The genomic and evolutionary landscapes of anaplastic thyroid carcinoma

Anaplastic thyroid carcinoma is arguably the most lethal human malignancy. It often co-occurs with differentiated thyroid cancers, yet the molecular origins of its aggressivity are unknown. We sequenced tumor DNA from 329 regions of thyroid cancer, including 213 from patients with primary anaplastic thyroid carcinomas. We also whole genome sequenced 9 patients using multi-region sequencing of both differentiated and anaplastic thyroid cancer components. Using these data, we demonstrate thatanaplastic thyroid carcinomas have a higher burden of mutations than other thyroid cancers, with distinct mutational signatures and molecular subtypes. Further, different cancer driver genes are mutated in anaplastic and differentiated thyroid carcinomas, even those arising in a single patient. Finally, we unambiguously demonstrate that anaplastic thyroid carcinomas share a genomic origin with co-occurring differentiated carcinomas and emerge from a common malignant field through acquisition of characteristic clonal driver mutations.

Abstract 3071: A reconstruction of evolutionary trajectories in primary tissue and PDTOs in a patient with metastatic osteosarcoma

Metastatic osteosarcoma is a rare and highly lethal cancer that affects children and young adults. The rarity of osteosarcoma and its highly heterogeneous genetic composition have resulted in a lack of curative treatments for recurrent and metastatic disease.

In this study, we present the functional and molecular characterization of a case of a pediatric patient with left distal femur osteosarcoma and pulmonary metastases at presentation. Through longitudinal sampling over the course of the patient’s illness, we have procured tissue from the initial treatment-naïve diagnostic biopsy, primary tumor resection and multiple subsequent lung metastasectomies, and have developed patient-derived tumor organoids (PDTOs) from the viable samples. PDTOs are useful pre-clinical models that are representative of the source tissue and allow further interrogations of the biology of tumors. These models can also help with the identification of effective personalized therapies (Al Shihabi et al, 2021). We applied our mini-ring organoid screening technology (Phan et al, 2019; Nguyen et al, 2020) to perform high-throughput drug screening with different pharmacologic agents. We also performed deep whole-genome sequencing on all collected samples and corresponding organoids to reconstruct their evolutionary history, identify driver mutations and quantify heterogeneity in mutational processes across time and space.

Our preliminary data show that the subclonal content of the tumor and derivative organoids as well as the PDTO drug responses vary with the patient’s treatment history. We identify the genomic makeup of the subclones and posit changes that may be responsible for chemoresistance. Furthermore, our data shows correlations between the subclonal genomic composition of the PDTOs and source tissue, thereby reinforcing that PDTOs are capable of accurately recapitulating the subclonal heterogeneity of the parental tumor.

Citation Format: Ardy Davarifar, Jane Yanagawa, Ahmad Al Shihabi, Huyen T. Nguyen, Lydia Y. Liu, Adriana Salcedo, Alfredo Gonzalez, Takafumi N. Yamaguchi, Nicholas Bernthal, Scott D. Nelson, Noah Federman, Paul C. Boutros, Alice Soragni. A reconstruction of evolutionary trajectories in primary tissue and PDTOs in a patient with metastatic osteosarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3071.

The relative role of plasticity and demographic history in Capsella bursa-pastoris: a common garden experiment in Asia and Europe

The colonization success of a species depends on the interplay between its phenotypic plasticity, adaptive potential and demographic history. Assessing their relative contributions during the different phases of a species range expansion is challenging, and requires large-scale experiments. Here, we investigated the relative contributions of plasticity, performance and demographic history to the worldwide expansion of the shepherd's purse, Capsella bursa-pastoris. We installed two large common gardens of the shepherd's purse, a young, self-fertilizing, allopolyploid weed with a worldwide distribution. One common garden was located in Europe, the other in Asia. We used accessions from three distinct genetic clusters (Middle East, Europe and Asia) that reflect the demographic history of the species. Several life-history traits were measured. To explain the phenotypic variation between and within genetic clusters, we analysed the effects of (i) the genetic clusters, (ii) the phenotypic plasticity and its association to fitness and (iii) the distance in terms of bioclimatic variables between the sampling site of an accession and the common garden, i.e. the environmental distance. Our experiment showed that (i) the performance of C. bursa-pastoris is closely related to its high phenotypic plasticity; (ii) within a common garden, genetic cluster was a main determinant of phenotypic differences; and (iii) at the scale of the experiment, the effect of environmental distance to the common garden could not be distinguished from that of genetic clusters. Phenotypic plasticity and demographic history both play important role at different stages of range expansion. The success of the worldwide expansion of C. bursa-pastoris was undoubtedly influenced by its strong phenotypic plasticity.

Transcriptional perturbation of protein arginine methyltransferase-5 exhibits MTAP-selective oncosuppression

We hypothesized that small molecule transcriptional perturbation could be harnessed to target a cellular dependency involving protein arginine methyltransferase 5 (PRMT5) in the context of methylthioadenosine phosphorylase (MTAP) deletion, seen frequently in malignant pleural mesothelioma (MPM). Here we show, that MTAP deletion is negatively prognostic in MPM. In vitro, the off-patent antibiotic Quinacrine efficiently suppressed PRMT5 transcription, causing chromatin remodelling with reduced global histone H4 symmetrical demethylation. Quinacrine phenocopied PRMT5 RNA interference and small molecule PRMT5 inhibition, reducing clonogenicity in an MTAP-dependent manner. This activity required a functional PRMT5 methyltransferase as MTAP negative cells were rescued by exogenous wild type PRMT5, but not a PRMT5E444Q methyltransferase-dead mutant. We identified c-jun as an essential PRMT5 transcription factor and a probable target for Quinacrine. Our results therefore suggest that small molecule-based transcriptional perturbation of PRMT5 can leverage a mutation-selective vulnerability, that is therapeutically tractable, and has relevance to 9p21 deleted cancers including MPM.

Reimagining physiology education with interactive content developed in H5P

The amalgamation of educational technologies in higher education is widespread and has become essential for contemporary practice on a large scale. Foundational anatomy and physiology knowledge is integral to all courses in health education. To tackle the volume and complexity of the content taught at the foundation level, the incorporation of online tools embedded within curricula provides a unique opportunity to engage students through active learning strategies in a blended design (Means B, Toyama Y, Murphy R, Baki M. Teach Coll Rec 115: 1-47, 2013). This article reports on the use of H5P as a platform to foster self-paced and self-directed learning, critically outlining the developmental process involved in scaffolding activities to learning outcomes. The H5P activities were embedded within the online learning management system, which enabled tracking of student access to these resources. Students were asked to complete an online survey about their perspectives on the effectiveness of H5P activities. This work is part of a comprehensive study evaluating the blended design for delivery of first-year physiology subjects.

A practical guide to cancer subclonal reconstruction from DNA sequencing

Subclonal reconstruction from bulk tumor DNA sequencing has become a pillar of cancer evolution studies, providing insight into the clonality and relative ordering of mutations and mutational processes. We provide an outline of the complex computational approaches used for subclonal reconstruction from single and multiple tumor samples. We identify the underlying assumptions and uncertainties in each step and suggest best practices for analysis and quality assessment. This guide provides a pragmatic resource for the growing user community of subclonal reconstruction methods.

Precision Radiotherapy: Reduction in Radiation for Oropharyngeal Cancer in the 30 ROC Trial

BACKGROUND

Patients with human papillomavirus-related oropharyngeal cancers have excellent outcomes but experience clinically significant toxicities when treated with standard chemoradiotherapy (70 Gy). We hypothesized that functional imaging could identify patients who could be safely deescalated to 30 Gy of radiotherapy.

METHODS

In 19 patients, pre- and intratreatment dynamic fluorine-18-labeled fluoromisonidazole positron emission tomography (PET) was used to assess tumor hypoxia. Patients without hypoxia at baseline or intratreatment received 30 Gy; patients with persistent hypoxia received 70 Gy. Neck dissection was performed at 4 months in deescalated patients to assess pathologic response. Magnetic resonance imaging (weekly), circulating plasma cell-free DNA, RNA-sequencing, and whole-genome sequencing (WGS) were performed to identify potential molecular determinants of response. Samples from an independent prospective study were obtained to reproduce molecular findings. All statistical tests were 2-sided.

RESULTS

Fifteen of 19 patients had no hypoxia on baseline PET or resolution on intratreatment PET and were deescalated to 30 Gy. Of these 15 patients, 11 had a pathologic complete response. Two-year locoregional control and overall survival were 94.4% (95% confidence interval = 84.4% to 100%) and 94.7% (95% confidence interval = 85.2% to 100%), respectively. No acute grade 3 radiation-related toxicities were observed. Microenvironmental features on serial imaging correlated better with pathologic response than tumor burden metrics or circulating plasma cell-free DNA. A WGS-based DNA repair defect was associated with response (P = .02) and was reproduced in an independent cohort (P = .03).

CONCLUSIONS

Deescalation of radiotherapy to 30 Gy on the basis of intratreatment hypoxia imaging was feasible, safe, and associated with minimal toxicity. A DNA repair defect identified by WGS was predictive of response. Intratherapy personalization of chemoradiotherapy may facilitate marked deescalation of radiotherapy.

Quantifying the influence of mutation detection on tumour subclonal reconstruction

Whole-genome sequencing can be used to estimate subclonal populations in tumours and this intra-tumoural heterogeneity is linked to clinical outcomes. Many algorithms have been developed for subclonal reconstruction, but their variabilities and consistencies are largely unknown. We evaluate sixteen pipelines for reconstructing the evolutionary histories of 293 localized prostate cancers from single samples, and eighteen pipelines for the reconstruction of 10 tumours with multi-region sampling. We show that predictions of subclonal architecture and timing of somatic mutations vary extensively across pipelines. Pipelines show consistent types of biases, with those incorporating SomaticSniper and Battenberg preferentially predicting homogenous cancer cell populations and those using MuTect tending to predict multiple populations of cancer cells. Subclonal reconstructions using multi-region sampling confirm that single-sample reconstructions systematically underestimate intra-tumoural heterogeneity, predicting on average fewer than half of the cancer cell populations identified by multi-region sequencing. Overall, these biases suggest caution in interpreting specific architectures and subclonal variants.

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.

A community effort to create standards for evaluating tumor subclonal reconstruction

Tumor DNA sequencing data can be interpreted by computational methods that analyze genomic heterogeneity to infer evolutionary dynamics. A growing number of studies have used these approaches to link cancer evolution with clinical progression and response to therapy. Although the inference of tumor phylogenies is rapidly becoming standard practice in cancer genome analyses, standards for evaluating them are lacking. To address this need, we systematically assess methods for reconstructing tumor subclonality. First, we elucidate the main algorithmic problems in subclonal reconstruction and develop quantitative metrics for evaluating them. Then we simulate realistic tumor genomes that harbor all known clonal and subclonal mutation types and processes. Finally, we benchmark 580 tumor reconstructions, varying tumor read depth, tumor type and somatic variant detection. Our analysis provides a baseline for the establishment of gold-standard methods to analyze tumor heterogeneity.

Abstract 3771: Oncogenes and tumour-suppressors drive differential retinoblastoma evolution

Unlike any other tumour type, retinoblastomas can be driven by only two tumour-initiating events: bi-allelic loss of the tumour suppressor RB1 or amplification of the MYCN oncogene. These mutations drive morphologically indistinguishable tumours that arise at different ages, providing a unique model system to evaluate the influence of initiating mutation on tumour evolution. We performed high-resolution copy number analysis of 101 retinoblastoma and whole genome sequencing of 23. These data reveal that different initiating mutations cause probabilistic changes in somatic point and copy number mutations, but large changes in genomic rearrangements and mitochondrial number. Independent of the initiating mutation, retinoblastomas harbour multiple subclonal populations that preferentially accrue point mutations after subclonal diversification. These subclonal structures suggest caution when choosing chemotherapeutic strategies for primary treatment. Overall, initiating mutations influence evolutionary trajectory more than specific driver mutations: RB1- and MYCN-driven tumours harbour distinct mutational processes, sequences of mutation acquisition and patterns of subclonal diversification. These data show how tumour-initiating mutations drive clinical behaviour by subtly biasing multiple evolutionary processes. Validation in other tumour types is underway.

Citation Format: Adriana Salcedo, John D. Watson, Hilary Racher, Diane Rushlow, Shadrielle Melijah G. Espiritu, Doroto H. Sendorek, Stephenie D. Prokopec, Donco Matveski, Fouad Yousif, Julie Livingstone, Brenda L. Gallie, Paul C. Boutros. Oncogenes and tumour-suppressors drive differential retinoblastoma evolution [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3771.

The impact of intratumoral heterogeneity on prognostic biomarkers in localized prostate cancer

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Background: Genomic biomarkers can identify patients that harbour aggressive disease. The utility of these biomarkers is uncertain due to genomic variation between prostate biopsy specimens. To quantify the robustness of genomic biomarkers, we performed spatio-genomic characterization of distinct tumor foci. We scored three validated DNA-based biomarkers of early biochemical recurrence: percentage of genome with a copy number aberration (PGA), a 100-loci biomarker, and an optimized 31- loci biomarker derived from the previous. For each biomarker, we determined their robustness to intratumoral heterogeneity in association with predicting early biochemical recurrence (eBCR; ≤18 months) and long term control (LTC; ≥48 months). Methods: We queried a registry of 1054 patients with high-risk prostate cancer who underwent a radical prostatectomy (RP). We developed a cohort (n = 42) risk matched by clinicopathologic prognostic indices. Half of the patients had eBCR, while the other half had LTC. We profiled multiple tumor foci per patient, analyzing 119 tumor foci. For each focus, CNA profiles were generated, and three biomarker scores were calculated. For each patient and biomarker, we calculated the score of the lowest-score region, the highest-score region, or sampling of all foci and use the mean score. Results: All three biomarkers distinguished LTC from eBCR. PGA scores separated the two groups with an area under the receiver operator curves (AUC) ranging from 0.75-0.80. The 100- and 31-loci signatures, had AUCs ranging from 0.76-0.85 and 0.76-0.80 respectively. Using Cox proportional hazards modeling, we found that PGA was associated with LTC (Hazard ratio (HR) range: 2.56-6.22; p < 0.05. This was replicated for the 100-loci signature (HR range: 3.55-5.23; p < 0.05). The 31-loci detected associations with eBCR independent of how different foci were summarized (log-rank p-value range: 5.1 x 10-4- 5.9 x 10-3). Conclusions: Despite divergence in biomarker scores, all three predicted eBCR. Our study suggests that genomic biomarkers can overcome intratumoral heterogeneity, making discrete samples potentially adequate in patients with high-risk disease to determine the risk of eBCR after radical treatment.

Parental legacy, demography, and admixture influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae)

Allopolyploidy is generally perceived as a major source of evolutionary novelties and as an instantaneous way to create isolation barriers. However, we do not have a clear understanding of how two subgenomes evolve and interact once they have fused in an allopolyploid species nor how isolated they are from their relatives. Here, we address these questions by analyzing genomic and transcriptomic data of allotetraploid Capsella bursa-pastoris in three differentiated populations, Asia, Europe, and the Middle East. We phased the two subgenomes, one descended from the outcrossing and highly diverse Capsella grandiflora (CbpCg) and the other one from the selfing and genetically depauperate Capsella orientalis (CbpCo). For each subgenome, we assessed its relationship with the diploid relatives, temporal changes of effective population size (Ne), signatures of positive and negative selection, and gene expression patterns. In all three regions, Ne of the two subgenomes decreased gradually over time and the CbpCo subgenome accumulated more deleterious changes than CbpCg. There were signs of widespread admixture between C. bursa-pastoris and its diploid relatives. The two subgenomes were impacted differentially depending on geographic region suggesting either strong interploidy gene flow or multiple origins of C. bursa-pastoris. Selective sweeps were more common on the CbpCg subgenome in Europe and the Middle East, and on the CbpCo subgenome in Asia. In contrast, differences in expression were limited with the CbpCg subgenome slightly more expressed than CbpCo in Europe and the Middle-East. In summary, after more than 100,000 generations of co-existence, the two subgenomes of C. bursa-pastoris still retained a strong signature of parental legacy but their evolutionary trajectory strongly varied across geographic regions.

A biopsy-based genomic classifier to predict biochemical failure after definitive radiation without hormone therapy in a prospective cohort of intermediate risk prostate cancer

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Background: Recently, NCCN adopted the Zumsteg-Spratt subclassification to define NCCN favorable and unfavorable intermediate-risk prostate cancer (IR-PCa). NCCN unfavorable disease is recommended to receive combination androgen deprivation therapy (ADT) and radiotherapy. To determine if genomics could help identify a subset who may safely avoid ADT, we evaluated the Decipher genomic classifier (GC) in IR-PCa treated with dose-escalated image-guided radiotherapy (DE-IGRT) alone. Methods: Our cohort comprised of 121 patients with NCCN favorable (N = 49, 40%) and unfavorable (N = 74, 60%) IR-PCa, who received 78 Gy without ADT. Diagnostic needle biopsies with the highest Gleason score (GS) and %tumor involvement were macrodissected for RNA extraction. GC scores were determined from the Decipher prostate cancer classifier assay (GenomeDx Biosciences, San Diego, CA). Primary clinical endpoint was biochemical relapse ([BCR], PSA nadir + 2ng/ml) post-DE-IGRT. We compared association with BCR against known clinicopathologic prognostic indices and the NCCN risk strata. Results: With a median follow up of 7.5y, 24 (19%) patients experienced BCR. Individual clinical indices did not predict BCR-free survival rate (BFS). NCCN risk strata was however associated with a small but significant difference in BFS (5-y 93%, favorable vs 88%, unfavourable, P = 0.046). GC scores stratified 85 (70%), 19 (16%), and 17 (14%) men into low, intermediate, and high risk of recurrence; 5-y BFS were 95%, 89%, and 59%, respectively (P < 0.001). On multivariable analysis, a hazard ratio of 4.71 (95% CI 1.81-12.28, P = 0.0015) for BCR was observed for the GC high risk group compared to low/intermediate; NCCN risk strata and intraductal variant did not achieve significance. Conclusions: In IR-PCa men treated with DE-IGRT monotherapy, Decipher GC was an independent predictor of BCR. While most men in this our cohort were stratified as NCCN unfavorable IR-PCa, the majority were GC low risk with excellent outcomes from DE-IGRT alone. In contrast, a minority with GC high risk had suboptimal outcomes, and may benefit from ADT intensification.

Abstract 5860: Genomic architecture of prostate cancer at recurrence following radiotherapy

Aim: Spatial intra-tumoural heterogeneity of prostate cancer is secondary to differential genomics and multi-clonality, even for tumours with the same Gleason grade. These unique features promote resistance to treatment. Here, we investigated if clonal selection or adaptation of new clones dominates in prostate cancer at the time of recurrence following high dose precision radiotherapy.

Methods: We identified 11 patients with biopsy-proven multi-focal recurrent prostate cancer following definitive image-guided radiotherapy/brachytherapy. Copy number aberration (CNA) profiling was performed on 33 anatomically distinct tumour foci with 11 matched-normals in the radio-resistant cohort. To assess clonality, 4 cases had matched pre-radiotherapy tumours for copy number profiling. We evaluated for recurrent driver amplifications and deletions, and genomic instability as measured by percent genome aberration (PGA). We also compared these genomic indices against 373 comprehensively profiled sporadic prostate cancers from the Canadian Prostate Cancer Gene Network [Fraser, et al., Nature, 2016].

Results: Independent of Gleason grade, we observed large intra-patient (COV of 0.66-1.13) and inter-patient heterogeneity (p &lt;0.001, one-way ANOVA) in the levels of genomic instability, as judged by PGA scores, among the radioresistant tumours. Interestingly, although total CNA counts did not differ between the radioresistant and sporadic (CPC-GENE) cohorts (median CNAs of 40, radioresistant vs 33, sporadic, p = 0.20], we observed a trend for increased genomic instability in the radioresistant cohort (median PGA of 8.8 vs 4.9, p = 0.059). This concurs with the findings on intra-tumoural spatial CNA analyses, which revealed the acquisition of CNAs that were both common and non-recurrent in the multi-focal radioresistant tumours, thus suggesting a common origin with subsequent divergent evolution. Importantly, we observed a mixture of CNAs, including known drivers of aggressive prostate cancer, namely NKX3-1, PTEN, TP53, CDKN1B, and CDH1, that was shared between pre-radiotherapy and radioresistant tumours, supporting a clonal selection process. We also discovered a novel deleted region on Chr3p, consisting of RAD18 and FANCD2, which was unique only in the radioresistant tumours.

Conclusions: Our novel observations in a small cohort of radioresistant prostate cancers favour the model of selection of radioresistant clones, as opposed to new-onset tumours. These results support the current approach of discovering biomarkers a priori, and molecular therapeutic targets for these radioresistant clones, so as to improve the therapeutic ratio of precision radiotherapy.

Citation Format: Melvin L.K. Chua, Erle Holgersen, Veronica Sabelnykova, Adriana Salcedo, Alice Meng, Michael Fraser, Theodorus van der Kwast, Paul C. Boutros, Robert G. Bristow. Genomic architecture of prostate cancer at recurrence following radiotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5860. doi:10.1158/1538-7445.AM2017-5860

Genomic architecture of radioresistant prostate cancer

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Background: Spatial intra-tumoral heterogeneity of prostate cancer is secondary to genomic diversity and multi-clonality. These unique features potentially promote resistance to treatment. Here, we investigated if clonal selection or adaptation of new clones dominates in prostate cancer at the time of recurrence following radiotherapy. Methods: We identified 11 patients with biopsy-proven multifocal recurrent prostate cancer following radiotherapy. Copy number aberration (CNA) profiling was performed on 33 anatomically distinct tumor foci with 11 matched-normals. 4 cases had matched pre-radiotherapy tumors for CNA profiling to assess for clonality. We evaluated for recurrent gene amplifications and deletions, and determined genomic instability by percent genome aberration (PGA). We also compared these genomic indices against 373 sporadic prostate cancers from the Canadian Prostate Cancer Gene Network. Results: We observed large intra- and inter-patient variation (p <0.001, one-way ANOVA) in PGA scores among the radioresistant tumors. Interestingly, although total CNA counts did not differ between the radioresistant and sporadic cohorts (median = 40, radioresistant vs 33, sporadic, p = 0.20], there was a trend for increased genomic instability in the radioresistant cohort (median PGA = 8.8 vs 4.9, p = 0.059). Spatial resolution of gene-level CNAs revealed the acquisition of CNAs that were both common and non-recurrent in the multi-focal radioresistant tumors, thus suggesting a common clonal origin, with subsequent divergent evolution. Importantly, we observed a mixture of CNAs, including known prognostic genes in prostate cancer, namely NKX3-1, PTEN, TP53, CDKN1B, and CDH1,that was shared between pre-treatment and radioresistant tumors, favoring clonal selection. We also discovered a novel deleted region on Chr3p, consisting of RAD18 and FANCD2, which was uniquely present in the radioresistant tumors. Conclusions: Our novel observations in a small cohort of radioresistant prostate cancers favor the model of clonal selection, as opposed to new-onset tumors. These results support the discovery of biomarkers a priori, and targeted treatment of these radioresistant clones to improve the therapeutic ratio of precision radiotherapy.

Genomic signature of successful colonization of Eurasia by the allopolyploid shepherd's purse (Capsella bursa-pastoris)

Polyploidization is a dominant feature of flowering plant evolution. However, detailed genomic analyses of the interpopulation diversification of polyploids following genome duplication are still in their infancy, mainly because of methodological limits, both in terms of sequencing and computational analyses. The shepherd's purse (Capsella bursa-pastoris) is one of the most common weed species in the world. It is highly self-fertilizing, and recent genomic data indicate that it is an allopolyploid, resulting from hybridization between the ancestors of the diploid species Capsella grandiflora and Capsella orientalis. Here, we investigated the genomic diversity of C. bursa-pastoris, its population structure and demographic history, following allopolyploidization in Eurasia. To that end, we genotyped 261 C. bursa-pastoris accessions spread across Europe, the Middle East and Asia, using genotyping-by-sequencing, leading to a total of 4274 SNPs after quality control. Bayesian clustering analyses revealed three distinct genetic clusters in Eurasia: one cluster grouping samples from Western Europe and Southeastern Siberia, the second one centred on Eastern Asia and the third one in the Middle East. Approximate Bayesian computation (ABC) supported the hypothesis that C. bursa-pastoris underwent a typical colonization history involving low gene flow among colonizing populations, likely starting from the Middle East towards Europe and followed by successive human-mediated expansions into Eastern Asia. Altogether, these findings bring new insights into the recent multistage colonization history of the allotetraploid C. bursa-pastoris and highlight ABC and genotyping-by-sequencing data as promising but still challenging tools to infer demographic histories of selfing allopolyploids.

Limited genomic consequences of mixed mating in the recently derived sister species pair, Collinsia concolor and Collinsia parryi

Highly selfing species often show reduced effective population sizes and reduced selection efficacy. Whether mixed mating species, which produce both self and outcross progeny, show similar patterns of diversity and selection remains less clear. Examination of patterns of molecular evolution and levels of diversity in species with mixed mating systems can be particularly useful for investigating the relative importance of linked selection and demographic effects on diversity and the efficacy of selection, as the effects of linked selection should be minimal in mixed mating populations, although severe bottlenecks tied to founder events could still be frequent. To begin to address this gap, we assembled and analysed the transcriptomes of individuals from a recently diverged mixed mating sister species pair in the self-compatible genus, Collinsia. The de novo assembly of 52 and 37 Mbp C. concolor and C. parryi transcriptomes resulted in ~40 000 and ~55 000 contigs, respectively, both with an average contig size ~945. We observed a high ratio of shared polymorphisms to fixed differences in the species pair and minimal differences between species in the ratio of synonymous to replacement substitutions or codon usage bias implying comparable effective population sizes throughout species divergence. Our results suggest that differences in effective population size and selection efficacy in mixed mating taxa shortly after their divergence may be minimal and are likely influenced by fluctuating mating systems and population sizes.

Antimicrobial therapy for pulmonary pathogenic colonisation and infection by Pseudomonas aeruginosa in cystic fibrosis patients

Pseudomonas aeruginosa colonisation has a negative effect on pulmonary function in cystic fibrosis patients. The organism can only be eradicated in the early stage of colonisation, while reduction of bacterial density is desirable during chronic colonisation or exacerbations. Monthly, or at least 3-monthly, microbiological culture is advisable for patients without previous evidence of P. aeruginosa colonisation. Cultures should be performed at least every 2-3 months in patients with well-established colonisation, and always during exacerbations or hospitalisations. Treatment of patients following the first isolation of P. aeruginosa, but with no clinical signs of colonisation, should be with oral ciprofloxacin (15-20 mg/kg twice-daily for 3-4 weeks) plus inhaled tobramycin or colistin (intravenous treatment with or without inhaled treatment can be used as an alternative), while patients with acute infection should be treated for 14-21 days with high doses of two intravenous antimicrobial agents, with or without an inhaled treatment during or at the end of the intravenous treatment. Maintenance treatment after development of chronic P. aeruginosa infection/colonisation (pathogenic colonisation) in stable patients (aged>6 years) should be with inhaled tobramycin (300 mg twice-daily) in 28-day cycles (on-off) or, as an alternative, colistin (1-3 million units twice-daily). Colistin is also a possible choice for patients aged<6 years. Treatment can be completed with oral ciprofloxacin (3-4 weeks every 3-4 months) for patients with mild pulmonary symptoms, or intravenously (every 3-4 months) for those with severe symptoms or isolates with ciprofloxacin resistance. Moderate and serious exacerbations can be treated with intravenous ceftazidime (50-70 mg/kg three-times-daily) or cefepime (50 mg/kg three-times-daily) plus tobramycin (5-10 mg/kg every 24 h) or amikacin (20-30 mg/kg every 24 h) for 2-3 weeks. Oral ciprofloxacin is recommended for patients with mild pulmonary disease. If multiresistant P. aeruginosa is isolated, antimicrobial agents that retain activity are recommended and epidemiological control measures should be established.

Prevalence and risk of cysticercosis and taeniasis in an urban population of soldiers and their relatives

To determine markers of Taenia solium transmission and risk factors in an urban community, we studied 1,000 soldiers from a military camp in Mexico City and their relatives. Serum samples were used to detect antigens and antibodies and fecal specimens were examined for Taenia coproantigens and helminth eggs. Prevalences of 12.2% and 5.8% for cysticercosis were found among soldiers and their relatives, respectively. Taeniasis was found in 0.5% and none of the groups, respectively. Relatives of soldiers positive for cysticercosis and taeniasis markers ate more pork from street stores than restaurants or markets compared with relatives of soldiers without these indicators of infection. Also, 12.0% of the relatives of positive soldiers had a history of expelling tapeworm proglottids in the feces in contrast to 3.7% of the family members of the control group. Prevalence values and risk factors in this urban population are similar to those of previous studies performed in rural populations.

[Atherosclerotic coronary ectasia or a lymphomucocutaneous syndrome in an adult (Kawasaki's disease)?]

We report the case of a 42-year-old man, who was admitted to hospital with an inferior myocardial infarction. He was treated with tissue plasminogen activator without complications in the acute phase. The stress testing performed before discharge showed residual myocardial ischemia. A catheterization study was indicated. The coronary angiogram demonstrated diffuse three vessel coronary artery aneurysmal disease. Two years before the patient had an aneurysm of the right iliac artery being operated on. The differential diagnosis of adult aneurysmal coronary disease is discussed with emphasis on Kawasaki's disease and atherosclerotic coronary artery ectasia.

[Thrombus in the thoracic aorta as cause of peripheral embolism diagnosed using transesophageal echocardiography]

The authors report the cases of two patients, with no risk factors for thromboembolism, in whom a mobile thrombus of the thoracic aorta was diagnosed by transesophageal echocardiography, after an episode of systemic embolism. The outcomes of the two cases were very different. In one patient the thrombus was no longer present after anticoagulant treatment with no recurrent embolic event. The other patient had a new embolic event and the thrombus persisted while having anticoagulant therapy. This patient underwent surgery, and the thrombus was removed. These cases illustrate the value of transesophageal echocardiography in the detection of embolic source.

[Risk factors in stable coronary disease. Relationship with ischemic threshold and prognostic implications]

BACKGROUND

To assess the clinical evolution, in a 5-year follow-up, of the development of acute coronary syndromes, in patients with angina clinically stable, establishing its relationship with the ischemic threshold (IT) and the main modifiable cardiovascular risk factors.

PATIENTS AND METHODS

120 patients, 86 males (71%), with an age of 57 +/- 8 years, with stable angina. The presence of smoking, hypercholesterolemia, hypertension and diabetes mellitus was evaluated. We performed exercise testings (baseline and after vasodilator drugs) in the beginning, in order to characterize the IT (which was fixed in 72 patients and variable in 48). The later group underwent exercise testing each term during the first year of follow-up. Lesion at least of 70% in a main coronary vessel was required as inclusion criteria. The development of acute myocardial infarction (AMI), unstable angina pectoris and cardiac death was recorded. Cox's hazard function analysis and multivariant analysis were applied.

RESULTS

106 patients (88%) had one or more risk factors (40% hypertension, 43% hypercholesterolemia, 22% diabetes mellitus and 56% were smokers or ex-smokers). A significant association was shown between male gender and smoking and diabetes mellitus and female gender. 6 cardiac deaths, 8 AMI and 9 unstable angina were recorded. Within the 72 patients with fixed IT, 12.5% (9) suffered some acute syndrome. In the 48 with variable IT, in the 30 who continued in it, 20% (6) developed acute coronary pathology and in the 18 who modified their IT to fixed, the prevalence was 44.5% (8). Patients with modification of IT to fixed had a higher risk of acute coronary syndrome in the follow-up (p < 0.01) and the presence of hypertension and hypercholesterolemia allowed the prediction of modification of the IT.

CONCLUSIONS

The prevalence of cardiovascular risk factors in the stable coronary artery disease is high (88%); male gender is associated smoking and female gender to diabetes mellitus. The presence of hypertension and hypercholesterolemia are associated to modification in the IT in patients with variable threshold, allowing the detection of a subgroup of high risk for the development of acute coronary pathology.

Classification of hypertensive cardiomyopathy

A clinical pathophysiological classification of hypertensive cardiomyopathy has been established on the basis of the degree to which the heart is affected by chronic, systemic arterial hypertension: Degree I: Asymptomatic patients without left ventricular hypertrophy but with left ventricular diastolic dysfunction according to Doppler mitral inversion relation (E/A < 0.9) or to gamma scintigraphy (peak filling rate reduction < or = 2.7 EDC.s-1. These patients are classified as Group 1. Degree II: Asymptomatic or mildly symptomatic patients (New York Heart Association class I) with echocardiographic left ventricular hypertrophy; classified as Group IIA or IIB according to whether weight-adjusted maximal oxygen uptake is normal or below normal, respectively. Degree III: The basic characteristic is the presence of congestive heart failure with normal ejection fraction (EF > or = 50%). Two subsets can be distinguished on the basis of degree of hypertrophy: Group IIIA, with a mass/volume index > 1.8, and IIIB with a mass/volume index < 1.8. The differences between the two are as follows: patients classified as IIIA had a lower rate of regional ischaemia, a higher ejection fraction, a more frequently audible fourth sound, rarely a third sound and a cardiothoracic ratio < 0.5; IIIB patients had a higher prevalence of regional ischaemia (thallium-positive), a frequently audible third sound and a cardiothoracic ratio > 0.5. Degree IV: This category is characterized by the presence of depressed contractility, which could cause heart failure, by an ejection fraction < 50% and an increase in ventricular volumes. Echocardiography shows increased distance between mitral point E and the septum.

[The effect of antihypertensive therapy on left ventricular mass and diastolic filling in light and moderate hypertension]

BACKGROUND

To valorate the effect of four antihypertensive drugs on the regression of cardiac mass and diastolic function, by echocardiography-Doppler, in not treated hypertensive subjects.

METHODS

60 mild-moderate hypertensive subjects were studied randomized in four groups of 15 patients each one: enalapril (10-40 mg/d), atenolol (25-100 mg/d), verapamil-retard (120-240 mg/d), alphametildopa (250 mg/8h to 3 g/d). The active drug therapy phase was 6 months, performing echo-Doppler, evaluating posterior-wall and septal-wall thicknesses, ventricular mass index, ratio of early to atrial peak diastolic filling velocity (E/A), the first-third filling fraction and atrial filling fraction.

RESULTS

The cardiac mass index decreased with the four drugs: with enalapril from 178 +/- 28 to 155 +/- 29 g/m2 (p < 0.05), with atenolol from 170 +/- 23 to 154 +/- 19 g/m2 (p < 0.05), with verapamil from 180 +/- 27 to 159 +/- 22 g/m2 (p < 0.05) and with alphametildopa from 176 +/- 30 to 142 +/- 22 g/m2 (p < 0.01). The E/A ratio and first-third filling fraction only improved in the atenolol subgroup, from 0.79 +/- 0.13 to 0.97 +/- 0.16 (p < 0.01) and from 36 +/- 5 to 44 +/- 9% (p < 0.01), decreasing atrial filling fraction from 37 +/- 6 to 30 +/- 8% (p < 0.01), without modifying with enalapril (0.74 +/- 0.14 to 0.76 +/- 0.20, 35 +/- 5% to 36 +/- 7%, 38 +/- 5 to 39 +/- 7%, p = NS), verapamil (0.69 +/- 0.12 to 0.74 +/- 0.17, 35 +/- 6% to 36 +/- 8% to 40 +/- 12%, p = NS) neither alphametildopa (0.72 +/- 0.14 to 0.71 +/- 0.21, 34 +/- 5% to 35 +/- 7%, 40 +/- 6% to 41 +/- 9%, p = NS). The heart rate decreased more with atenolol than with the other drugs (61 +/- 15 vs 71 +/- 12, p < 0.01).

CONCLUSIONS

In hypertensive patients the decreasing of cardiac mass is not accompanied of improvement of the diastolic function except in patients treated with atenolol, probably due to bradycardia.

Usefulness of exercise testing performed with vasodilators for predicting the severity of myocardial ischaemia during daily activities and treatment

Fifty patients (aged 53 +/- 7 years) with confirmed coronary disease performed two stress tests (baseline and following treatment with vasodilators) and were divided into two groups: (A) fixed ischaemic threshold (n = 27), and (B) variable ischaemic threshold (n = 23). All patients underwent 24-h baseline Holter monitoring and monitoring following treatment with nifedipine, placebo, propranolol and nifedipine + propranolol. In Group A, 92% of ischaemic episodes occurred at heart rates similar to those found during exercise testing. In Group B, the heart rate was lower in 66%. In Group A, positive stress testing before the first 3 min of exercise, or at < 140 beat,min-1 with ST segment depressions > or = 0.02 mV, correlated with higher Holter indexes. In Group A, propranolol reduced both the number of episodes and total ischaemia time. In Group B, the best effects were achieved with nifedipine and combined treatment. Our results further emphasize the contrasts between patients with angina and fixed and variable ischaemic thresholds and suggest that therapy tailored to the physiopathology may be most efficacious.

Congestive heart failure from left ventricular diastolic dysfunction in systemic hypertension

Previous studies have pointed out that congestive heart failure (CHF) with normal ejection fraction presents a uniform clinical profile that is indistinguishable from heart failure with low ejection fraction. Thirty-six patients with systemic hypertension who had recently experienced CHF with normal ejection fraction (> or = 50%) and no clinical history of ischemic cardiomyopathy were studied. The patients were divided into 2 groups according to degree of echocardiographic hypertrophy: group A (19 patients) with a ventricular mass/volume ratio > 1.8, and group B (17 patients) with a ratio < 1.8. Group A patients had a higher ejection fraction (67 +/- 6 vs 57 +/- 3%, p < 0.01), smaller ventricular diameters and a lower thallium-201 positive rate at peak stress (10 vs 70% in group B, p < 0.001), with 8 of 10 showing severe coronary stenosis. Clinically, group A had a more frequent audible fourth sound (79 vs 17%, p < 0.001), a low incidence of audible third sound (5 vs 55%, p < 0.001) and a cardiothoracic ratio < or = 0.5 (63 vs 17%, p < 0.01). The degree of radionuclide-detected resting diastolic dysfunction and exercise intolerance was similar in both groups. In conclusion, CHF with normal ejection fraction in hypertensive patients presents 2 different profiles: one characterized by severe hypertrophy and the other by a high rate of myocardial regional ischemia. Therapy should be aimed at pathophysiologic regression of the hypertrophy in the first case, and at improvement of the ischemia in the second.