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3.
Blood Cancer J ; 5: e346, 2015 Aug 28.
Article in English | MEDLINE | ID: mdl-26314988

ABSTRACT

Lack of remission or early relapse remains a major clinical issue in diffuse large B-cell lymphoma (DLBCL), with 30% of patients failing standard of care. Although clinical factors and molecular signatures can partially predict DLBCL outcome, additional information is needed to identify high-risk patients, particularly biologic factors that might ultimately be amenable to intervention. Using whole-exome sequencing data from 51 newly diagnosed and immunochemotherapy-treated DLBCL patients, we evaluated the association of somatic genomic alterations with patient outcome, defined as failure to achieve event-free survival at 24 months after diagnosis (EFS24). We identified 16 genes with mutations, 374 with copy number gains and 151 with copy number losses that were associated with failure to achieve EFS24 (P<0.05). Except for FOXO1 and CIITA, known driver mutations did not correlate with EFS24. Gene losses were localized to 6q21-6q24.2, and gains to 3q13.12-3q29, 11q23.1-11q23.3 and 19q13.12-19q13.43. Globally, the number of gains was highly associated with poor outcome (P=7.4 × 10(-12)) and when combined with FOXO1 mutations identified 77% of cases that failed to achieve EFS24. One gene (SLC22A16) at 6q21, a doxorubicin transporter, was lost in 54% of EFS24 failures and our findings suggest it functions as a doxorubicin transporter in DLBCL cells.


Subject(s)
Exome/genetics , Lymphoma, Large B-Cell, Diffuse/genetics , Organic Cation Transport Proteins/genetics , Aged , Aged, 80 and over , Biological Transport , Combined Modality Therapy , DNA Copy Number Variations , DNA Mutational Analysis , Doxorubicin/metabolism , Female , Genetic Association Studies , Genome, Human , Humans , Kaplan-Meier Estimate , Lymphoma, Large B-Cell, Diffuse/mortality , Lymphoma, Large B-Cell, Diffuse/therapy , Male , Middle Aged , Sequence Deletion , Treatment Outcome
5.
J Thromb Haemost ; 10(8): 1521-31, 2012 Aug.
Article in English | MEDLINE | ID: mdl-22672568

ABSTRACT

OBJECTIVES: To identify venous thromboembolism (VTE) disease-susceptibility genes. PATIENTS AND METHODS: We performed in silico genome wide association scan (GWAS) analyses using genotype data imputed to approximately 2.5 million single-nucleotide polymorphisms (SNPs) from adults with objectively-diagnosed VTE (n=1503), and controls frequency matched on age and gender (n=1459; discovery population). Single-nucleotide polymorphisms exceeding genome-wide significance were replicated in a separate population (VTE cases, n=1407; controls, n=1418). Genes associated with VTE were re-sequenced. RESULTS: Seven SNPs exceeded genome-wide significance (P<5×10(-8)): four on chromosome 1q24.2 (F5 rs6025 [factor V Leiden], BLZF1 rs7538157, NME7 rs16861990 and SLC19A2 rs2038024) and three on chromosome 9q34.2 (ABO rs2519093 [ABO intron 1], rs495828, rs8176719 [ABO blood type O allele]). The replication study confirmed a significant association of F5, NME7 and ABO with VTE. However, F5 was the main signal on 1q24.2 as only ABO SNPs remained significantly associated with VTE after adjusting for F5 rs6025. This 1q24.2 region was shown to be inherited as a haplotype block. ABO re-sequencing identified 15 novel single nucleotide variations (SNV) in ABO intron 6 and the ABO 3' UTR that were strongly associated with VTE (P<10(-4)) and belonged to three distinct linkage disequilibrium (LD) blocks; none were in LD with ABO rs8176719 or rs2519093. Our sample size provided 80% power to detect odds ratios (ORs)=2.0 and 1.51 for minor allele frequencies=0.05 and 0.5, respectively (α=1×10(-8); 1% VTE prevalence). CONCLUSIONS: Apart from F5 rs6025, ABO rs8176719, rs2519093 and F2 rs1799963, additional common and high VTE-risk SNPs among whites are unlikely.


Subject(s)
Chromosomes, Human, Pair 1 , Chromosomes, Human, Pair 9 , Polymorphism, Single Nucleotide , Venous Thromboembolism/genetics , ABO Blood-Group System/genetics , Case-Control Studies , Computer Simulation , Factor V/genetics , Gene Frequency , Genetic Predisposition to Disease , Genome-Wide Association Study , Haplotypes , Humans , Linkage Disequilibrium , Logistic Models , Minnesota/epidemiology , Models, Genetic , Odds Ratio , Prevalence , Prothrombin/genetics , Risk Assessment , Risk Factors , Venous Thromboembolism/ethnology , White People/genetics
6.
Blood Cancer J ; 1(6): e24, 2011 Jun.
Article in English | MEDLINE | ID: mdl-22829168

ABSTRACT

MicroRNAs (miRNAs) are involved in the regulation of many cellular processes including hematopoiesis, with the aberrant expression of differentiation-stage specific miRNA associated with lymphomagenesis. miRNA profiling has been essential for understanding the underlying biology of many hematological malignancies; however the miRNA signature of the diverse tumor clone associated with Waldenstrom's macroglobulinemia (WM), consisting of B lymphocytes, plasmacytes and lymphoplasmacytic cells, has not been characterized. We have investigated the expression of over 13 000 known and candidate miRNAs in both CD19(+) and CD138(+) WM tumor cells, as well as in their malignant and non-malignant counterparts. Although neither CD19(+) nor CD138(+) WM cells were defined by a distinct miRNA profile, the combination of all WM cells revealed a unique miRNA transcriptome characterized by the dysregulation of many miRNAs previously identified as crucial for normal B-cell lineage differentiation. Specifically, miRNA-9(*)/152/182 were underexpressed in WM, whereas the expression of miRNA-21/125b/181a/193b/223/363 were notably increased (analysis of variance; P<0.0001). Future studies focusing on the effects of these dysregulated miRNAs will provide further insight into the mechanisms responsible for the pathogenesis of WM.

7.
Mol Pharmacol ; 58(5): 911-9, 2000 Nov.
Article in English | MEDLINE | ID: mdl-11040037

ABSTRACT

The secretin receptor is prototypic of the class II family of G protein-coupled receptors, with a long extracellular amino-terminal domain containing six highly conserved Cys residues and one Cys residue (Cys(11)) that is present only in the most closely related family members. This domain is critical for function, with some component Cys residues believed to be involved in key disulfide bonds, although these have never been directly demonstrated. Here, we examine the functional importance of each of these residues and determine their involvement in disulfide bonds. Secretin binding was markedly diminished after treating cells with cell-impermeant reducing reagents, supporting the presence of important extracellular disulfide bonds. To determine whether the amino-terminal domain was covalently attached to the receptor body by disulfide linkage, a strategy was implemented that involved introduction of an acid-labile Asp-Pro sequence to enable specific cleavage at the boundary of these domains. Under nonreducing conditions, the amino terminus was released from the receptor body, supporting the absence of covalent association between these domains. Quantitative [(14)C]iodoacetamide incorporation into the isolated amino-terminal domain of the receptor in the absence and presence of chemical reduction established the ratio of free to total Cys residues as 1:7, consistent with three disulfide bonds. Mutagenesis of each of the amino-terminal Cys residues to Ala was tolerated only for Cys(11), suggesting that these bonds linked the conserved Cys residues. This was further supported by treatment of intact cells expressing wild-type or C11A mutant secretin receptor with a cell-impermeant sulfhydryl-reactive reagent. Thus, the functionally important amino terminus of the secretin receptor represents a structurally independent, highly folded, and disulfide-bonded domain, with a pattern that is likely critical and conserved throughout this receptor family.


Subject(s)
Cysteine/chemistry , Cystine/chemistry , Disulfides/metabolism , Receptors, Gastrointestinal Hormone/chemistry , Animals , CHO Cells , Cricetinae , Cysteine/genetics , Cystine/genetics , Disulfides/chemistry , Mutagenesis, Site-Directed , Protein Conformation , Rats , Receptors, G-Protein-Coupled , Receptors, Gastrointestinal Hormone/genetics
8.
J Biol Chem ; 275(34): 26032-9, 2000 Aug 25.
Article in English | MEDLINE | ID: mdl-10859300

ABSTRACT

The carboxyl-terminal domains of secretin family peptides have been shown to contain key determinants for high affinity binding to their receptors. In this work, we have examined the interaction between carboxyl-terminal residues within secretin and the prototypic secretin receptor. We previously utilized photoaffinity labeling to demonstrate spatial approximation between secretin residue 22 and the receptor domain that includes the first 30 residues of the amino terminus (Dong, M., Wang, Y., Pinon, D. I., Hadac, E. M., and Miller, L. J. (1999) J. Biol. Chem. 274, 903-909). Here, we further refined the site of labeling with the p-benzoyl-phenylalanine (Bpa(22)) probe to receptor residue Leu(17) using progressive cleavage of wild type and mutant secretin receptors (V13M and V16M) and sequence analysis. We also developed a new probe incorporating a photolabile Bpa at position 26 of secretin, closer to its carboxyl terminus. This analogue was also a potent agonist (EC(50) = 72 +/- 6 pm) and bound to the secretin receptor specifically and with high affinity (K(i) = 10.3 +/- 2.4 nm). It covalently labeled the secretin receptor at a single site saturably and specifically. This was localized to the segment between residues Gly(34) and Ala(41) using chemical and enzymatic cleavage of labeled wild type and A41M mutant receptor constructs and immunoprecipitation of epitope-tagged receptor fragments. Radiochemical sequencing identified the site of covalent attachment as residue Leu(36). These new insights, along with our recent report of contact between residue 6 within the amino-terminal half of secretin and this same amino-terminal region of this receptor (Dong, M., Wang, Y., Hadac, E. M., Pinon, D. I., Holicky, E. L., and Miller, L. J. (1999) J. Biol. Chem. 274, 19161-19167), support a key role for this region, making the molecular details of this interaction of major interest.


Subject(s)
Receptors, Gastrointestinal Hormone/chemistry , Secretin/chemistry , Alanine/metabolism , Amino Acid Sequence , Animals , CHO Cells , Cricetinae , Glycine/metabolism , Kinetics , Ligands , Molecular Sequence Data , Molecular Weight , Phenylalanine/analogs & derivatives , Phenylalanine/metabolism , Photoaffinity Labels/metabolism , Protein Structure, Secondary , Receptors, G-Protein-Coupled , Receptors, Gastrointestinal Hormone/metabolism , Secretin/metabolism , Structure-Activity Relationship
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