Changes in prostate cancer detection rate of MRI-TRUS fusion vs systematic biopsy over time: evidence of a learning curve.

BACKGROUND: To determine the effect of urologist and radiologist learning curves and changes in MRI-TRUS fusion platform during 9 years of NCI's experience with multiparametric magnetic resonance imaging (mpMRI)/TRUS fusion biopsy. METHODS: A prospectively maintained database of patients undergoing mpMRI followed by fusion biopsy (Fbx) and systematic biopsy (Sbx) from 2007 to 2016 was reviewed. The patients were stratified based on the timing of first biopsy. Cohort 1 (7/2007-12/2010) accounted for learning curve. Cohort 2 (1/2011-5/2013) and cohort 3 (5/2013-4/2016) included patients biopsied prior to and after debut of a new software platform, respectively. Clinically significant (CS) disease was defined as Gleason 7 (3+4) or higher. McNemar's test compared cancer detection rates (CDRs) of Sbx and Fbx between time periods. RESULTS: 1528 patients were included in the study with 230, 537 and 761 patients included in three respective cohorts. Median age (interquartile range) was 61.0 (±9.0), 62.0 (±7.3), and 64.0 (±11.0) years in three cohorts, respectively (P<0.001). Fbx and Sbx had comparable CS CDR in cohort 1 (24.8 vs 22.2%, P=0.377). Fbx detected significantly more CS disease compared to Sbx in the following two periods (cohort 2: 31.5 vs 25.0%, P=0.001; cohort 3: 36.4 vs 30.3%, P<0.001) and detected significantly less low risk disease in the same period (cohort 2: 14.5 vs 19.6%, P<0.001; cohort 3: 12.6 vs 16.7%, P<0.001). Even after multivariate adjustment with age, PSA, race, clinical stage and MRI suspicion score, Fbx CS cancer detection increased in successive cohorts (cohort 2: OR 2.23, P=0.043; cohort 3: OR 2.92, P=0.007). CONCLUSIONS: In the past 9 years, there has been significant improvement in the accuracy of Fbx. Our results show that after an early learning period, Fbx detected higher rates of CS cancer and lower rates of clinically insignificant cancer than Sbx. Software advances allowed for even greater detection of CS disease.

Direct interaction in T-cells between thetaPKC and the tyrosine kinase p59fyn.

The protein kinase C (PKC) family has been clearly implicated in T-cell activation as have several nonreceptor protein-tyrosine kinases associated with the T-cell receptor, including p59fyn. This report demonstrates that thetaPKC and p59fyn specifically interact in vitro, in the yeast two-hybrid system, and in T-cells. Further indications of direct interaction are that p59fyn potentiates thetaPKC catalytic activity and that thetaPKC is a substrate for tyrosine phosphorylation by p59fyn. This interaction may account for the localization of thetaPKC following T-cell activation, pharmacological disruption of which results in specific cell-signaling defects. The demonstration of a physical interaction between a PKC and a protein-tyrosine kinase expands the class of PKC-anchoring proteins (receptors for activated C kinases (RACKs)) and demonstrates a direct connection between these two major T-cell-signaling pathways.

Glubodies: randomized libraries of glutathione transferase enzymes.

BACKGROUND: The immunoglobulin framework has been mutagenized to engineer recombinant libraries of proteins as potential diagnostics and novel catalysts, although the often shallow binding cleft may limit the utility of this framework for binding diverse small organic molecules. By contrast, the glutathione S-transferase (GST) family of enzymes contains a deep binding cleft, which has evolved to accommodate a broad range of hydrophobic xenobiotics. We set out to determine whether GST molecules with novel ligand-binding characteristics could be produced by random mutagenesis of segments of the binding cleft. RESULTS: We have identified two ligand-recognition segments (LRSs) in human GST P1, which are near the active site in the folded protein, but have characteristics indicating that the integrity of their sequence is not essential for the overall structure or activity of the protein. Libraries of GST P1-derived proteins were produced by substituting randomized sequences for an LRS or inserting random sequences into an LRS. The recombinant proteins in the libraries, collectively designated as 'glubodies,' generally retain enzymatic activity but differ markedly both from each other and from the parent enzyme in sensitivity to inhibition by diverse small organic compounds. In some instances, a glubody is inhibited by completely novel structures. CONCLUSIONS: We have shown that a non-antibody framework can be used to create large libraries of proteins with a wide range of binding specificities for small organic molecules. The glubodies provide a rich source of data for correlating the structural and functional features of proteins relevant to ligand binding. The criteria applied for identifying an LRS in GST P1 are generally applicable to other protein frameworks.

Mutagenesis using trinucleotide beta-cyanoethyl phosphoramidites.

There is no easy way to selectively introduce mixtures of codon triplets into mutagenesis libraries. Solid-phase-supported DNA synthesis using successive coupling of mixtures of mononucleotides can be made to supply 32 codons, which gives redundancies in coding for 20 natural amino acids, as well as an often unwanted stop codon. Resin-splitting methods have been described, but the representation of all permutations is limited by mechanical factors for a large library, and the method is experimentally cumbersome. To demonstrate a third, improved method, the 3'-cyanoethyl phosphoramidite codon triplets dATA, dCTT, dATC, dATG and dAGC were made by solution-phase methods, with protecting groups fully compatible with modern automated phosphoramidite DNA synthesis chemistry. The reagents were then used to synthesize a 54-mer DNA fragment, wherein 15 internal base pairs were randomized by coupling a mixture of the five codons five times. The fragment was amplified as a cDNA pool, which was subcloned into a phagemid vector, and 16 randomly selected recombinants from this mini-library were sequenced. These clones showed random incorporation of the proper transcribed codon sequences at the correct location. Other functional tests involving the trinucleotide phosphoramidites showed modest (ca. 70%) coupling efficiencies and structural integrity of the DNA produced.