal models, the discovery of new cellular targets, and novel techniques for in situ immune cell reprogramming.
Subject(s)
Biocompatible Materials , Macrophages , Animals , Biocompatible Materials/pharmacology , Biocompatible Materials/therapeutic use , Immunity , Prostheses and ImplantsABSTRACT
Basement membranes (BMs) are thin sheet-like specialized extracellular matrices found at the basal surface of epithelia and endothelial tissues. They have been conserved across evolution and are required for proper tissue growth, organization, differentiation and maintenance. The major constituents of BMs are two independent networks of Laminin and Type IV Collagen in addition to the proteoglycan Perlecan and the glycoprotein Nidogen/entactin (Ndg). The ability of Ndg to bind in vitro Collagen IV and Laminin, both with key functions during embryogenesis, anticipated an essential role for Ndg in morphogenesis linking the Laminin and Collagen IV networks. This was supported by results from cultured embryonic tissue experiments. However, the fact that elimination of Ndg in C. elegans and mice did not affect survival strongly questioned this proposed linking role. Here, we have isolated mutations in the only Ndg gene present in Drosophila. We find that while, similar to C.elegans and mice, Ndg is not essential for overall organogenesis or viability, it is required for appropriate fertility. We also find, alike in mice, tissue-specific requirements of Ndg for proper assembly and maintenance of certain BMs, namely those of the adipose tissue and flight muscles. In addition, we have performed a thorough functional analysis of the different Ndg domains in vivo. Our results support an essential requirement of the G3 domain for Ndg function and unravel a new key role for the Rod domain in regulating Ndg incorporation into BMs. Furthermore, uncoupling of the Laminin and Collagen IV networks is clearly observed in the larval adipose tissue in the absence of Ndg, indeed supporting a linking role. In light of our findings, we propose that BM assembly and/or maintenance is tissue-specific, which could explain the diverse requirements of a ubiquitous conserved BM component like Nidogen.
Subject(s)
Basement Membrane/physiology , Drosophila Proteins/physiology , Drosophila/physiology , Membrane Glycoproteins/physiology , Adipose Tissue/cytology , Adipose Tissue/metabolism , Animals , Animals, Genetically Modified , Female , Fertility/physiology , Male , Muscles/cytology , Muscles/metabolism , Mutation , Organ Specificity/physiology , Organogenesis/physiology , Protein Domains/physiologyABSTRACT
Cell-extracellular-matrix adhesion is mediated by cell receptors, mainly integrins and transmembrane proteoglycans, which can functionally interact. How these receptors are regulated and coordinated is largely unknown. We show that the conserved transmembrane Drosophila proteoglycan Kon-tiki (Kon, also known as Perdido) interacts with the αPS2ßPS integrin (αPS2 is encoded by inflated and ßPS by myospheroid) to mediate muscle-tendon adhesion. kon and inflated double mutant embryos show a synergistic increase in muscle detachment. Furthermore, Kon modulates αPS2ßPS signaling at the muscle attachment, since phosphorylated Fak is reduced in kon mutants. This reduction in integrin signaling can be rescued by the expression of a truncated Kon protein containing its transmembrane and extracellular domains, suggesting that these domains are sufficient to mediate this signaling. We show that these domains are sufficient to properly localize the αPS2ßPS ligand, Thrombospondin, to the muscle attachment, and to partially rescue Kon-dependent muscle-tendon adhesion. We propose that Kon can engage in a protein complex with αPS2ßPS and enhance integrin-mediated signaling and adhesion by recruiting its ligand, which would increase integrin-binding affinity to the extracellular matrix, resulting in the consolidation of the myotendinous junction.
Subject(s)
Drosophila Proteins/metabolism , Drosophila melanogaster/metabolism , Integrin alpha Chains/metabolism , Muscles/metabolism , Nerve Tissue Proteins/metabolism , Tendons/metabolism , Thrombospondins/metabolism , Animals , Cell Adhesion , Cell Line , Drosophila Proteins/chemistry , Drosophila melanogaster/embryology , Embryo, Nonmammalian/metabolism , Epistasis, Genetic , Focal Adhesion Protein-Tyrosine Kinases/metabolism , Ligands , Nerve Tissue Proteins/chemistry , Phosphorylation , Protein Domains , Protein Subunits/metabolism , Signal Transduction , Structure-Activity RelationshipABSTRACT
Muscle differentiation requires the assembly of high-order structures called myofibrils, composed of sarcomeres. Even though the molecular organization of sarcomeres is well known, the mechanisms underlying myofibrillogenesis are poorly understood. It has been proposed that integrin-dependent adhesion nucleates myofibrils at the periphery of the muscle cell to sustain sarcomere assembly. Here, we report a role for the gene perdido (perd, also known as kon-tiki, a transmembrane chondroitin proteoglycan) in myofibrillogenesis. Expression of perd RNAi in muscles, prior to adult myogenesis, can induce misorientation and detachment of Drosophila adult abdominal muscles. In comparison to controls, perd-depleted muscles contain fewer myofibrils, which are localized at the cell periphery. These myofibrils are detached from each other and display a defective sarcomeric structure. Our results demonstrate that the extracellular matrix receptor Perd has a specific role in the assembly of myofibrils and in sarcomeric organization. We suggest that Perd acts downstream or in parallel to integrins to enable the connection of nascent myofibrils to the Z-bands. Our work identifies the Drosophila adult abdominal muscles as a model to investigate in vivo the mechanisms behind myofibrillogenesis.
Subject(s)
Drosophila Proteins/metabolism , Drosophila/growth & development , Membrane Proteins/metabolism , Muscle Proteins/metabolism , Proteoglycans/metabolism , Sarcomeres/physiology , Animals , Drosophila/metabolism , Drosophila Proteins/genetics , Membrane Proteins/genetics , Muscle Development , Sarcomeres/metabolismABSTRACT
The mechanisms behind the pro-healing effects of multicellular, bioengineered allogeneic cellularized constructs (BACC) are not known. Macrophages are key regulators of every phase of the wound healing process and the primary cells that mediate the response to biomaterials. It is hypothesized that cells within the BACC modulate macrophage behavior, which may contribute to the mechanism by which BACC promotes healing. To probe the influence of cells within the BACC compared to effects of the underlying collagen substrate, primary human macrophages are cultured in direct or indirect contact with BACC or with the same collagen substrate used in the BACC manufacturing. Macrophage phenotype is characterized over time via multiplex gene expression, protein secretion, multidimensional flow cytometry, and functional assays with fibroblasts and endothelial cells. The BACC causes macrophages to exhibit a predominately reparative phenotype over time compared to relevant collagen substrate controls, with multiple subpopulations expressing both pro-inflammatory and reparative markers. Conditioned media from macrophage-BACC co-cultures causes distinct effects on fibroblast and endothelial cell proliferation, migration, and network formation. Given the critical role of the reparative macrophage phenotype in wound healing, these results suggest that modulation of macrophage phenotype may be a critical part of the mechanisms behind BACC's pro-healing effects.
ABSTRACT
Therapeutic cells are usually administered as living agents, despite the risks of undesired cell migration and acquisition of unpredictable phenotypes. Additionally, most cell-based therapies rely on the administration of single cells, often associated with rapid in vivo clearance. 3D cellular materials may be useful to prolong the effect of cellular therapies and offer the possibility of creating structural volumetric constructs. Here, the manufacturing of shape-versatile fixed cell-based materials with immunomodulatory properties is reported. Living cell aggregates with different shapes (spheres and centimeter-long fibers) are fixed using a method compatible with maintenance of structural integrity, robustness, and flexibility of 3D constructs. The biological properties of living cells can be modulated before fixation, rendering an in vitro anti-inflammatory effect toward human macrophages, in line with a decreased activation of the nuclear factor kappa B (NF-κB) pathway that preponderantly correlated with the surface area of the materials. These findings are further corroborated in vivo in mouse skin wounds. Contact with fixed materials also reduces the proliferation of activated primary T lymphocytes, while promoting regulatory populations. The fixation of cellular constructs is proposed as a versatile phenotypic stabilization method that can be easily implemented to prepare immunomodulatory materials with therapeutic potential.
Subject(s)
Immunomodulation , Animals , Humans , Immunomodulation/drug effects , Mice , Macrophages/drug effects , Macrophages/metabolism , Macrophages/immunology , Macrophages/cytology , NF-kappa B/metabolism , Cell Proliferation/drug effects , T-Lymphocytes/immunology , T-Lymphocytes/cytology , Wound Healing/drug effectsABSTRACT
Soil salinity restricts plant growth and productivity. Na(+) represents the major ion causing toxicity because it competes with K(+) for binding sites at the plasma membrane. Inoculation with arbuscular mycorrhizal fungi (AMF) can alleviate salt stress in the host plant through several mechanisms. These may include ion selection during the fungal uptake of nutrients from the soil or during transfer to the host plant. AM benefits could be enhanced when native AMF isolates are used. Thus, we investigated whether native AMF isolated from an area with problems of salinity and desertification can help maize plants to overcome the negative effects of salinity stress better than non-AM plants or plants inoculated with non-native AMF. Results showed that plants inoculated with two out the three native AMF had the highest shoot dry biomass at all salinity levels. Plants inoculated with the three native AMF showed significant increase of K(+) and reduced Na(+) accumulation as compared to non-mycorrhizal plants, concomitantly with higher K(+) /Na(+) ratios in their tissues. For the first time, these effects have been correlated with regulation of ZmAKT2, ZmSOS1 and ZmSKOR genes expression in the roots of maize, contributing to K(+) and Na(+) homeostasis in plants colonized by native AMF.
Subject(s)
Adaptation, Physiological , Homeostasis , Mycorrhizae/physiology , Salinity , Zea mays/microbiology , Zea mays/physiology , Biomass , Chlorides/metabolism , Gene Expression Regulation, Plant , Ion Transport/genetics , Ions/metabolism , Mediterranean Region , Minerals/metabolism , Plant Proteins/genetics , Plant Proteins/metabolism , Plant Shoots/growth & development , Plant Shoots/metabolism , Potassium/metabolism , Proline/metabolism , Sodium/metabolism , Spain , Symbiosis , Zea mays/geneticsABSTRACT
Introduction: Different analyses of the profiles of tortillas have been made using the traditional method, whether from landraces or hybrids versus those made with dry masa flour in which significant variability (p < 0.05) is reported in favor or against each type of tortilla which may be due to various factors such as the type of maize or the processing methods. Methods: Twenty-two samples including hybrids, hybrid mixtures, varieties, landraces and dry masa flours were processed to masa and tortilla under similar and controlled conditions and tortilla quality evaluated. In total, 70 characteristics were analyzed as physicochemical properties of the maize (e.g., hectoliter weight and dimensions), processability characteristics, masa characteristics [e.g. viscoamylographic parameters (RVA)], and quality parameters of tortillas (e.g., sensory performance, color and texture). Results and discussión: The studied materials presented variability among genotypes, especially within landraces. The physical and chemical properties of corn affected the processability and quality characteristics of tortillas (sensory and composition), and it was found that high producing hybrids and varieties (p < 0.05) were better and more consistent in all stages of processing. Forty percent of the landraces yielded masa with poor machinability. Conclusion: Landraces averaged 1.27 percentage points more protein (p < 0.05) than other analyzed samples and they comparatively yielded tortillas with lower extensibility (12.34%) compared to counterparts produced from hybrids and varieties. This work provides valuable information on how the chemical and physical characteristics of different types of maize genotypes affect the nixtamalization process and the quality of tortillas to provide more elements in the selection of the most appropriate genotypes for tortilla production.
ABSTRACT
In the scientific literature there are different analyses of the nutritional profiles of maize tortillas, whether they are landraces or hybrid maize versus those made with dry masa flour (DMF). In general terms, there is agreement in the reported content of moisture. However, for the other nutrients, a great disparity is reported for each type of tortilla which may be due to various factors such as the type of maize or processing methods. In this study, the nutritional aspects of maize tortillas made with different genotypes (five hybrids, two varieties, five landraces, six hybrid mixtures and six dry masa flours) under controlled conditions, were compared. More than 30 characteristics were analyzed. High performance hybrids and varieties (HPHV) and landraces had the highest (p < 0.05) antioxidant capacity (58.8% free, 150.2% bound). In terms of vitamins contents, the tortillas produced from DMF contained 11.2 and 3.5 times more B1, 18.6 and 7.8 times more B2, and 2.7 and 5.3 times more B3 than HPHV and landraces respectively; and only in these samples was detected folic acid. DMF tortilla samples contained 1.75 times more sodium and 2.75 times more iron than the other groups, and 0.75 times less calcium than HPHV. Zinc was present in higher concentration (p < 0.05) in DMF tortilla samples. The landraces had the highest protein content (average 10.28%), but the tortillas produced from DMF presented the highest protein quality evaluated by protein digestibility-corrected amino acid score (PDCAAS) (p < 0.05) that represents 27, 25 and 19% more than hybrids mixture, HPHV and landraces, respectively. This work gives valuable information on how different types of grains differ in the nutritional quality affecting the final product to provide more elements in the decision-making of processors. There is no a perfect maize, but there are genotypes that can be combined as mixtures and the processing method to design superior nutritional tortillas and related products for populations that highly consume them and improve their human health.
ABSTRACT
It has been reported that pineapple (Ananas comosus) contains healthy nutrients and phytochemicals associated with antioxidant and anti-inflammatory capacities. However, a substantial amount of pineapple residue is produced due to a lack of valorization applications at the industrial scale, resulting in the loss of valuable nutrients. Solid-state fermentation (SSF) is proposed as an innovative strategy to enhance the release of bound phenolics from pineapple residues. In this work, the effects of SSF of pineapple peels with Lactobacillus plantarum, Lactobacillus rhamnosus, and Aspergillus oryzae on the release of phenolic compounds and their antioxidant and anti-inflammatory activities were evaluated, respectively. Pineapple peel extracts after SSF showed an increase in the release of phenolic compounds (248.11% with L. plantarum, 182% with A. oryzae, and 180.10% with L. rhamnosus), which led to an increase in the cellular antioxidant (81.94% with L. rhamnosus) and anti-inflammatory potential (nitric oxide inhibition of 62% with L. rhamnosus) compared to non-fermented extracts. Therefore, SSF of pineapple peels with L. plantarum, L. rhamnosus, and A. oryzae thrives as a new approach for the production of secondary metabolites with remarkable biological benefits, which can be the precursors for novel biofortified and nutraceutical-enriched foods that meet the needs of the most demanding and health-conscious consumers.
ABSTRACT
Macrophages are major regulators of angiogenesis in response to injury, but the mechanisms behind their diverse and phenotypically specific functions are still poorly understood. In particular, the effects of interleukin-4 (IL-4) on macrophage behavior have been well studied in vitro, but it remains unclear whether the release of IL-4 from biomaterials can be used to control macrophage phenotype and subsequent effects on angiogenesis in vivo. We used the murine hindlimb ischemia model to investigate the effects of IL-4-releasing poly(lactic-co-glycolic acid) microparticles co-delivered with IL-4-polarized macrophages on host macrophage phenotype and angiogenesis in vivo. We established a minimum dose of IL-4 required to modulate macrophage phenotype in vivo and evaluated effects on macrophage subpopulation diversity using multidimensional flow cytometry and pseudotime analysis. The delivery of IL-4-releasing microparticles did not affect the density or size of blood vessels as measured by immunohistochemical (IHC) analysis, but it did increase perfused tissue volume as measured by 3D microcomputed tomography (microCT). In contrast, the co-delivery of IL-4-releasing microparticles and exogenously IL-4-polarized macrophages increased the size of blood vessels as measured by IHC, but without effects on perfused tissue volume via microCT. These effects occurred in spite of low recovery of adoptively transferred macrophages at 4 days after administration. Spatial analysis of macrophage-blood vessel interactions via IHC showed that macrophages closely interacted with blood vessels, which was slightly influenced by treatment, and that blood vessel size was positively correlated with number of macrophages in close proximity. Altogether, these findings indicate that delivery of IL-4-releasing microparticles and exogenously IL-4-polarized macrophages can be beneficial for angiogenesis, but further mechanistic investigations are required.
Subject(s)
Interleukin-4 , Macrophages , Animals , Mice , X-Ray Microtomography , Immunomodulation , Adoptive TransferABSTRACT
[This corrects the article DOI: 10.3389/fcell.2021.749723.].
ABSTRACT
Mesenchymal stromal cells (MSCs) have unique immunomodulatory capacities. We investigated hair follicle-derived MSCs (HF-MSCs) from the dermal sheath, which are advantageous as an alternative source because of their relatively painless and minimally risky extraction procedure. These cells expressed neural markers upon isolation and maintained stemness for a minimum of 10 passages. Furthermore, HF-MSCs showed responsiveness to pro-inflammatory environments by expressing type-II major histocompatibility complex antigens (MHC)-II to a lesser extent than adipose tissue-derived MSCs (AT-MSCs). HF-MSCs effectively inhibited the proliferation of peripheral blood mononuclear cells equivalently to AT-MSCs. Additionally, HF-MSCs promoted the induction of CD4+CD25+FOXP3+ regulatory T cells to the same extent as AT-MSCs. Finally, HF-MSCs, more so than AT-MSCs, skewed M0 and M1 macrophages towards M2 phenotypes, with upregulation of typical M2 markers CD163 and CD206 and downregulation of M1 markers such as CD64, CD86, and MHC-II. Thus, we conclude that HF-MSCs are a promising source for immunomodulation.
ABSTRACT
Muscle development is a multistep process that involves cell specification, myoblast fusion, myotube migration, and attachment to the tendons. In spite of great efforts trying to understand the basis of these events, little is known about the molecular mechanisms underlying myotube migration. Knowledge of the few molecular cues that guide this migration comes mainly from studies in Drosophila. The migratory process of Drosophila embryonic muscles involves a first phase of migration, where muscle progenitors migrate relative to each other, and a second phase, where myotubes migrate searching for their future attachment sites. During this phase, myotubes form extensive filopodia at their ends oriented preferentially toward their attachment sites. This myotube migration and the subsequent muscle attachment establishment are regulated by cell adhesion receptors, such as the conserved proteoglycan Kon-tiki/Perdido. Laminins have been shown to regulate the migratory behavior of many cell populations, but their role in myotube migration remains largely unexplored. Here, we show that laminins, previously implicated in muscle attachment, are indeed required for muscle migration to tendon cells. Furthermore, we find that laminins genetically interact with kon-tiki/perdido to control both myotube migration and attachment. All together, our results uncover a new role for the interaction between laminins and Kon-tiki/Perdido during Drosophila myogenesis. The identification of new players and molecular interactions underlying myotube migration broadens our understanding of muscle development and disease.
ABSTRACT
Edible insects are being accepted by a growing number of consumers in recent years not only as a snack but also as a side dish or an ingredient to produce other foods. Most of the edible insects belong to one of these groups of insects such as caterpillars, butterflies, moths, wasps, beetles, crickets, grasshoppers, bees, and ants. Insect properties are analyzed and reported in the articles reviewed here, and one common feature is nutrimental content, which is one of the most important characteristics mentioned, especially proteins, lipids, fiber, and minerals. On the other hand, insects can be used as a substitute for flour of cereals for the enrichment of snacks because of their high content of proteins, lipids, and fiber. Technological properties are not altered when these insects-derived ingredients are added and sensorial analysis is satisfactory, and only in some cases, change in color takes place. Insects can be used as substitute ingredients in meat products; the products obtained have higher mineral content than traditional ones, and some texture properties (like elasticity) can be improved. In extruded products, insects are an alternative source of proteins to feed livestock, showing desirable characteristics. Isolates of proteins of insects have demonstrated bioactive activity, and these can be used to improve food formulations. Bioactive compounds, as antioxidant agents, insulin regulators, and anti-inflammatory peptides, are high-value products that can be obtained from insects. Fatty acids that play a significant role in human health and lipids from insects have showed positive impacts on coronary disease, inflammation, and cancer. Insects can be a vector for foodborne microbial contamination, but the application of good manufacturing practices and effective preservation techniques jointly with the development of appropriate safety regulations will decrease the appearance of such risks. However, allergens presented in some insects are a hazard that must be analyzed and taken into account. Despite all the favorable health-promoting characteristics present in insects and insects-derived ingredients, willingness to consume them has yet to be generalized.
ABSTRACT
An important but largely unmet challenge in understanding the mechanisms that govern the formation of specific organs is to decipher the complex and dynamic genetic programs exhibited by the diversity of cell types within the tissue of interest. Here, we use an integrated genetic, genomic, and computational strategy to comprehensively determine the molecular identities of distinct myoblast subpopulations within the Drosophila embryonic mesoderm at the time that cell fates are initially specified. A compendium of gene expression profiles was generated for primary mesodermal cells purified by flow cytometry from appropriately staged wild-type embryos and from 12 genotypes in which myogenesis was selectively and predictably perturbed. A statistical meta-analysis of these pooled datasets--based on expected trends in gene expression and on the relative contribution of each genotype to the detection of known muscle genes--provisionally assigned hundreds of differentially expressed genes to particular myoblast subtypes. Whole embryo in situ hybridizations were then used to validate the majority of these predictions, thereby enabling true-positive detection rates to be estimated for the microarray data. This combined analysis reveals that myoblasts exhibit much greater gene expression heterogeneity and overall complexity than was previously appreciated. Moreover, it implicates the involvement of large numbers of uncharacterized, differentially expressed genes in myogenic specification and subsequent morphogenesis. These findings also underscore a requirement for considerable regulatory specificity for generating diverse myoblast identities. Finally, to illustrate how the developmental functions of newly identified myoblast genes can be efficiently surveyed, a rapid RNA interference assay that can be scored in living embryos was developed and applied to selected genes. This integrated strategy for examining embryonic gene expression and function provides a substantially expanded framework for further studies of this model developmental system.
Subject(s)
Computational Biology/methods , Gene Expression Regulation, Developmental , Genetic Techniques , Myoblasts/physiology , Animals , Drosophila melanogaster , Gene Expression Regulation , Genotype , In Situ Hybridization , Mesoderm/metabolism , Muscle Development , Muscles/metabolism , Myoblasts/metabolism , RNA InterferenceABSTRACT
Different oregano species have been traditionally used as infusions in folk medicine. Oregano medicinal properties, such as antioxidant and anti-inflammatory, have been partially attributed to its polyphenolic content. However, information regarding bioaccessibility of oregano polyphenols is limited. Cell-based antioxidant activity, and in vitro hypoglycemic, and hypolipidemic properties of polyphenolic extracts from three species of oregano species, namely, Hedeoma patens (HP), Lippia graveolens (LG) and Lippia palmeri (LP), subjected to simulated gastrointestinal digestion were evaluated. LC-TOF-MS analysis of HP, LG and LP allowed the identification of 9 flavonoids and 6 hydroxycinnamic acid derivatives with nutraceutical significance. Oregano polyphenolic extracts and digests from HP, LG, and LP exhibited cellular antioxidant capacity, hypoglycemic and hypolipidemic properties. Altogether, our results suggest that HP, LG and LP polyphenols exhibit potential for use as hypoglycemic, hypolipidemic, and antioxidant agents.
Subject(s)
Antioxidants/pharmacology , Digestion , Glycoside Hydrolase Inhibitors/pharmacology , Hypolipidemic Agents/pharmacology , Lipase/antagonists & inhibitors , Origanum/chemistry , Plant Extracts/pharmacology , Polyphenols/pharmacology , Antioxidants/isolation & purification , Caco-2 Cells , Chromatography, High Pressure Liquid , Gastric Acid/chemistry , Glycoside Hydrolase Inhibitors/isolation & purification , Humans , Hypolipidemic Agents/isolation & purification , Intestinal Secretions/chemistry , Lipase/metabolism , Oxidation-Reduction , Oxidative Stress/drug effects , Plant Extracts/isolation & purification , Polyphenols/isolation & purification , Spectrometry, Mass, Electrospray IonizationABSTRACT
We have developed an integrated genetic, genomic, and computational approach to identify and characterize genes involved in myoblast fusion in Drosophila. We first used fluorescence-activated cell sorting to purify mesodermal cells both from wild-type embryos and from 12 variant genotypes in which muscle development is perturbed in known ways. Then, we obtained gene expression profiles for the purified cells by hybridizing isolated mesodermal RNA to Affymetrix GeneChip arrays. These data were subsequently compounded into a statistical metaanalysis that predicts myoblast subtype-specific gene expression signatures that were later validated by in situ hybridization experiments. Finally, we analyzed the myogenic functions of a subset of these myoblast genes using a double-stranded RNA interference assay in living embryos expressing green fluorescent protein under control of a muscle-specific promoter. This experimental strategy led to the identification of several previously uncharacterized genes required for myoblast fusion in Drosophila.
Subject(s)
Cell Fusion/methods , Drosophila melanogaster/cytology , Drosophila melanogaster/genetics , Genomics/methods , Myoblasts/cytology , Animals , Drosophila melanogaster/embryology , Embryo, Nonmammalian/cytology , Embryo, Nonmammalian/metabolism , Flow Cytometry , Gene Expression Profiling , Gene Expression Regulation, Developmental , Genes, Insect , Green Fluorescent Proteins/metabolism , Oligonucleotide Array Sequence Analysis , RNA/isolation & purification , RNA Interference , Reproducibility of ResultsABSTRACT
While combinatorial models of transcriptional regulation can be inferred for metazoan systems from a priori biological knowledge, validation requires extensive and time-consuming experimental work. Thus, there is a need for computational methods that can evaluate hypothesized cis regulatory codes before the difficult task of experimental verification is undertaken. We have developed a novel computational framework (termed "CodeFinder") that integrates transcription factor binding site and gene expression information to evaluate whether a hypothesized transcriptional regulatory model (TRM; i.e., a set of co-regulating transcription factors) is likely to target a given set of co-expressed genes. Our basic approach is to simultaneously predict cis regulatory modules (CRMs) associated with a given gene set and quantify the enrichment for combinatorial subsets of transcription factor binding site motifs comprising the hypothesized TRM within these predicted CRMs. As a model system, we have examined a TRM experimentally demonstrated to drive the expression of two genes in a sub-population of cells in the developing Drosophila mesoderm, the somatic muscle founder cells. This TRM was previously hypothesized to be a general mode of regulation for genes expressed in this cell population. In contrast, the present analyses suggest that a modified form of this cis regulatory code applies to only a subset of founder cell genes, those whose gene expression responds to specific genetic perturbations in a similar manner to the gene on which the original model was based. We have confirmed this hypothesis by experimentally discovering six (out of 12 tested) new CRMs driving expression in the embryonic mesoderm, four of which drive expression in founder cells.