Uncovering Clinically Relevant Gene Fusions with Integrated Genomic and Transcriptomic Profiling of Metastatic Cancers

PURPOSE

Gene fusions are important oncogenic drivers and many are actionable. Whole-genome and transcriptome (WGS and RNA-seq, respectively) sequencing can discover novel clinically relevant fusions.

EXPERIMENTAL DESIGN

Using WGS and RNA-seq, we reviewed the prevalence of fusions in a cohort of 570 patients with cancer, and compared prevalence to that predicted with commercially available panels. Fusions were annotated using a consensus variant calling pipeline (MAVIS) and required that a contig of the breakpoint could be constructed and supported from ≥2 structural variant detection approaches.

RESULTS

In 570 patients with advanced cancer, MAVIS identified 81 recurrent fusions by WGS and 111 by RNA-seq, of which 18 fusions by WGS and 19 by RNA-seq were noted in at least 3 separate patients. The most common fusions were EML4-ALK in thoracic malignancies (9/69, 13%), and CMTM8-CMTM7 in colorectal cancer (4/73, 5.5%). Combined genomic and transcriptomic analysis identified novel fusion partners for clinically relevant genes, such as NTRK2 (novel partners: SHC3, DAPK1), and NTRK3 (novel partners: POLG, PIBF1).

CONCLUSIONS

Utilizing WGS/RNA-seq facilitates identification of novel fusions in clinically relevant genes, and detected a greater proportion than commercially available panels are expected to find. A significant benefit of WGS and RNA-seq is the innate ability to retrospectively identify variants that becomes clinically relevant over time, without the need for additional testing, which is not possible with panel-based approaches.

MAVIS: merging, annotation, validation, and illustration of structural variants

Summary

Reliably identifying genomic rearrangements and interpreting their impact is a key step in understanding their role in human cancers and inherited genetic diseases. Many short read algorithmic approaches exist but all have appreciable false negative rates. A common approach is to evaluate the union of multiple tools increasing sensitivity, followed by filtering to retain specificity. Here we describe an application framework for the rapid generation of structural variant consensus, unique in its ability to visualize the genetic impact and context as well as process both genome and transcriptome data.

Availability and implementation

http://mavis.bcgsc.ca.

Supplementary information

Supplementary data are available at Bioinformatics online.

The Genome of the Beluga Whale (Delphinapterus leucas)

The beluga whale is a cetacean that inhabits arctic and subarctic regions, and is the only living member of the genus Delphinapterus. The genome of the beluga whale was determined using DNA sequencing approaches that employed both microfluidic partitioning library and non-partitioned library construction. The former allowed for the construction of a highly contiguous assembly with a scaffold N50 length of over 19 Mbp and total reconstruction of 2.32 Gbp. To aid our understanding of the functional elements, transcriptome data was also derived from brain, duodenum, heart, lung, spleen, and liver tissue. Assembled sequence and all of the underlying sequence data are available at the National Center for Biotechnology Information (NCBI) under the Bioproject accession number PRJNA360851A.

The Genome of the Northern Sea Otter (Enhydra lutris kenyoni)

The northern sea otter inhabits coastal waters of the northern Pacific Ocean and is the largest member of the Mustelidae family. DNA sequencing methods that utilize microfluidic partitioned and non-partitioned library construction were used to establish the sea otter genome. The final assembly provided 2.426 Gbp of highly contiguous assembled genomic sequences with a scaffold N50 length of over 38 Mbp. We generated transcriptome data derived from a lymphoma to aid in the determination of functional elements. The assembled genome sequence and underlying sequence data are available at the National Center for Biotechnology Information (NCBI) under the BioProject accession number PRJNA388419.

Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer

We report a comprehensive analysis of 412 muscle-invasive bladder cancers characterized by multiple TCGA analytical platforms. Fifty-eight genes were significantly mutated, and the overall mutational load was associated with APOBEC-signature mutagenesis. Clustering by mutation signature identified a high-mutation subset with 75% 5-year survival. mRNA expression clustering refined prior clustering analyses and identified a poor-survival "neuronal" subtype in which the majority of tumors lacked small cell or neuroendocrine histology. Clustering by mRNA, long non-coding RNA (lncRNA), and miRNA expression converged to identify subsets with differential epithelial-mesenchymal transition status, carcinoma in situ scores, histologic features, and survival. Our analyses identified 5 expression subtypes that may stratify response to different treatments.

Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling

BACKGROUND

The Amoebozoa constitute one of the primary divisions of eukaryotes, encompassing taxa of both biomedical and evolutionary importance, yet its genomic diversity remains largely unsampled. Here we present an analysis of a whole genome assembly of Acanthamoeba castellanii (Ac) the first representative from a solitary free-living amoebozoan.

RESULTS

Ac encodes 15,455 compact intron-rich genes, a significant number of which are predicted to have arisen through inter-kingdom lateral gene transfer (LGT). A majority of the LGT candidates have undergone a substantial degree of intronization and Ac appears to have incorporated them into established transcriptional programs. Ac manifests a complex signaling and cell communication repertoire, including a complete tyrosine kinase signaling toolkit and a comparable diversity of predicted extracellular receptors to that found in the facultatively multicellular dictyostelids. An important environmental host of a diverse range of bacteria and viruses, Ac utilizes a diverse repertoire of predicted pattern recognition receptors, many with predicted orthologous functions in the innate immune systems of higher organisms.

CONCLUSIONS

Our analysis highlights the important role of LGT in the biology of Ac and in the diversification of microbial eukaryotes. The early evolution of a key signaling facility implicated in the evolution of metazoan multicellularity strongly argues for its emergence early in the Unikont lineage. Overall, the availability of an Ac genome should aid in deciphering the biology of the Amoebozoa and facilitate functional genomic studies in this important model organism and environmental host.

FeatureStack: Perl module for comparative visualization of gene features

SUMMARY

FeatureStack is a Perl module for the automatic generation of multi-gene images. FeatureStack takes BioPerl-compliant gene or transcript features as input and renders them side by side using a user-defined BioPerl glyph. Output images can be generated in SVG or PNG format. FeatureStack comes with a new BioPerl glyph, decorated_gene, which can highlight protein features on top of gene models. Used in combination, FeatureStack and decorated_gene enable rapid and automated generation of annotation-rich images of stacked gene models that greatly facilitate evolutionary studies of related gene structures and gene families.

AVAILABILITY AND IMPLEMENTATION

Bio-Draw-FeatureStack and Bio-Graphics-glyph-decorated_gene are freely available at the Comprehensive Perl Archive Network (CPAN) and GitHub.

CONTACT

chenn@sfu.ca

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Changes in Spinal Reflex Excitability in a Countermanded Timed Response Task

Subjects (N = 8) performed a timed response task in which they attempted to synchronize an impulsive foot-press response with the last in a series of four regularly spaced tones. In Experiment 1, the response was countermanded on one third of the trials (stop trials) by a stop signal that appeared at a predetermined delay after the third tone. No stop signal appeared on the remaining trials (go trials). All subjects showed a systematic transition from withholding the response on stop trials in which the stop signal appeared shortly after the third tone to executing the response on trials in which a single stop signal delay had been chosen so that a response would be made on about 50% of the stop trials. We elicited Hoffmann (H) reflexes from the soleus muscle on all trials to determine whether the reflexes were augmented on occasions on which a response was prepared but withheld. Mean H-reflex amplitudes on go trials and on stop trials on which the response was executed were similar and showed a marked augmentation beginning about 250 ms before response onset; mean H-reflex amplitudes on stop trials on which the response was withheld showed less pronounced augmentation. Inspection of individual H-reflex amplitudes revealed that on stop trials on which the response was withheld the reflexes could be augmented to the same extent as on trials on which the response was executed. This dissociation of H-reflex augmentation and response execution shows that H-reflex augmentation reflects a controlled response process. Ballistic response processes therefore must be limited to a brief duration.

Extracellular matrix proteins protect small cell lung cancer cells against apoptosis: a mechanism for small cell lung cancer growth and drug resistance in vivo

Resistance to chemotherapy is a principal problem in the treatment of small cell lung cancer (SCLC). We show here that SCLC is surrounded by an extensive stroma of extracellular matrix (ECM) at both primary and metastatic sites. Adhesion of SCLC cells to ECM enhances tumorigenicity and confers resistance to chemotherapeutic agents as a result of beta1 integrin-stimulated tyrosine kinase activation suppressing chemotherapy-induced apoptosis. SCLC may create a specialized microenvironment, and the survival of cells bound to ECM could explain the partial responses and local recurrence of SCLC often seen clinically after chemotherapy. Strategies based on blocking beta1 integrin-mediated survival signals may represent a new therapeutic approach to improve the response to chemotherapy in SCLC.

Reduced glucose degradation products in bicarbonate/lactate-buffered peritoneal dialysis solutions produced in two-chambered bags

OBJECTIVES

The aims of the current study were: (1) to determine the effects of peritoneal dialysis (PD) solutions at different glucose concentrations on the growth of cultured cells; (2) to determine whether a bicarbonate/lactate-based solution, as a result of the configuration of its components during heat sterilization in a two-chambered bag, was lower in glucose degradation products than a corresponding lactate-based PD solution; and (3) to determine whether lower glucose degradation corresponded to a decreased inhibition of cell growth.

DESIGN

Growth inhibition of cells exposed to lactate-based PD solutions at three different glucose concentrations was determined. Bicarbonate/lactate-based and lactate-based solutions at high glucose concentration (3.86%) were further analyzed for presence of glucose degradation products and inhibition of cell growth.

METHODS

Cell growth was determined by neutral red uptake, measured by optical density at 540 nm. Glucose degradation to acetaldehyde or fructose was determined by gas chromatography-mass spectroscopy and high-performance liquid chromatography.

RESULTS

Only 3.86% glucose lactate-based PD solution caused significant inhibition of cell growth (p < 0.05). The heat-sterilized, bicarbonate/dlactate-based solution (3.86% glucose) had lower levels of fructose and acetaldehyde than a conventional heat-sterilized, lactate-based solution with the same glucose concentration. Growth of cultured cells exposed to the bicarbonate/lactate-based solution was significantly improved (p < 0.05) over growth in the conventional solution.

CONCLUSIONS

The bicarbonate/lactate-based solutions, manufactured and heat-sterilized in two-chambered bags, were lower in glucose degradation products than that corresponding lactate-based PD solutions, and demonstrated improved in vitro biocompatibility as measured by the growth of cultured cells.

Correction of oriental epiblepharon by anterior lamellar reposition

Epiblepharon commonly occurs in Oriental infants and children, but usually corrects itself with age. Epiblepharon in adults is not uncommon and may be misdiagnosed or detected late. It causes symptoms of ocular irritation and inferior punctate corneal epithelial erosion. These can persist if surgical treatment is ineffective. A series of 15 lower lid epiblepharon in 10 adults is presented with the clinical features and surgical treatment by anterior lamellar reduction and repositioning. The surgical technique is discussed. All patients had significant symptomatic relief and correction of lash-corneal touch. Among 15 cases of epiblepharon, 3 with residual trichiasis post-operatively were further corrected by skin reduction and debulking of pretarsal orbicularis oculi to achieve total correction. Adequate skin reduction and debulking of orbicularis oculi, especially the pretarsal muscle, are essential in the anterior lamellar repositioning and effective correction of this condition.