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1.
Ann Pharm Fr ; 82(1): 137-145, 2024 Jan.
Article in French | MEDLINE | ID: mdl-37827213

ABSTRACT

OBJECTIVES: The decree concerning quality management of implantable medical device circuits came into force in healthcare establishments on 26 May 2022. The aim of this project is to assess the level of safety of this circuit within the pharmacy, in order to improve it and bring it into line with this future regulation. METHODS: A grid for compliance with the decree was drawn up, enabling compliance rates to be calculated. A second grid was drawn up in accordance with internal procedures. All these criteria were audited in pairs. Priority areas for improvement were identified and working groups were formed. The action plan was monitored by the Steering Committee. Control audits ensure the implementation and relevance of the action plan, as well as the effective securing of the circuit. RESULTS: The rate of circuit compliance with the decree rose from 58% (initial audits) to 72% (control audits). Over a period of 18 months, six workgroups were set to implement improvement measures allowing to ensure regulatory compliance and circuit security. Obstacles (equipment, IT) nevertheless hindered the presence of the unique identifier for medical devices at every stages of the circuit. CONCLUSIONS: This cross-functional project was carried out in "project mode", thanks to the involvement of field staff. It will be pursued at hospital level by the person in charge of the quality management system.


Subject(s)
Hospitals , Prostheses and Implants , Humans
2.
Bioorg Med Chem Lett ; 28(17): 2985-2992, 2018 09 15.
Article in English | MEDLINE | ID: mdl-30122227
3.
J Dermatol Sci ; 2018 May 17.
Article in English | MEDLINE | ID: mdl-29779986

ABSTRACT

BACKGROUND: Actinic keratoses (AK) are proliferations of neoplastic keratinocytes in the epidermis resulting from cumulative exposure to ultraviolet radiation (UVR), which are liable to transform into squamous cell carcinoma (SCC). Organ Transplant Recipients (OTR) have an increased risk of developing SCC as a consequence of long-term immunosuppressive therapy. The aim of this study was to determine the molecular signature of AKs from OTR prior to treatment with methyl aminolevulinate-photodynamic therapy (MAL-PDT), and to assess what impact the treatment has on promoting remodeling of the photo-damaged skin. METHODS: Seven patients were enrolled on a clinical trial to assess the effect of MAL-PDT with biopsies taken at screening prior to the first treatment session (week 1), and six weeks after completion of final treatment (week 18). Whole-genome gene expression analysis was carried out on skin biopsies isolated from an AK lesion, an area surrounding the lesion, and a non-sun exposed region of the body. Quantitative PCR was utilized to confirm the differential expression of key genes. RESULTS: MAL-PDT treatment corrected abnormal proliferation-related gene profiles, corrected aberrantly expressed cancer-associated genes and induced expression of dermal extracellular matrix genes in photo-exposed skin. CONCLUSION: The efficacy of the MAL-PDT on AK lesions was confirmed at whole-genome gene expression level. A transcriptional signature of remodeling, identified through assessing the effect of MAL-PDT on photodamaged skin, supports the use of MAL-PDT for treating photodamaged skin and field cancerized areas.

4.
J Med Chem ; 61(9): 4030-4051, 2018 05 10.
Article in English | MEDLINE | ID: mdl-29648825

ABSTRACT

The use of an interleukin ß antibody is currently being investigated in the clinic for the treatment of acne, a dermatological disorder affecting 650M persons globally. Inhibiting the protease responsible for the cleavage of inactive pro-IL1ß into active IL-1ß, caspase-1, could be an alternative small molecule approach. This report describes the discovery of uracil 20, a potent (38 nM in THP1 cells assay) caspase-1 inhibitor for the topical treatment of inflammatory acne. The uracil series was designed according to a published caspase-1 pharmacophore model involving a reactive warhead in P1 for covalent reversible inhibition and an aryl moiety in P4 for selectivity against the apoptotic caspases. Reversibility was assessed in an enzymatic dilution assay or by using different substrate concentrations. In addition to classical structure-activity-relationship exploration, topical administration challenges such as phototoxicity, organic and aqueous solubility, chemical stability in solution, and skin metabolic stability are discussed and successfully resolved.


Subject(s)
Acne Vulgaris/drug therapy , Caspase 1/metabolism , Caspase Inhibitors/administration & dosage , Caspase Inhibitors/pharmacology , Drug Design , Acne Vulgaris/enzymology , Administration, Topical , Animals , Caspase 1/chemistry , Caspase Inhibitors/pharmacokinetics , Caspase Inhibitors/therapeutic use , Cell Line , Humans , Mice , Models, Molecular , Protein Conformation , Solvents/chemistry , Tissue Distribution
5.
Exp Dermatol ; 27(4): 358-365, 2018 04.
Article in English | MEDLINE | ID: mdl-29380443

ABSTRACT

Staphylococcus aureus colonization is thought to contribute to the pathophysiology of atopic dermatitis (AD). AD patients exhibit reduced levels of cutaneous antimicrobial peptides (AMPs), which may explain their increased susceptibility to infections. Using an in vitro reconstructed human epidermis (RHE) model, we sought to determine whether topical application of a non-replicating probiotic, heat-treated Lactobacillus johnsonii NCC 533 (HT La1), could inhibit S. aureus adhesion to skin and boost cutaneous innate immunity. We found that application of HT La1 suspension to RHE samples reduced the binding of radiolabelled S. aureus by up to 74%. To investigate a potential effect of HT La1 on innate immunity, we analysed the expression of nine AMP genes, including those encoding beta defensins and S100 proteins, following topical application of HT La1 in suspension or in a daily moisturizer lotion. Analysed genes were induced by up to fourfold in a dose-dependent manner by HT La1 in suspension and by up to 2.4-fold by HT La1 in the moisturizer lotion. Finally, using ELISA and immunohistochemical detection, we evaluated the expression and secretion of the AMPs hBD-2 and psoriasin and determined that both proteins were induced by topical HT La1, particularly in the stratum corneum of the RHE. These findings demonstrate that a topically applied, non-replicating probiotic can modulate endogenous AMP expression and inhibit binding of S. aureus to an RHE model in vitro. Moreover, they suggest that a topical formulation containing HT La1 could benefit atopic skin by enhancing cutaneous innate immunity and reducing S. aureus colonization.


Subject(s)
Bacterial Adhesion/drug effects , Epidermis/immunology , Epidermis/metabolism , Lactobacillus johnsonii , Probiotics/pharmacology , S100 Proteins/genetics , Staphylococcus aureus/physiology , beta-Defensins/genetics , Administration, Topical , Epidermis/microbiology , Gene Expression/drug effects , Hot Temperature , Humans , Immunity, Innate/drug effects , Probiotics/administration & dosage , S100 Calcium Binding Protein A7/genetics , S100 Calcium Binding Protein A7/metabolism , S100 Proteins/metabolism , beta-Defensins/metabolism
6.
Sci Rep ; 7(1): 2954, 2017 06 07.
Article in English | MEDLINE | ID: mdl-28592806

ABSTRACT

Autologous fat grafting is a gold standard therapy for soft tissue defects, but is hampered by unpredictable postoperative outcomes. Fat graft enrichment with adipose-derived stromal cell (ASCs) was recently reported to enhance graft survival. Platelet-rich plasma (PRP) has also emerged as a biologic scaffold that promotes fat graft viability. Combined ASC/PRP fat grafting enrichment is thus a promising new regenerative medicine approach. The effects of PRP on ASC proliferation are well documented, but the impact of PRP on ASC differentiation has yet to be investigated in depth to further elucidate the PRP clinical effects. Here we analyzed the human ASC fate upon PRP treatment. PRP was found to sharply reduce the potential of ASCs to undergo differentiation into adipocytes. Interestingly, the PRP anti-adipogenic effect was accompanied by the generation of myofibroblast-like cells. Among the various factors released from PRP, TGFß pathway activators played a critical role in both the anti-adipogenic and pro-myofibroblastic PRP effects. Overall, these data suggest that PRP participates in maintaining a pool of ASCs and in the repair process by promoting ASC differentiation into myofibroblast-like cells. TGFß may provide an important target pathway to improve PRP clinical outcomes.


Subject(s)
Adipogenesis , Adipose Tissue/cytology , Cell Differentiation , Myofibroblasts/cytology , Myofibroblasts/metabolism , Platelet-Rich Plasma/metabolism , Stromal Cells/cytology , Stromal Cells/metabolism , Transforming Growth Factor beta/metabolism , Adipocytes/cytology , Adipocytes/metabolism , Aged , Benzamides/pharmacology , Cells, Cultured , Dioxoles/pharmacology , Female , Humans , Infant , Male , Phenotype
7.
J Invest Dermatol ; 135(9): 2198-2208, 2015 Sep.
Article in English | MEDLINE | ID: mdl-25848978

ABSTRACT

Rosacea is a common chronic inflammatory skin disease of unknown etiology. Our knowledge about an involvement of the adaptive immune system is very limited. We performed detailed transcriptome analysis, quantitative real-time reverse-transcriptase-PCR, and quantitative immunohistochemistry on facial biopsies of rosacea patients, classified according to their clinical subtype. As controls, we used samples from patients with facial lupus erythematosus and healthy controls. Our study shows significant activation of the immune system in all subtypes of rosacea, characterizing erythematotelangiectatic rosacea (ETR) already as a disease with significant influx of proinflammatory cells. The T-cell response is dominated by Th1/Th17-polarized immune cells, as demonstrated by significant upregulation of IFN-γ or IL-17, for example. Chemokine expression patterns support a Th1/Th17 polarization profile of the T-cell response. Macrophages and mast cells are increased in all three subtypes of rosacea, whereas neutrophils reach a maximum in papulopustular rosacea. Our studies also provide evidence for the activation of plasma cells with significant antibody production already in ETR, followed by a crescendo pattern toward phymatous rosacea. In sum, Th1/Th17 polarized inflammation and macrophage infiltration are an underestimated hallmark in all subtypes of rosacea. Therapies directly targeting the Th1/Th17 pathway are promising candidates in the future treatment of this skin disease.


Subject(s)
Adaptive Immunity/physiology , Rosacea/immunology , Th1 Cells/immunology , Th17 Cells/immunology , Adaptive Immunity/immunology , Adult , Biopsy, Needle , Case-Control Studies , Cell Proliferation , Chemokines/metabolism , Female , Humans , Immunohistochemistry , Inflammation/immunology , Inflammation/physiopathology , Macrophages/immunology , Male , Mast Cells/immunology , Middle Aged , Molecular Targeted Therapy/methods , Reference Values , Rosacea/drug therapy , Rosacea/pathology
8.
Stem Cells Int ; 2015: 592090, 2015.
Article in English | MEDLINE | ID: mdl-25733979

ABSTRACT

Animal study findings have revealed that individual fat depots are not functionally equivalent and have different embryonic origins depending on the anatomic location. Mouse bone regeneration studies have also shown that it is essential to match the Hox code of transplanted cells and host tissues to achieve correct repair. However, subcutaneous fat depots from any donor site are often used in autologous fat grafting. Our study was thus carried out to determine the embryonic origins of human facial (chin) and limb (knee) fat depots and whether they had similar features and molecular matching patterns. Paired chin and knee fat depots were harvested from 11 subjects and gene expression profiles were determined by DNA microarray analyses. Adipose-derived stromal cells (ASCs) from both sites were isolated and analyzed for their capacity to proliferate, form clones, and differentiate. Chin and knee fat depots expressed a different HOX code and could have different embryonic origins. ASCs displayed a different phenotype, with chin-ASCs having the potential to differentiate into brown-like adipocytes, whereas knee-ASCs differentiated into white adipocytes. These results highlighted different features for these two fat sites and indicated that donor site selection might be an important factor to be considered when applying adipose tissue in cell-based therapies.

9.
Int J Infect Dis ; 29: 176-7, 2014 Dec.
Article in English | MEDLINE | ID: mdl-25449254

ABSTRACT

We report here the presence of Bartonella quintana in a demodex. Demodex are arthropods associated with acnea. Bartonella quintana was found by broad Spectrum 16rDNA PCR amplification and sequencing, and confirmed by specific PCR. Bartonella quintana may parasite several arthropods and not only lice.


Subject(s)
Bartonella quintana/isolation & purification , Mites/microbiology , Rosacea/microbiology , Adult , Animals , Bartonella quintana/genetics , Female , Humans , Middle Aged
10.
J Dermatol Sci ; 75(1): 49-54, 2014 Jul.
Article in English | MEDLINE | ID: mdl-24802713

ABSTRACT

BACKGROUND: The facial erythema of rosacea is recognized as the most prevalent and most difficult manifestation of rosacea to treat. A recent approach in patients with rosacea has been to reduce this erythema through vasoconstriction of cutaneous blood vessels by selectively targeting α2-adrenergic receptors with brimonidine. OBJECTIVE: To further investigate the pharmacodynamic profile of brimonidine, its vasoconstrictive effects and its anti-inflammatory properties. METHODS: The potency for the α1A, α1B, α2A, α2B and α2C receptors of brimonidine was measured, as well as performing a large target profiling study in order to determine the target selectivity profile of brimonidine. The vasoconstrictive effects of brimonidine were measured using ex vivo wire myography and human skin biopsy neuroinflammation models. The anti-inflammatory properties of brimonidine were measured using two in vivo mice ear inflammation models. RESULTS: Brimonidine was found to be highly selective for the α2A adrenoreceptor (EC50 0.45nM) over the other α-adrenoreceptors. Additionally, the large target profiling study demonstrated the high selectivity of brimonidine with minimal off-target effects. The ex vivo wire myography model showed that brimonidine is a potent vasoconstrictor of human subcutaneous vessels with a diameter of less than 200µm (EC50 0.4nM). The ex vivo human skin biopsy neuroinflammation model demonstrated that brimonidine completely inhibited vasodilation induced by capsaicin. Both in vivo mouse ear inflammation models highlighted that brimonidine inhibited ear edema (up to 76%) when compared to vehicle. CONCLUSION: The selectivity, vasoconstrictive and anti-inflammatory properties of brimonidine that have been described in these studies are in agreement with the benefits observed with this compound in the treatment of facial erythema in rosacea.


Subject(s)
Adrenergic alpha-2 Receptor Agonists/pharmacology , Anti-Inflammatory Agents/pharmacology , Inflammation/prevention & control , Quinoxalines/pharmacology , Receptors, Adrenergic, alpha-2/drug effects , Skin/blood supply , Vasoconstrictor Agents/pharmacology , Vasodilation/drug effects , Animals , Biopsy , Brimonidine Tartrate , Disease Models, Animal , Female , Humans , Inflammation/chemically induced , Inflammation/metabolism , Mice, Inbred BALB C , Receptors, Adrenergic, alpha-2/metabolism , Tissue Culture Techniques
11.
Microb Pathog ; 71-72: 37-40, 2014.
Article in English | MEDLINE | ID: mdl-24768927

ABSTRACT

Proliferation of Demodex mites is associated with rosacea. Furthermore, Demodex-associated bacteria were suggested to play a role in the pathogenesis of rosacea. We decided to analyze Demodex microbiota. Mites were collected by standardized skin surface biopsies from patients with erythematotelangiectatic, papulopustular rosacea or from control subjects. The microbiota from each mite was characterized by 16S rRNA clone library approach. The 16S rRNA clone library consisted of 367 clones obtained from 73 extracts originating from 5 samples per study group (ETR, PPR or healthy subjects). A total of 86 species were identified with 36 as Demodex-specific microbiota. In the papulopustular group, proportions of Proteobacteria and Firmicutes increased whereas proportion of Actinobacteria decreased. Here, we report preliminary results on the microbiota of Demodex mites based on a molecular approach showing an unexpected diversity. Differences according to the host status need to be confirmed but open new perspectives for diagnostic of rosacea.


Subject(s)
Acari/microbiology , Biota , Rosacea/parasitology , Acari/growth & development , Adult , Aged , Animals , Cluster Analysis , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , Female , Humans , Male , Middle Aged , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA
12.
J Invest Dermatol ; 132(4): 1253-62, 2012 Apr.
Article in English | MEDLINE | ID: mdl-22189789

ABSTRACT

Rosacea is a frequent chronic inflammatory skin disease of unknown etiology. Because early rosacea reveals all characteristics of neurogenic inflammation, a central role of sensory nerves in its pathophysiology has been discussed. Neuroinflammatory mediators and their receptors involved in rosacea are poorly defined. Good candidates may be transient receptor potential (TRP) ion channels of vanilloid type (TRPV), which can be activated by many trigger factors of rosacea. Interestingly, TRPV2, TRPV3, and TRPV4 are expressed by both neuronal and non-neuronal cells. Here, we analyzed the expression and distribution of TRPV receptors in the various subtypes of rosacea on non-neuronal cells using immunohistochemistry, morphometry, double immunoflourescence, and quantitative real-time PCR (qRT-PCR) as compared with healthy skin and lupus erythematosus. Our results show that dermal immunolabeling of TRPV2 and TRPV3 and gene expression of TRPV1 is significantly increased in erythematotelangiectatic rosacea (ETR). Papulopustular rosacea (PPR) displayed an enhanced immunoreactivity for TRPV2, TRPV4, and also of TRPV2 gene expression. In phymatous rosacea (PhR)-affected skin, dermal immunostaining of TRPV3 and TRPV4 and gene expression of TRPV1 and TRPV3 was enhanced, whereas epidermal TRPV2 staining was decreased. Thus, dysregulation of TRPV channels also expressed by non-neuronal cells may be critically involved in the initiation and/or development of rosacea. TRP ion channels may be targets for the treatment of rosacea.


Subject(s)
Rosacea/metabolism , Skin/metabolism , TRPV Cation Channels/metabolism , Antigens, CD/metabolism , Antigens, Differentiation, Myelomonocytic/metabolism , Biopsy , Case-Control Studies , Humans , Lupus Erythematosus, Systemic/metabolism , Lupus Erythematosus, Systemic/pathology , Rosacea/pathology , Skin/pathology , Tryptases/metabolism
13.
J Investig Dermatol Symp Proc ; 15(1): 2-11, 2011 Dec.
Article in English | MEDLINE | ID: mdl-22076321

ABSTRACT

Rosacea is a chronic inflammatory skin disease of unknown etiology. Although described centuries ago, the pathophysiology of this disease is still poorly understood. Epidemiological studies indicate a genetic component, but a rosacea gene has not been identified yet. Four subtypes and several variants of rosacea have been described. It is still unclear whether these subtypes represent a "developmental march" of different stages or are merely part of a syndrome that develops independently but overlaps clinically. Clinical and histopathological characteristics of rosacea make it a fascinating "human disease model" for learning about the connection between the cutaneous vascular, nervous, and immune systems. Innate immune mechanisms and dysregulation of the neurovascular system are involved in rosacea initiation and perpetuation, although the complex network of primary induction and secondary reaction of neuroimmune communication is still unclear. Later, rosacea may result in fibrotic facial changes, suggesting a strong connection between chronic inflammatory processes and skin fibrosis development. This review highlights recent molecular (gene array) and cellular findings and aims to integrate the different body defense mechanisms into a modern concept of rosacea pathophysiology.


Subject(s)
Rosacea/pathology , Rosacea/physiopathology , Chronic Disease , Female , Fibrosis , Humans , Incidence , Male , Prevalence , Rosacea/immunology , Sex Factors , Vasodilation/physiology
14.
J Investig Dermatol Symp Proc ; 15(1): 53-62, 2011 Dec.
Article in English | MEDLINE | ID: mdl-22076328

ABSTRACT

Rosacea is a common skin disease with a high impact on quality of life. Characterized by erythema, edema, burning pain, immune infiltration, and facial skin fibrosis, rosacea has all the characteristics of neurogenic inflammation, a condition induced by sensory nerves via antidromically released neuromediators. To investigate the hypothesis of a central role of neural interactions in the pathophysiology, we analyzed molecular and morphological characteristics in the different subtypes of rosacea by immunohistochemistry, double immunofluorescence, morphometry, real-time PCR, and gene array analysis, and compared the findings with those for lupus erythematosus or healthy skin. Our results showed significantly dilated blood and lymphatic vessels. Signs of angiogenesis were only evident in phymatous rosacea. The number of mast cells and fibroblasts was increased in rosacea, already in subtypes in which fibrosis is not clinically apparent, indicating early activation. Sensory nerves were closely associated with blood vessels and mast cells, and were increased in erythematous rosacea. Gene array studies and qRT-PCR confirmed upregulation of genes involved in vasoregulation and neurogenic inflammation. Thus, dysregulation of mediators and receptors implicated in neurovascular and neuroimmune communication may be crucial at early stages of rosacea. Drugs that function on neurovascular and/or neuroimmune communication may be beneficial for the treatment of rosacea.


Subject(s)
Neurogenic Inflammation/immunology , Neurogenic Inflammation/physiopathology , Rosacea/immunology , Rosacea/physiopathology , Skin/innervation , Skin/physiopathology , Fibroblasts/immunology , Fibroblasts/physiology , Gene Expression Profiling , Humans , Lupus Erythematosus, Systemic/genetics , Lupus Erythematosus, Systemic/immunology , Lupus Erythematosus, Systemic/physiopathology , Lymphatic Vessels/immunology , Lymphatic Vessels/physiopathology , Mast Cells/immunology , Mast Cells/physiology , Neovascularization, Pathologic/genetics , Neovascularization, Pathologic/immunology , Neovascularization, Pathologic/physiopathology , Neurogenic Inflammation/genetics , Neurogenic Inflammation/pathology , Rosacea/genetics , Rosacea/pathology , Skin/blood supply , Skin/pathology , Up-Regulation , Vasodilation/genetics , Vasodilation/immunology , Vasodilation/physiology , Vimentin/analysis , Vimentin/immunology
15.
J Invest Dermatol ; 131(8): 1692-700, 2011 Aug.
Article in English | MEDLINE | ID: mdl-21562572

ABSTRACT

Melasma is a commonly acquired hyperpigmentary disorder of the face, but its pathogenesis is poorly understood and its treatment remains challenging. We conducted a comparative histological study on lesional and perilesional normal skin to clarify the histological nature of melasma. Significantly, higher amounts of melanin and of melanogenesis-associated proteins were observed in the epidermis of lesional skin, and the mRNA level of tyrosinase-related protein 1 was higher in lesional skin, indicating regulation at the mRNA level. However, melanocyte numbers were comparable between lesional and perilesional skin. A transcriptomic study was undertaken to identify genes involved in the pathology of melasma. A total of 279 genes were found to be differentially expressed in lesional and perilesional skin. As was expected, the mRNA levels of a number of known melanogenesis-associated genes, such as tyrosinase, were found to be elevated in lesional skin. Bioinformatics analysis revealed that the most lipid metabolism-associated genes were downregulated in lesional skin, and this finding was supported by an impaired barrier function in melasma. Interestingly, a subset of Wnt signaling modulators, including Wnt inhibitory factor 1, secreted frizzled-related protein 2, and Wnt5a, were also found to be upregulated in lesional skin. Immunohistochemistry confirmed the higher expression of these factors in melasma lesions.


Subject(s)
Gene Expression Profiling , Lipid Metabolism/genetics , Melanosis/genetics , Melanosis/metabolism , Wnt Proteins/genetics , Wnt Proteins/metabolism , Adaptor Proteins, Signal Transducing/genetics , Adaptor Proteins, Signal Transducing/metabolism , Adult , Frizzled Receptors/genetics , Frizzled Receptors/metabolism , Humans , Immunohistochemistry , In Situ Hybridization , Melanocytes/physiology , Melanosis/pathology , Membrane Glycoproteins/genetics , Membrane Glycoproteins/metabolism , Middle Aged , Oxidoreductases/genetics , Oxidoreductases/metabolism , Proto-Oncogene Proteins/genetics , Proto-Oncogene Proteins/metabolism , Receptors, G-Protein-Coupled/genetics , Receptors, G-Protein-Coupled/metabolism , Repressor Proteins/genetics , Repressor Proteins/metabolism , Wnt-5a Protein , Wnt1 Protein/genetics , Wnt1 Protein/metabolism
16.
Bioinformatics ; 20(16): 2726-37, 2004 Nov 01.
Article in English | MEDLINE | ID: mdl-15145801

ABSTRACT

MOTIVATION: Microarray technology has become a powerful research tool in many fields of study; however, the cost of microarrays often results in the use of a low number of replicates (k). Under circumstances where k is low, it becomes difficult to perform standard statistical tests to extract the most biologically significant experimental results. Other more advanced statistical tests have been developed; however, their use and interpretation often remain difficult to implement in routine biological research. The present work outlines a method that achieves sufficient statistical power for selecting differentially expressed genes under conditions of low k, while remaining as an intuitive and computationally efficient procedure. RESULTS: The present study describes a Global Error Assessment (GEA) methodology to select differentially expressed genes in microarray datasets, and was developed using an in vitro experiment that compared control and interferon-gamma treated skin cells. In this experiment, up to nine replicates were used to confidently estimate error, thereby enabling methods of different statistical power to be compared. Gene expression results of a similar absolute expression are binned, so as to enable a highly accurate local estimate of the mean squared error within conditions. The model then relates variability of gene expression in each bin to absolute expression levels and uses this in a test derived from the classical ANOVA. The GEA selection method is compared with both the classical and permutational ANOVA tests, and demonstrates an increased stability, robustness and confidence in gene selection. A subset of the selected genes were validated by real-time reverse transcription-polymerase chain reaction (RT-PCR). All these results suggest that GEA methodology is (i) suitable for selection of differentially expressed genes in microarray data, (ii) intuitive and computationally efficient and (iii) especially advantageous under conditions of low k. AVAILABILITY: The GEA code for R software is freely available upon request to authors.


Subject(s)
Algorithms , Gene Expression Profiling/methods , Gene Expression Regulation/physiology , Models, Genetic , Sequence Alignment/methods , Sequence Analysis, DNA/methods , Skin/metabolism , Analysis of Variance , Animals , Cell Line , Humans , Interferon-gamma/pharmacology , Models, Statistical , Oligonucleotide Array Sequence Analysis , Skin/drug effects , Software , Statistics as Topic/methods
17.
Proc Natl Acad Sci U S A ; 100 Suppl 1: 11836-41, 2003 Sep 30.
Article in English | MEDLINE | ID: mdl-12923295

ABSTRACT

The transcription factor Sox1 is the earliest and most specific known marker for mammalian neural progenitors. During fetal development, Sox1 is expressed by proliferating progenitor cells throughout the central nervous system and in no tissue but the lens. We generated a reporter mouse line in which egfp is inserted into the Sox1 locus. Sox1GFP animals faithfully recapitulate the expression of the endogenous gene. We have used the GFP reporter to purify neuroepithelial cells by fluorescence-activated cell sorting from embryonic day 10.5 embryos. RNAs prepared from Sox1GFP+ and Sox1GFP- embryo cells were then used to perform a pilot screen of subtracted cDNAs prepared from differentiating embryonic stem cells and arrayed on a glass chip. Fifteen unique differentially expressed genes were identified, all previously associated with fetal or adult neural tissue. Whole mount in situ hybridization against two genes of previously unknown embryonic expression, Lrrn1 and Musashi2, confirmed the selectivity of this screen for early neuroectodermal markers.


Subject(s)
Cell Separation/methods , DNA-Binding Proteins/genetics , High Mobility Group Proteins/genetics , Neurons/cytology , Neurons/metabolism , Stem Cells/cytology , Stem Cells/metabolism , Animals , Female , Flow Cytometry , Gene Expression Profiling , Green Fluorescent Proteins , In Situ Hybridization , Luminescent Proteins/genetics , Male , Mice , Mice, Transgenic , Oligonucleotide Array Sequence Analysis , RNA, Messenger/genetics , RNA, Messenger/metabolism , Recombinant Fusion Proteins/genetics , SOXB1 Transcription Factors
18.
Nat Biotechnol ; 20(12): 1240-5, 2002 Dec.
Article in English | MEDLINE | ID: mdl-12447396

ABSTRACT

The multilineage differentiation capacity of mouse embryonic stem (ES) cells offers a potential testing platform for gene products that mediate mammalian lineage determination and cellular specialization. Identification of such differentiation regulators is crucial to harnessing ES cells for pharmaceutical discovery and cell therapy. Here we describe the use of episomal expression technology for functional evaluation of cDNA clones during ES-cell differentiation in vitro. Several candidate cDNAs identified by subtractive cloning and expression profiling were introduced into ES cells in episomal expression constructs. Subsequent differentiation revealed that the Wnt antagonist Sfrp2 stimulates production of neural progenitors. The significance of this observation was substantiated by forced expression of Wnt-1 and treatment with lithium chloride, both of which inhibit neural differentiation. These findings reveal the importance of Wnt signaling in regulating ES-cell lineage diversification. More generally, this study establishes a path for rapid and direct validation of candidate genes in ES cells.


Subject(s)
Cell Differentiation/physiology , Membrane Proteins , Neurons/physiology , Proteins/metabolism , Proto-Oncogene Proteins/physiology , Stem Cells/physiology , Zebrafish Proteins , Animals , Cells, Cultured , Embryo, Mammalian/cytology , Gene Expression Profiling/methods , Gene Expression Regulation, Developmental/physiology , Genetic Testing/methods , Mice , Neurons/cytology , Plasmids/genetics , Proteins/genetics , Proto-Oncogene Proteins/genetics , Wnt Proteins , Wnt1 Protein
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