Global gene expression profile progression in Gaucher disease mouse models.

Abstract:

BACKGROUND:Gaucher disease is caused by defective glucocerebrosidase activity and the consequent accumulation of glucosylceramide. The pathogenic pathways resulting from lipid laden macrophages (Gaucher cells) in visceral organs and their abnormal functions are obscure. RESULTS:To elucidate this pathogenic pathway, developmental global gene expression analyses were conducted in distinct Gba1 point-mutated mice (V394L/V394L and D409 V/null). About 0.9 to 3% of genes had altered expression patterns (≥ ± 1.8 fold change), representing several categories, but particularly macrophage activation and immune response genes. Time course analyses (12 to 28 wk) of INFγ-regulated pro-inflammatory (13) and IL-4-regulated anti-inflammatory (11) cytokine/mediator networks showed tissue differential profiles in the lung and liver of the Gba1 mutant mice, implying that the lipid-storage macrophages were not functionally inert. The time course alterations of the INFγ and IL-4 pathways were similar, but varied in degree in these tissues and with the Gba1 mutation. CONCLUSIONS:Biochemical and pathological analyses demonstrated direct relationships between the degree of tissue glucosylceramides and the gene expression profile alterations. These analyses implicate IFNγ-regulated pro-inflammatory and IL-4-regulated anti-inflammatory networks in differential disease progression with implications for understanding the Gaucher disease course and pathophysiology.

journal_name

BMC Genomics

journal_title

BMC genomics

authors

Xu YH,Jia L,Quinn B,Zamzow M,Stringer K,Aronow B,Sun Y,Zhang W,Setchell KD,Grabowski GA

doi

10.1186/1471-2164-12-20

subject

Has Abstract

pub_date

2011-01-11 00:00:00

pages

20

issn

1471-2164

pii

1471-2164-12-20

journal_volume

12

pub_type

杂志文章
  • CEG: a database of essential gene clusters.

    abstract:BACKGROUND:Essential genes are indispensable for the survival of living entities. They are the cornerstones of synthetic biology, and are potential candidate targets for antimicrobial and vaccine design. DESCRIPTION:Here we describe the Cluster of Essential Genes (CEG) database, which contains clusters of orthologous ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-14-769

    authors: Ye YN,Hua ZG,Huang J,Rao N,Guo FB

    更新日期:2013-11-09 00:00:00

  • A genomic perspective on the potential of Actinobacillus succinogenes for industrial succinate production.

    abstract:BACKGROUND:Succinate is produced petrochemically from maleic anhydride to satisfy a small specialty chemical market. If succinate could be produced fermentatively at a price competitive with that of maleic anhydride, though, it could replace maleic anhydride as the precursor of many bulk chemicals, transforming a multi...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-11-680

    authors: McKinlay JB,Laivenieks M,Schindler BD,McKinlay AA,Siddaramappa S,Challacombe JF,Lowry SR,Clum A,Lapidus AL,Burkhart KB,Harkins V,Vieille C

    更新日期:2010-11-30 00:00:00

  • Comparative analyses of genotype dependent expressed sequence tags and stress-responsive transcriptome of chickpea wilt illustrate predicted and unexpected genes and novel regulators of plant immunity.

    abstract:BACKGROUND:The ultimate phenome of any organism is modulated by regulated transcription of many genes. Characterization of genetic makeup is thus crucial for understanding the molecular basis of phenotypic diversity, evolution and response to intra- and extra-cellular stimuli. Chickpea is the world's third most importa...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-10-415

    authors: Ashraf N,Ghai D,Barman P,Basu S,Gangisetty N,Mandal MK,Chakraborty N,Datta A,Chakraborty S

    更新日期:2009-09-05 00:00:00

  • Profile and functional analysis of small RNAs derived from Aspergillus fumigatus infected with double-stranded RNA mycoviruses.

    abstract:BACKGROUND:Mycoviruses are viruses that naturally infect and replicate in fungi. Aspergillus fumigatus, an opportunistic pathogen causing fungal lung diseases in humans and animals, was recently shown to harbour several different types of mycoviruses. A well-characterised defence against virus infection is RNA silencin...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-017-3773-8

    authors: Özkan S,Mohorianu I,Xu P,Dalmay T,Coutts RHA

    更新日期:2017-05-30 00:00:00

  • Microarray analysis of Foxa2 mutant mouse embryos reveals novel gene expression and inductive roles for the gastrula organizer and its derivatives.

    abstract:BACKGROUND:The Spemann/Mangold organizer is a transient tissue critical for patterning the gastrula stage vertebrate embryo and formation of the three germ layers. Despite its important role during development, there are still relatively few genes with specific expression in the organizer and its derivatives. Foxa2 is ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-9-511

    authors: Tamplin OJ,Kinzel D,Cox BJ,Bell CE,Rossant J,Lickert H

    更新日期:2008-10-30 00:00:00

  • Deciphering the heterogeneity in DNA methylation patterns during stem cell differentiation and reprogramming.

    abstract:BACKGROUND:Human induced pluripotent stem cells (iPSCs) have a wide range of applications throughout the fields of basic research, disease modeling and drug screening. Epigenetic instable iPSCs with aberrant DNA methylation may divide and differentiate into cancer cells. Unfortunately, little effort has been taken to c...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-978

    authors: Shao X,Zhang C,Sun MA,Lu X,Xie H

    更新日期:2014-11-18 00:00:00

  • Transcriptome profiling in fast versus slow-growing rainbow trout across seasonal gradients.

    abstract:BACKGROUND:Circannual rhythms in vertebrates can influence a wide variety of physiological processes. Some notable examples include annual reproductive cycles and for poikilotherms, seasonal changes modulating growth. Increasing water temperature elevates growth rates in fishes, but increases in photoperiod regime can ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-016-2363-5

    authors: Danzmann RG,Kocmarek AL,Norman JD,Rexroad CE 3rd,Palti Y

    更新日期:2016-01-15 00:00:00

  • Transcriptome profile analysis of flowering molecular processes of early flowering trifoliate orange mutant and the wild-type [Poncirus trifoliata (L.) Raf.] by massively parallel signature sequencing.

    abstract:BACKGROUND:After several years in the juvenile phase, trees undergo flowering transition to become mature (florally competent) trees. This transition depends on the balanced expression of a complex network of genes that is regulated by both endogenous and environmental factors. However, relatively little is known about...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-12-63

    authors: Zhang JZ,Ai XY,Sun LM,Zhang DL,Guo WW,Deng XX,Hu CG

    更新日期:2011-01-26 00:00:00

  • RNA sequencing identifies common pathways between cigarette smoke exposure and replicative senescence in human airway epithelia.

    abstract:BACKGROUND:Aging is affected by genetic and environmental factors, and cigarette smoking is strongly associated with accumulation of senescent cells. In this study, we wanted to identify genes that may potentially be beneficial for cell survival in response to cigarette smoke and thereby may contribute to development o...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-5409-z

    authors: Voic H,Li X,Jang JH,Zou C,Sundd P,Alder J,Rojas M,Chandra D,Randell S,Mallampalli RK,Tesfaigzi Y,Ryba T,Nyunoya T

    更新日期:2019-01-09 00:00:00

  • A SNP in intron 8 of CD46 causes a novel transcript associated with mastitis in Holsteins.

    abstract:BACKGROUND:The membrane protein CD46, a ubiquitous cell surface pathogen receptor, can bind Streptococcus to trigger cell autophagy, which is a critical step in the control of infection. RESULTS:In this study, we found a new splice variant designated CD46 transcript variant (CD46-TV). The splice variant is characteriz...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-630

    authors: Wang X,Zhong J,Gao Y,Ju Z,Huang J

    更新日期:2014-07-28 00:00:00

  • Fluorescent amplification for next generation sequencing (FA-NGS) library preparation.

    abstract:BACKGROUND:Next generation sequencing (NGS) has become a universal practice in modern molecular biology. As the throughput of sequencing experiments increases, the preparation of conventional multiplexed libraries becomes more labor intensive. Conventional library preparation typically requires quality control (QC) tes...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-020-6481-8

    authors: Chiniquy J,Garber ME,Mukhopadhyay A,Hillson NJ

    更新日期:2020-01-28 00:00:00

  • Population-based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing.

    abstract:BACKGROUND:Rare genetic variation in the human population is a major source of pathophysiological variability and has been implicated in a host of complex phenotypes and diseases. Finding disease-related genes harboring disparate functional rare variants requires sequencing of many individuals across many genomic regio...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-683

    authors: Ramos E,Levinson BT,Chasnoff S,Hughes A,Young AL,Thornton K,Li A,Vallania FL,Province M,Druley TE

    更新日期:2012-12-06 00:00:00

  • Association of the matrix attachment region recognition signature with coding regions in Caenorhabditis elegans.

    abstract:BACKGROUND:Matrix attachment regions (MAR) are the sites on genomic DNA that interact with the nuclear matrix. There is increasing evidence for the involvement of MAR in regulation of gene expression. The unsuitability of experimental detection of MAR for genome-wide analyses has led to the development of computational...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-8-418

    authors: Anthony A,Blaxter M

    更新日期:2007-11-15 00:00:00

  • A comparative approach to elucidate chloroplast genome replication.

    abstract:BACKGROUND:Electron microscopy analyses of replicating chloroplast molecules earlier predicted bidirectional Cairns replication as the prevalent mechanism, perhaps followed by rounds of a rolling circle mechanism. This standard model is being challenged by the recent proposition of homologous recombination-mediated rep...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-10-237

    authors: Krishnan NM,Rao BJ

    更新日期:2009-05-20 00:00:00

  • Topology and expressed repertoire of the Felis catus T cell receptor loci.

    abstract:BACKGROUND:The domestic cat (Felis catus) is an important companion animal and is used as a large animal model for human disease. However, the comprehensive study of adaptive immunity in this species is hampered by the lack of data on lymphocyte antigen receptor genes and usage. The objectives of this study were to ann...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-6431-5

    authors: Radtanakatikanon A,Keller SM,Darzentas N,Moore PF,Folch G,Nguefack Ngoune V,Lefranc MP,Vernau W

    更新日期:2020-01-06 00:00:00

  • Comparative genomic analysis of eutherian fibroblast growth factor genes.

    abstract:BACKGROUND:The eutherian fibroblast growth factors were implicated as key regulators in developmental processes. However, there were major disagreements in descriptions of comprehensive eutherian fibroblast growth factors gene data sets including either 18 or 22 homologues. The present analysis attempted to revise and ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-020-06958-4

    authors: Premzl M

    更新日期:2020-08-05 00:00:00

  • MS2CNN: predicting MS/MS spectrum based on protein sequence using deep convolutional neural networks.

    abstract:BACKGROUND:Tandem mass spectrometry allows biologists to identify and quantify protein samples in the form of digested peptide sequences. When performing peptide identification, spectral library search is more sensitive than traditional database search but is limited to peptides that have been previously identified. An...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-6297-6

    authors: Lin YM,Chen CT,Chang JM

    更新日期:2019-12-24 00:00:00

  • Pangenome analysis of Bifidobacterium longum and site-directed mutagenesis through by-pass of restriction-modification systems.

    abstract:BACKGROUND:Bifidobacterial genome analysis has provided insights as to how these gut commensals adapt to and persist in the human GIT, while also revealing genetic diversity among members of a given bifidobacterial (sub)species. Bifidobacteria are notoriously recalcitrant to genetic modification, which prevents explora...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-1968-4

    authors: O'Callaghan A,Bottacini F,O'Connell Motherway M,van Sinderen D

    更新日期:2015-10-21 00:00:00

  • Endogenous circadian time genes expressions in the liver of mice under constant darkness.

    abstract:BACKGROUND:The circadian rhythms regulate physiological functions and metabolism. Circadian Time (CT) is a unit to quantify the rhythm of endogenous circadian clock, independent of light influence. To understand the gene expression changes throughout CT, C57BL/6 J mice were maintained under constant darkness (DD) for 6...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-020-6639-4

    authors: Li H,Zhang S,Zhang W,Chen S,Rabearivony A,Shi Y,Liu J,Corton CJ,Liu C

    更新日期:2020-03-12 00:00:00

  • Zooplankton diversity analysis through single-gene sequencing of a community sample.

    abstract:BACKGROUND:Oceans cover more than 70% of the earth's surface and are critical for the homeostasis of the environment. Among the components of the ocean ecosystem, zooplankton play vital roles in energy and matter transfer through the system. Despite their importance, understanding of zooplankton biodiversity is limited...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-10-438

    authors: Machida RJ,Hashiguchi Y,Nishida M,Nishida S

    更新日期:2009-09-17 00:00:00

  • Transcriptional response to sulfide in the Echiuran Worm Urechis unicinctus by digital gene expression analysis.

    abstract:BACKGROUND:Urechis unicinctus, an echiuran worm inhabiting the U-shaped burrows in the coastal mud flats, is an important commercial and ecological invertebrate in Northeast Asian countries, which has potential applications in the study of animal evolution, coastal sediment improvement and marine drug development. Furt...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-2094-z

    authors: Liu X,Zhang L,Zhang Z,Ma X,Liu J

    更新日期:2015-10-21 00:00:00

  • Improving ancient DNA read mapping against modern reference genomes.

    abstract:BACKGROUND:Next-Generation Sequencing has revolutionized our approach to ancient DNA (aDNA) research, by providing complete genomic sequences of ancient individuals and extinct species. However, the recovery of genetic material from long-dead organisms is still complicated by a number of issues, including post-mortem D...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-178

    authors: Schubert M,Ginolhac A,Lindgreen S,Thompson JF,Al-Rasheid KA,Willerslev E,Krogh A,Orlando L

    更新日期:2012-05-10 00:00:00

  • Transcriptomic response to heat stress among ecologically divergent populations of redband trout.

    abstract:BACKGROUND:As ectothermic organisms have evolved to differing aquatic climates, the molecular basis of thermal adaptation is a key area of research. In this study, we tested for differential transcriptional response of ecologically divergent populations of redband trout (Oncorhynchus mykiss gairdneri) that have evolved...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-1246-5

    authors: Narum SR,Campbell NR

    更新日期:2015-02-21 00:00:00

  • Comparison of gene coverage of mouse oligonucleotide microarray platforms.

    abstract:BACKGROUND:The increasing use of DNA microarrays for genetical genomics studies generates a need for platforms with complete coverage of the genome. We have compared the effective gene coverage in the mouse genome of different commercial and noncommercial oligonucleotide microarray platforms by performing an in-house g...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-7-58

    authors: Verdugo RA,Medrano JF

    更新日期:2006-03-21 00:00:00

  • Comparison of gene expression of Paramecium bursaria with and without Chlorella variabilis symbionts.

    abstract:BACKGROUND:The ciliate Paramecium bursaria harbors several hundred cells of the green-alga Chlorella sp. in their cytoplasm. Irrespective of the mutual relation between P. bursaria and the symbiotic algae, both cells retain the ability to grow without the partner. They can easily reestablish endosymbiosis when put in c...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-183

    authors: Kodama Y,Suzuki H,Dohra H,Sugii M,Kitazume T,Yamaguchi K,Shigenobu S,Fujishima M

    更新日期:2014-03-10 00:00:00

  • Genome-wide investigation of calcium-dependent protein kinase gene family in pineapple: evolution and expression profiles during development and stress.

    abstract:BACKGROUND:Calcium-dependent protein kinase (CPK) is one of the main Ca2+ combined protein kinase that play significant roles in plant growth, development and response to multiple stresses. Despite an important member of the stress responsive gene family, little is known about the evolutionary history and expression pa...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-020-6501-8

    authors: Zhang M,Liu Y,He Q,Chai M,Huang Y,Chen F,Wang X,Liu Y,Cai H,Qin Y

    更新日期:2020-01-23 00:00:00

  • Colorectal cancer cell-derived microvesicles are enriched in cell cycle-related mRNAs that promote proliferation of endothelial cells.

    abstract:BACKGROUND:Various cancer cells, including those of colorectal cancer (CRC), release microvesicles (exosomes) into surrounding tissues and peripheral circulation. These microvesicles can mediate communication between cells and affect various tumor-related processes in their target cells. RESULTS:We present potential r...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-10-556

    authors: Hong BS,Cho JH,Kim H,Choi EJ,Rho S,Kim J,Kim JH,Choi DS,Kim YK,Hwang D,Gho YS

    更新日期:2009-11-25 00:00:00

  • Hierarchical transcriptional control regulates Plasmodium falciparum sexual differentiation.

    abstract:BACKGROUND:Malaria pathogenesis relies on sexual gametocyte forms of the malaria parasite to be transmitted between the infected human and the mosquito host but the molecular mechanisms controlling gametocytogenesis remains poorly understood. Here we provide a high-resolution transcriptome of Plasmodium falciparum as i...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-6322-9

    authors: van Biljon R,van Wyk R,Painter HJ,Orchard L,Reader J,Niemand J,Llinás M,Birkholtz LM

    更新日期:2019-12-03 00:00:00

  • Identification of prohormones and pituitary neuropeptides in the African cichlid, Astatotilapia burtoni.

    abstract:BACKGROUND:Cichlid fishes have evolved remarkably diverse reproductive, social, and feeding behaviors. Cell-to-cell signaling molecules, notably neuropeptides and peptide hormones, are known to regulate these behaviors across vertebrates. This class of signaling molecules derives from prohormone genes that have undergo...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-016-2914-9

    authors: Hu CK,Southey BR,Romanova EV,Maruska KP,Sweedler JV,Fernald RD

    更新日期:2016-08-19 00:00:00

  • ChlamyNET: a Chlamydomonas gene co-expression network reveals global properties of the transcriptome and the early setup of key co-expression patterns in the green lineage.

    abstract:BACKGROUND:Chlamydomonas reinhardtii is the model organism that serves as a reference for studies in algal genomics and physiology. It is of special interest in the study of the evolution of regulatory pathways from algae to higher plants. Additionally, it has recently gained attention as a potential source for bio-fue...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-016-2564-y

    authors: Romero-Campero FJ,Perez-Hurtado I,Lucas-Reina E,Romero JM,Valverde F

    更新日期:2016-03-12 00:00:00