30 research outputs found
Next-generation sequencing of advanced prostate cancer treated with androgen-deprivation therapy
<b>Background:</b>
Androgen-deprivation therapy (ADT) is standard treatment for locally advanced or metastatic prostate cancer (PCa). Many patients develop castration resistance (castration-resistant PCa [CRPC]) after approximately 2â3 yr, with a poor prognosis. The molecular mechanisms underlying CRPC progression are unclear.<p></p>
<b>Objective:</b>
To undertake quantitative tumour transcriptome profiling prior to and following ADT to identify functionally important androgen-regulated pathways or genes that may be reactivated in CRPC.<p></p>
<b>Design, setting, and participants:</b>
RNA sequencing (RNA-seq) was performed on tumour-rich, targeted prostatic biopsies from seven patients with locally advanced or metastatic PCa before and approximately 22 wk after ADT initiation. Differentially regulated genes were identified in treatment pairs and further investigated by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) on cell lines and immunohistochemistry on a separate CRPC patient cohort. Functional assays were used to determine the effect of pathway modulation on cell phenotypes.<p></p>
<b>Outcome measurements and statistical analysis:</b>
We searched for gene expression changes affecting key cell signalling pathways that may be targeted as proof of principle in a CRPC in vitro cell line model.<p></p>
<b>Results and limitations:</b>
We identified ADT-regulated signalling pathways, including the Wnt/ÎČ-catenin signalling pathway, and observed overexpression of ÎČ-catenin in a subset of CRPC by immunohistochemistry. We validated 6 of 12 (50%) pathway members by qRT-PCR on LNCaP/LNCaP-AI cell RNAs, of which 4 (67%) demonstrated expression changes consistent with RNA-seq data. We show that the tankyrase inhibitor XAV939 (which promotes ÎČ-catenin degradation) reduced androgen-independent LNCaP-AI cell line growth compared with androgen-responsive LNCaP cells via an accumulation of cell proportions in the G0/G1 phase and reduction in the S and G2/M phases. Our biopsy protocol did not account for tumour heterogeneity, and pathway inhibition was limited to pharmacologic approaches.<p></p>
<b>Conclusions:</b>
RNA-seq of paired PCa samples revealed ADT-regulated signalling pathways. Proof-of-principle inhibition of the Wnt/ÎČ-catenin signalling pathway specifically delays androgen-independent PCa cell cycle progression and proliferation and warrants further investigation as a potential target for therapy for CRPC.<p></p>
Developing and applying heterogeneous phylogenetic models with XRate
Modeling sequence evolution on phylogenetic trees is a useful technique in
computational biology. Especially powerful are models which take account of the
heterogeneous nature of sequence evolution according to the "grammar" of the
encoded gene features. However, beyond a modest level of model complexity,
manual coding of models becomes prohibitively labor-intensive. We demonstrate,
via a set of case studies, the new built-in model-prototyping capabilities of
XRate (macros and Scheme extensions). These features allow rapid implementation
of phylogenetic models which would have previously been far more
labor-intensive. XRate's new capabilities for lineage-specific models,
ancestral sequence reconstruction, and improved annotation output are also
discussed. XRate's flexible model-specification capabilities and computational
efficiency make it well-suited to developing and prototyping phylogenetic
grammar models. XRate is available as part of the DART software package:
http://biowiki.org/DART .Comment: 34 pages, 3 figures, glossary of XRate model terminolog
Accurate reconstruction of insertion-deletion histories by statistical phylogenetics
The Multiple Sequence Alignment (MSA) is a computational abstraction that
represents a partial summary either of indel history, or of structural
similarity. Taking the former view (indel history), it is possible to use
formal automata theory to generalize the phylogenetic likelihood framework for
finite substitution models (Dayhoff's probability matrices and Felsenstein's
pruning algorithm) to arbitrary-length sequences. In this paper, we report
results of a simulation-based benchmark of several methods for reconstruction
of indel history. The methods tested include a relatively new algorithm for
statistical marginalization of MSAs that sums over a stochastically-sampled
ensemble of the most probable evolutionary histories. For mammalian
evolutionary parameters on several different trees, the single most likely
history sampled by our algorithm appears less biased than histories
reconstructed by other MSA methods. The algorithm can also be used for
alignment-free inference, where the MSA is explicitly summed out of the
analysis. As an illustration of our method, we discuss reconstruction of the
evolutionary histories of human protein-coding genes.Comment: 28 pages, 15 figures. arXiv admin note: text overlap with
arXiv:1103.434
Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis
The combined application of next-generation sequencing platforms has provided an economical approach to unlocking the potential of the turkey genome
Guidelines and Recommendations on Yeast Cell Death Nomenclature
Elucidating the biology of yeast in its full complexity has major implications for science, medicine and industry. One of the most critical processes determining yeast life and physiology is cellular demise. However, the investigation of yeast cell death is a relatively young field, and a widely accepted set of concepts and terms is still missing. Here, we propose unified criteria for the definition of accidental, regulated, and programmed forms of cell death in yeast based on a series of morphological and biochemical criteria. Specifically, we provide consensus guidelines on the differential definition of terms including apoptosis, regulated necrosis, and autophagic cell death, as we refer to additional cell death routines that are relevant for the biology of (at least some species of) yeast. As this area of investigation advances rapidly, changes and extensions to this set of recommendations will be implemented in the years to come. Nonetheless, we strongly encourage the authors, reviewers and editors of scientific articles to adopt these collective standards in order to establish an accurate framework for yeast cell death research and, ultimately, to accelerate the progress of this vibrant field of research
Identification of a candidate prognostic gene signature by transcriptome analysis of matched pre-and post-treatment prostatic biopsies from patients with advanced prostate cancer
Background: Although chemotherapy for prostate cancer (PCa) can improve patient survival, some tumours are
chemo-resistant. Tumour molecular profiles may help identify the mechanisms of drug action and identify potential
prognostic biomarkers. We performed in vivo transcriptome profiling of pre- and post-treatment prostatic biopsies
from patients with advanced hormone-naive prostate cancer treated with docetaxel chemotherapy and androgen
deprivation therapy (ADT) with an aim to identify the mechanisms of drug action and identify prognostic biomarkers.
Methods: RNA sequencing (RNA-Seq) was performed on biopsies from four patients before and ~22 weeks after
docetaxel and ADT initiation. Gene fusion products and differentially-regulated genes between treatment pairs were
identified using TopHat and pathway enrichment analyses undertaken. Publically available datasets were interrogated
to perform survival analyses on the gene signatures identified using cBioportal.
Results: A number of genomic rearrangements were identified including the TMPRSS2/ERG fusion and 3 novel gene
fusions involving the ETS family of transcription factors in patients, both pre and post chemotherapy. In total, gene
expression analyses showed differential expression of at least 2 fold in 575 genes in post-chemotherapy biopsies. Of
these, pathway analyses identified a panel of 7 genes (ADAM7, FAM72B, BUB1B, CCNB1, CCNB2, TTK, CDK1), including
a cell cycle-related geneset, that were differentially-regulated following treatment with docetaxel and ADT. Using
cBioportal to interrogate the MSKCC-Prostate Oncogenome Project dataset we observed a statistically-significant
reduction in disease-free survival of patients with tumours exhibiting alterations in gene expression of the above
panel of 7 genes (p = 0.015).
Conclusions: Here we report on the first âreal-timeâ in vivo RNA-Seq-based transcriptome analysis of clinical PCa from
pre- and post-treatment TRUSS-guided biopsies of patients treated with docetaxel chemotherapy plus ADT. We identify
a chemotherapy-driven PCa transcriptome profile which includes the down-regulation of important positive regulators
of cell cycle progression. A 7 gene signature biomarker panel has also been identified in high-risk prostate cancer
patients to be of prognostic value. Future prospective study is warranted to evaluate the clinical value of this panel
Insights into hominid evolution from the gorilla genome sequence.
Gorillas are humans' closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago. In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution
Mouse genomic variation and its effect on phenotypes and gene regulation
We report genome sequences of 17 inbred strains of laboratory mice and identify almost ten times more variants than previously known. We use these genomes to explore the phylogenetic history of the laboratory mouse and to examine the functional consequences of allele-specific variation on transcript abundance, revealing that at least 12% of transcripts show a significant tissue-specific expression bias. By identifying candidate functional variants at 718 quantitative trait loci we show that the molecular nature of functional variants and their position relative to genes vary according to the effect size of the locus. These sequences provide a starting point for a new era in the functional analysis of a key model organism
Guidelines and recommendations on yeast cell death nomenclature
Elucidating the biology of yeast in its full complexity has major implications for science, medicine and industry. One of the most critical processes determining yeast life and physiology is cel-lular demise. However, the investigation of yeast cell death is a relatively young field, and a widely accepted set of concepts and terms is still missing. Here, we propose unified criteria for the defi-nition of accidental, regulated, and programmed forms of cell death in yeast based on a series of morphological and biochemical criteria. Specifically, we provide consensus guidelines on the differ-ential definition of terms including apoptosis, regulated necrosis, and autophagic cell death, as we refer to additional cell death rou-tines that are relevant for the biology of (at least some species of) yeast. As this area of investigation advances rapidly, changes and extensions to this set of recommendations will be implemented in the years to come. Nonetheless, we strongly encourage the au-thors, reviewers and editors of scientific articles to adopt these collective standards in order to establish an accurate framework for yeast cell death research and, ultimately, to accelerate the pro-gress of this vibrant field of research