Edits: an electronic tool for cancer registry data quality.

Edits are a standardized tool for cancer registry data quality. The development of edits is overseen by the North American Association of Central Cancer Registries Edits Workgroup. Edit software tools are supported by the National Program of Cancer Registries. Collaborative Stage (CS) edits are available to support registrar coding of the CS data items. Edits enforce consistent coding across multiple related data items. Understanding where to look for information on edit logic and how to read the edit documents will enable registrars to correctly resolve data discrepancies identified by edit reports.

The Collaborative Stage Version 2 Data Validation Project, 2010.

The Collaborative Stage Data Collection System (CS), used to collect cancer information and derive stage values, was extensively revised in response to revisions in the American Joint Committee on Cancer's AJCC Cancer Staging Manual seventh edition, published in 2010. CSv2 was released to the cancer registry community for use in January 2010. In February 2010 the CSv2 Project management team authorized the data validation project to review the content and formatting of the data tables and make recommendations to the CSv2 mapping team for modifications to the tables. This article describes the review process, problems identified and resolved, and results: 1453 new codes, 340 converted codes, 301 codes marked for manual review, 6 new types of data tags, 3 new version numbers, changes in table notes, changes in construction of intermediate tables, and changes in tables which combine AJCC TNM components into stage assignments. The purpose of this article is to help software vendors, registry users, and data analysts understand the changes they will see as they implement the new version, CSv2:V0203. Also, as vendors, users, and analysts become aware of the complexities and limitations of the current system and processes, and the considerations involved in modifying the system, evident to those working on the project, it is hoped that the review presented in this article will inform ongoing discussions about the future management and development of the Collaborative Stage Data Collection System.

Cloning the human vitamin D receptor into the pTwin-1 expression vector.

Many of the actions of 1alpha,25-dihydroxyvitamin D3 [1,25(OH)2D3] are mediated by binding to the nuclear vitamin D receptor (VDR). VDR is a member of a superfamily of nuclear receptors that are ligand-dependent transcription factors. Ligand binding induces conformational changes in the VDR that enable the receptor to interact with other coactivators to modulate gene transcription. In order to better characterize the binding of the VDR to 1,25(OH)2D3 and to analogs of 1,25(OH)2D3, we have cloned the cDNA for the human VDR into the pTwin1 expression system. The expression system results in the cDNA for a chitin-binding peptide and a yeast intein fused in frame with the N-terminal end of the cDNA for VDR. The intein cDNA codes for a self-cleaving peptide that can release VDR, without any additional amino acids, from a chitin column by changing the pH of the buffer. Western blot analysis of the VDR-fusion protein indicates that a protein of approximately 75 kDA was obtained as expected.

Residues of the human nuclear vitamin D receptor that form hydrogen bonding interactions with the three hydroxyl groups of 1alpha,25-dihydroxyvitamin D3.

Most of the biological effects of 1,25-dihydroxyvitamin D(3) (hormone D) are mediated through the nuclear vitamin D receptor (VDR). Hormone binding induces conformational changes in VDR that enable the receptor to activate gene transcription. It is known that residues S237 and R274 form hydrogen bonds with the 1-hydroxyl group of hormone D, while residues Y143 and S278, and residues H305 and H397 form hydrogen bonds with the 3-hydroxyl and the 25-hydroxyl groups of the hormone. A series of VDR mutations were constructed (S237A, R274A, R274Q, Y143F, Y143A, S278A, H305A, and H397F; double mutants: S237A/R274A, Y143F/S278A, Y143A/S278A, and H305A/H397F). The relative binding affinities of the wild-type and variant VDRs were assessed. All of the mutants except H397F resulted in lower binding affinity compared to wild-type VDR. Binding to hormone was barely detectable in Y143F, H305A, and H305A/H397F mutants, and undetectable in mutants R274A, R274Q, Y143A, S237A/R274A, and Y143A/S278A, indicating the importance of these residues. Ability to activate gene transcription was also assessed. All of the VDR mutants, except the single mutant S278A, required higher doses of hormone D for half-maximal response. Defining the role of hormone D-VDR binding will lead to a better understanding of the vitamin D signal transduction pathway.

Effect of 25-hydroxyl group orientation on biological activity and binding to the 1alpha,25-dihydroxy vitamin D3 receptor.

The hormonal form of vitamin D, 1alpha,25-dihydroxyvitamin D(3) (1,25D), generates many biological actions by interactions with its nuclear receptor (VDR). The presence of a carbon-25 hydroxyl group is necessary for optimizing binding to the VDR. To examine the effect of spatial orientation of the 25-hydroxyl, two pairs of 22,23-allene sidechain analogs were studied. The 22R orientation in analogs HR (52+/-2%) and LA (154+/-19%) resulted in higher affinity binding than the 22S orientation of analogs HQ (21+/-3%) and LB (3.5+/-1.3%; 1,25D=100%). Limited trypsin proteolysis showed that 22R analogs induced VDR conformational changes better able to protect VDR from digestion than 22S analogs. 22R analogs were also able to induce gene transcription at 10-100-fold lower concentrations than 1,25D; 22S analogs were less effective. Analog LA was at least 10-fold more potent than 1,25D at inducing differentiation, while the other analogs were less potent. None of the analogs were as potent as 1,25D in promoting in vivo intestinal calcium absorption or bone calcium mobilization. LA was the most potent of the analogs but required 20-30-fold higher doses than 1,25D. The 25-hydroxyl orientation combined with the 16,17-ene functionality of analog LA enhances its ability to interact with VDR and induce biological actions.

Role of residues 143 and 278 of the human nuclear Vitamin D receptor in the full-length and Delta165-215 deletion mutant.

Most of the actions of 1,25-dihydroxyvitamin D(3) [1,25(OH)(2)D(3)] are mediated by binding to the Vitamin D nuclear receptor (VDR). The crystal structure of a deletion mutant (Delta165-215) of the VDR ligand-binding domain (LBD) bound to 1,25(OH)(2)D(3) indicates that amino acid residues tyrosine-143 and serine-278 form hydrogen bonding interactions with the 3-hydroxyl group of 1,25(OH)(2)D(3). Studies of VDR and three mutants (Y143F, S278A, and Y143F/S278A) did not indicate any differences in the binding affinity between the variant receptors and the wild-type receptor. This might indicate that the 3-hydroxyl group binds differently to the full-length VDR than the to deletion mutant. To further investigate, four deletion VDR mutants were constructed: VDR(Delta165-215), VDR(Delta165-215) (Y143F), VDR(Delta165-215) (S278A), VDR(Delta165-215) (Y143F/S278A). There were no significant differences in binding affinity between the wild-type receptor and the deletion mutants except for VDR(Delta165-215) (Y143F/S278A). In gene activation assays, VDR constructs with the single mutation Y143F and the double mutation Y143F/S278A, but not the single mutation S278A required higher doses of 1,25(OH)(2)D(3) for half-maximal response. This suggests that there are some minor structural and functional differences between the wild-type VDR and the Delta165-215 deletion mutant and that Y143 residue is more important for receptor function than residue S278.

Flexibility of BIV TAR-Tat: models of peptide binding.

A new approach in determining local residue flexibility from base-amino acid contact frequencies is applied to the twelve million lattice chains modeling BIV Tat peptide binding to TAR RNA fragment. Many of the resulting key features in flexibility correspond to RMSD calculations derived from a set of five NMR derived structures (X. Ye, R. A. Kumar, and D. J. Patel, Protein Data Bank: Database of three-dimensional structures determined from NMR (1996)) and binding studies of mutants (L. Chen and A. D. Frankel, Proc. Natl. Acad. Sci. USA 92, 5077-5081 (1995)). The lattice and RMSD calculations facilitate the identification of peptide hinge regions that can best utilize the introduction of Gly or other flexible residues. This approach for identifying potential sites amenable to substitution of more flexible residues to enhance peptide binding to RNA targets could be a useful design tool.