Detection of prostate cancer recurrence using an ultrasensitive nanoparticle-based PSA assay

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Approximately 400,000 men are diagnosed each year with prostate cancer worldwide, and many of those patients undergo radical prostatectomy in an attempt to cure the disease. Although prostatectomy is effective for a majority of patients, approximately 15 to 40 % will experience prostate cancer recurrence within 5 years, and a majority of those patients will die from the disease (JAMA. 2008;299:2760-2769). Currently, prostate cancer recurrence is determined by monitoring prostate specific antigen (PSA) levels in patients following treatment, and those patients whose PSA levels rise above the clinical cutoff of 200 pg/mL PSA are defined as having recurrent prostate cancer. For those that do recur and have high PSA doubling times, early salvage radiotherapy confers a significant increase in prostate cancer specific survival (1). We have developed an ultrasensitive assay that measures PSA levels with a limit of detection of 0.5 pg/mL PSA with a CV of less than 20 % at 2 pg/mL. This assay utilizes functionalized gold nanoparticles to label PSA targets captured onto antibody coated glass substrates. The amount of PSA is quantified through silver enhancement of the functionalized gold. In this presentation, we describe the application of this technology in monitoring PSA levels in patients that are approximately 400 fold below the current clinical cutoff as a means of diagnosing prostate cancer recurrence at a much earlier timepoint than current assays.

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Ultra-sensitive detection of biomarkers and applications in pharmaceutical discovery and development. Example application to rat cardiac troponin I assay via nanoparticle probes

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Although specific to heart, rat cardiac troponin I (cTnI) is an example of an important biomarker for assessing drug-induced cardiotoxicity in animal models used in various phases of drug discovery and development. Current commercially available assays can only detect 10 ∼ 100 pg/mL in serum at the lowest limits. To improve the sensitivity of rat cTnI assay, we have developed a generically applicable, microarray based nano-probe test. Our rat cTnI assay algorithm uses a multi-step robotic process, which relies on non- isotropically oriented antibodies on functionalized glass as multiplexed microarrays to capture cTnI from serum. Functionalized, 130 angstrom diameter gold nano-probes (measured by static light scattering, 5 nm S.D.) also bind to the troponin through a molecular-scale complex containing antibodies. The troponin-bound molecular complex is then quantified through silver enhancement of the functionalized gold. Assays in this format can be rapidly configured and implemented for a wide array of potential biomarkers. For cTnI we have demonstrated a robust and ultra-sensitive assay with an LOD of less than 500 femtograms of rat cTnI per mL serum, and an overall CV of less than 20%. The assay also shows very low background, a broad dynamic range and over 3 logs of linear dose response. As an example of the potential of high sensitivity, the nanoparticle-based rat cTnI assay could significantly increase the effectiveness of measuring drug-induced heart damage at very low drug dosages and early times. Such sensitive and early measurements can improve examination of the safety of drug candidates while correspondingly reducing drug development time and cost.

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Biomarkers in cancer: Survey of diagnostic needs

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Background: Much ongoing work in the field of diagnostics is related to identifying novel and clinically useful tumor markers. However, it is not clear that this discovery is focused on the clinical uses that are most important to physicians. Methods: Consequently, we conducted a survey to assess these needs. Our survey of oncologists, specialists and primary care physicians received 236 responses. Of these, 214 doctors provided their view, ranking with an 8 point Likert scale, for which of eight aspects of cancer that they would like to better differentially diagnose. Of the respondents, 45% were oncologists, 17% primary care, 16% urology and 15% OB/Gyn. Of the physicians surveyed, 57% were in private practice and 32% were in academic medicine, with the remaining 11% in a variety of other settings. Results: As may be unexpected, respondents believed that they still could benefit most from diagnosis itself (indexed score 6.1), followed closely by improving earlier diagnosis or identifying latent disease (5.6), as opposed to simple screening (4.82). The aspects that they believed required the least improvement were prognosis for metastasis (3.6) and prognosis for progression (4.0). Surprisingly, desire for the ability for better treatment planning was unremarkable as well (4.3). We also gauged the respondents familiarity with tumor markers using a 5 point Likert scale. 29% considered themselves very familiar, and only 13% considered themselves with less than average familiarity. Conclusions: The results of the survey suggest it may be useful to consider evaluation of biomarkers which aid early diagnosis rather than disease prognosis.

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A genome scan in multigenerational families with dyslexia: Identification of a novel locus on chromosome 2q that contributes to phonological decoding efficiency

Dyslexia is a common and complex developmental disorder manifested by unexpected difficulty in learning to read. Multiple different measures are used for diagnosis, and may reflect different biological pathways related to the disorder. Impaired phonological decoding (translation of written words without meaning cues into spoken words) is thought to be a core deficit. We present a genome scan of two continuous measures of phonological decoding ability: phonemic decoding efficiency (PDE) and word attack (WA). PDE measures both accuracy and speed of phonological decoding, whereas WA measures accuracy alone. Multipoint variance component linkage analyses (VC) and Markov chain Monte-Carlo (MCMC) multipoint joint linkage and segregation analyses were performed on 108 families. A strong signal was observed on chromosome 2 for PDE using both VC (LOD=2.65) and MCMC methods (intensity ratio (IR)=32.1). The IR is an estimate of the ratio of the posterior to prior probability of linkage in MCMC analysis. The chromosome 2 signal was not seen for WA. More detailed mapping with additional markers provided statistically significant evidence for linkage of PDE to chromosome 2, with VC-LOD=3.0 and IR=59.6 at D2S1399. Parametric analyses of PDE, using a model obtained by complex segregation analysis, provided a multipoint maximum LOD=2.89. The consistency of results from three analytic approaches provides strong evidence for a locus on chromosome 2 that influences speed but not accuracy of phonological decoding.

Pharmacotherapy for severe aggression in a child with autism: "open label" evaluation of multiple medications on response frequency and intensity of behavioral intervention

Many persons who have developmental disabilities and challenging behaviors are treated with multiple medications combined with nonpharmacological approaches. However, the comparative effects from pharmacotherapy frequently are not assessed empirically, do not include corollary behavioral measures, and are not evaluated in the long term. The present single-case study incorporated behavioral assessment methodology in an "open label" evaluation of anticonvulsant (clonazepam), beta-blocking (propanolol), and antidepressant (sertraline and clomipramine) medications on severe aggression in a child with autism. Clinically significant reductions in aggressive behavior were attained with the administration of clomipramine and the reductive effects from the medication persisted for 1.7 years. In addition, clomipramine was associated with the elimination of crisis intervention procedures that had been required to manage the child's aggression. These findings add to the clinical literature describing effective treatment of serious behavior disorders in persons with developmental disabilities using antidepressant medication.

Sequence-tagged connectors: a sequence approach to mapping and scanning the human genome

The sequence-tagged connector (STC) strategy proposes to generate sequence tags densely scattered (every 3.3 kilobases) across the human genome by arraying 450,000 bacterial artificial chromosomes (BACs) with randomly cleaved inserts, sequencing both ends of each, and preparing a restriction enzyme fingerprint of each. The STC resource, containing end sequences, fingerprints, and arrayed BACs, creates a map where the interrelationships of the individual BAC clones are resolved through their STCs as overlapping BAC clones are sequenced. Once a seed or initiation BAC clone is sequenced, the minimum overlapping 5' and 3' BAC clones can be identified computationally and sequenced. By reiterating this "sequence-then-map by computer analysis against the STC database" strategy, a minimum tiling path of clones can be sequenced at a rate that is primarily limited by the sequencing throughput of individual genome centers. As of February 1999, we had deposited, together with The Institute for Genomic Research (TIGR), into GenBank 314,000 STCs ( approximately 135 megabases), or 4.5% of human genomic DNA. This genome survey reveals numerous genes, genome-wide repeats, simple sequence repeats (potential genetic markers), and CpG islands (potential gene initiation sites). It also illustrates the power of the STC strategy for creating minimum tiling paths of BAC clones for large-scale genomic sequencing. Because the STC resource permits the easy integration of genetic, physical, gene, and sequence maps for chromosomes, it will be a powerful tool for the initial analysis of the human genome and other complex genomes.

The structure of VanX reveals a novel amino-dipeptidase involved in mediating transposon-based vancomycin resistance

VanX is a zinc-dependent D-alanyl-D-alanine dipeptidase that is a critical component in a system that mediates transposon-based vancomycin resistance in enterococci. It is also a key drug target in circumventing clinical vancomycin resistance. The structure of VanX from E. faecium has been solved by X-ray crystallography and reveals a Zn(2+)-dipeptidase with a unique overall fold and a well-defined active site confined within a cavity of limited size. The crystal structures of VanX, the VanX:D-alanyl-D-alanine complex, the VanX:D-alanine complex, and VanX in complex with phosphonate and phosphinate transition-state analog inhibitors, are also presented at high resolution. Structural homology searches of known structures revealed that the fold of VanX is similar to those of two proteins: the N-terminal fragment of murine Sonic hedgehog and the Zn(2+)-dependent N-acyl-D-alanyl-D-alanine carboxypeptidase of S. albus G.

1H, 13C and 15N backbone assignments of cyclophilin when bound to cyclosporin A (CsA) and preliminary structural characterization of the CsA binding site

The backbone 1H, 13C and 15N chemical shifts of cyclophilin (CyP) when bound to cyclosporin A (CsA) have been assigned from heteronuclear two- and three-dimensional NMR experiments involving selectively 15N- and uniformly 15N- and 15N,13C-labeled cyclophilin. From an analysis of the 1H and 15N chemical shifts of CyP that change upon binding to CsA and from CyP/CsA NOEs, we have determined the regions of cyclophilin involved in binding to CsA.

Extended femoro-distal bypasses for limb salvage: are they worthwhile?

In this report on 93 patients with limb-threatening leg ischemia the surgical procedures applied were malleolar bypasses (14), sequential bypasses (12) and femoro-distal bypasses with adjunct AV fistulas (67). The first two methods resulted in favourable limb-salvage and patency rates. However the results of such reconstructions essentially depend on the quality of primary and secondary foot arcades. In peripheral calf and foot arterial occlusions we have applied a distal arteriovenous fistula as an adjunct measure to maintain bypass patency in the crural region. 67 patients were operated on according to this method: 30 females and 37 males with an average age of 70.3 years. 29% had rest-pain and 71% had gangrene. The majority had already been operated on at least once. 7 patients had been amputated contralaterally.

RESULTS

79% of the patients had a patent graft after one month. The incidence of limb salvage was 77%. At two years 47% of all grafts are still patent and the incidence of limb-salvage is 52%. However, this operation should be exclusively designed for limb-salvage and for cases with extremely poor run-off.

A computer terminal program to evaluate cardiovascular functional limits and estimate coronary event risks

A system of computer terminals was set up in a group of office practices, industrial medical departments and hospitals and connected to a central computer. This service provides a means of analyzing treadmill exercise results, which are displayed graphically on the computer printout. The system also provides estimates of probabilities of primary or secondary coronary heart disease events developing based on the exercise responses.