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Cryptic and Complex Chromosomal Aberrations in Early-Onset Neuropsychiatric Disorders

AMERICAN JOURNAL OF HUMAN GENETICS 2014年第4期95卷 454-461页

作者： Brand, Harrison Pillalamarri, Vamsee Collins, Ryan L. Eggert, Stacey O'Dushlaine, Colm Braaten, Ellen B. Stone, Matthew R. Chambert, Kimberly Doty, Nathan D. Hanscom, Carrie Rosenfeld, Jill A. Ditmars, Hillary Blais, Jessica Mills, Ryan Lee, Charles Gusella, James F. McCarroll, Steven Smoller, Jordan W. Talkowski, Michael E. Doyle, Alysa E. Massachusetts Gen Hosp Ctr Human Genet Res Mol Neurogenet Unit Psychiat & Neurodev Genet Unit Boston MA 02114 USA Massachusetts Gen Hosp Dept Neurol Boston MA 02114 USA Harvard Univ Sch Med Boston MA 02114 USA Harvard Univ Sch Med Dept Genet Boston MA 02115 USA Broad Inst Stanley Ctr Psychiat Res Cambridge MA 02141 USA Broad Inst Program Med & Populat Genet Cambridge MA 02141 USA Massachusetts Gen Hosp Dept Psychiat Boston MA 02114 USA PerkinElmer Inc Signature Genom Labs Spokane WA 99207 USA Univ Michigan Med Ctr Dept Computat Med Ann Arbor MI 48109 USA Univ Michigan Med Ctr Dept Bioinformat & Human Genet Ann Arbor MI 48109 USA Jackson Lab Genom Med Farmington CT 06030 USA

Structural variation (SV) is a significant component of the genetic etiology of both neurodevelopmental and psychiatric disorders;however, routine guidelines for clinical genetic screening have been established only in the former category. Genome-wide chromosomal microarray (CMA) can detect genomic imbalances such as copy-number variants (CNVs), but balanced chromosomal abnormalities (BCAs) still require karyotyping for clinical detection. Moreover, submicroscopic BCAs and subarray threshold CNVs are intractable, or cryptic, to both CMA and karyotyping. Here, we performed whole-genome sequencing using large-insert jumping libraries to delineate both cytogenetically visible and cryptic SVs in a single test among 30 clinically referred youth representing a range of severe neuropsychiatric conditions. We detected 96 SVs per person on average that passed filtering criteria above our highest-confidence resolution (6,305 bp) and an additional 111 SVs per genome below this resolution. These SVs rearranged 3.8 Mb of genomic sequence and resulted in 42 putative loss-of-function (LoF) or gain-of-function mutations per person. We estimate that 80% of the LoF variants were cryptic to clinical CMA. We found myriad complex and cryptic rearrangements, including a "paired" duplication (360 kb, 169 kb) that flanks a 5.25 Mb inversion that appears in 7 additional cases from clinical CNV data among 47,562 individuals. Following convergent genomic profiling of these independent clinical CNV data, we interpreted three SVs to be of potential clinical significance. These data indicate that sequence-based delineation of the full SV mutational spectrum warrants exploration in youth referred for neuropsychiatric evaluation and clinical diagnostic SV screening more broadly.

关键词： CHROMOSOME abnormalities NEUROBEHAVIORAL disorders DISEASES -- Causes & theories of causation DEVELOPMENTAL neurobiology GENETIC testing microarray technology DNA sequencing

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Lactobacillus reuteri 100-23 Modulates Urea Hydrolysis in the Murine Stomach

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APPLIED AND ENVIRONMENTAL MICROBIOLOGY 2014年第19期80卷 6104-6113页

作者： Wilson, Charlotte M. Loach, Diane Lawley, Blair Bell, Tracey Sims, Ian M. O'Toole, Paul W. Zomer, Aldert Tannock, Gerald W. Univ Otago Dept Microbiol & Immunol Dunedin New Zealand Victoria Univ Wellington Ferrier Res Inst Wellington New Zealand Natl Univ Ireland Univ Coll Cork Sch Microbiol Cork Ireland Natl Univ Ireland Univ Coll Cork Alimentary Pharmabiot Ctr Cork Ireland

Comparisons of in vivo (mouse stomach) and in vitro (laboratory culture) transcriptomes of Lactobacillus reuteri strain 100-23 were made by microarray analysis. These comparisons revealed the upregulation of genes associated with acid tolerance, including urease production, in the mouse stomach. Inactivation of the ureC gene reduced the acid tolerance of strain 100-23 in vitro, and the mutant was outcompeted by the wild type in the gut of ex-Lactobacillus-free mice. Urine analysis showed that stable iso-tope-labeled urea, administered by gavage, was metabolized to a greater extent in Lactobacillus-free mice than animals colonized by strain 100-23. This surprising observation was associated with higher levels of urease activity and fecal-type bacteria in the stomach digesta of Lactobacillus-free mice. Despite the modulation of urea hydrolysis in the stomach, recycling of urea nitrogen in the murine host was not affected since the essential amino acid isoleucine, labeled with a stable isotope, was detected in the livers of both Lactobacillus-free and 100-23-colonized animals. Therefore, our experiments reveal a new and unexpected impact of Lactobacillus colonization on urea hydrolysis in the murine gut.

关键词： LACTOBACILLUS reuteri microarray technology UREA ANIMAL models in research NITROGEN excretion

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Total Analysis Systems with Thermochromic Etching Discs technology

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ANALYTICAL CHEMISTRY 2014年第24期86卷 12037-12046页

作者： Avella-Oliver, Miguel Morais, Sergi Carrascosa, Javier Puchades, Rosa Maquieira, Angel Univ Politecn Valencia Dept Quim IDM Valencia 46022 Spain

A new analytical system based on Thermochromic Etching Discs (TED) technology is presented. TED comprises a number of attractive features such as track independency, selective irradiation, a high power laser, and the capability to create useful assay platforms. The analytical versatility of this tool opens up a wide range of possibilities to design new compact disc-based total analysis systems applicable in chemistry and life sciences. In this paper, TED analytical implementation is described and discussed, and their analytical potential is supported by several applications. microarray immunoassay, immunofiltration assay, solution measurement, and cell culture approaches are herein addressed in order to demonstrate the practical capacity of this system. The analytical usefulness of TED technology is herein demonstrated, describing how to exploit this tool for developing truly integrated analytical systems that provide solutions within the point of care framework.

关键词： IMMUNOASSAY microarray technology NANOtechnology IRRADIATION LIFE sciences

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Micropatterned Arrays of ZnSe Nanospheres as Antireflection Coatings

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AUSTRALIAN JOURNAL OF CHEMISTRY 2014年第10期67卷 1427-1433页

作者： Florence, S. Sasi Sachan, Priyanka Gupta, Raju Kumar John, Rita Mahalingam, Umadevi Mother Teresa Womens Univ Dept Phys Kodaikanal 624101 Tamil Nadu India Indian Inst Technol Dept Chem Engn Kanpur 208016 Uttar Pradesh India Indian Inst Technol DST Unit Nanosci Kanpur 208016 Uttar Pradesh India Univ Madras Dept Theoret Phys Madras 600005 Tamil Nadu India

In this work, we demonstrate deposition of micro-arrays of ZnSe nanospheres on Si (100) substrate using simple thermal evaporation on a self-assembled sacrificial polystyrene (PS) mask. The results have been compared with the deposition on unpatterned gold catalyst- and SU-8 (negative photoresist)-coated Si substrates. The deposited ZnSe nanospheres properties were characterised by X-ray diffraction, atomic force microscopy (AFM), scanning electron microscopy (SEM), Raman, photoluminescence, and UV-vis spectroscopies. The X-ray diffraction patterns of the films exhibited reflection corresponding to the cubic (111) phase and showed polycrystallinity with a cubic (zinc blende) structure. The SEM and AFM images indicated that the particles were well dispersed and spherical in shape. The micro-arrays of ZnSe nanospheres on a self-assembled sacrificial PS mask showed excellent structural, morphological, and optical properties and demonstrated its usage in photovoltaic devices as an improved superior antireflective coating. The reflectance of the micro-arrays of ZnSe nanospheres on a self-assembled sacrificial PS mask decreased to nearly half of that of the ZnSe nanospheres fabricated on Au- and SU-8-coated Si substrates in the range of 300-800nm. Due to the well aligned and patterned surfaces, these noble textured ZnSe nanospheres may be suitable for low cost, large area photovoltaic devices and other antireflection applications.

关键词： ZINC selenide ANTIREFLECTIVE coatings microarray technology POLYSTYRENE GOLD catalysts PHOTOLUMINESCENCE X-ray diffraction

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FOXP1 directly represses transcription of proapoptotic genes and cooperates with NF-κB to promote survival of human B cells

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BLOOD 2014年第23期124卷 3431-3440页

作者： van Keimpema, Martine Gruneberg, Leonie J. Mokry, Michal van Boxtel, Ruben Koster, Jan Coffer, Paul J. Pals, Steven T. Spaargaren, Marcel Univ Amsterdam Acad Med Ctr Dept Pathol NL-1105 AZ Amsterdam Netherlands Univ Amsterdam Acad Med Ctr Lymphoma & Myeloma Ctr Amsterdam NL-1105 AZ Amsterdam Netherlands Univ Med Ctr Utrecht Wilhelmina Childrens Hosp Div Pediat Utrecht Netherlands Royal Netherlands Acad Arts & Sci Hubrecht Inst Dev Biol & Stem Cell Res Utrecht Netherlands Univ Med Ctr Utrecht Utrecht Netherlands Univ Amsterdam Acad Med Ctr Dept Oncogen NL-1105 AZ Amsterdam Netherlands Univ Med Ctr Utrecht Dept Cell Biol Utrecht Netherlands

The forkhead transcription factor FOXP1 is involved in B-cell development and function and is generally regarded as an oncogene in activated B-cell-like subtype of diffuse large B-cell lymphoma (DLBCL) and mucosa-associated lymphoid tissue lymphoma, lymphomas relying on constitutive nuclear factor kappa B (NF-kappa B) activity for survival. However, the mechanism underlying its putative oncogenic activity has not been established. By gene expression microarray, upon overexpression or silencing of FOXP1 in primary human B cells and DLBCL cell lines, combined with chromatin immunoprecipitation followed by next-generation sequencing, we established that FOXP1 directly represses a set of 7 proapoptotic genes. Low expression of these genes, encoding the BH3-only proteins BIK and Harakiri, the p53-regulatory proteins TP63, RASSF6, and TP53INP1, and AIM2 and EAF2, is associated with poor survival in DLBCL patients. In line with these findings, we demonstrated that FOXP1 promotes the expansion of primary mature human B cells by inhibiting caspase-dependent apoptosis, without affecting B-cell proliferation. Furthermore, FOXP1 is dependent upon, and cooperates with, NF-kappa B signaling to promote B-cell expansion and survival. Taken together, our data indicate that, through direct repression of proapoptotic genes, (aberrant) expression of FOXP1 complements (constitutive) NF-kappa B activity to promote B-cell survival and can thereby contribute to B-cell homeostasis and lymphomagenesis.

关键词： APOPTOTIC bodies B cells LYMPHOID tissue microarray technology MUCOUS membrane

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The Role of Transforming Growth Factor β Signaling in Fibroblast-like Synoviocytes From Patients With Oligoarticular Juvenile Idiopathic Arthritis Dysregulation of Transforming Growth Factor β Signaling, Including Overexpression of Bone Morphogenetic Protein 4, May Lead to a Chondrocyte Phenotype and May Contribute to Bony Hypertrophy

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ARTHRITIS & RHEUMATOLOGY 2014年第5期66卷 1352-1362页

作者： Brescia, AnneMarie C. Simonds, Megan M. McCahan, Suzanne M. Fawcett, Paul T. Rose, Carlos D. Thomas Jefferson Univ Philadelphia PA 19107 USA Alfred I DuPont Hosp Children Nemours Wilmington DE 19803 USA Nemours Biomed Res Wilmington DE USA

Objective. This study was designed to investigate the pathogenic contributions of fibroblast-like synoviocytes (FLS) to juvenile idiopathic arthritis (JIA) by identifying pathways with dysregulated gene expression in FLS from patients with oligoarticular JIA. Methods. FLS were derived from synovial fluid obtained by arthrocentesis from patients with JIA undergoing intraarticular steroid injections and from orthopedic control patients. Gene expression profiles of the JIA and control FLS were obtained using the Affymetrix platform, with application of Ingenuity Path-way Analysis and Gene Set Enrichment Analysis software to define gene sets in dysregulated pathways and networks of potential pathologic relevance in this disease. Biologically relevant differentially expressed genes were confirmed by RNA and protein analysis. Results. Exploration of global gene expression profiles of the JIA FLS revealed important dysregulated pathways, including the transforming growth factor beta (TGF beta) signaling, as well as endochondral bone formation, cartilage formation, and beta-catenin networks. Importantly, bone morphogenetic protein 4 (BMP-4) was significantly overexpressed in the JIA FLS. FLS from patients with oligoarticular JIA exhibit a chondrocyte phenotype, as evidenced by expression of type II collagen and aggrecan. Conclusion. Dysregulation of the pathways involved in the pathogenesis of oligoarticular JIA were revealed through gene expression profiling. JIA FLS displayed dysregulated TGF beta signaling and exhibited a hypertrophic chondrocyte phenotype. These characteristics, along with contributions from the beta-catenin network may have implications for endochondral bone formation and local growth disturbances in oligoarticular JIA. Overexpression of BMP-4 in FLS from patients with oligoarticular JIA in particular may play an important role in disease pathogenesis, with a direct effect on functional outcome and with implications for future treatment.

关键词： EXOSTOSIS ACADEMIC medical centers ENZYME-linked immunosorbent assay GENES POLYMERASE chain reaction FINANCING of research RHEUMATOID arthritis in children WESTERN immunoblotting REVERSE transcriptase polymerase chain reaction DATA analysis software microarray technology GENE expression profiling DESCRIPTIVE statistics DISEASE complications RISK factors

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The Plasma Cell Signature in Autoimmune Disease

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ARTHRITIS & RHEUMATOLOGY 2014年第1期66卷 173-184页

作者： Streicher, Katie Morehouse, Christopher A. Groves, Christopher J. Rajan, Bhargavi Pilataxi, Fernanda Lehmann, Kim P. Brohawn, Philip Z. Higgs, Brandon W. McKeever, Kathleen Greenberg, Steven A. Fiorentino, David Richman, Laura K. Jallal, Bahija Herbst, Ronald Yao, Yihong Ranade, Koustubh MedImmune Gaithersburg MD USA Brigham & Womens Hosp Boston MA 02115 USA Harvard Univ Sch Med Boston MA USA Stanford Univ Sch Med Stanford CA 94305 USA

Objective. Production of pathogenic autoantibodies by self-reactive plasma cells (PCs) is a hallmark of autoimmune diseases. We undertook this study to investigate the prevalence of PCs and their relationship to known pathogenic pathways to increase our understanding of the role of PCs in disease progression and treatment response. Methods. We developed a sensitive gene expression-based method to overcome the challenges of measuring PCs using flow cytometry. Whole-genome microarray analysis of sorted cellular fractions identified a panel of genes, IGHA1, IGJ, IGKC, IGKV4-1, and TNFRSF17, expressed predominantly in PCs. The sensitivity of the PC signature score created from the combined expression levels of these genes was assessed through ex vivo experiments with sorted cells. This PC gene expression signature was used for monitoring changes in PC levels following anti-CD19 therapy, for evaluating the relationship between PCs and other autoimmune disease-related genes, and for estimating PC levels in affected blood and tissue from patients with multiple autoimmune diseases. Results. The PC signature was highly sensitive and capable of detecting a change in as few as 360 PCs. The PC signature was reduced more than 90% in scleroderma patients following anti-CD19 treatment, and this reduction was highly correlated (r = 0.80) with inhibition of collagen gene expression. Evaluation of multiple autoimmune diseases revealed that 30-35% of lupus and rheumatoid arthritis patients had increased levels of PCs. Conclusion. This newly developed PC signature provides a robust and accurate method of measuring PC levels in the clinic. Our results highlight subsets of patients across multiple autoimmune diseases who may benefit from PC-depleting therapy.

关键词： LEUCOCYTES PHYSIOLOGY PATIENT monitoring METHODOLOGY AUTOANTIBODIES AUTOIMMUNE diseases FLOW cytometry PLACEBOS (Medicine) POLYMERASE chain reaction REGRESSION analysis STATISTICS SYSTEMIC scleroderma T-test (Statistics) U-statistics GENOMICS DATA analysis RANDOMIZED controlled trials BLIND experiment DATA analysis software microarray technology

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Reverse Interferon Signature Is Characteristic of Antigen-Presenting Cells in Human and Rat Spondyloarthritis

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ARTHRITIS & RHEUMATOLOGY 2014年第4期66卷 841-851页

作者： Fert, Ingrid Cagnard, Nicolas Glatigny, Simon Letourneur, Franck Jacques, Sebastien Smith, Judith A. Colbert, Robert A. Taurog, Joel D. Chiocchia, Gilles Araujo, Luiza M. Breban, Maxime Univ Paris 05 Sorbonne Paris Cite Lab Excellence Inflamex Inst Cochin Paris France CNRS UMR 8104 INSERM U1016 Paris France Univ Paris 05 Paris France Hop Necker Enfants Malad Paris France Univ Paris 05 Inst Cochin Paris France Univ Wisconsin Madison Sch Med & Publ Hlth Madison WI 53706 USA NIAMSD NIH Bethesda MD 20892 USA Univ Texas SW Med Ctr Dallas Dallas TX 75390 USA Hop Ambroise Pare F-92100 Boulogne France Versailles St Quentin En Yvelines Univ Boulogne France

Objective. In HLA-B27-transgenic rats, the development of a disorder that mimics spondyloarthritis (SpA) is highly correlated with dendritic cell (DC) dysfunction. The present study was undertaken to analyze the underlying mechanisms of this via transcriptome analysis. Methods. Transcriptome analysis of ex vivo-purified splenic CD103 + CD4 + DCs from B27-transgenic rats and control rats was performed. Transcriptional changes in selected genes were confirmed by quantitative reverse transcriptase-polymerase chain reaction. A meta-analysis of our rat data and published data on gene expression in macrophages from ankylosing spondylitis (AS) patients was further performed. Results. Interferon (IFN) signaling was the most significantly affected pathway in DCs from B27-transgenic rats;the majority of genes connected to IFN were underexpressed in B27-transgenic rats as compared to controls. This pattern was already present at disease onset, persisted over time, and was conserved in 2 disease-prone B27-transgenic rat lines. In DCs from B27-transgenic rats, we further found an up-regulation of suppressor of cytokine signaling 3 (which may account for reverse IFN signaling) and a down-regulation of interleukin-27 (a cytokine that opposes Th17 differentiation and promotes Treg cells). The meta-analysis of data on conventional DCs from rats and data on monocyte-derived macrophages from humans revealed 7 IFN-regulated genes that were negatively regulated in both human and rat SpA (i. e., IRF1, STAT1, CXCL9, CXCL10, IFIT3, DDX60, and EPSTI1). Conclusion. Our results suggest that expression of HLA-B27 leads to a defect in IFN gamma signaling in antigen-presenting cells in both B27-transgenic rats and SpA patients, which may result in Th17 expansion and Treg cell alteration (as shown in B27-transgenic rats) and contribute to disease pathogenesis.

关键词： ANIMAL experimentation CELLULAR signal transduction DENDRITIC cells INTERFERONS POLYMERASE chain reaction PROBABILITY theory RATS FINANCING of research SPONDYLOARTHROPATHIES T-test (Statistics) HLA-B27 antigen REVERSE transcriptase polymerase chain reaction microarray technology GENE expression profiling DESCRIPTIVE statistics

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Methotrexate Inhibits NF-κB Activity Via Long Intergenic (Noncoding) RNA-p21 Induction

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ARTHRITIS & RHEUMATOLOGY 2014年第11期66卷 2947-2957页

作者： Spurlock, Charles F., III Tossberg, John T. Matlock, Brittany K. Olsen, Nancy J. Aune, Thomas M. Vanderbilt Univ Sch Med Nashville TN 37232 USA Vanderbilt Univ Med Ctr Nashville TN 37232 USA Penn State Milton S Hershey Med Ctr Hershey PA USA

Objective. To determine interrelationships between the expression of long intergenic (noncoding) RNA-p21 (lincRNA-p21), NF-kappa B activity, and responses to methotrexate (MTX) in rheumatoid arthritis (RA) by analyzing patient blood samples and cell culture models. Methods. Expression levels of long noncoding RNA and messenger RNA (mRNA) were determined by quantitative reverse transcription-polymerase chain reaction. Western blotting and flow cytometry were used to quantify levels of intracellular proteins. Intracellular NF-kappa B activity was determined using an NF-kappa B luciferase reporter plasmid. Results. Patients with RA expressed reduced basal levels of lincRNA-p21 and increased basal levels of phosphorylated p65 (RelA), a marker of NF-kappa B activation. Patients with RA who were not treated with MTX expressed lower levels of lincRNA-p21 and higher levels of phosphorylated p65 compared with RA patients treated with low-dose MTX. In cell culture using primary cells and transformed cell lines, MTX induced lincRNA-p21 through a DNA-dependent protein kinase catalytic subunit (DNA PKcs)-dependent mechanism. Deficiencies in the levels of PRKDC mRNA in patients with RA were also corrected by MTX in vivo. Furthermore, MTX reduced NF-kappa B activity in tumor necrosis factor alpha-treated cells through a DNA PKcs-dependent mechanism via induction of lincRNA-p21. Finally, we observed that depressed levels of TP53 and lincRNA-p21 increased NF-kappa B activity in cell lines. Decreased levels of lincRNA-p21 did not alter NFKB1 or RELA transcripts;rather, lincRNA-p21 physically bound to RELA mRNA. Conclusion. Our findings support a model whereby depressed levels of lincRNA-p21 in RA contribute to increased NF-kappa B activity. MTX decreases basal levels of NF-kappa B activity by increasing lincRNA-p21 levels through a DNA PKcs-dependent mechanism

关键词： CELL culture FLOW cytometry GENE expression LONGITUDINAL method METHOTREXATE POLYMERASE chain reaction PROBABILITY theory PROTEINS FINANCING of research RHEUMATOID arthritis RNA STATISTICAL hypothesis testing T-test (Statistics) WESTERN immunoblotting REVERSE transcriptase polymerase chain reaction DATA analysis software microarray technology CHEMICAL inhibitors

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Induction of Dopaminergic Neurons From Human Wharton's Jelly Mesenchymal Stem Cell by Forskolin

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JOURNAL OF CELLULAR PHYSIOLOGY 2014年第2期229卷 232-244页

作者： Paldino, Emanuela Cenciarelli, Carlo Giampaolo, Adele Milazzo, Luisa Pescatori, Mario Hassan, Hamisa Jane Casalbore, Patrizia CNR Inst Cell Biol & Neurobiol I-00143 Rome Italy CNR Inst Translat Pharmacol I-00143 Rome Italy Ist Super Sanita Dept Hematol Oncol & Mol Med I-00161 Rome Italy Erasmus MC Dept Surg Rotterdam Netherlands Healthesolutions Rotterdam Netherlands

The purpose of this study was to investigate the Wharton's jelly mesenchymal stem cells differentiation ability toward neuronal fate. Human Wharton's jelly mesenchymal stem cells (hWJMSC) have been isolated from human umbilical cord of full-term births and characterized by flow cytometry analysis for their stem mesenchymal properties through specific surface markers expression (CD73, CD90, and CD105). hWJMSC mesodermal lineage differentiation ability and karyotype analysis were assessed. The trans-differentiation of hWJMSC into neural lineage was investigated in presence of forskolin, an agent known to increase the intracellular levels of cAMP. A molecular profile of differentiated hWJMSC was performed by microarray technology which revealed 1,532 statistically significant modulated genes respect to control cells. Most of these genes are mainly involved in functional neuronal signaling pathways and part of them are specifically required for the neuronal dopaminergic induction. The acquisition of the dopaminergic phenotype was evaluated via immunocytochemistry and Western blot analysis revealed the significant induction of Nurr1, NeuroD1, and TH proteins expression in forskolin-induced hWJMSC. Moreover, the treatment with forskolin promoted, in hWJMSC, a strong upregulation of the neurotrophin Trk receptors related to the high release of brain-derived neurotrophic factor. Taken together these findings show that hWJMSC may be represent an optimal therapeutic strategy for neurological diseases. J. Cell. Physiol. 229: 232-244, 2014. (c) 2013 Wiley Periodicals, Inc.

关键词： Stem Cells Brain-Derived Neurotrophic Factor Colforsin Mesenchymal Stem Cells Nervous System Diseases Intracellular levels microarray technology Dopaminergic Neurons Term Birth Umbilical Cord Immunocytochemistry Immunoblotting Karyotyping Immunology

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