ABSTRACT
BACKGROUND: Emergency admissions in England for alcohol-related liver disease (ArLD) have increased steadily for decades. Statistics based on administrative data typically focus on the ArLD-specific code as the primary diagnosis and are therefore at risk of excluding ArLD admissions defined by other coding combinations. AIM: To deploy the Liverpool ArLD Algorithm (LAA), which accounts for alternative coding patterns (e.g., ArLD secondary diagnosis with alcohol/liver-related primary diagnosis), to national and local datasets in the context of studying trends in ArLD admissions before and during the COVID-19 pandemic. METHODS: We applied the standard approach and LAA to Hospital Episode Statistics for England (2013-21). The algorithm was also deployed at 28 hospitals to discharge coding for emergency admissions during a common 7-day period in 2019 and 2020, in which eligible patient records were reviewed manually to verify the diagnosis and extract data. RESULTS: Nationally, LAA identified approximately 100% more monthly emergency admissions from 2013 to 2021 than the standard method. The annual number of ArLD-specific admissions increased by 30.4%. Of 39,667 admissions in 2020/21, only 19,949 were identified with standard approach, an estimated admission cost of £70 million in under-recorded cases. Within 28 local hospital datasets, 233 admissions were identified using the standard approach and a further 250 locally verified cases using the LAA (107% uplift). There was an 18% absolute increase in ArLD admissions in the seven-day evaluation period in 2020 versus 2019. There were no differences in disease severity or mortality, or in the proportion of admissions with decompensation of cirrhosis or alcoholic hepatitis. CONCLUSIONS: The LAA can be applied successfully to local and national datasets. It consistently identifies approximately 100% more cases than the standard coding approach. The algorithm has revealed the true extent of ArLD admissions. The pandemic has compounded a long-term rise in ArLD admissions and mortality.
Subject(s)
COVID-19 , Liver Diseases , Humans , Pandemics , COVID-19/epidemiology , Hospitalization , Liver Diseases/diagnosis , Liver Diseases/epidemiology , Hospitals , England/epidemiology , AlgorithmsABSTRACT
Background: Environmental sensitivity is commonly reported by people with fibromyalgia syndrome. People living with fibromyalgia syndrome frequently report hypersensitivity to noxious and non-noxious sensations. To date, there has been little empirical validation of sensory disturbance to non-noxious triggers. Environmental sensitivity is used as a diagnostic feature only in Bennet's alternative criteria for diagnosis of fibromyalgia, where it was ranked the second most important of the components for diagnosis, after number of pain sites. The aim of this study was to use a validated sensory measure to determine if people with fibromyalgia have greater sensory disturbances compared to people with other chronic pain conditions. Methods: This study used the Sensory Perception Quotient (SPQ) 92 question survey in adults with chronic pain conditions. A fibromyalgia group (n = 135) and a non-fibromyalgia chronic pain control group (n = 45) were recruited. All participants completed the SPQ as a self-report measure of sensory processing. In addition to the original SPQ scoring method, the Revised Scoring of the Sensory Perception Quotient (SPQ-RS) method was used to investigate self-reported hypersensitivity and hyposensitivity and the vision, hearing, taste, touch, and smell subscales. Chi-squared tests were used for categorical variables and Mann Whitney U, or Kruskal-Wallis H test were used to compare groups. Results: The fibromyalgia group reported significantly more sensitivity compared to the control group (p = 0.030). The fibromyalgia group reported significantly greater hypersensitivity (p = 0.038), but not more hyposensitivity (p = 0.723) compared to controls. The average fibromyalgia SPQ score (92.64 ± 23.33) was similar to that previously reported for adults with autism (92.95 ± 26.61). However, whereas adults with autism had broad range hypersensitivity, the fibromyalgia group reported significantly more hypersensitivity compared to the control group, but the range was restricted to vision (p = 0.033), smell (p = 0.049) and touch (0.040). Conclusions: These findings demonstrate greater sensory hypersensitivity in people with fibromyalgia compared to people with other chronic pain disorders. Greater hypersensitivity was restricted to touch, vision, and smell, all of which have previously been demonstrated to crosstalk with nociception.
ABSTRACT
BACKGROUND AND AIMS: SARS-CoV-2 and consequent pandemic has presented unique challenges. Beyond the direct COVID-related mortality in those with liver disease, we sought to determine the effect of lockdown on people with liver disease in Scotland. The effect of lockdown on those with alcohol-related disease is of interest; and whether there were associated implications for a change in alcohol intake and consequent presentations with decompensated disease. METHODS: We performed a retrospective analysis of patients admitted to seven Scottish hospitals with a history of liver disease between 1 April and 30 April 2020 and compared across the same time in 2017, 2018 and 2019. We also repeated an intermediate assessment based on a single centre to examine for delayed effects between 1 April and 31 July 2020. RESULTS: We found that results and outcomes for patients admitted in 2020 were similar to those in previous years in terms of morbidity, mortality, and length of stay. In the Scotland-wide cohort: admission MELD (Model for End-stage Liver Disease) (16 (12-22) vs 15 (12-19); p=0.141), inpatient mortality ((10.9% vs 8.6%); p=0.499) and length of stay (8 days (4-15) vs 7 days (4-13); p=0.140). In the Edinburgh cohort: admission MELD (17 (12-23) vs 17 (13-21); p=0.805), inpatient mortality ((13.7% vs 10.1%; p=0.373) and length of stay (7 days (4-14) vs 7 days (3.5-14); p=0.525)). CONCLUSION: This assessment of immediate and medium-term lockdown impacts on those with chronic liver disease suggested a minimal effect on the presentation of decompensated liver disease to secondary care.
Subject(s)
COVID-19 , End Stage Liver Disease , Communicable Disease Control , Humans , Retrospective Studies , SARS-CoV-2 , Scotland/epidemiology , Severity of Illness IndexABSTRACT
Liver transplantation is a highly successful treatment for all types of liver failure, some non-liver failure indications and liver cancer. Most referrals come from secondary care. This first part of a two-part guideline outlines who to refer, and how that referral should be made, including patient details and additional issues such as those relevant to alcohol and drug misuse. The process of liver transplant assessment involves the confirmation of the diagnosis and non-reversibility, an evaluation of comorbidities and exclusion of contraindications. Finally, those making it onto the waiting list require monitoring and optimising. Underpinning this process is a need for good communication between patient, their carers, secondary care and the liver transplant service, synchronised by the transplant coordinator. Managing expectation and balancing the uncertainty of organ availability against the inevitable progression of underlying liver disease requires sensitivity and honesty from all healthcare providers and the assessment of palliative care needs is an integral part of this process.
ABSTRACT
Survival rates for patients following liver transplantation exceed 90% at 12 months and approach 70% at 10 years. Part 1 of this guideline has dealt with all aspects of liver transplantation up to the point of placement on the waiting list. Part 2 explains the organ allocation process, organ donation and organ type and how this influences the choice of recipient. After organ allocation, the transplant surgery and the critical early post-operative period are, of necessity, confined to the liver transplant unit. However, patients will eventually return to their referring secondary care centre with a requirement for ongoing supervision. Part 2 of this guideline concerns three key areas of post liver transplantation care for the non-transplant specialist: (1) overseeing immunosuppression, including interactions and adherence; (2) the transplanted organ and how to initiate investigation of organ dysfunction; and (3) careful oversight of other organ systems, including optimising renal function, cardiovascular health and the psychosocial impact. The crucial significance of this holistic approach becomes more obvious as time passes from the transplant, when patients should expect the responsibility for managing the increasing number of non-liver consequences to lie with primary and secondary care.
ABSTRACT
BACKGROUND: The Ts1Cje mouse model of Down syndrome (DS) has partial triplication of mouse chromosome 16 (MMU16), which is partially homologous to human chromosome 21. These mice develop various neuropathological features identified in DS individuals. We analysed the effect of partial triplication of the MMU16 segment on global gene expression in the cerebral cortex, cerebellum and hippocampus of Ts1Cje mice at 4 time-points: postnatal day (P)1, P15, P30 and P84. RESULTS: Gene expression profiling identified a total of 317 differentially expressed genes (DEGs), selected from various spatiotemporal comparisons, between Ts1Cje and disomic mice. A total of 201 DEGs were identified from the cerebellum, 129 from the hippocampus and 40 from the cerebral cortex. Of these, only 18 DEGs were identified as common to all three brain regions and 15 were located in the triplicated segment. We validated 8 selected DEGs from the cerebral cortex (Brwd1, Donson, Erdr1, Ifnar1, Itgb8, Itsn1, Mrps6 and Tmem50b), 18 DEGs from the cerebellum (Atp5o, Brwd1, Donson, Dopey2, Erdr1, Hmgn1, Ifnar1, Ifnar2, Ifngr2, Itgb8, Itsn1, Mrps6, Paxbp1, Son, Stat1, Tbata, Tmem50b and Wrb) and 11 DEGs from the hippocampus (Atp5o, Brwd1, Cbr1, Donson, Erdr1, Itgb8, Itsn1, Morc3, Son, Tmem50b and Wrb). Functional clustering analysis of the 317 DEGs identified interferon-related signal transduction as the most significantly dysregulated pathway in Ts1Cje postnatal brain development. RT-qPCR and western blotting analysis showed both Ifnar1 and Stat1 were over-expressed in P84 Ts1Cje cerebral cortex and cerebellum as compared to wild type littermates. CONCLUSIONS: These findings suggest over-expression of interferon receptor may lead to over-stimulation of Jak-Stat signaling pathway which may contribute to the neuropathology in Ts1Cje or DS brain. The role of interferon mediated activation or inhibition of signal transduction including Jak-Stat signaling pathway has been well characterized in various biological processes and disease models including DS but information pertaining to the role of this pathway in the development and function of the Ts1Cje or DS brain remains scarce and warrants further investigation.
Subject(s)
Brain/metabolism , Down Syndrome/genetics , Interferons/metabolism , Animals , Cerebral Cortex/metabolism , Cluster Analysis , Disease Models, Animal , Female , Gene Expression , Gene Expression Profiling , Hippocampus/metabolism , Interferons/genetics , Janus Kinases/genetics , Janus Kinases/metabolism , Male , Mice , Mice, Inbred C57BL , Oligonucleotide Array Sequence Analysis , Real-Time Polymerase Chain Reaction , Receptor, Interferon alpha-beta/genetics , Receptor, Interferon alpha-beta/metabolism , STAT1 Transcription Factor/genetics , STAT1 Transcription Factor/metabolism , Signal Transduction/genetics , TrisomyABSTRACT
The Ts1Cje mouse model of Down syndrome (DS) has partial trisomy of mouse chromosome 16 (MMU16), which is syntenic to human chromosome 21 (HSA21). It develops various neuropathological features demonstrated by DS patients such as reduced cerebellar volume [1] and altered hippocampus-dependent learning and memory [2,3]. To understand the global gene expression effect of the partially triplicated MMU16 segment on mouse brain development, we performed the spatiotemporal transcriptome analysis of Ts1Cje and disomic control cerebral cortex, cerebellum and hippocampus harvested at four developmental time-points: postnatal day (P)1, P15, P30 and P84. Here, we provide a detailed description of the experimental and analysis procedures of the microarray dataset, which has been deposited in the Gene Expression Omnibus (GSE49050) database.
ABSTRACT
BACKGROUND: The Kimba mouse carries a human vascular endothelial growth factor transgene causing retinal neovascularisation similar to that seen in diabetic retinopathy. Here, we examine the relationship between differential gene expression induced by vascular endothelial growth factor overexpression and the architectural changes that occur in the retinae of these mice. METHODS: Retinal gene expression changes in juvenile and adult Kimba mice were assayed by microarray and compared with age-matched wild-type littermates. Transcription of selected genes was validated by quantitative real-time polymerase chain reaction. Protein translation was determined using immunohistochemistry and enzyme-linked immunosorbent assay. RESULTS: Semaphorin 3C was upregulated, and nuclear receptor subfamily 2, group 3, member 3 (Nr2e3) was downregulated in juvenile Kimba mice. Betacellulin and endothelin 2 were upregulated in adults. Semaphorin 3C colocalized with glial fibrillary acidic protein in Müller cells of Kimba retinae at greater signal intensities than in wild type. Endothelin 2 colocalised to Müller cell end feet and extended into the outer limiting membrane. Endothelin receptor type B staining was most pronounced in the inner nuclear layer, the region containing Müller cell somata. CONCLUSIONS: An early spike in vascular endothelial growth factor induced significant long-term retinal neovascularisation associated with changes to the retinal ganglion, photoreceptor and Müller cells. Overexpression of vascular endothelial growth factor led to dysregulation of photoreceptor metabolism through differential expression of Nr2e3, endothelin 2, betacellulin and semaphorin 3C. Alterations in the expression of these genes may therefore play key roles in the pathological mechanisms that result from retinal neovascularisation.
Subject(s)
Diabetic Retinopathy/genetics , Gene Expression Regulation/physiology , Retinal Neovascularization/genetics , Vascular Endothelial Growth Factor A/genetics , Animals , Betacellulin , Diabetic Retinopathy/metabolism , Endothelin-2/metabolism , Enzyme-Linked Immunosorbent Assay , Gene Expression Profiling , Immunohistochemistry , Intercellular Signaling Peptides and Proteins/metabolism , Mice , Mice, Transgenic , Orphan Nuclear Receptors/metabolism , Real-Time Polymerase Chain Reaction , Retinal Neovascularization/metabolism , Semaphorins/metabolismSubject(s)
Alcoholic Beverages/poisoning , Central Nervous System Depressants/poisoning , Ethanol/poisoning , Adolescent , Adult , Alcoholism/epidemiology , Alcoholism/mortality , Chemical and Drug Induced Liver Injury/pathology , Disinfectants/poisoning , Female , Guanidines/poisoning , Humans , Male , Middle Aged , Poisoning/epidemiology , Poisoning/therapy , Russia/epidemiology , Young AdultABSTRACT
Protein isoforms produced by alternative splicing (AS) of many genes have been implicated in several aspects of cancer genesis and progression. These observations motivated a genome-wide assessment of AS in breast cancer. We accomplished this by measuring exon level expression in 31 breast cancer and nonmalignant immortalized cell lines representing luminal, basal, and claudin-low breast cancer subtypes using Affymetrix Human Junction Arrays. We analyzed these data using a computational pipeline specifically designed to detect AS with a low false-positive rate. This identified 181 splice events representing 156 genes as candidates for AS. Reverse transcription-PCR validation of a subset of predicted AS events confirmed 90%. Approximately half of the AS events were associated with basal, luminal, or claudin-low breast cancer subtypes. Exons involved in claudin-low subtype-specific AS were significantly associated with the presence of evolutionarily conserved binding motifs for the tissue-specific Fox2 splicing factor. Small interfering RNA knockdown of Fox2 confirmed the involvement of this splicing factor in subtype-specific AS. The subtype-specific AS detected in this study likely reflects the splicing pattern in the breast cancer progenitor cells in which the tumor arose and suggests the utility of assays for Fox-mediated AS in cancer subtype definition and early detection. These data also suggest the possibility of reducing the toxicity of protein-targeted breast cancer treatments by targeting protein isoforms that are not present in limiting normal tissues.
Subject(s)
Breast Neoplasms/genetics , Breast Neoplasms/metabolism , Exons , RNA, Messenger/genetics , RNA, Messenger/metabolism , Alternative Splicing , Binding Sites , Breast Neoplasms/pathology , Cell Growth Processes/genetics , Cell Line, Tumor , Female , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Humans , Microarray Analysis , Protein Isoforms , Sequence Analysis, DNA , TransfectionABSTRACT
BACKGROUND: Down syndrome (DS) individuals suffer mental retardation with further cognitive decline and early onset Alzheimer's disease. METHODOLOGY/PRINCIPAL FINDINGS: To understand how trisomy 21 causes these neurological abnormalities we investigated changes in gene expression networks combined with a systematic cell lineage analysis of adult neurogenesis using the Ts1Cje mouse model of DS. We demonstrated down regulation of a number of key genes involved in proliferation and cell cycle progression including Mcm7, Brca2, Prim1, Cenpo and Aurka in trisomic neurospheres. We found that trisomy did not affect the number of adult neural stem cells but resulted in reduced numbers of neural progenitors and neuroblasts. Analysis of differentiating adult Ts1Cje neural progenitors showed a severe reduction in numbers of neurons produced with a tendency for less elaborate neurites, whilst the numbers of astrocytes was increased. CONCLUSIONS/SIGNIFICANCE: We have shown that trisomy affects a number of elements of adult neurogenesis likely to result in a progressive pathogenesis and consequently providing the potential for the development of therapies to slow progression of, or even ameliorate the neuronal deficits suffered by DS individuals.
Subject(s)
Down Syndrome/metabolism , Down Syndrome/pathology , Gene Regulatory Networks/genetics , Neurogenesis/physiology , Animals , Apoptosis/genetics , Apoptosis/physiology , Aurora Kinase A , Aurora Kinases , BRCA2 Protein/genetics , Cell Cycle Proteins/genetics , Cell Differentiation/genetics , Cell Differentiation/physiology , Cell Movement/genetics , Cell Movement/physiology , Cells, Cultured , DNA-Binding Proteins/genetics , Disease Models, Animal , Down Syndrome/genetics , Female , Fluorescent Antibody Technique , Immunohistochemistry , Male , Mice , Mice, Inbred C57BL , Minichromosome Maintenance Complex Component 7 , Neurogenesis/genetics , Neurons/cytology , Neurons/metabolism , Nuclear Proteins/genetics , Oligonucleotide Array Sequence Analysis , Protein Serine-Threonine Kinases/genetics , Reverse Transcriptase Polymerase Chain Reaction , Stem Cells/cytology , Stem Cells/metabolism , Trisomy/geneticsABSTRACT
Previous diffusion tensor imaging (DTI) studies indicated microstructural disruption of white matter in alcohol dependence. To investigate the microstructure of primary neurocircuitry involved in alcohol use disorders, the present study used Tract-Based Spatial Statistics (TBSS) of DTI measures as well as probabilistic tractography. Eleven recovering alcoholics in their first week of abstinence from alcohol were compared with 10 light-drinking controls; diffusion measures were correlated with measures of neurocognition and drinking severity. Regions characterized by low fractional anisotropy and high mean diffusivity included cortico-striatal fibers and those in frontal white matter and limbic pathways. Greater diffusion abnormalities in sections of commissural fibers (inter-hemispheric connections) were associated with greater drinking severity, and lower fractional anisotropy measures in frontal and limbic fiber tracts correlated with lower visuospatial memory performance. These study findings provide direct evidence of compromised integrity of the motivational brain circuitry in alcohol use disorders. These abnormalities in fiber connections could be partially responsible for deficiencies in executive functions, behavioral regulation, and impulse control commonly described in alcohol dependence.
Subject(s)
Alcohol-Related Disorders/pathology , Alcohol-Related Disorders/psychology , Brain/pathology , Cognition , Diffusion Magnetic Resonance Imaging , Motivation , Adult , Alcohol Drinking/pathology , Alcohol Drinking/psychology , Anisotropy , Cerebral Cortex/pathology , Corpus Striatum/pathology , Frontal Lobe/pathology , Humans , Image Processing, Computer-Assisted , Male , Memory , Middle Aged , Neural Pathways/pathology , Neuropsychological Tests , Severity of Illness Index , Space Perception , Visual PerceptionABSTRACT
Hepatotoxicity associated with the therapeutic ingestion of the vitamin A metabolite acitretin is well recognized. No reported cases of hepatic dysfunction as a consequence of acitretin overdose are, however, present. Here for the first time we report a case of fulminant hepatic failure following an intentional overdose of 600 mg of acitretin. The patient fulfilled the King's College Hospital poor prognostic criteria by 66 h after overdose, but demonstrated a rapid improvement thereafter and did not require liver transplantation. Given the known association between psoriasis and depression, and the possible association of acitretin with psychiatric illness, this is an important potential adverse event.
Subject(s)
Acitretin/poisoning , Keratolytic Agents/poisoning , Liver Failure, Acute/chemically induced , Acitretin/therapeutic use , Adult , Drug Overdose , Female , Humans , Keratolytic Agents/therapeutic use , Psoriasis/drug therapy , Psoriasis/psychology , Suicide, AttemptedABSTRACT
BACKGROUND: The RUNX1 transcription factor gene is frequently mutated in sporadic myeloid and lymphoid leukemia through translocation, point mutation or amplification. It is also responsible for a familial platelet disorder with predisposition to acute myeloid leukemia (FPD-AML). The disruption of the largely unknown biological pathways controlled by RUNX1 is likely to be responsible for the development of leukemia. We have used multiple microarray platforms and bioinformatic techniques to help identify these biological pathways to aid in the understanding of why RUNX1 mutations lead to leukemia. RESULTS: Here we report genes regulated either directly or indirectly by RUNX1 based on the study of gene expression profiles generated from 3 different human and mouse platforms. The platforms used were global gene expression profiling of: 1) cell lines with RUNX1 mutations from FPD-AML patients, 2) over-expression of RUNX1 and CBFbeta, and 3) Runx1 knockout mouse embryos using either cDNA or Affymetrix microarrays. We observe that our datasets (lists of differentially expressed genes) significantly correlate with published microarray data from sporadic AML patients with mutations in either RUNX1 or its cofactor, CBFbeta. A number of biological processes were identified among the differentially expressed genes and functional assays suggest that heterozygous RUNX1 point mutations in patients with FPD-AML impair cell proliferation, microtubule dynamics and possibly genetic stability. In addition, analysis of the regulatory regions of the differentially expressed genes has for the first time systematically identified numerous potential novel RUNX1 target genes. CONCLUSION: This work is the first large-scale study attempting to identify the genetic networks regulated by RUNX1, a master regulator in the development of the hematopoietic system and leukemia. The biological pathways and target genes controlled by RUNX1 will have considerable importance in disease progression in both familial and sporadic leukemia as well as therapeutic implications.
Subject(s)
Computational Biology , Core Binding Factor Alpha 2 Subunit/genetics , Gene Expression Profiling/methods , Animals , Blood Platelet Disorders/genetics , Cell Line, Transformed , Core Binding Factor beta Subunit/genetics , Gene Expression Regulation , Gene Regulatory Networks , Genetic Predisposition to Disease , HeLa Cells , Humans , Leukemia, Myeloid, Acute/genetics , Mice , Mice, Inbred BALB C , Oligonucleotide Array Sequence Analysis , Point MutationABSTRACT
Rapid production of interferon-gamma (IFN-gamma) in response to malaria by the innate immune system may determine resistance to infection, or inflammatory disease. However, conflicting reports exist regarding the identity of IFN-gamma-producing cells that rapidly respond to Plasmodium falciparum. To clarify this area, we undertook detailed phenotyping of IFN-gamma-producing cells across a panel of naive human donors following 24-h exposure to live schizont-infected red blood cells (iRBC). Here, we show that NK cells comprise only a small proportion of IFN-gamma-responding cells and that IFN-gamma production is unaffected by NK cell depletion. Instead, gammadelta-T cells represent the predominant source of innate IFN-gamma, with the majority of responding gammadelta-T cells expressing NK receptors. Malaria-responsive gammadelta-T cells more frequently expressed NKG2A compared to non-responding gammadelta-T cells, while non-responding gammadelta-T cells more frequently expressed CD158a/KIR2DL1. Unlike long-term gammadelta-T cell responses to iRBC, alphabeta-T cell help was not required for innate gammadelta-T cell responses. Diversity was observed among donors in total IFN-gamma output. This was positively associated with CD94 expression on IFN-gamma(+) NK-like gammadelta-T cells. Applied to longitudinal cohort studies in endemic regions, similar comparative phenotyping should allow assessment of the contribution of diverse cell populations and regulatory receptors to risk of infection and disease.
Subject(s)
Interferon-gamma/biosynthesis , Killer Cells, Natural/immunology , Malaria, Falciparum/immunology , Receptors, Antigen, T-Cell, gamma-delta/immunology , Receptors, Immunologic/immunology , T-Lymphocyte Subsets/immunology , Enzyme-Linked Immunosorbent Assay , Flow Cytometry , Humans , Interferon-gamma/immunology , Lymphocyte Activation/immunology , NK Cell Lectin-Like Receptor Subfamily C , NK Cell Lectin-Like Receptor Subfamily D/immunology , Phenotype , Receptors, Antigen, T-Cell, gamma-delta/metabolism , Receptors, KIR , Receptors, KIR2DL1 , Receptors, Natural Killer CellABSTRACT
BACKGROUND: The apicomplexan parasite Plasmodium falciparum causes the most severe form of malaria in humans. After invasion into erythrocytes, asexual parasite stages drastically alter their host cell and export remodeling and virulence proteins. Previously, we have reported identification and functional analysis of a short motif necessary for export of proteins out of the parasite and into the red blood cell. RESULTS: We have developed software for the prediction of exported proteins in the genus Plasmodium, and identified exported proteins conserved between malaria parasites infecting rodents and the two major causes of human malaria, P. falciparum and P. vivax. This conserved 'exportome' is confined to a few subtelomeric chromosomal regions in P. falciparum and the synteny of these and surrounding regions is conserved in P. vivax. We have identified a novel gene family PHIST (for Plasmodium helical interspersed subtelomeric family) that shares a unique domain with 72 paralogs in P. falciparum and 39 in P. vivax; however, there is only one member in each of the three species studied from the P. berghei lineage. CONCLUSION: These data suggest radiation of genes encoding remodeling and virulence factors from a small number of loci in a common Plasmodium ancestor, and imply a closer phylogenetic relationship between the P. vivax and P. falciparum lineages than previously believed. The presence of a conserved 'exportome' in the genus Plasmodium has important implications for our understanding of both common mechanisms and species-specific differences in host-parasite interactions, and may be crucial in developing novel antimalarial drugs to this infectious disease.
Subject(s)
Erythrocytes/parasitology , Plasmodium falciparum/genetics , Protozoan Proteins/blood , Protozoan Proteins/genetics , Amino Acid Sequence , Animals , Conserved Sequence , Humans , Malaria, Falciparum/blood , Multigene Family , Open Reading Frames , SoftwareABSTRACT
SUMMARY: affylmGUI is a graphical user interface (GUI) to an integrated workflow for Affymetrix microarray data. The user is able to proceed from raw data (CEL files) to QC and pre-processing, and eventually to analysis of differential expression using linear models with empirical Bayes smoothing. Output of the analysis (tables and figures) can be exported to an HTML report. The GUI provides user-friendly access to state-of-the-art methods embodied in the Bioconductor software repository. AVAILABILITY: affylmGUI is an R package freely available from http://www.bioconductor.org. It requires R version 1.9.0 or later and tcl/tk 8.3 or later and has been successfully tested on Windows 2000, Windows XP, Linux (RedHat and Fedora distributions) and Mac OS/X with X11. Further documentation is available at http://bioinf.wehi.edu.au/affylmGUI CONTACT: keith@wehi.edu.au.
Subject(s)
Computer Graphics , Gene Expression Profiling/methods , Linear Models , Oligonucleotide Array Sequence Analysis/methods , Software , User-Computer Interface , Bayes TheoremABSTRACT
Leukemia inhibitory factor (LIF) is required to maintain pluripotency and permit self-renewal of murine embryonic stem (ES) cells. LIF binds to a receptor complex of LIFR-beta and gp130 and signals via the Janus kinase-signal transducer and activator of transcription (JAK-STAT) pathway, with signalling attenuated by suppressor of cytokine signalling (SOCS) proteins. Recent in vivo studies have highlighted the role of SOCS-3 in the negative regulation of signalling via gp130. To determine the role of SOCS-3 in ES cell biology, SOCS-3-null ES cell lines were generated. When cultured in LIF levels that sustain self-renewal of wild-type cells, SOCS-3-null ES cell lines exhibited less self-renewal and greater differentiation into primitive endoderm. The absence of SOCS-3 enhanced JAK-STAT and extracellular signal-related kinase 1/2 (ERK-1/2)-mitogen-activated protein kinase (MAPK) signal transduction via gp130, with higher levels of phosphorylated STAT-1, STAT-3, SH-2 domain-containing cytoplasmic protein tyrosine phosphatase 2 (SHP-2), and ERK-1/2 in steady state and in response to LIF stimulation. Attenuation of ERK signalling by the addition of MAPK/ERK kinase (MEK) inhibitors to SOCS-3-null ES cell cultures rescued the differentiation phenotype, but did not restore proliferation to wild-type levels. In summary, SOCS-3 plays a crucial role in the regulation of the LIF signalling pathway in murine ES cells. Its absence perturbs the balance between activation of the JAK-STAT and SHP-2-ERK-1/2-MAPK pathways, resulting in less self-renewal and a greater potential for differentiation into the primitive endoderm lineage.
Subject(s)
Cell Differentiation/genetics , Cell Proliferation , Embryo, Mammalian/metabolism , MAP Kinase Signaling System/genetics , Stem Cells/metabolism , Suppressor of Cytokine Signaling Proteins/deficiency , Animals , Cell Differentiation/drug effects , Cell Lineage/genetics , Cell Proliferation/drug effects , Cells, Cultured , Embryo, Mammalian/cytology , Endoderm/cytology , Endoderm/metabolism , Interleukin-6/pharmacology , Leukemia Inhibitory Factor , MAP Kinase Signaling System/drug effects , Mice , Mice, Mutant Strains , Protein-Tyrosine Kinases/metabolism , Stem Cells/cytology , Suppressor of Cytokine Signaling 3 Protein , Suppressor of Cytokine Signaling Proteins/genetics , Suppressor of Cytokine Signaling Proteins/metabolismABSTRACT
Microarray-based gene expression analysis demonstrated that laser photocoagulation (LPC) of mouse eyes had a long-term effect on the expression of genes functionally related to tissue repair, cell migration, proliferation, ion, protein and nucleic acid metabolism, cell signaling, and angiogenesis. Six structural genes, including five crystallins (Cryaa, Cryba1, Crybb2, Crygc, Crygs) and keratin 1-12 (Krt1-12), the anti-angiogenic factor thrombospondin 1 (Tsp1), the retina- and brain-specific putative transcription factor tubby-like protein 1 (Tulp1), and transketolase (Tkt), a key enzyme in the pentose-phosphate pathway, were all shown to be up-regulated by real-time PCR and/or Western blotting. Immunohistochemistry localized five of these proteins to the laser lesions and surrounding tissue within the retina and pigmented epithelium. This is the first study demonstrating long-term changes in the expression of these genes associated with LPC. Therefore, it suggests that modulated gene expression might contribute to the long-term inhibitory effect of LPC. In addition, these genes present novel targets for gene-based therapies aimed at treating microangiopathies, especially diabetic retinopathy, a disease currently only treatable with LPC.