Tolerability and efficacy of anti-androgen manipulation versus taxotere and anti-androgen manipulation in patients with hormone-naive, high-risk/metastatic prostate cancer: A phase II, open-labeled, randomized study

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Background: Anti-androgen manipulation (AA) is considered the standard initial therapy for high-risk/metastatic prostate cancer. The role of chemotherapy and anti-androgen manipulation (TAA) is still undefined in this group. GenTax is a phase II trial investigating clinical outcome and gene profiling in prostate cancer before and after AA or TAA. Here we present the clinical outcome data.

Methods: Patients with T3/4 disease, PSA ≥ 50 ng/ml or Gleason score ≥ 8, or metastatic disease were enrolled. Patients were randomised at histological diagnosis to AA or TAA (goserelin 3.6 mgs q28 ± taxotere 75 mg/m2 q21 for 6 cycles). TRUS biopsies were taken at randomisation and 22 weeks after treatment initiation. Clinical assessment including KPS, QOL using QLQ-C30, bloods/PSA were measured 3 weekly until 22 weeks then 3 monthly. Data was analysed for PFS, OS, toxicities and QOL.

Results: 30 patients were recruited with 15 patients in each arm from 10/13/2005 to 12/02/2009. The median age was 62.2 yrs (range 48.9-75.1). All patients had a KPS of ≥ 90%. 12 (40%) and 18 (60%) of patients had stage 3 and 4 disease respectively. At randomization 10 patients had bone and 4 had visceral metastases. 29 had a Gleason score of ≥ 7. There were no statistical differences for age, KPS, disease stage or Gleason score between the two arms. Treatment was well tolerated in both groups with no G3-4 toxicity in the AA arm. In the TAA arm, 4 patients had dose delays or reductions; with one G3 incidence of neutropenia. G3-4 non-hematological toxicities were infrequent; fatigue and one episode of anaphylaxis occurring in separate patients. Median PFS and OS between the two treatments have not been reached at median follow up of 25 months. The 2-year PFS rate was not significantly different, (50% vs 60% p = 0.788) between the AA and TAA groups. There were no significant differences in QOL measures.

Conclusions: Combination therapy of taxotere and anti-androgen manipulation is safe and well tolerated. The gene profiling results may provide important information in selecting patients who will benefit from more aggressive initial therapy.

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Dissecting quantitative resistance against blast disease using heterogeneous inbred family lines in rice

SHZ-2 is an indica rice cultivar that exhibits broad-spectrum resistance to rice blast; it is widely used as a resistance donor in breeding programs. To dissect the QTL responsible for broad-spectrum blast resistance, we crossed SHZ-2 to TXZ-13, a blast susceptible indica variety, to produce 244 BC(4)F(3) lines. These lines were evaluated for blast resistance in greenhouse and field conditions. Chromosomal introgressions from SHZ-2 into the TXZ-13 genome were identified using a single feature polymorphism microarray, SSR markers and gene-specific primers. Segregation analysis of the BC(4)F(3) population indicated that three regions on chromosomes 2, 6, and 9, designated as qBR2.1, qBR6.1, and qBR9.1, respectively, was associated with blast resistance and contributed 16.2, 14.9, and 22.3%, respectively, to the phenotypic variance of diseased leaf area (DLA). We further narrowed the three QTL regions using pairs of sister lines extracted from heterogeneous inbred families (HIF). Pairwise comparison of these lines enabled the determination of the relative contributions of individual QTL. The qBR9.1 conferred strong resistance, whereas qBR2.1 or qBR6.1 individually did not reduce disease under field conditions. However, when qBR2.1 and qBR6.1 were combined, they reduced disease by 19.5%, suggesting that small effect QTLs contribute to reduction of epidemics. The qBR6.1 and qBR9.1 regions contain nucleotide-binding sites and leucine rich repeats (NBS-LRR) sequences, whereas the qBR2.1 did not. In the qBR6.1 region, the patterns of expression of adjacent NBS-LRR genes were consistent in backcross generations and correlated with blast resistance, supporting the hypothesis that multiple resistance genes within a QTL region can contribute to non-race-specific quantitative resistance.

Genetic variation in biomass traits among 20 diverse rice varieties

Biofuels provide a promising route of producing energy while reducing reliance on petroleum. Developing sustainable liquid fuel production from cellulosic feedstock is a major challenge and will require significant breeding efforts to maximize plant biomass production. Our approach to elucidating genes and genetic pathways that can be targeted for improving biomass production is to exploit the combination of genomic tools and genetic diversity in rice (Oryza sativa). In this study, we analyzed a diverse set of 20 recently resequenced rice varieties for variation in biomass traits at several different developmental stages. The traits included plant size and architecture, aboveground biomass, and underlying physiological processes. We found significant genetic variation among the 20 lines in all morphological and physiological traits. Although heritability estimates were significant for all traits, heritabilities were higher in traits relating to plant size and architecture than for physiological traits. Trait variation was largely explained by variety and breeding history (advanced versus landrace) but not by varietal groupings (indica, japonica, and aus). In the context of cellulosic biofuels development, cell wall composition varied significantly among varieties. Surprisingly, photosynthetic rates among the varieties were inversely correlated with biomass accumulation. Examining these data in an evolutionary context reveals that rice varieties have achieved high biomass production via independent developmental and physiological pathways, suggesting that there are multiple targets for biomass improvement. Future efforts to identify loci and networks underlying this functional variation will facilitate the improvement of biomass traits in other grasses being developed as energy crops.

An expedited stroke triage pathway: the key to shortening the door-to-needle time in delivery of thrombolysis

OBJECTIVES

To assess time management of stroke thrombolysis triage and functional outcomes in patients receiving recombinant tissue plasminogen activator for hyperacute stroke, and identify bottlenecks in delivery of the treatment.

DESIGN

Prospective study.

SETTING

A university teaching hospital in Hong Kong.

PATIENTS

Patients with suspected hyperacute stroke referred to the stroke thrombolysis team during October 2008 to September 2009.

MAIN OUTCOME MEASURES

Time performance records including door-to-stroke team, door-to-needle, and onset-to-thrombolysis times. Functional outcomes by modified Rankin Scale score at 3 months, and thrombolysis-related complications including haemorrhagic transformations and mortality.

RESULTS

During the 12-month period, 95 thrombolysis calls were received; recombinant tissue plasminogen activator was given intravenously to 17 (18%) of the patients and intra-arterially to 11 (12%). The mean (standard deviation) door-to-stroke team and the door-to-needle times for intravenous recombinant tissue plasminogen activator patients were 33 (25) and 80 (25) minutes, respectively; both were about 20 minutes longer than that recommended by the National Institute of Neurological Disorders and Stroke. The mean National Institute of Health Stroke Scale score for patients received intravenous recombinant tissue plasminogen activator was 16 (standard deviation, 7). The mean (standard deviation) onset-to-treatment time was 144 (42) minutes. Nine (53%) patients who received intravenous recombinant tissue plasminogen activator achieved favourable outcomes at 3 months, with a modified Rankin Scale score of 0 to 1. Symptomatic haemorrhage and mortality occurred in one (6%) patient.

CONCLUSION

A dedicated stroke triage pathway is essential to ensure efficient and safe delivery of thrombolysis therapy. Improvements in door-to-stroke team time through integration with emergency medicine staff and neuroradiologists may improve thrombolysis eligibility.

More genomic resources for less-studied crops

Many of the crop species considered to be minor on a global scale, yet are important locally for food security in the developing world, have remained less-studied crops. Recent years have witnessed the development of large-scale genomic and genetic resources, including simple sequence repeat, single nucleotide polymorphism and diversity array technology markers, expressed sequence tags or transcript reads, bacterial artificial chromosome libraries, genetic and physical maps, and genetic stocks with rich genetic diversity, such as core reference sets and introgression lines in these crops. These resources have the potential to accelerate gene discovery and initiate molecular breeding in these crops, thereby enhancing crop productivity to ensure food security in developing countries.

Relationship between Phylogeny and Pathotype for the Bacterial Blight Pathogen of Rice

Several transposable elements were isolated from the genome of Xanthomonas oryzae pv. oryzae. These elements and an avirulence gene isolated from X. oryzae pv. oryzae were used as hybridization probes for a collection of X. oryzae pv. oryzae strains from the Philippines. Each of the sequences was present in multiple copies in all strains examined and showed distinct patterns of hybridizing bands. Phenograms were derived from the restriction fragment length polymorphism data obtained for each of the individual probes and for pooled data from multiple probes. The phenograms derived from the different probes differed in topology and, on the basis of bootstrap analysis, were not equally robust. For all of the probes, including the avirulence gene, some groups (even some haplotypes) consisted of multiple races. The strains were grouped into four major clusters on the basis of the two probes giving the highest bootstrap values. These groups were inferred to represent phylogenetic lineages. Three of the six races of X. oryzae pv. oryzae appeared in more than one of the lineages, and another was present in two sublineages. For three of the races, strains representing different phenetic groups were inoculated on rice cultivars carrying 10 resistance genes. Two new races were differentiated, corresponding to pathogen lineages identified by DNA typing. On the basis of DNA and pathotypic analyses, together with information on the spatial and temporal distribution of the pathogen types from this and other studies, a general picture of X. oryzae pv. oryzae evolution in the Philippines is presented.

Single nucleotide polymorphisms in a gene for translation initiation factor (eIF4G) of rice (Oryza sativa) associated with resistance to Rice tungro spherical virus

Rice tungro disease (RTD) is a serious constraint to rice production in South and Southeast Asia. RTD is caused by Rice tungro spherical virus (RTSV) and Rice tungro bacilliform virus. Rice cv. Utri Merah is resistant to RTSV. To identify the gene or genes involved in RTSV resistance, the association of genotypic and phenotypic variations for RTSV resistance was examined in backcross populations derived from Utri Merah and rice germplasm with known RTSV resistance. Genetic analysis revealed that resistance to RTSV in Utri Merah was controlled by a single recessive gene (tsv1) mapped within an approximately 200-kb region between 22.05 and 22.25 Mb of chromosome 7. A gene for putative translation initiation factor 4G (eIF4G(tsv1)) was found in the tsv1 region. Comparison of eIF4G(tsv1) gene sequences among susceptible and resistant plants suggested the association of RTSV resistance with one of the single nucleotide polymorphism (SNP) sites found in exon 9 of the gene. Examination of the SNP site in the eIF4G(tsv1) gene among various rice plants resistant and susceptible to RTSV corroborated the association of SNP or deletions in codons for Val(1060-1061) of the predicted eIF4G(tsv1) with RTSV resistance in rice.

Genetic analysis and gene mapping of a new rolled-leaf mutant in rice (Oryza sativa L.)

To understand the development of rice leaf blades, we identified a new rolled-leaf mutant, w32, from indica cultivar IR64 through EMS mutagenesis. The mutant showed a stable rolled-leaf phenotype throughout the life cycle. Two F2 populations were developed by crossing w32 to cultivar IR24 and PA64. Genetic analysis showed that the rolled-leaf phenotype was controlled by a single recessive gene. To determine the location of the gene, bulked segregant analysis was carried out using mutant and wild-type DNA pools and 1846 mutant-type F2 individuals derived from the cross w32/PA64 were genotyped to locate the gene on the short arm of chromosome 7. The rolled-leaf gene, tentatively named rl11(t), is likely a new gene as no other rolled-leaf genes have been identified near the region. By developing new SSR and InDel markers, the gene was delimited to a 52 kb region near the end of the short chromosome arm. Further fine mapping and cloning of the gene are currently underway.

Reversible Cerebral Vasoconstriction Syndrome with Posterior Leucoencephalopathy after Oral Contraceptive Pills

Reversible cerebral vasoconstriction syndrome (RCVS) is characterized by sudden-onset recurrent ‘thunderclap’ headaches with reversible multifocal narrowing of the cerebral arteries, often associated with focal neurological deficits from ischaemic or haemorrhagic stroke. It has been associated with exposure to vasoconstrictive drugs, pregnancy, migraine, and a variety of other conditions. Whereas the pathophysiology of RCVS remains unclear, changes in the levels of female hormones are considered important because RCVS predominantly affects women and is frequently associated with pregnancy. We report a patient with angiographically confirmed RCVS whose MRI showed reversible brain oedema, suggesting an overlap between RCVS and the reversible posterior leucoencephalopathy syndrome. The only identified risk factor was oral contraceptive pills started 1 month prior to onset, supporting a role for female reproductive hormones in precipitating this overlap syndrome.

Detection of genomic deletions in rice using oligonucleotide microarrays

BACKGROUND

The induction of genomic deletions by physical- or chemical- agents is an easy and inexpensive means to generate a genome-saturating collection of mutations. Different mutagens can be selected to ensure a mutant collection with a range of deletion sizes. This would allow identification of mutations in single genes or, alternatively, a deleted group of genes that might collectively govern a trait (e.g., quantitative trait loci, QTL). However, deletion mutants have not been widely used in functional genomics, because the mutated genes are not tagged and therefore, difficult to identify. Here, we present a microarray-based approach to identify deleted genomic regions in rice mutants selected from a large collection generated by gamma ray or fast neutron treatment. Our study focuses not only on the utility of this method for forward genetics, but also its potential as a reverse genetics tool through accumulation of hybridization data for a collection of deletion mutants harboring multiple genetic lesions.

RESULTS

We demonstrate that hybridization of labeled genomic DNA directly onto the Affymetrix Rice GeneChip allows rapid localization of deleted regions in rice mutants. Deletions ranged in size from one gene model to approximately 500 kb and were predicted on all 12 rice chromosomes. The utility of the technique as a tool in forward genetics was demonstrated in combination with an allelic series of mutants to rapidly narrow the genomic region, and eventually identify a candidate gene responsible for a lesion mimic phenotype. Finally, the positions of mutations in 14 mutants were aligned onto the rice pseudomolecules in a user-friendly genome browser to allow for rapid identification of untagged mutations http://irfgc.irri.org/cgi-bin/gbrowse/IR64_deletion_mutants/.

CONCLUSION

We demonstrate the utility of oligonucleotide arrays to discover deleted genes in rice. The density and distribution of deletions suggests the feasibility of a database saturated with deletions across the rice genome. This community resource can continue to grow with further hybridizations, allowing researchers to quickly identify mutants that harbor deletions in candidate genomic regions, for example, regions containing QTL of interest.

A germin-like protein gene family functions as a complex quantitative trait locus conferring broad-spectrum disease resistance in rice

Plant disease resistance governed by quantitative trait loci (QTL) is predicted to be effective against a broad spectrum of pathogens and long lasting. Use of these QTL to improve crop species, however, is hindered because the genes contributing to the trait are not known. Five disease resistance QTL that colocalized with defense response genes were accumulated by marker-aided selection to develop blast-resistant varieties. One advanced backcross line carrying the major-effect QTL on chromosome (chr) 8, which included a cluster of 12 germin-like protein (OsGLP) gene members, exhibited resistance to rice (Oryza sativa) blast disease over 14 cropping seasons. To determine if OsGLP members contribute to resistance and if the resistance was broad spectrum, a highly conserved portion of the OsGLP coding region was used as an RNA interference trigger to silence a few to all expressed chr 8 OsGLP family members. Challenge with two different fungal pathogens (causal agents of rice blast and sheath blight diseases) revealed that as more chr 8 OsGLP genes were suppressed, disease susceptibility of the plants increased. Of the 12 chr 8 OsGLPs, one clustered subfamily (OsGER4) contributed most to resistance. The similarities of sequence, gene organization, and roles in disease resistance of GLP family members in rice and other cereals, including barley (Hordeum vulgare) and wheat (Triticum aestivum), suggest that resistance contributed by the chr 8 OsGLP is a broad-spectrum, basal mechanism conserved among the Gramineae. Natural selection may have preserved a whole gene family to provide a stepwise, flexible defense response to pathogen invasion.

Agreement between initial and final diagnosis of first seizures, epilepsy and non-epileptic events: a prospective study

BACKGROUND

Differentiating between first seizure, epilepsy and a non-epileptic event is a challenging clinical exercise for many physicians as it may lead to different therapeutic implications. This study aims to investigate the agreement between the initial diagnosis at the accident and emergency (A&E) department and the final diagnosis following inpatient neurological evaluation of seizure disorders.

METHOD

A prospective observational study between April 2004 and June 2005 in a regional hospital in Hong Kong recruited 1701 patients from the A&E to neurology/medical wards with initial diagnoses/labels matching any one of 12 predefined keywords which were categorised as either "seizure specific" or "non-specific".

RESULTS

Among the 1170 patients with "non-specific" initial diagnoses/labels, 58 (5%) were finally diagnosed as having had a first seizure or epilepsy. Among 531 patients with "seizure specific" initial diagnoses/labels, 27 (5.1%) were subsequently diagnosed as having had non-epileptic events. The kappa value for agreement between the initial and final diagnosis was 0.88. Of the 154 patients with a final diagnosis of first seizure, 34 (22%) had "non-specific" initial labels. Among these patients, components of the evaluation contributing to revision of diagnosis included retrieval of witness accounts (47%), epileptiform discharges on EEG (47%), short term monitoring in patients suspected of acute symptomatic seizures (28%) and panel discussion of cases (22%).

CONCLUSION

There was generally a high degree of agreement between the initial and final diagnosis, but first seizures were often missed initially. Careful history taking, judicious use of EEG, selective short term monitoring and liaison with specialists are important in reaching an accurate diagnosis.

SPIN1, a K homology domain protein negatively regulated and ubiquitinated by the E3 ubiquitin ligase SPL11, is involved in flowering time control in rice

The rice (Oryza sativa) E3 ligase SPOTTED LEAF11 (SPL11) negatively regulates programmed cell death and disease resistance. We demonstrate here that SPL11 also regulates flowering via interaction with SPIN1 (for SPL11-interacting protein1), a Signal Transduction and Activation of RNA family member. SPIN1 binds RNA and DNA in vitro and interacts with SPL11 in the nucleus. Spl11 mutants have delayed flowering under long-day conditions. Spin1 overexpression causes late flowering independently of daylength; expression analyses of flowering marker genes in these lines suggested that SPIN1 represses flowering by downregulating the flowering promoter gene Heading date3a (Hd3a) via Hd1-dependent mechanisms in short days and by targeting Hd1-independent factors in long days. Both Spin1 and Spl11 are regulated diurnally in opposing phases. SPL11 negatively regulates Spin1 transcript levels, while SPIN1 also affects Spl11 expression. Moreover, we show that coincidence of high accumulation of Spin1 mRNA with the light in the morning and early evening is needed to repress flowering. SPIN1 is monoubiquitinated by SPL11, suggesting that it is not targeted for degradation. Our data are consistent with a model in which SPIN1 acts as a negative regulator of flowering that itself is negatively regulated by SPL11, possibly via ubiquitination.

Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in rice

BACKGROUND

We report the development of a microarray platform for rapid and cost-effective genetic mapping, and its evaluation using rice as a model. In contrast to methods employing whole-genome tiling microarrays for genotyping, our method is based on low-cost spotted microarray production, focusing only on known polymorphic features.

RESULTS

We have produced a genotyping microarray for rice, comprising 880 single feature polymorphism (SFP) elements derived from insertions/deletions identified by aligning genomic sequences of the japonica cultivar Nipponbare and the indica cultivar 93-11. The SFPs were experimentally verified by hybridization with labeled genomic DNA prepared from the two cultivars. Using the genotyping microarrays, we found high levels of polymorphism across diverse rice accessions, and were able to classify all five subpopulations of rice with high bootstrap support. The microarrays were used for mapping of a gene conferring resistance to Magnaporthe grisea, the causative organism of rice blast disease, by quantitative genotyping of samples from a recombinant inbred line population pooled by phenotype.

CONCLUSION

We anticipate this microarray-based genotyping platform, based on its low cost-per-sample, to be particularly useful in applications requiring whole-genome molecular marker coverage across large numbers of individuals.

Categories and inheritance of resistance to Nilaparvata lugens (Hemiptera: Delphacidae) in mutants of indica rice 'IR64'

Varietal mutants can be useful for developing durable resistance, understanding categories of resistance, and identifying candidate genes involved in defense responses. We used mutants of rice 'IR64' to isolate new sources of resistance to the planthopper Nilaparvata lugens (Stål) (Hemiptera: Delphacidae). We compared two mutants that showed a gain and loss of resistance to N. lugens, to determine the categories of resistance to this pest. Under choice tests, female planthoppers avoided settling and laid fewer eggs on the resistant mutant 'D518' than on the susceptible mutant D1131, susceptible check 'TN1', and wild-type IR64, indicating that antixenosis was the resistance category. Similarly, under no-choice conditions, planthoppers laid 29% fewer eggs in D518 than in IR64, but they oviposited more in 'D1131' and TN1. Honeydew excretion was greater on D1131 seedlings but slightly lower on D518 than on IR64. Nymphal survival and adult female weight did not differ among rice cultivars. D518 showed higher tolerance of N. lugens infestations than IR64. Genetic analysis of the F1, F2, and F3 populations derived from D518 x IR64 revealed that resistance in D518 is dominant and controlled by a single gene. Despite the variation in resistance to N. lugens, both mutants and IR64 performed similarly in the field. The mutant D518 is a new source of durable resistance to N. lugens, mainly due to enhanced antixenosis to female hoppers for settling and oviposition.

Stressed genomics-bringing relief to rice fields

Active research in rice genetics aided by full-genome sequence has generated results to address multiple problems caused by biotic and abiotic stresses. The main challenges are achieving stability of resistance against variable biological agents and defining the genetic basis of traits influenced strongly by genotypexenvironment interactions. As shown in bacterial blight disease, detailed knowledge of host-pathogen interactions has enabled a predictive strategy to combine specific genes to provide durable resistance. Large-effect QTLs conferring tolerance to submergence, salinity, and drought have been identified. Marker-aided incorporation of the submergence tolerance gene into popular rice varieties illustrates how gene discovery can be rapidly converted into useful products. Extensive use of parallel whole-genome expression and mapping analyses is expected to improve our understanding of QTL. To accelerate conversion of discoveries into products, much can be gained by using agronomically proven genotypes and by testing in multiple environments.

Finding the missing link between ictal bradyarrhythmia, ictal asystole, and sudden unexpected death in epilepsy

Basic science studies of the human brain have supported the cortical representation of cardiovascular responses, including heart rate variability. Clinical observations of ictal bradyarrhythmia may be mechanistically explained by the influence of the central autonomic network, although the localization and lateralization issues need to be considered in the light of patterns of seizure spread, hand dominance, and presence of lesions. Ictal bradyarrhythmia also offers a mechanistic explanation of sudden unexpected death in epilepsy (SUDEP), though it may explain only some but not all cases of SUDEP. The missing links are (1) clinical evidence of common factors shared by patients with ictal bradyarrhythmia and patients who die from SUDEP, (2) evidence of arrhythmia as a risk factor for SUDEP from epidemiological studies, and, (3) determination of the importance of ictal bradyarrhythmia in SUDEP with respect to other proposed mechanisms including apnea and intrinsic cardiac abnormalities. There remains a need to review the seizure mechanisms in cases of SUDEP and to step up the amount of concurrent ECG/intracranial EEG analysis in both ictal bradyarrhythmia and SUDEP cases.