Characterizing the KRAS G12C mutation in metastatic colorectal cancer: a population-based cohort and assessment of expression differences in The Cancer Genome Atlas

Introduction

In metastatic colorectal cancer (mCRC), RAS mutations impart inferior survival and resistance to anti-epidermal growth factor receptor (EGFR) antibodies. KRAS G12C inhibitors have been developed and we evaluated how KRAS G12C differs from other RAS mutations.

Patients and Methods

This retrospective review evaluated patients in British Columbia, Canada with mCRC and RAS testing performed between 1 January 2016 and 31 December 2018. Sequencing information from The Cancer Genome Analysis (TCGA) was also obtained and analysed.

Results

Age at diagnosis, sex, anatomic location and stage at diagnosis did not differ by RAS mutation type. Progression free survival on first chemotherapy for patients with metastatic KRAS G12C tumours was 11 months. Median overall survival did not differ by RAS mutation type but was worse for both KRAS G12C (27 months) and non-G12C alterations (29 months) than wildtype (43 months) (p = 0.01). Within the TCGA, there was no differential gene expression between KRAS G12C and other RAS mutations. However, eight genes with copy number differences between the G12C and non-G12C RAS mutant groups were identified after adjusting for multiple comparisons (FITM2, PDRG1, POFUT1, ERGIC3, EDEM2, PIGU, MANBAL and PXMP4). We also noted that other RAS mutant mCRCs had a higher tumour mutation burden than those with KRAS G12C mutations (median 3.05 vs 2.06 muts/Mb, p = 4.2e-3) and that KRAS G12C/other RAS had differing consensus molecular subtype distribution from wildtype colorectal cancer (CRC) (p < 0.0001) but not each other (p = 0.14).

Conclusion

KRAS G12C tumours have similar clinical presentation to other RAS mutant tumours, however, are associated with differential copy number alterations.

Effect of preexamination conditions in a centralized-testing model of non-invasive prenatal screening

OBJECTIVES

Non-invasive prenatal testing requires the presence of fetal DNA in maternal plasma. Understanding how preexamination conditions affect the integrity of cell-free DNA (cfDNA) and fetal fraction (FF) are a prerequisite for test implementation. Therefore, we examined the adjusted effect that EDTA and Streck tubes have on the cfDNA quantity and FF.

METHODS

A total of 3,568 maternal blood samples across Canada were collected in either EDTA, or Streck tubes, and processing metrics, maternal body mass index (BMI), gestational age and fetal karyotype and sex were recorded. Plasma samples were sequenced using two different sequencing platforms in separate laboratories. Sequencing data were processed with SeqFF to estimate FF. Linear regression and multivariate imputation by chained equations were used to estimate the adjusted effect of tube type on cfDNA and FF.

RESULTS

We found a positive association between cfDNA quantity and blood shipment time in EDTA tubes, which is significantly reduced with the use of Streck tubes. Furthermore, we show the storage of plasma at -80 °C is associated with a 4.4% annual relative decrease in cfDNA levels. FF was not associated with collection tube type when controlling for confounding variables. However, FF was positively associated with gestational age and trisomy 21, while negatively associated with BMI, male fetus, trisomy 18, Turners syndrome and triploidy.

CONCLUSIONS

Preexamination, maternal and fetal variables are associated with cfDNA quantity and FF. The consideration of these variables in future studies may help to reduce the number of pregnant women with inconclusive tests as a result of low FF.

Use of Treatment-Focused Tumor Sequencing to Screen for Germline Cancer Predisposition

Next-generation sequencing assays are capable of identifying cancer patients eligible for targeted therapies and can also detect germline variants associated with increased cancer susceptibility. However, these capabilities have yet to be routinely harmonized in a single assay because of challenges with accurately identifying germline variants from tumor-only data. We have developed the Oncology and Hereditary Cancer Program targeted capture panel, which uses tumor tissue to simultaneously screen for both clinically actionable solid tumor variants and germline variants across 45 genes. Validation using 14 tumor specimens, composed of patient samples and cell lines analyzed in triplicate, demonstrated high coverage with sensitive and specific identification of single-nucleotide variants and small insertions and deletions. Average coverage across all targets remained >2000× in 198 additional patient tumor samples. Analysis of 55 formalin-fixed, paraffin-embedded tumor samples for the detection of known germline variants within a subset of cancer-predisposition genes, including one multiexon deletion, yielded a 100% detection rate, demonstrating that germline variants can be reliably detected in tumor samples using a single panel. Combining targetable somatic and actionable germline variants into a single tumor tissue assay represents a streamlined approach that can inform treatment for patients with advanced cancers as well as identify those with potential germline variants who are eligible for confirmatory testing, but would not otherwise have been identified.

Assessing Limit of Detection in Clinical Sequencing

Clinical reporting of solid tumor sequencing requires reliable assessment of the accuracy and reproducibility of each assay. Somatic mutation variant allele fractions may be below 10% in many samples due to sample heterogeneity, tumor clonality, and/or sample degradation in fixatives such as formalin. The toolkits available to the clinical sequencing community for correlating assay design parameters with assay sensitivity remain limited, and large-scale empirical assessments are often relied upon due to the lack of clear theoretical grounding. To address this uncertainty, a theoretical model was developed for predicting the expected variant calling sensitivity for a given library complexity and sequencing depth. Binomial models were found to be appropriate when assay sensitivity was only limited by library complexity or sequencing depth, but functional scaling for library complexity was necessary when both library complexity and sequencing depth were co-limiting. This model was empirically validated with sequencing experiments by using a series of DNA input amounts and sequencing depths. Based on these findings, a workflow is proposed for determining the limiting factors to sensitivity in different assay designs, and the formulas for these scenarios are presented. The approach described here provides designers of clinical assays with the methods to theoretically predict assay design outcomes a priori, potentially reducing burden in clinical tumor assay design and validation efforts.

Population-based Screening for BRAF V600E in Metastatic Colorectal Cancer Reveals Increased Prevalence and Poor Prognosis

PURPOSE

BRAF ^V600E mutations portend poor prognosis in metastatic colorectal cancer (mCRC); however, the true prevalence and prognosis are unknown, as unwell patients may not undergo BRAF sequencing.

EXPERIMENTAL DESIGN

We reviewed a population-based cohort of 1,898 patients with colorectal cancer that underwent reflexive IHC mismatch repair (MMR) and BRAF ^V600E testing. Outcomes among IHC-detected BRAF ^V600E mCRC (BRAF _IHC) were compared with patients with next-generation sequencing (NGS)-identified BRAF ^V600E-mutated mCRC from two institutions (BRAF _NGS) with patients spanning from 2004 to 2018.

RESULTS

All-stage population prevalence of BRAF ^V600E was 12.5% (238/1,898) and did not differ between early and metastatic stages (P = 0.094). Prevalence among mCRC was 10.6% (61/575), of whom 51 (83.6%) were referred to oncology and 26 (42.6%) had NGS testing. BRAF _IHC had worse median overall survival (mOS) than BRAF _NGS [5.5 vs. 20.4 months; HR, 2.90; 95% confidence interval (CI), 1.89-4.45; P < 0.0001], which persisted in multivariate analysis (P < 0.0001). Across a combined NGS and IHC cohort, BRAF ^V600E tumors with deficient MMR showed worse mOS compared with MMR proficient tumors (8.9 vs. 17.2 months; HR, 1.46; 95% CI, 0.96-2.27; P = 0.043). In this combined cohort, first-line progression-free survival was 5.9 months, with minimal differences between regimens. Within the population-based cohort, attrition between treatment lines was high with only 60.7% receiving first-line chemotherapy and 26.2% receiving second line.

CONCLUSIONS

Patients with BRAF ^V600E-mutated mCRC have a worse prognosis than previously suggested, potentially arising from referral bias for testing. High attrition between lines of therapy suggests efficacious therapies need to be prioritized early for patients to benefit.

0039 The Clinical Utility of Dim Light Melatonin Onset in Treatment of Delayed Sleep-Wake Phase Disorder: Preliminary Findings

Introduction

Delayed sleep-wake phase disorder (DSWPD) is common, debilitating, and challenging to treat. In an ongoing randomized trial, we are comparing exogenous melatonin treatment outcomes in DSWPD participants for whom dim light melatonin onset (DLMO) is measured objectively vs. estimated.

Methods

Thus far, 13 participants (27±6 years old, 67% female) have completed a randomized, controlled, double-blind 4-week trial of 0.5 mg of exogenous melatonin timed to either 3 h before measured DLMO (M-DLMO, n = 6) or 3 h before DLMO estimated at 2 h before average sleep onset time based on at least 7 days of wrist actigraphy and sleep diary (E-DLMO, n = 7). All participants met International Classification of Sleep Disorders-3 diagnostic criteria for DSWPD and were otherwise healthy. Participants completed 4 weekly treatment sessions with a blinded psychologist; time of melatonin administration and bed-rise schedule were advanced up to 1 h/week. A validated home saliva collection kit measured DLMO in all participants. Between-group t-tests and Hedges’ g effect sizes (ES) were calculated at post-treatment for the following outcomes: DLMO; Pittsburgh Sleep Quality Index (PSQI) global score; Morningness-Eveningness Questionnaire (MEQ); and the actigraphy parameters sleep efficiency (SE) and clock time of sleep onset and offset. A paired-sample t-test compared the measured vs. estimated DLMO at baseline.

Results

The M-DLMO group had a 65±88 mins DLMO advance vs. 27±30 mins in the E-DLMO group (ES=0.51 p=.381). PSQI scores were similar between groups (M-DLMO=6.67±2.06, E-DLMO=7.1± 1.57, ES=-0.24, p=.646), as were MEQ scores (M-DLMO=43±4.98, E-DLMO=48±12.72, ES=-0.47, p=.387). Sleep onset time (M-DLMO=0:32±1:02, E-DLMO=0:31±1:38, ES=0.01, p=.98) and offset time (M-DLMO=8:05±1:03, E-DLMO=8:08±2:14, ES=-0.02, p=.968) were similar between the groups, although sleep was more efficient in M-DLMO vs. E-DLMO (84%±3% vs. 76%±10%, ES=0.94, p=.096). On average, baseline measured DLMO occurred 123±83 mins earlier than estimated DLMO (p=.001).

Conclusion

We are continuing to enroll participants in this trial. Preliminary results suggest some potential benefit of measuring the DLMO, but results will need to be clarified in a larger sample.

Support

American Sleep Medicine Foundation Strategic Research Award

Evidence for adult age-invariance in associative false recognition

Older people are more prone to memory distortions and errors than young people, but do not always show greater false recognition in the Deese-Roediger-McDermott (DRM) task. We report two preregistered experiments investigating whether recent findings of age-invariant false recognition extend to designs in which studied items are blocked. According to (Tun, P. A., Wingfield, A., Rosen, M. J., & Blanchard, L. (1998). Response latencies for false memories: Gist-based processes in normal aging. Psychology and Aging, 13(2), 230-241.), age effects on false recognition in the DRM task are due to a greater reliance on gist processing which is enhanced under blocked study conditions. Experiment 1 assessed false recognition in an online variant of the DRM task where words were presented visually, with incidental encoding. The results showed Bayesian evidence against greater false recognition by older adults, whether lures were semantically associated with studied lists, or perceptually related (presented in the same distinctive font as studied lists) or both. Experiment 2 used a typical DRM procedure with auditory lists and intentional encoding, closely reproducing (Tun, P. A., Wingfield, A., Rosen, M. J., & Blanchard, L. (1998). Response latencies for false memories: Gist-based processes in normal aging. Psychology and Aging, 13(2), 230-241.) Experiment 2 but omitting an initial test of recall. The results showed evidence against an age-related increase in critical lure false recognition under these conditions. Together, the data suggest that older people do not make more associative memory errors in recognition tests than young people.

P2427The development of a computational fluid dynamics pipeline for the study of tetralogy of Fallot and coarctation of the aorta in a developing world context

Background

Tetralogy of Fallot (ToF) and coarctation of the aorta (CoA) each constitute approximately 7% of congenital heart disease (CHD) births worldwide. Compared to developed countries, developing countries have a disparate level of access to prompt diagnosis and treatment for these diseases. Computational fluid dynamics (CFD) approaches implemented on routinely available non-invasive imaging data may yield low-cost improvements to the management of these patients.

Purpose

The purpose of this research is to develop a patient-specific computational pipeline that allows the modelling of blood flow in diseased arteries of patients suffering from ToF and CoA. The project aims to prove the feasible use of broadly available imaging techniques - CT angiograms (CTA) and echocardiographs (echo) - for achieving this in low-to-middle income countries. The capability of the pipeline will be demonstrated through a qualitative study of the effects of different systemic to pulmonary shunt configurations used in the palliative treatment of ToF. In addition, the effects of idealised stent configurations on the blood flow through the aorta of a patient with CoA will be studied.

Methods

A retrospective search through the hospital database was conducted to select suitable CTA data for a CoA and ToF case. Data for patient A, a five-month-old child with typical CoA, and patient B, a twelve-month-old child with typical ToF who had a central shunt in place, was found. Echo data was obtained for patient A through an investigation protocol which focused on CFD application whereas there was no echo data available for patient B. As a result, idealised volume flow rate data was implemented for patient B. Geometries for patient A and patient B were extracted and volume discretisation was implemented for grid independence testing. The Navier-Stokes governing equations for fluid flow were solved using the open source software, OpenFOAM, for the transient case where inlet volume flow rate was defined for four cardiac cycles. Figure 1 shows key features of the flow in the shunt and pulmonary branches (A), the aortic arch (B), the inlet at the ascending aorta (C) and the descending aorta (D) for the geometry extracted from the data set of patient B.

Figure 1. Key flow features of patient B

Results and discussion

We have implemented CFD models which are able to qualitatively assess the favourable or unfavourable impact of different approaches to ToF and CoA repairs on the characteristics of blood flow in the aorta and pulmonary arteries. An echo investigation protocol has been developed and successfully applied. CTA studies have been shown as feasible sources of geometry data in spite of the restriction on quality by the important requirement for low doses of radiation in paediatric patients. This project represents progress towards an advanced tool that may be broadly implemented in both well-resourced and minimally-resourced hospitals.

Acknowledgement/Funding

National Research Fund, British Heart Foundation, Newton Fund (UK MRC, South African Medical Research Council), University of Cape Town

Population-based screening for BRAF V600E in metastatic colorectal cancer (mCRC) to reveal true prognosis

3579

Background: BRAFV600E ( BRAF) mutations (mts) portend poor prognosis in mCRC and patients (pts) may die before ascertainment. Since 2014, Vancouver Coastal Health (VCH) has performed reflex hereditary screening of CRCs with BRAF and mismatch repair (MMR) immunohistochemistry (IHC). We evaluated this BRAF mt population-based cohort ( BRAFPOP) to establish the true prognosis of BRAF mts in mCRC. Methods: We reviewed all mCRCs from VCH between 4/2014 and 5/2018 for BRAF by IHC (VE1 antibody). Overall survival (OS) from stage IV diagnosis was compared to mCRCs with next generation sequencing (NGS) determined BRAF mts ( BRAFNGS) from BC Cancer & MD Anderson. BRAFNGS OS did not differ by center (p = 0.77). Results: See table for BRAF cohort baseline characteristic comparison. BRAFPOP pts had worse OS than BRAFNGS pts (HR 2.5, 95% CI 1.6 – 3.9, P < 0.0001). Median OS for all BRAF mt pts was 17.9 mos. Both groups had worse OS than wild type pts (P < 0.0001). 52 (81%) of BRAFPOP pts were referred to oncology, 40 (63%) received chemotherapy, and 12 (19%) had NGS BRAF testing. BRAFPOP pts who had NGS testing with BRAF mts had OS comparable to other BRAFNGS pts (P = 0.89) and better OS than BRAFPOP pts that never had NGS testing (HR 0.37, 95% CI 0.18-0.76, P = 0.030). Pts with BRAF mts and MMR deficiency (dMMR) (n = 40) had worse OS than MMR proficiency (pMMR, n = 202) (1.6, 95% CI 1.0-2.5, P = 0.011). This was driven by BRAFPOP dMMR pts (HR 1.9, 95% CI 0.9-4.0, P = 0.036) as no difference was seen by MMR in BRAFNGS pts (HR 1.3, 95% CI 0.8-2.2, P = 0.30). Conclusions: Current estimates of prognosis for mCRC with BRAF mts likely underestimate its impact due to referral bias for NGS testing. BRAF mts with dMMR are associated with worse prognosis than pMMR. This appears driven by BRAFPOP pts. [Table: see text]

Fixation Effects on Variant Calling in a Clinical Resequencing Panel

Formalin fixation is the standard method for the preservation of tissue for diagnostic purposes, including pathologic review and molecular assays. However, this method is known to cause artifacts that can affect the accuracy of molecular genetic test results. We assessed the applicability of alternative fixatives to determine whether these perform significantly better on next-generation sequencing assays, and whether adequate morphology is retained for primary diagnosis, in a prospective study using a clinical-grade, laboratory-developed targeted resequencing assay. Several parameters relating to sequencing quality and variant calling were examined and quantified in tumor and normal colon epithelial tissues. We identified an alternative fixative that suppresses many formalin-related artifacts while retaining adequate morphology for pathologic review.

Src family kinases Fyn and Lyn are constitutively activated and mediate plasmacytoid dendritic cell responses

Plasmacytoid dendritic cells (pDC) are type I interferon-producing cells with critical functions in a number of human illnesses; however, their molecular regulation is incompletely understood. Here we show the role of Src family kinases (SFK) in mouse and human pDCs. pDCs express Fyn and Lyn and their activating residues are phosphorylated both before and after Toll-like receptor (TLR) stimulation. Fyn or Lyn genetic ablation as well as treatment with SFK inhibitors ablate pDC (but not conventional DC) responses both in vitro and in vivo. Inhibition of SFK activity not only alters TLR-ligand localization and inhibits downstream signalling events, but, independent of ex-vivo TLR stimulation, also affects constitutive phosphorylation of BCAP, an adaptor protein bridging PI3K and TLR pathways. Our data identify Fyn and Lyn as important factors that promote pDC responses, describe the mechanisms involved and highlight a tonic SFK-mediated signalling that precedes pathogen encounter, raising the possibility that small molecules targeting SFKs could modulate pDC responses in human diseases.

pH responsive highly branched poly(N-isopropylacrylamide) with trihistidine or acid chain ends

Thermally responsive highly branched poly(N-isopropyl acrylamide)s (HB-PNIPAM) were prepared and end-functionalised to give polymers with acid or trihistidine end groups. ​The ionisation of the end groups affects the swelling of desolvated globules.

Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies

Background

Chimeric transcripts, including partial and internal tandem duplications (PTDs, ITDs) and gene fusions, are important in the detection, prognosis, and treatment of human cancers.

Results

We describe Barnacle, a production-grade analysis tool that detects such chimeras in de novo assemblies of RNA-seq data, and supports prioritizing them for review and validation by reporting the relative coverage of co-occurring chimeric and wild-type transcripts. We demonstrate applications in large-scale disease studies, by identifying PTDs in MLL, ITDs in FLT3, and reciprocal fusions between PML and RARA, in two deeply sequenced acute myeloid leukemia (AML) RNA-seq datasets.

Conclusions

Our analyses of real and simulated data sets show that, with appropriate filter settings, Barnacle makes highly specific predictions for three types of chimeric transcripts that are important in a range of cancers: PTDs, ITDs, and fusions. High specificity makes manual review and validation efficient, which is necessary in large-scale disease studies. Characterizing an extended range of chimera types will help generate insights into progression, treatment, and outcomes for complex diseases.

Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia

BACKGROUND

Many mutations that contribute to the pathogenesis of acute myeloid leukemia (AML) are undefined. The relationships between patterns of mutations and epigenetic phenotypes are not yet clear.

METHODS

We analyzed the genomes of 200 clinically annotated adult cases of de novo AML, using either whole-genome sequencing (50 cases) or whole-exome sequencing (150 cases), along with RNA and microRNA sequencing and DNA-methylation analysis.

RESULTS

AML genomes have fewer mutations than most other adult cancers, with an average of only 13 mutations found in genes. Of these, an average of 5 are in genes that are recurrently mutated in AML. A total of 23 genes were significantly mutated, and another 237 were mutated in two or more samples. Nearly all samples had at least 1 nonsynonymous mutation in one of nine categories of genes that are almost certainly relevant for pathogenesis, including transcription-factor fusions (18% of cases), the gene encoding nucleophosmin (NPM1) (27%), tumor-suppressor genes (16%), DNA-methylation-related genes (44%), signaling genes (59%), chromatin-modifying genes (30%), myeloid transcription-factor genes (22%), cohesin-complex genes (13%), and spliceosome-complex genes (14%). Patterns of cooperation and mutual exclusivity suggested strong biologic relationships among several of the genes and categories.

CONCLUSIONS

We identified at least one potential driver mutation in nearly all AML samples and found that a complex interplay of genetic events contributes to AML pathogenesis in individual patients. The databases from this study are widely available to serve as a foundation for further investigations of AML pathogenesis, classification, and risk stratification. (Funded by the National Institutes of Health.).

Dissect: detection and characterization of novel structural alterations in transcribed sequences

Motivation: Computational identification of genomic structural variants via high-throughput sequencing is an important problem for which a number of highly sophisticated solutions have been recently developed. With the advent of high-throughput transcriptome sequencing (RNA-Seq), the problem of identifying structural alterations in the transcriptome is now attracting significant attention.

In this article, we introduce two novel algorithmic formulations for identifying transcriptomic structural variants through aligning transcripts to the reference genome under the consideration of such variation. The first formulation is based on a nucleotide-level alignment model; a second, potentially faster formulation is based on chaining fragments shared between each transcript and the reference genome. Based on these formulations, we introduce a novel transcriptome-to-genome alignment tool, Dissect (DIScovery of Structural Alteration Event Containing Transcripts), which can identify and characterize transcriptomic events such as duplications, inversions, rearrangements and fusions. Dissect is suitable for whole transcriptome structural variation discovery problems involving sufficiently long reads or accurately assembled contigs.

Results: We tested Dissect on simulated transcripts altered via structural events, as well as assembled RNA-Seq contigs from human prostate cancer cell line C4-2. Our results indicate that Dissect has high sensitivity and specificity in identifying structural alteration events in simulated transcripts as well as uncovering novel structural alterations in cancer transcriptomes.

Availability: Dissect is available for public use at: http://dissect-trans.sourceforge.net

Contact:denizy@mit.edu; fhach@cs.sfu.ca; cenk@cs.sfu.ca

Luminescence techniques and characterization of the morphology of polymer latices

Five poly(n-butyl methacrylate), PBMA, latex dispersions have been prepared, each incorporating a different fluorescent label, via a two-stage seeded emulsion polymerization. The resultant latices contain ca. 35% by weight total solids and are of 80 (+/-10) nm diameter as determined by photon correlation spectrometry. Luminescence spectroscopic techniques, namely fluorescence (and phosphorescence) excited state lifetime measurements in addition to time-resolved anisotropy experiments have provided useful information regarding the morphology, microviscosity and water permeability of the resultant particles. A picture of the PBMA colloid emerges of an interior which is highly viscous and water impermeable in nature. Indeed, the environment is protective enough to sustain room temperature stabilized phosphorescence from both an acenaphthylene and 9-phenanthrylmethyl methacrylate labeled dispersion through simple nitrogen purging of the solutions. However, the current spectroscopic measurements should be viewed with the knowledge that each luminescent label may fashion its own distinctive microenvironment within the latex during polymerization.

Luminescence techniques and characterization of the morphology of polymer latices. 3. An investigation of the microenvironments within stabilized aqueous latex dispersions of poly(n-butyl methacrylate) and polyurethane

Fluorescence techniques (including time-resolved anisotropy measurements, TRAMS) have been used to probe differences in morphology between two stabilized aqueous latex dispersions (poly(n-butyl methacrylate), PBMA, and polyurethane, PU). Use of the emission characteristics of probes such as pyrene and phenanthrene dispersed within particles reveals that the PU latices are more heterogeneous in nature: evidence exists, particularly from quenching measurements and TRAMS, that voids and channels of water permeate the PU structure, resulting in a relatively soft, open particle, swollen by ingress of the bulk aqueous phase. Fluorescence measurements indicate that PBMA colloids, however, are composed of relatively hard, hydrophobic particles. In addition, TRAMS are considered to be a valuable tool both for probing the morphological characteristics of such dispersions and in estimating the average particle size.

Modulation of beta-amyloid production and fibrillization

Alzheimer's disease (AD) is the most common cause of dementia in old age and presently affects an estimated 4 million people in the U.S.A. and 0.75 million people in the U.K. It is a relentless, degenerative brain disease, characterized by progressive cognitive impairment. In the final stages of the disease, patients are often bedridden, doubly incontinent and unable to speak or to recognize close relatives. Pathological changes of Alzheimer's disease include extensive neuronal loss and the presence of numerous neurofibrillary tangles and senile plaques in the brain. The senile plaques contain amyloid fibrils derived from a 39-43-amino-acid peptide referred to as beta-amyloid or A beta. The basic theory of the so-called 'amyloid hypothesis' is that the deposition of aggregated forms of A beta in the brain parenchyma triggers a pathological cascade of events that leads to neurofibrillary tangle formation, neuronal loss and the associated dementia [1]. Here we discuss progress towards the identification of inhibitors of A beta production and fibrillization.

Structure-based design of non-peptide HIV protease inhibitors

A number of structurally novel P2-ligands have been designed and synthesized. Incorporation of these ligands in the (R)-(hydroxyethyl)sulfonamide isostere provided a series of potent non-peptidyl HIV protease inhibitors.

Fluorescence anisotropy: a method for early detection of Alzheimer beta-peptide (Abeta) aggregation

Time-resolved anisotropy measurements (TRAMS) have been used to study the aggregation of the beta-amyloid (Abeta) peptide which is suspected of playing a central role in the pathogenesis of Alzheimer's Disease (AD). The experiments, which employ small quantities of fluorescently-labelled Abeta, in addition to the untagged peptide, have shown that the sensitive TRAMS technique detects the presence of preformed "seed" particles in freshly prepared solutions of Abeta. More importantly, as 100 microM solutions of Abeta containing tagged Abeta at a concentration level of either 0.5 or 1 microM are incubated, the TRAMS prove capable of detection of the peptide aggregation process through the appearance of a continuously increasing "residual anisotropy" within the time-resolved fluorescence data. The method detects Abeta aggregation in its earliest stages, well before complexation becomes apparent in more conventional methods such as the thioflavin T fluorescence assay. The TRAMS approach promises to provide a most attractive route for establishment of a high-throughput procedure for the early detection of the presence of amyloid aggregates in the screening of biological samples.

On the fine structure of the pes Hippocampi major (with plates XIII-XXIII). 1886

We have provided a translation of Golgi's original paper on the mammalian hippocampus (first published in 1883 and reprinted numerous times), along with a preface on its historical context. Golgi believed that this part of the cerebral hemisphere showed best the exact relationship between nerve cells and nerve fibers, the most important problem in 19th century neuroscience.

Some differences between English plural noun inflections and third singular verb inflections in the input: the contributions of frequency, sentence position, and duration

Grammatical inflections such as the English plural noun -s and third person singular verb -s are acquired at different points in time by young children. This finding is typically attributed to factors such as relative semantic salience or the distinction between lexical and functional categories. In this study input frequency, sentence position, and duration were examined as possible contributing factors. In both conversations with and stories aimed at young children, noun plural inflections were found to be more frequent than third singular verb inflections, especially in sentence-final position. Analysis of the speech of four mothers reading stories to their two-year-old children confirmed that duration differences also exist in the input. Because fricatives were lengthened in sentence-final position and plural nouns were much more likely to appear in these positions than were third singular verb forms, plural nouns were significantly longer than third singular inflections on average. The possible implications of these findings for language learnability theories and accounts of grammatical deficits in specific language impairment are discussed.

Serum prolactin concentrations in the captive female African elephant (Loxodonta africana): potential effects of season and steroid hormone interactions

Research was conducted to determine whether seasonal changes in prolactin secretion occur in nonpregnant female African elephants and to examine potential functional interrelationships between secretion of prolactin, cortisol, and progesterone. Weekly blood samples were taken for 18 months from four female African elephants and the sera were analyzed by RIA for progesterone, cortisol, and prolactin concentrations. There was no significant effect of season on serum concentrations of prolactin. Estrous cycles averaged 14 weeks in length and were composed of a 9-week luteal phase and a 5-week follicular phase (based on progesterone concentrations consistently >200 and <200 pg/ml, respectively). Estrous cycle synchronicity was evident between pairs of elephants. Serum concentrations of prolactin (3.91 +/- 0.69 ng/ml; range: 0.84-15.8 ng/ml) were significantly lower during the luteal, compared with the follicular, phase (P < 0.0001; t test) and were positively correlated with serum concentrations of cortisol (r = 0.14; P < 0.05). Mean (+/-SE) serum concentration of cortisol was 5.7 +/- 1.3 ng/ml (range: 1.4-19.3 ng/ml), and concentrations of this adrenal steroid were negatively correlated with progesterone concentrations (r = -0.15; P < 0.01). Increased serum concentrations of prolactin detected during the follicular phase suggest that this hormone may be regulated by ovarian estrogens and may play a role in modulating ovarian function in the elephant.

Solving stubborn-wound problem could save millions, team says

Why do some wounds refuse to heal? A team in London, Ont., is attempting to determine the cellular and molecular clues that could lead to better treatment of recalcitrant wounds.

Reliability of taurine concentrations measured in single urine samples obtained from dogs eight hours after eating

OBJECTIVE

To evaluate the reliability of taurine concentrations measured in a single urine sample obtained from dogs 8 hours after eating, compared with taurine concentrations measured in 24-hour urine samples.

ANIMALS

18 healthy Beagles.

PROCEDURE

After emptying the urinary bladder by transurethral catheterization, dogs were fed a canned maintenance diet. Approximately 8 hours later, urine, plasma, and serum samples were obtained for determination of fractional urinary excretion of taurine and urine taurine-to-creatinine concentration ratios (Utaur:Ucr). Results were compared with 24-hour urinary taurine excretion rate.

RESULTS

Unbound and total fractional urinary taurine excretion correlated well with unbound and total 24-hour urinary taurine excretion. However, bound fractional urinary taurine excretion correlated poorly with bound 24-hour urinary taurine excretion. Unbound and total Utaur:Ucr correlated well with unbound and total 24-hour urinary taurine excretion. However, bound Utaur:Ucr correlated poorly with bound 24-hour urinary taurine excretion.

CONCLUSION AND CLINICAL RELEVANCE

Fractional urinary excretion of unbound and total taurine, and unbound and total Utaur:Ucr are reliable indicators of 24-hour urinary unbound and total taurine excretion in healthy dogs. However, determination of 24-hour urinary taurine excretion is recommended for evaluating urinary bound taurine concentrations of dogs.

Cochlear implants: the head-on collision between medical technology and the right to be deaf

The debate over using cochlear implants to help deaf people communicate with those who can hear continues to rage. Some have welcomed the new technology, but others say the deaf have their own culture and do not need to be "cured".

Radiation-induced apoptosis is not enhanced by expression of either p53 or BAX in SW626 ovarian cancer cells

The p53 protein is known to play a central role in mediating G1 arrest or apoptosis in response to ionizing radiation in some cell types. It has been proposed that the link between p53 and induction of apoptosis is provided in part by p53-mediated upregulation of BAX. In this study, we used the human SW626 ovarian cancer cell line, which lacks functional p53, to further investigate the relationship between wildtype p53, BAX, and apoptosis. SW626 cells expressing a temperature sensitive (ts) p53 mutant did not undergo G1 arrest or apoptosis and did not exhibit enhanced sensitivity to radiation at the permissive temperature of 32 degrees C. The tsp53 protein was functional in these cells as evidenced by rapid induction of p21 at 32 degrees C, but not at 37 degrees C. Interestingly, restoration of wildtype p53 function at 32 degrees C was not associated with BAX upregulation. In addition, stable overexpression of BAX in SW626 cells was not capable of enhancing apoptotic cell death in response to radiation. Thus, failure of p53 to upregulate BAX is not the sole reason for its inability to promote radiation-induced apoptosis in SW626 cells. Taken together, our data suggest that neither p53 nor BAX upregulation is sufficient for the induction of apoptosis in response to genotoxic damage in some cell types.