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1.
Blood ; 128(5): 699-709, 2016 08 04.
Article in English | MEDLINE | ID: mdl-27207795

ABSTRACT

Human blood cell counts are tightly maintained within narrow physiologic ranges, largely controlled by cytokine-integrated signaling and transcriptional circuits that regulate multilineage hematopoietic specification. Known genetic loci influencing blood cell production account for <10% of platelet and red blood cell variability, and thrombopoietin/cellular myeloproliferative leukemia virus liganding is dispensable for definitive thrombopoiesis, establishing that fundamentally important modifier loci remain unelucidated. In this study, platelet transcriptome sequencing and extended thrombocytosis cohort analyses identified a single loss-of-function mutation (BLVRB(S111L)) causally associated with clonal and nonclonal disorders of enhanced platelet production. BLVRB(S111L) encompassed within the substrate/cofactor [α/Ɵ dinucleotide NAD(P)H] binding fold is a functionally defective redox coupler using flavin and biliverdin (BV) IXƟ tetrapyrrole(s) and results in exaggerated reactive oxygen species accumulation as a putative metabolic signal leading to differential hematopoietic lineage commitment and enhanced thrombopoiesis. These data define the first physiologically relevant function of BLVRB and implicate its activity and/or heme-regulated BV tetrapyrrole(s) in a unique redox-regulated bioenergetic pathway governing terminal megakaryocytopoiesis; these observations also define a mechanistically restricted drug target retaining potential for enhancing human platelet counts.


Subject(s)
Heme/metabolism , Metabolic Networks and Pathways , Mutation/genetics , Oxidoreductases Acting on CH-CH Group Donors/genetics , Thrombopoiesis/genetics , Alleles , Antigens, CD34/metabolism , Blood Platelets/metabolism , Cell Lineage , Cohort Studies , Erythroid Cells/cytology , Erythroid Cells/enzymology , Genetic Association Studies , Hematopoiesis , Humans , Megakaryocytes/cytology , Megakaryocytes/enzymology , Oxidation-Reduction , Polymorphism, Single Nucleotide/genetics , Reactive Oxygen Species/metabolism , Risk Factors , Sequence Analysis, RNA , Thrombocytosis/genetics
2.
Chemistry ; 23(8): 1891-1900, 2017 Feb 03.
Article in English | MEDLINE | ID: mdl-27897348

ABSTRACT

Biliverdin reductase IXƟ (BLVRB) is a crucial enzyme in heme metabolism. Recent studies in humans have identified a loss-of-function mutation (Ser111Leu) that unmasks a fundamentally important role in hematopoiesis. We have undertaken experimental and thermodynamic modeling studies to provide further insight into the role of the cofactor in substrate accessibility and protein folding properties regulating BLVRB catalytic mechanisms. Site-directed mutagenesis with molecular dynamic (MD) simulations establish the critical role of NAD(P)H-dependent conformational changes on substrate accessibility by forming the "hydrophobic pocket", along with identification of a single key residue (Arg35) modulating NADPH/NADH selectivity. Loop80 and Loop120 block the hydrophobic substrate binding pocket in apo BLVRB (open), whereas movement of these structures after cofactor binding results in the "closed" (catalytically active) conformation. Both enzymatic activity and thermodynamic stability are affected by mutation(s) involving Ser111, which is located in the core of the BLVRB active site. This work 1)Ć¢Ā€Ā…elucidates the crucial role of Ser111 in enzymatic catalysis and thermodynamic stability by active site hydrogen bond network; 2)Ć¢Ā€Ā…defines a dynamic model for apo BLVRB extending beyond the crystal structure of the binary BLVRB/NADP+ complex; 3)Ć¢Ā€Ā…provides a structural basis for the "encounter" and "equilibrium" states of the binary complex, which are regulated by NAD(P)H.


Subject(s)
Oxidoreductases Acting on CH-CH Group Donors/chemistry , Serine/chemistry , Animals , Binding Sites , Catalytic Domain , Hydrogen Bonding , Kinetics , Molecular Dynamics Simulation , Mutagenesis, Site-Directed , NAD/chemistry , Oxidoreductases Acting on CH-CH Group Donors/genetics , Oxidoreductases Acting on CH-CH Group Donors/metabolism , Protein Stability , Serine/metabolism , Substrate Specificity , Thermodynamics
3.
Proc Natl Acad Sci U S A ; 109(21): 8241-6, 2012 May 22.
Article in English | MEDLINE | ID: mdl-22493262

ABSTRACT

Aristolochic acid, a potent human carcinogen produced by Aristolochia plants, is associated with urothelial carcinoma of the upper urinary tract (UUC). Following metabolic activation, aristolochic acid reacts with DNA to form aristolactam (AL)-DNA adducts. These lesions concentrate in the renal cortex, where they serve as a sensitive and specific biomarker of exposure, and are found also in the urothelium, where they give rise to a unique mutational signature in the TP53 tumor-suppressor gene. Using AL-DNA adducts and TP53 mutation spectra as biomarkers, we conducted a molecular epidemiologic study of UUC in Taiwan, where the incidence of UUC is the highest reported anywhere in the world and where Aristolochia herbal remedies have been used extensively for many years. Our study involves 151 UUC patients, with 25 patients with renal cell carcinomas serving as a control group. The TP53 mutational signature in patients with UUC, dominated by otherwise rare A:T to T:A transversions, is identical to that observed in UUC associated with Balkan endemic nephropathy, an environmental disease. Prominent TP53 mutational hotspots include the adenine bases of (5')AG (acceptor) splice sites located almost exclusively on the nontranscribed strand. A:T to T:A mutations also were detected at activating positions in the FGFR3 and HRAS oncogenes. AL-DNA adducts were present in the renal cortex of 83% of patients with A:T to T:A mutations in TP53, FGFR3, or HRAS. We conclude that exposure to aristolochic acid contributes significantly to the incidence of UUC in Taiwan, a finding with significant implications for global public health.


Subject(s)
Aristolochic Acids/adverse effects , Carcinoma, Renal Cell/chemically induced , Carcinoma, Transitional Cell/chemically induced , Drugs, Chinese Herbal/adverse effects , Kidney Neoplasms/chemically induced , Ureteral Neoplasms/chemically induced , Adult , Aged , Aged, 80 and over , Carcinoma, Renal Cell/epidemiology , Carcinoma, Renal Cell/genetics , Carcinoma, Transitional Cell/epidemiology , Carcinoma, Transitional Cell/genetics , DNA Adducts/genetics , Female , Humans , Kidney Neoplasms/epidemiology , Kidney Neoplasms/genetics , Male , Middle Aged , Mutagens/adverse effects , Oncogenes/drug effects , Oncogenes/genetics , Taiwan/epidemiology , Tumor Suppressor Protein p53/genetics , Ureteral Neoplasms/epidemiology , Ureteral Neoplasms/genetics , Urothelium/drug effects , Urothelium/pathology
4.
Blood ; 120(17): 3575-85, 2012 Oct 25.
Article in English | MEDLINE | ID: mdl-22869791

ABSTRACT

Posttranscriptional and translational controls mediated by microRNAs (miRNA) regulate diverse biologic processes. We dissected regulatory effects of miRNAs relevant to megakaryocytopoiesis and platelet biology by analyzing expression patterns in 79 subjects with thrombocytosis and controls, and integrated data with transcriptomic and proteomic platforms. We validated a unique 21-miRNA genetic fingerprint associated with thrombocytosis, and demonstrated that a 3-member subset defines essential thrombocythemia (ET). The genetic signature includes functional guide and passenger strands of the previously uncharacterized miR 490 (5p and 3p), which displayed restricted, low-level expression in megakaryocytes/platelets (compared with leukocytes), and aberrant expression during thrombocytosis, most profound in ET. Overexpression of miR 490 in a bilineage differentiation model of megakaryocyte/erythroid progenitor formation was insufficient for hematopoietic colony differentiation and/or lineage specification. Integration of transcriptomic and mass spectrometric datasets with functional reporter assays identified dishevelled associated activator of morphogenesis 1 (DAAM1) as a miR 490 5p protein target demonstrating decreased expression in ET platelets, putatively by translational control (and not by mRNA target degradation). Our data define a dysregulated miRNA fingerprint in thrombocytosis and support a developmentally restricted function of miR 490 (and its putative DAAM1 target) to conditions associated with exaggerated megakaryocytopoiesis and/or proplatelet formation.


Subject(s)
Adaptor Proteins, Signal Transducing/genetics , Blood Platelets/metabolism , Gene Expression Regulation, Developmental , Megakaryocytes/metabolism , MicroRNAs/genetics , Thrombocythemia, Essential/genetics , Adaptor Proteins, Signal Transducing/metabolism , Binding Sites , Blood Platelets/pathology , Cell Differentiation , Cell Lineage/genetics , Cells, Cultured , Female , Gene Expression Profiling , Genes, Reporter , Humans , Lentivirus , Luciferases , Male , Mass Spectrometry , Megakaryocytes/pathology , MicroRNAs/metabolism , Microfilament Proteins , Oligonucleotide Array Sequence Analysis , Protein Binding , Proteomics , Thrombocythemia, Essential/metabolism , Thrombocythemia, Essential/pathology , Thrombopoiesis/genetics , rho GTP-Binding Proteins
5.
Proc Natl Acad Sci U S A ; 108(34): 14294-9, 2011 Aug 23.
Article in English | MEDLINE | ID: mdl-21844368

ABSTRACT

Adeno-associated virus (AAV) is a single-stranded parvovirus retaining the unique capacity for site-specific integration into a transcriptionally silent region of the human genome, a characteristic requiring the functional properties of the Rep 78/68 polypeptide in conjunction with AAV terminal repeat integrating elements. Previous strategies designed to assemble these genetic elements into adenoviral (Ad) backbones have been limited by the general intolerability of AAV Rep sequences, prompting us to computationally reengineer the Rep gene by using synonymous codon pair recoding. Rep mutants generated by using de novo genome synthesis maintained the polypeptide sequence and endonuclease properties of Rep 78, while dramatically enhancing Ad replication and viral titer yields, characteristics indistinguishable from adenovirus lacking coexpressed Rep. Parallel approaches using domain swaps encompassing WT and recoded genomic segments, coupled with iterative computational algorithms, collectively established that 3' cis-acting Rep genetic elements (and not the Rep 78 polypeptide) retain dominant-acting sequences inhibiting Ad replication. These data provide insights into the molecular relationships of AAV Rep and Ad replication, while expanding the applicability of synonymous codon pair reengineering as a strategy to effect phenotypic endpoints.


Subject(s)
Computational Biology/methods , Dependovirus/genetics , Genetic Vectors/genetics , Viral Proteins/genetics , Base Sequence , Codon/genetics , Dependovirus/physiology , Endonucleases/metabolism , Genes, Viral/genetics , HEK293 Cells , HeLa Cells , Humans , Mutation/genetics , Viral Proteins/metabolism , Virus Replication/physiology
6.
Blood ; 115(1): 7-14, 2010 Jan 07.
Article in English | MEDLINE | ID: mdl-19773543

ABSTRACT

Criteria for distinguishing among etiologies of thrombocytosis are limited in their capacity to delineate clonal (essential thrombocythemia [ET]) from nonclonal (reactive thrombocytosis [RT]) etiologies. We studied platelet transcript profiles of 126 subjects (48 controls, 38 RT, 40 ET [24 contained the JAK2V(617)F mutation]) to identify transcript subsets that segregated phenotypes. Cross-platform consistency was validated using quantitative real-time polymerase chain reaction (RT-PCR). Class prediction algorithms were developed to assign phenotypic class between the thrombocytosis cohorts, and by JAK2 genotype. Sex differences were rare in normal and ET cohorts (< 1% of genes) but were male-skewed for approximately 3% of RT genes. An 11-biomarker gene subset using the microarray data discriminated among the 3 cohorts with 86.3% accuracy, with 93.6% accuracy in 2-way class prediction (ET vs RT). Subsequent quantitative RT-PCR analysis established that these biomarkers were 87.1% accurate in prospective classification of a new cohort. A 4-biomarker gene subset predicted JAK2 wild-type ET in more than 85% patient samples using either microarray or RT-PCR profiling, with lower predictive capacity in JAK2V(617)F mutant ET patients. These results establish that distinct genetic biomarker subsets can predict thrombocytosis class using routine phlebotomy.


Subject(s)
Models, Genetic , Thrombocytosis/classification , Thrombocytosis/genetics , Adult , Aged , Cohort Studies , Discriminant Analysis , Female , Gene Expression Profiling , Genetic Markers , Genotype , Humans , Janus Kinase 2/genetics , Janus Kinase 2/metabolism , Male , Middle Aged , Oligonucleotide Array Sequence Analysis , Sex Characteristics , Thrombocytosis/enzymology
7.
J Thromb Haemost ; 20(11): 2632-2645, 2022 11.
Article in English | MEDLINE | ID: mdl-35962592

ABSTRACT

BACKGROUND: Developmental ontogeny of neonatal thrombopoiesis retains characteristics that are distinct from adults although molecular mechanisms remain unestablished. METHODS: We applied multiparameter quantitative platelet responses with integrated ribosome profiling/transcriptomic studies to better define gene/pathway perturbations regulating the neonatal-to-adult transition. A bioinformatics pipeline was developed to identify stable, neonatal-restricted platelet biomarkers for clinical application. RESULTS: Cord blood (CB) platelets retained the capacity for linear agonist-receptor coupling linked to phosphatidylserine (PS) exposure and α-granule release, although a restricted block in cross-agonist activation pathways was evident. Functional immaturity of synergistic signaling pathways was due to younger ontogenetic age and singular underdevelopment of the protein secretory gene network, with reciprocal expansion of developmental pathways (E2F, G2M checkpoint, c-Myc) important for megakaryocytopoiesis. Genetic perturbations regulating vesicle transport and fusion (TOM1L1, VAMP3, SNAP23, and DNM1L) and PS exposure and procoagulant activity (CLCN3) were the most significant, providing a molecular explanation for globally attenuated responses. Integrated transcriptomic and ribosomal footprints identified highly abundant (ribosome-protected) DEFA3 (encoding human defensin neutrophil peptide 3) and HBG1 as stable biomarkers of neonatal thrombopoiesis. Studies comparing CB- or adult-derived megakaryocytopoiesis confirmed inducible and abundant DEFA3 antigenic expression in CB megakaryocytes, ~3.5-fold greater than in leukocytes (the most abundant source in humans). An initial feasibility cohort of at-risk pregnancies manifested by maternal/fetal hemorrhage (chimerism) were applied for detection and validation of platelet HBG1 and DEFA3 as neonatal thrombopoiesis markers, most consistent for HBG1, which displayed gestational age-dependent expression. CONCLUSIONS: These studies establish an ontogenetically divergent stage of neonatal thrombopoiesis, and provide initial feasibility studies to track disordered fetal-to-adult megakaryocytopoiesis in vivo.


Subject(s)
Blood Platelets , Phosphatidylserines , Infant, Newborn , Pregnancy , Female , Humans , Blood Platelets/metabolism , Phosphatidylserines/metabolism , Vesicle-Associated Membrane Protein 3/metabolism , Thrombopoiesis/genetics , Megakaryocytes/metabolism , Peptides/metabolism , Defensins/metabolism , Adaptor Proteins, Signal Transducing/metabolism
8.
Blood Adv ; 6(16): 4884-4900, 2022 08 23.
Article in English | MEDLINE | ID: mdl-35381074

ABSTRACT

Inflammatory stimuli have divergent effects on peripheral platelet counts, although the mechanisms of thrombocytopenic and thrombocytotic responses remain poorly understood. A candidate gene approach targeting 326 polymorphic genes enriched in thrombopoietic and cytokine signaling pathways was applied to identify single nucleotide variants (SNVs) implicated in enhanced platelet responses in cohorts with reactive thrombocytosis (RT) or essential (myeloproliferative neoplasm [MPN]) thrombocytosis (ET). Cytokine profiles incorporating a 15-member subset, pathway topology, and functional interactive networks were distinct between ET and RT, consistent with distinct regulatory pathways of exaggerated thrombopoiesis. Genetic studies using aggregate (ET + RT) or ET-restricted cohorts identified associations with 2 IFNA16 (interferon-α16) SNVs, and the ET associations were validated in a second independent cohort (P = .0002). Odds ratio of the combined ET cohort (n = 105) was 4.92, restricted to the JAK2V617F-negative subset (odds ratio, 5.01). ET substratification analysis by variant IFNA16 exhibited a statistically significant increase in IFN-α16 levels (P = .002) among 16 quantifiable cytokines. Recombinantly expressed variant IFN-α16 encompassing 3 linked non-synonymous SNVs (E65H95P133) retained comparable antiviral and pSTAT signaling profiles as native IFN-α16 (V65D95A133) or IFN-α2, although both native and variant IFN-α16 showed stage-restricted differences (compared with IFN-α2) of IFN-regulated genes in CD34+-stimulated megakaryocytes. These data implicate IFNA16 (IFN-α16 gene product) as a putative susceptibility locus (driver) within the broader disrupted cytokine network evident in MPNs, and they provide a framework for dissecting functional interactive networks regulating stress or MPN thrombopoiesis.


Subject(s)
Myeloproliferative Disorders , Thrombocytosis , Humans , Cytokines , Megakaryocytes , Myeloproliferative Disorders/genetics , Thrombocytosis/complications , Thrombocytosis/genetics , Thrombopoiesis/genetics
9.
Data Brief ; 36: 107080, 2021 Jun.
Article in English | MEDLINE | ID: mdl-34026977

ABSTRACT

Genetic pathways regulating hematopoietic lineage commitment at critical stages of development remain incompletely characterized.Ā  To better delineate genetic sources of variability regulating cellular speciation during steady-state hematopoiesis, we applied a factorial single-cell latent variable model (f-scLVM) to decompose single-cell transcriptome heterogeneity into interpretable biological factors (refined pathway annotations or gene sets without annotation) dynamically regulating cell fate. Ā Hematopoietic single cell transcriptomic raw sequencing data extracted from 1,920 hematopoietic stem and progenitor cells (HSPCs) derived from 12-week-old female mice were used for data analysis and model development. These single cell RNA sequencing data were subsequently analyzed using the factorial single-cell latent variable model (f-scLVM), with their heterogeneity decomposed into interpretable biological factors. The top biological factors underlying the basal hematopoiesis were subsequently identified for the aggregate, and lineage-restricted (myeloid, megakaryocyte, erythroid) progenitor cells. For a subset of factors, data were independently verified experimentally in a companion research paper [1]. These data facilitate the identification of novel subpopulations and adjust gene sets to discover new marker genes and hidden confounding factors driving basal hematopoiesis.

10.
Free Radic Biol Med ; 164: 164-174, 2021 02 20.
Article in English | MEDLINE | ID: mdl-33359909

ABSTRACT

Cytoprotective mechanisms of heme oxygenases function by derivatizing heme to generate carbon monoxide, ferrous iron, and isomeric biliverdins, followed by rapid NAD(P)H-dependent biliverdin reduction to the antioxidant bilirubin using two non-overlapping biliverdin reductases that display biliverdin isomer-restricted redox activity. Although cytoprotective functions of heme oxygenases are widely recognized, concomitant effects of downstream biliverdin reductases remain incomplete. A computational model predicated on murine hematopoietic single-cell transcriptomic data identified Blvrb as a biological driver linked to the tumor necrosis factor stress pathway as a predominant source of variation defining hematopoietic cell heterogeneity. In vivo studies using Blvrb-deficient mice established the dispensable role of Blvrb in steady-state hematopoiesis, although model validation using aged Blvrb-deficient mice established an important cytoprotective function in stress hematopoiesis with dichotomous megakaryocyte-biased hematopoietic recovery. Defective stress erythropoiesis was evident in Blvrb-/- spleens and in bone marrow erythroid development, occurring in conjunction with defective lipid peroxidation as a marker of oxidant mishandling. Cell autonomous effects on megakaryocyte lineage bias were documented using multipotential progenitor assays. These data provide the first physiological function of murine Blvrb in a non-redundant pathway of stress cytoprotection. Divergent effects on erythroid/megakaryocyte lineage speciation impute a novel redox-regulated mechanism for lineage partitioning.


Subject(s)
Hematopoiesis , Megakaryocytes , Oxidoreductases Acting on CH-CH Group Donors/genetics , Animals , Biliverdine , Cell Lineage , Hematopoiesis/genetics , Heme , Mice , Mice, Knockout
11.
BMC Gastroenterol ; 10: 125, 2010 Oct 26.
Article in English | MEDLINE | ID: mdl-20977743

ABSTRACT

BACKGROUND: IQGAP1 and IQGAP2 are homologous members of the IQGAP family of scaffold proteins. Accumulating evidence implicates IQGAPs in tumorigenesis. We recently reported that IQGAP2 deficiency leads to the development of hepatocellular carcinoma (HCC) in mice. In the current study we extend these findings, and investigate IQGAP1 and IQGAP2 expression in human HCC. METHODS: IQGAP1 and IQGAP2 protein expression was assessed by Western blotting and immunohistochemistry. IQGAP mRNA was measured by quantitative RT-PCR. The methylation status of the Iqgap2 promoter was determined by pyrosequencing of bisulfite-treated genomic DNA. RESULTS: IQGAP1 and IQGAP2 expression was reciprocally altered in 6/6 liver cancer cell lines. Similarly, immunohistochemical staining of 82 HCC samples showed that IQGAP2 protein expression was reduced in 64/82 (78.0%), while IQGAP1 was present in 69/82 (84.1%). No IQGAP1 staining was detected in 23/28 (82.1%) normal livers, 4/4 (100.0%) hepatic adenomas and 23/23 (100.0%) cirrhosis cases, while IQGAP2 was increased in 22/28 (78.6%), 4/4 (100.0%) and 23/23 (100.0%), respectively. Although the Iqgap2 promoter was not hypermethylated in HCC at any of the 25 CpG sites studied (N = 17), IQGAP2 mRNA levels were significantly lower in HCC specimens (N = 23) than normal livers (N = 6). CONCLUSIONS: We conclude that increased IQGAP1 and/or decreased IQGAP2 contribute to the pathogenesis of human HCC. Furthermore, downregulation of IQGAP2 in HCC occurs independently of hypermethylation of the Iqgap2 promoter. Immunostaining of IQGAP1 and IQGAP2 may aid in the diagnosis of HCC, and their pharmacologic modulation may represent a novel therapeutic strategy for the treatment of liver cancer.


Subject(s)
Carcinoma, Hepatocellular/genetics , DNA, Neoplasm/genetics , Gene Expression Regulation, Neoplastic , Liver Neoplasms/genetics , ras GTPase-Activating Proteins/genetics , Adult , Aged , Aged, 80 and over , Biopsy , Blotting, Western , Carcinoma, Hepatocellular/metabolism , Carcinoma, Hepatocellular/pathology , Female , Genetic Predisposition to Disease , Humans , Immunohistochemistry , Liver Neoplasms/metabolism , Liver Neoplasms/pathology , Male , Middle Aged , Polymerase Chain Reaction , Tumor Cells, Cultured , ras GTPase-Activating Proteins/biosynthesis
12.
Curr Opin Hematol ; 16(5): 329-33, 2009 Sep.
Article in English | MEDLINE | ID: mdl-19550320

ABSTRACT

PURPOSE OF REVIEW: The proteome is the pool of proteins expressed at a given time and circumstance. The word 'proteomics' summarizes several technologies for visualization, quantitation and identification of these proteins. Recent advances in these techniques are helping to elucidate platelet processes which are relevant to bleeding and clotting disorders, transfusion medicine and regulation of angiogenesis. RECENT FINDINGS: Over 1100 platelet proteins have been identified using proteomic techniques. Various subproteomes have been characterized, including platelet releasates (the 'secretome'), alpha and dense granules, membrane and cytoskeletal proteins, platelet-derived microparticles, and the platelet 'phosphoproteome'. Proteomic data about platelets have become increasingly available in integrated databases. SUMMARY: Proteomic experiments in resting and activated platelets have identified novel signaling pathways and secreted proteins which may represent therapeutic targets, as well as potential cancer biomarkers.


Subject(s)
Blood Platelets/chemistry , Proteome/analysis , Cell-Derived Microparticles , Humans , Platelet Activation , Proteomics/methods , Signal Transduction
13.
Methods Mol Biol ; 496: 245-72, 2009.
Article in English | MEDLINE | ID: mdl-18839115

ABSTRACT

Platelets are anucleated cells that are generated from megakaryocytes via thrombopoiesis. They lack genomic DNA but have a pool of individual mRNA transcripts. Taken together, these mRNAs constitute a platelet transcriptome. Platelets have a unique and reproducible transcript profile, which includes approximately 1,600-3,000 individual transcripts. In this chapter, we will focus on platelet purification and on transcript profiling using an Affymetrix microarray platform and serial analysis of gene expression (SAGE). Platelet purification is described in detail. Large-scale platelet purification schema is designed to purify platelets from apheresis platelet bags (approximately 3-5 x 10(11) platelets/bag). Modification of this schema --small-scale platelet purification--is designed to isolate platelets from 20 ml of peripheral blood. This chapter provides detailed protocols for microarray and SAGE transcript profiling. We also discuss peculiarities of platelet purification, RNA isolation, and transcript profiling.


Subject(s)
Blood Platelets/metabolism , Gene Expression Profiling/methods , Oligonucleotide Array Sequence Analysis/methods , RNA, Messenger/biosynthesis , Blood Platelets/cytology , Humans , Plateletpheresis/methods , RNA, Messenger/genetics , RNA, Messenger/isolation & purification
14.
Thromb Haemost ; 100(5): 929-36, 2008 Nov.
Article in English | MEDLINE | ID: mdl-18989540

ABSTRACT

Human platelets have unique and reproducible mRNA profiles, with evidence for distinct profiles in haematopoietic stem cell disorders associated with thrombocytosis. Platelet transcript profiling is traditionally studied by microarray analysis, quantitative reverse transcription-PCR or serial analysis of gene expression, techniques that are labor- and technically-intensive. We have now applied a novel multiplex-based platform for quantitative transcript profiling of human platelets. Simultaneous quantification of 17 platelet transcripts was assayed using intact platelet-rich plasma or gel-filtered platelets lysed in vitro. Accurate and reproducible profiles could be obtained from as few as 5 x 10(7) platelets (a platelet mass corresponding to approximately 100 microl of whole blood), even for the low-abundant platelet transcripts. Correlation coefficients of this 17-member gene set to platelet Affymetrix microarrays were excellent (r(2) = 0.949, p < 1 x 10(-10)), with no correlation to in kind-derived leukocyte profiles, highlighting the cell-specificity of the platform. These data demonstrate that transcript multiplexing using fluorescent microspheres can be adapted for rapid molecular profiling using intact platelets (bypassing the need for RNA isolation methods), with potential applicability irrespective of baseline platelet counts.


Subject(s)
Blood Platelets/chemistry , Fluorescent Dyes , Gene Expression Profiling/methods , Microspheres , Oligonucleotide Array Sequence Analysis , RNA, Messenger/blood , Spectrometry, Fluorescence , Humans , Reproducibility of Results
15.
Thromb Haemost ; 100(6): 1111-22, 2008 Dec.
Article in English | MEDLINE | ID: mdl-19132238

ABSTRACT

Ectopic delivery of factor VIII (FVIII) to megakaryocytes (Mk) represents a viable approach for localized tenase generation by concentrating the FVIIIa/FIXa enzyme-cofactor complex onto activated platelet membranes. We utilized a core rat platelet factor 4 (PF4) promoter for Mk/platelet-restricted expression of human B-domain-deleted (hBDD) FVIII within the background of a haemophilia A mouse (rPF4/hBDD/FVIII-/-). Platelets from rPF4/hBDD/FVIII(-/-) mice contained approximately 122 mU FVIII:C/1 x 10(9) platelets/ml with no detectable plasmatic FVIII:C, and with no effect on alpha-granule-derived platelet factor V/Va function. Paired tenase assays (+/- thrombin) confirmed that platelet (pt) FVIII (unlike platelet FV) required thrombin cleavage for complete activation. rPF4/hBDD/FVIII(-/-) mice exposed to a thrombocytotic stimulus (thrombopoietin, TPO) demonstrated a statistically-significant 66% reduction in molar ptFVIII activity with a non-significant reduction in total ptFVIII biomass. Decreased molar ptFVIII concentration correlated with loss of phenotypic correction as evaluated using a haemostatic tail-snip assay. Comparative studies using a transgenic mouse expressing human amyloid-beta-precursor protein (hAbetaPP) from the rPF4 promoter confirmed diminished hAbetaPP expression without affecting endogenous alpha-granule PF4, establishing generalizability of these observations. While Mk/platelet-released ptFVIII (unlike pFV) is proteolytically inactive, we also conclude that thrombocytotic stimuli negatively affect ptFVIII bioavailability and phenotypic efficacy, results which correlate best with molar ptFVIII concentration, and not systemically available ptFVIII.


Subject(s)
Blood Coagulation , Blood Platelets/metabolism , Factor VIII/metabolism , Genetic Therapy/methods , Hemophilia A/therapy , Megakaryocytes/metabolism , Thrombocytosis/blood , Amyloid beta-Protein Precursor/genetics , Animals , Blood Coagulation/genetics , Blood Coagulation Tests , Cysteine Endopeptidases/metabolism , Cytoplasmic Granules/metabolism , Disease Models, Animal , Factor VIII/genetics , Factor Xa/metabolism , Hemophilia A/blood , Hemophilia A/genetics , Humans , Mice , Mice, Inbred C57BL , Mice, Knockout , Mice, Transgenic , Neoplasm Proteins/metabolism , Phenotype , Platelet Activation , Platelet Count , Platelet Factor 4/genetics , Rats , Thrombin/metabolism , Thrombocytosis/chemically induced , Thrombocytosis/genetics , Thrombopoietin , Time Factors
16.
Semin Thromb Hemost ; 34(6): 532-8, 2008 Sep.
Article in English | MEDLINE | ID: mdl-19085652

ABSTRACT

The transcriptome is the mRNA pool found within a cell. Transcriptomic discovery approaches include microarray-based technologies as well as sequencing-based technologies. Transcriptomic experiments provide dynamic information about gene expression at the tissue level. The proteome is the pool of proteins expressed at a given time and circumstance. The word PROTEOMICS summarizes several technologies for visualization, quantitation, and identification of these proteins. Protein separation can be accomplished by two-dimensional electrophoresis, use of protein chips with an affinity matrix, or by a variety of advanced chromatographic methods. Mass spectrometry is used to identify the proteins in conjunction with protein sequence databases. Recent proteomic experiments in resting and activated platelets have identified novel signaling pathways and secreted proteins. Platelet transcriptomic studies in essential thrombocythemia, atherosclerotic disease, sickle cell disease, and an inherited platelet defect are reviewed. Transcript profiling has the potential to distinguish molecular signatures in normal and diseased platelets and to classify prothrombotic patient phenotypes to tailor their therapy.


Subject(s)
Blood Platelet Disorders/diagnosis , Blood Platelets/metabolism , Genomics , Proteomics , Blood Platelet Disorders/genetics , Blood Platelet Disorders/metabolism , Gene Expression Profiling , Humans , Proteome/genetics , Proteome/metabolism
17.
Thromb Haemost ; 94(2): 412-21, 2005 Aug.
Article in English | MEDLINE | ID: mdl-16113833

ABSTRACT

Human blood platelets have important, regulatory functions in diverse hemostatic and pathological disorders, including vascular remodeling, inflammation, and wound repair. Microarray analysis was used to study the molecular basis of essential thrombocythemia, a myeloproliferative disorder with quantitative and qualitative platelet defects associated with cardiovascular and thrombohemorrhagic symptoms, not infrequently neurological. A platelet-expressed gene (HSD17B3) encoding type 3 17beta-hydroxysteroid dehydrogenase (previously characterized as a testis-specific enzyme catalyzing the final step in gonadal synthesis of testosterone) was selectively down-regulated in ET platelets, with reciprocal induction of the type 12 enzyme (HSD17B12). Functional 17beta-HSD3 activity corresponding to approximately 10% of that found in murine testis was demonstrated in normal platelets. The induction of HSD17B12 in ET platelets was unassociated with a concomitant increase in androgen biosynthesis, suggesting distinct functions and/or substrate specificities of the types 3 and 12 enzymes. Application of a molecular assay distinguished ET from normal platelets in 20 consecutive patients (p < 0.0001). These data provide the first evidence that distinct subtypes of steroidogenic 17beta-HSDs are functionally present in human blood platelets, and that the expression patterns of HSD17B3 and HSD17B12 are associated with an uncommon platelet disorder manifest by quantitative and qualitative platelet defects.


Subject(s)
17-Hydroxysteroid Dehydrogenases/metabolism , Blood Platelets/enzymology , Thrombocytosis/blood , Thrombocytosis/pathology , Adult , Aged , Animals , Blood Platelets/metabolism , Computational Biology , Down-Regulation , Female , Gene Expression Regulation , Humans , Male , Mice , Middle Aged , Phenotype , Phylogeny , RNA, Messenger/metabolism , Reverse Transcriptase Polymerase Chain Reaction , Testis/metabolism , Thrombocytosis/enzymology , Time Factors , Up-Regulation
18.
Exp Hematol ; 32(10): 991-9, 2004 Oct.
Article in English | MEDLINE | ID: mdl-15504554

ABSTRACT

OBJECTIVE: Two major protease-activated receptors (PARs), PAR1 and PAR4, are involved in the activation of human platelets by thrombin. A third, PAR3, is preferentially expressed by tissues of hematopoietic origin and megakaryocytes. Although PAR3 is also a thrombin substrate, its low-level expression on human platelets suggests a function distinct from that of PAR1, the major receptor involved in thrombin-mediated platelet activation. We studied the expression of PARs during megakaryocyte differentiation of human erythroleukemia (HEL) cells in order to determine the role of PAR3 in megakaryocytopoiesis. METHODS: HEL cells exposed to phorbol 12-myristate 13-acetate (PMA) to induce megakaryocyte differentiation were examined by light microscopy and flow cytometry (DNA ploidy, surface expression of PAR1, PAR3, GPIIb-IIIa). Northern blot, RT-PCR, and quantitative RT-PCR were used to evaluate the expression of PARs 1, 3, and 4 mRNA. HEL cells were also exposed to thrombin and thrombopoietin (TPO). RESULTS: In baseline studies, unstimulated HEL cells were found to express comparable levels of PAR1 and PAR3 by Northern blot. Minimal expression of PAR4 was detected by RT-PCR, but not by Northern analysis. Exposure to PMA, but not thrombin or TPO, resulted in megakaryocytic differentiation as evident by increased cell size and nuclear complexity, increased ploidy, and enhanced expression of GPIIb-IIIa, a specific marker of megakaryocytes/platelets. PMA-stimulated HEL cells showed enhanced PAR3 cell-surface expression (approximately threefold increase by day 2) by flow cytometry. In contrast, there was no change in cell-surface PAR1 expression. Northern blot analysis (approximately 10-fold) and quantitative RT-PCR (approximately threefold) confirmed the upregulation of PAR3 mRNA expression (by 24 hours) in cells exposed to PMA. This did not occur with exposure to TPO. CONCLUSION: These data demonstrate increased expression of PAR3 mRNA and protein in HEL cells undergoing megakaryocytic maturation following PMA exposure, suggesting a developmental role for PAR3. Furthermore, regulation of PAR3 expression appears to be specifically coupled to the protein kinase C system, but independent of the Ras/Raf/MAP kinase pathway.


Subject(s)
Gene Expression Regulation, Neoplastic , Leukemia, Erythroblastic, Acute/pathology , Megakaryocytes/cytology , Receptors, Proteinase-Activated/genetics , Receptors, Thrombin/genetics , Cell Differentiation , Cell Line, Tumor , Cell Lineage , DNA/analysis , Humans , Megakaryocytes/immunology , RNA, Messenger/analysis , Receptors, Cell Surface/analysis , Signal Transduction , Tetradecanoylphorbol Acetate , Up-Regulation
19.
PLoS One ; 10(6): e0129314, 2015.
Article in English | MEDLINE | ID: mdl-26047140

ABSTRACT

IQ motif-containing GTPase-activating protein 2 (IQGAP2) is a multidomain scaffolding protein that plays a role in cytoskeleton regulation by juxtaposing Rho GTPase and Ca2+/calmodulin signals. While IQGAP2 suppresses tumorigenesis in liver, its role in pathophysiology of the gastrointestinal tract remains unexplored. Here we report that IQGAP2 is required for the inflammatory response in colon. Mice lacking Iqgap2 gene (Iqgap2-/- mice) were resistant to chemically-induced colitis. Unlike wild-type controls, Iqgap2-/- mice treated with 3% dextran sulfate sodium (DSS) in water for 13 days displayed no injury to colonic epithelium. Mechanistically, resistance to colitis was associated with suppression of colonic NF-κB signaling and IL-6 synthesis, along with diminished neutrophil and macrophage production and recruitment in Iqgap2-/- mice. Finally, alterations in IQGAP2 expression were found in colons of patients with inflammatory bowel disease (IBD). Our findings indicate that IQGAP2 promotes inflammatory response at two distinct levels; locally, in colonic epithelium through TLR4/NF-κB signaling pathway, and systemically, via control of maturation and recruitment of myeloid immune cells. This work identifies a novel mechanism of colonic inflammation mediated by signal transducing scaffolding protein IQGAP2. IQGAP2 domain-specific blocking agents may represent a conceptually novel strategy for therapy of IBD and other inflammation-associated disorders, including cancer.


Subject(s)
Colitis/genetics , Colon/metabolism , Drug Resistance/genetics , ras GTPase-Activating Proteins/genetics , Animals , Blotting, Western , Colitis/chemically induced , Colitis/metabolism , Colon/pathology , Dextran Sulfate , Disease Models, Animal , Female , Gene Expression , Goblet Cells/metabolism , Goblet Cells/pathology , Humans , Hyperplasia , Interleukin-10/genetics , Interleukin-10/metabolism , Interleukin-6/genetics , Interleukin-6/metabolism , Leukocyte Count , Mice, 129 Strain , Mice, Knockout , Microscopy, Fluorescence , NF-kappa B/metabolism , Reverse Transcriptase Polymerase Chain Reaction , Signal Transduction , ras GTPase-Activating Proteins/metabolism
20.
Thromb Haemost ; 92(2): 317-27, 2004 Aug.
Article in English | MEDLINE | ID: mdl-15269828

ABSTRACT

We have generated an E1a/E1b/E3-deleted adeno/adeno-associated (Ad/AAV) hybrid virus driven by a small nuclear RNA (pHU1-1) promoter for expression of a B domain-deleted (Thr761-Asn1639) factor VIII transgene (FVIIIDelta761-1639). Productive replication of Ad/AAV/FVIIIDelta761-1639 in AAV rep-expressing cells resulted in generation of monomeric and dimeric mini-adenoviral (mAd) replicative forms that retained the AAV integration elements (mAd/FVIIIDelta761-1639). In vitro studies using Ad/AAV/FVIIIDelta761-1639 generated approximately 2-logs greater FVIII activity than mAd/FVIIIDelta761-1639. To determine its capacity for in vivo excision and/or genomic integration, Ad/AAV/FVIIIDelta761-1639 was injected by tail vein into three groups of hemophilia A mice (2 x 10(11) vp [n = 3]; 4 x 10(11) vp [n = 3]; 8 x 10(11) vp [n = 3]), with clear concentration-dependent increase in FVIII activity (range 160-510 mU/ml; plasma activity 16%-51% of normal). Peak activity was seen by Day (D) 5, with slow return to baseline by D28 (0.1-0.9% activity); in only 3/9 mice was loss of FVIII activity associated with development of anti-FVIII antibodies. Quantitative-PCR using genomic DNA isolated from D28 liver, spleen, heart, lungs, and kidney demonstrated the highest concentration in liver (approximately 10 genomes/cell), with little to no organ toxicity at early (D5 or 6) or late (D28) post-infusion time points. There was no evidence for spontaneous transgene excision or genomic integration in vivo as evaluated by quantitative PCR and genomic blotting. These data establish (i) the feasibility and applicability of developing high-titer Ad/AAV hybrid viruses for FVIII delivery using a small cellular promoter, (ii) the potential utility of this virus for generation of "gutted" monomeric and dimeric mAD/FVIII retaining AAV integration elements, and (iii) that the development of strategies for regulated Rep68/78 co-expression may provide a novel approach for excision, integration, and long-term FVIII transgene expression.


Subject(s)
Adenoviridae/genetics , Dependovirus/genetics , Factor VIII/biosynthesis , Gene Transfer Techniques , Hemophilia A/genetics , Animals , Base Sequence , COS Cells , Cell Line , DNA Primers/chemistry , Dimerization , Genetic Therapy , HeLa Cells , Hepatocytes/metabolism , Humans , Mice , Mice, Transgenic , Models, Genetic , Molecular Sequence Data , Plasmids/metabolism , Polymerase Chain Reaction , RNA, Small Nuclear/metabolism , Time Factors , Transgenes
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