Miniaturised interaction proteomics on a microfluidic platform with ultra-low input requirements

Essentially all cellular processes are orchestrated by protein-protein interactions (PPIs). In recent years, affinity purification coupled to mass spectrometry (AP-MS) has been the preferred method to identify cellular PPIs. Here we present a microfluidic-based AP-MS workflow, called on-chip AP-MS, to identify PPIs using minute amounts of input material. By using this automated platform we purify the human Cohesin, CCC and Mediator complexes from as little as 4 micrograms of input lysate, representing a 50─100-fold downscaling compared to regular microcentrifuge tube-based protocols. We show that our platform can be used to affinity purify tagged baits as well as native cellular proteins and their interaction partners. As such, our method holds great promise for future biological and clinical AP-MS applications in which sample amounts are limited.

Chondroprotection by urocortin involves blockade of the mechanosensitive ion channel Piezo1

Osteoarthritis (OA) is characterised by progressive destruction of articular cartilage and chondrocyte cell death. Here, we show the expression of the endogenous peptide urocortin1 (Ucn1) and two receptor subtypes, CRF-R1 and CRF-R2, in primary human articular chondrocytes (AC) and demonstrate its role as an autocrine/paracrine pro-survival factor. This effect could only be removed using the CRF-R1 selective antagonist CP-154526, suggesting Ucn1 acts through CRF-R1 when promoting chondrocyte survival. This cell death was characterised by an increase in p53 expression, and cleavage of caspase 9 and 3. Antagonism of CRF-R1 with CP-154526 caused an accumulation of intracellular calcium (Ca2+) over time and cell death. These effects could be prevented with the non-selective cation channel blocker Gadolinium (Gd3+). Therefore, opening of a non-selective cation channel causes cell death and Ucn1 maintains this channel in a closed conformation. This channel was identified to be the mechanosensitive channel Piezo1. We go on to determine that this channel inhibition by Ucn1 is mediated initially by an increase in cyclic adenosine monophosphate (cAMP) and a subsequent inactivation of phospholipase A2 (PLA2), whose metabolites are known to modulate ion channels. Knowledge of these novel pathways may present opportunities for interventions that could abrogate the progression of OA.

Genetic differentiation in spite of high gene flow in the dominant rainforest tree of southeastern Australia, Nothofagus cunninghamii

Nothofagus cunninghamii is a long-lived, wind-pollinated tree species that dominates the cool temperate rainforests of southeastern Australia. The species' distribution is more or less continuous in western Tasmania but is fragmented elsewhere. However, it is unknown whether this fragmentation has affected the species' genetic architecture. Thus, we examined N. cunninghamii using 12 nuclear microsatellites and 633 individuals from 18 populations spanning the species' natural range. Typical of wind-pollinated trees, there was low range-wide genetic structure (FST=0.04) consistent with significant gene flow across most of the species' range. However, gene flow was not high enough to overcome the effects of drift across some disjunctions. Victorian populations (separated from Tasmania by the 240 km wide Bass Strait) formed a genetic group distinct from Tasmanian populations, had lower diversity (mean allelic richness (Ar)=5.4 in Victoria versus 6.9 in Tasmania) and were significantly more differentiated from one another than those in Tasmania (FST=0.045 in Victoria versus 0.012 in Tasmania). Evidence for bottlenecking was found in small populations that were at least 20 km from other populations. Interestingly, we found little divergence in microsatellite markers between the extremes of genetically based morphological and physiological altitudinal clines suggesting adaptive differentiation is strongly driven by selection because it is likely to be occurring in the presence of gene flow. Even though the cool temperate rainforests of Australia are highly relictual, the species is relatively robust to population fragmentation due to high levels of genetic diversity and gene flow, especially in Tasmania.

Pathogenicity and molecular characteristics of infectious bronchitis virus (IBV) strains isolated from broilers showing diarrhoea and respiratory disease

Abstract 1. The possibility that infectious bronchitis virus (IBV) variants isolated from broilers with enteric and respiratory problems have a different tropism and pathological outcome from those IBV strains causing classical respiratory disease was investigated. 2. IBV variants were isolated from broiler flocks with enteric and respiratory problems in two regions of Brazil. The USP-10 isolate, of enteric origin, was inoculated via the oral oroculonasal routes into IBV-antibody-free broilers and specific pathogen-free (SPF) chickens to determine tissue tropism and pathogenicity and compared with an IBV variant (USP-50) isolated from chickens showing signs of respiratory disease only. 3. Both USP-10 and USP-50 strains caused similar pathological patterns by either route of inoculation. Both variants were detected in respiratory and non-respiratory tissues, including the kidney, intestine and testis. 4. Broilers were more susceptible to infection than SPF chickens, and seroconversion was detected in all of the chicks.

Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex

Large-scale surveys of single-cell gene expression have the potential to reveal rare cell populations and lineage relationships, but require efficient methods for cell capture and mRNA sequencing^1–4. Although cellular barcoding strategies allow parallel sequencing of single cells at ultra-low depths⁵, the limitations of shallow sequencing have not been directly investigated. By capturing 301 single cells from 11 populations using microfluidics and analyzing single-cell transcriptomes across downsampled sequencing depths, we demonstrate that shallow single-cell mRNA sequencing (~50,000 reads per cell) is sufficient for unbiased cell-type classification and biomarker identification. In developing cortex we identify diverse cell types including multiple progenitor and neuronal subtypes, and we identify EGR1 and FOS as previously unreported candidate targets of Notch signaling in human but not mouse radial glia. Our strategy establishes an efficient method for unbiased analysis and comparison of cell populations from heterogeneous tissue by microfluidic single-cell capture and low-coverage sequencing of many cells.

A review of the Institute of Medicine's analysis of using chimpanzees in biomedical research

We argue that the recommendations made by the Institute of Medicine's 2011 report, Chimpanzees in Biomedical and Behavioral Research: Assessing the Necessity, are methodologically and ethically confused. We argue that a proper understanding of evolution and complexity theory in terms of the science and ethics of using chimpanzees in biomedical research would have had led the committee to recommend not merely limiting but eliminating the use of chimpanzees in biomedical research. Specifically, we argue that a proper understanding of the difference between the gross level of examination of species and examinations on finer levels can shed light on important methodological and ethical inconsistencies leading to ignorance of potentially unethical practices and policies regarding the use of animals in scientific research.

Chiropractors as Primary Spine Care Providers: precedents and essential measures

Chiropractors have the potential to address a substantial portion of spinal disorders; however the utilization rate of chiropractic services has remained low and largely unchanged for decades. Other health care professions such as podiatry/chiropody, physiotherapy and naturopathy have successfully gained public and professional trust, increases in scope of practice and distinct niche positions within mainstream health care. Due to the overwhelming burden of spine care upon the health care system, the establishment of a 'primary spine care provider' may be a worthwhile niche position to create for society's needs. Chiropractors could fulfill this role, but not without first reviewing and improving its approach to the management of spinal disorders. Such changes have already been achieved by the chiropractic profession in Switzerland, Denmark, and New Mexico, whose examples may serve as important templates for renewal here in Canada.

A microfluidic device for preparing next generation DNA sequencing libraries and for automating other laboratory protocols that require one or more column chromatography steps

Library preparation for next-generation DNA sequencing (NGS) remains a key bottleneck in the sequencing process which can be relieved through improved automation and miniaturization. We describe a microfluidic device for automating laboratory protocols that require one or more column chromatography steps and demonstrate its utility for preparing Next Generation sequencing libraries for the Illumina and Ion Torrent platforms. Sixteen different libraries can be generated simultaneously with significantly reduced reagent cost and hands-on time compared to manual library preparation. Using an appropriate column matrix and buffers, size selection can be performed on-chip following end-repair, dA tailing, and linker ligation, so that the libraries eluted from the chip are ready for sequencing. The core architecture of the device ensures uniform, reproducible column packing without user supervision and accommodates multiple routine protocol steps in any sequence, such as reagent mixing and incubation; column packing, loading, washing, elution, and regeneration; capture of eluted material for use as a substrate in a later step of the protocol; and removal of one column matrix so that two or more column matrices with different functional properties can be used in the same protocol. The microfluidic device is mounted on a plastic carrier so that reagents and products can be aliquoted and recovered using standard pipettors and liquid handling robots. The carrier-mounted device is operated using a benchtop controller that seals and operates the device with programmable temperature control, eliminating any requirement for the user to manually attach tubing or connectors. In addition to NGS library preparation, the device and controller are suitable for automating other time-consuming and error-prone laboratory protocols requiring column chromatography steps, such as chromatin immunoprecipitation.

Enteric viruses in Brazilian turkey flocks: single and multiple virus infection frequency according to age and clinical signs of intestinal disease

Poult enteritis complex has been associated with enteritis and reduction in growth rates in commercial turkeys worldwide. Intestinal samples from 76 turkey flocks from different Brazilian states affected or not with intestinal disorders were evaluated for the presence of adenovirus groups 1 and 2 (TAV), astrovirus types 1 and 2 (TAstV-1 and TAstV-2), turkey coronavirus (TCoV), reovirus, rotavirus, and avian nephritis virus (ANV) using PCR. The percentage of positive samples was categorized according to the geographic origin, age of the flocks, and presence of clinical signs of intestinal disease. The percentage of samples that were positive for at least one virus was 93.4%, whereas the percentage of samples that were positive for more than one virus was 69.7%. An average of 3.20 viruses per sample was detected in turkeys in the growing phase of the production cycle (1 to 4 wk of age). The TAstV-1 and TCoV were the most frequently observed viruses in growing phase turkeys and occurred simultaneously in 85% of these samples. In turkeys in the finishing phase of development (5 to 18 wk), a lower average number of viruses was observed (2.41), and the most frequent viruses isolated in these turkeys were TAstV-1 (57.1%) and rotavirus (51.8%). Overall, every virus was detected more frequently in growing phase turkeys than in finishing phase turkeys with the exception of TAV. Samples from flocks exhibiting clinical signs of intestinal disease showed a higher rate of positivity, and TAstV-1, TAstV-2, and TCoV were the most frequently occurring viruses in this cohort. Birds without clinical signs most frequently harbored TAstV-1 and rotavirus. Future studies should focus on the description and elucidation of the role of each virus, as well as the pathogenic and immunological implications of the different combinations of viruses in turkeys.

Effect of T-cell suppression by cyclosporin on primary and persistent infections of infectious bronchitis virus in chickens

Two-week-old white leghorn (WL) chickens were inoculated intra-nasally with 4.51ogio median ciliostatic doses (CD50) of IBV strain M41. Cyclosporin (CSP) (100 mg/kg body weight) was injected intra-muscularly 3 days before virus infection and every 3 days till day 15 post-infection (p.i.). Significant reduction in proliferation responses of whole blood lymphocytes to a T-cell mitogen, concanavalin A were induced, but not to a B and T-cell mitogen, pokeweed mitogen. Mortality in the IBV + CSP group was 18%, but in the IBV group it was 2%. No significant differences in the total number of virus isolations were seen between the two groups. Virus titres in trachea, lung and kidneys of the T-cell suppressed chickens were slightly higher and histopathological lesions more severe. Thus it appeared that T-cells may play a major role in limiting severity and lethality of IBV infections rather than clearing virus. To confirm this, another experiment was performed in which 2-week-old brown leghorn (BrL) chickens, relatively resistant to IBV were infected with a pool of IBV strains. Mortality was 43% in the IBV + CSP group and zero with IBV alone. Earlier reports using the same pool of IBV strains have shown a mortality of 47% in line 151 chicks, a line sensitive to IBV infection. Thus, a resistant line was induced to behave like a susceptible line by T-cell suppression. Virus titres were always 1 to 3 logs higher in the kidneys of T-cell suppressed BrL chicks. Attempts to induce re-excretion of virus by CSP treatment of WL chickens infected with the IBV strain M41 when 2 weeks old were unsuccessful, but when chicks were infected with the same strain at day-old and given CSP injections from 5 weeks p.i., virus re-excretion was primarily seen from the kidneys and not the caecal tonsil. Thus the kidney appears to be the primary site of IBV persistence. The pathogenesis of the disease in T-cell suppressed chickens is discussed.

Effect of heterophil depletion by 5-fluorouracil on infectious bronchitis virus infection in chickens

An anti-tumour drug, 5-fluorouracil (5 FU) was used to deplete heterophils in 11-day-old white leghorn chickens. The reduction in heterophil numbers was monitored by total and differential white cell counts in the peripheral blood. Three days after injection of 5 FU, when the heterophil numbers were significantly reduced, chickens were infected with the Massachusetts strain of infectious bronchitis virus (IBV). Following infection, although the numbers of birds exhibiting clinical signs (nasal exudate) were significantly higher in the 5 FU treated group, the consistency of the nasal exudate was characteristically thin and watery. No significant differences were seen in the virus titres in trachea, lung and kidney between normal and heteropaenic chickens infected with IBV. However, the epithelial cell damage in the tracheal sections was less in the heterophil-depleted chickens.

An in vitro comparison of the virulence of seven strains of infectious bronchitis virus using tracheal and oviduct organ cultures

The virulence of seven infectious bronchitis virus (IBV) strains for tracheal and oviduct ciliated epithelium was assessed using an in vitro tracheal organ culture (TOC) and oviduct organ culture (OOC) system. The OOC were prepared using oviducts obtained from oestrogen-treated chicks. All strains tested stopped ciliary beating in the oviduct by day 5 post-inoculation (p.i.) and in the trachea by day 3 p.i. This corresponded with the absence of immunofluorescent-stained cells in the epithelium at that time. The time taken for a 50% reduction of relative ciliary activity (RCA) of oviduct cilia was shortest for strain 6 (serotype D207) and longest for strain G (enterotropic variant). Strains 7 (serotype D3896) and M41 were the most pathogenic for tracheal cilia, while strains 6 and G were less pathogenic. A calmod-ulin (CAM) assay was standardized to quantify the epithelial cell damage to oviducts caused by IBV. It was found that strains 6 and M41 were the most pathogenic. The use of time taken to achieve a 50% reduction in RCA and the CAM assay for in vitro pathotyping of IBV isolates is discussed. The susceptibility of OOC or TOC for five IBV strains was compared. It was found that strains 25 and 793B had equal predilection for both, while for 25, G and M41, TOC was more susceptible.

Cross-reactive cellular immune responses in chickens vaccinated with live infectious bronchitis virus vaccine

Two-week-old chickens were vaccinated intra-nasally with a live infectious bronchitis virus (IBV) vaccine (H120). On days 4, 7, 11 and 14 post-vaccination (p.v.) spleen mononuclear cells (MNC) prepared from control and vaccinated chickens were stimulated in vitro with homologous (strain M41) and heterologous (strains 7 and 793/B) virus antigens. Antigen-specific lymphoproliferation and interleukin-2 (IL-2) and interferon-y (IFN) production were used to measure cross-reactive cell mediated immune responses. In antigen-specific lymphoproliferation assays, it was found that while 4/16 vaccinated birds responded to the homologous antigen, only one responded to an heterologous antigen (strain 7). However, IL-2 production was seen in the supernatants of spleen MNC from vaccinated chickens stimulated with all three antigens. Production of IFN was also demonstrated in samples stimulated with the homologous and one heterologous (strain 7) antigen. Thus it appears that, following vaccination of chickens with live IBV vaccine, cross-reactive cellular immune responses occur that vary in magnitude with the strain of IBV used for in vitro stimulation.

Susceptibility of organ cultures from chicken tissues for strains of infectious bronchitis virus isolated from the intestine

Organ cultures were prepared from various levels of intestine and kidney of 2 to 4-week old specific-pathogen-free chickens, and their susceptibility to ten strains of infectious bronchitis virus isolated from the chicken intestine and the Massachusetts strain M41 was investigated. The ability of a virus to grow depended on the strain of virus and size of the inoculum. While proventriculus, bursa and kidney were found to be universally susceptible to all viruses tested, some strains did not grow in caecal tonsils or rectum. Strain M41 showed little difference in pattern of tissue replication compared with several other strains isolated from the gut and actually grew in a wider range than some. Duodenum, jejunum and ileum were found to be non-permissive to all strains tested, even after a high input inoculum.

Microwave or autoclave treatments destroy the infectivity of infectious bronchitis virus and avian pneumovirus but allow detection by reverse transcriptase-polymerase chain reaction

A method is described for enabling safe transit of denatured virus samples for polymerase chain reaction (PCR) identification without the risk of unwanted viable viruses. Cotton swabs dipped in avian infectious bronchitis virus (IBV) or avian pneumovirus (APV) were allowed to dry. Newcastle disease virus and avian influenza viruses were used as controls. Autoclaving and microwave treatment for as little as 20 sec destroyed the infectivity of all four viruses. However, both IBV and APV could be detected by reverse transcriptase (RT)-PCR after autoclaving and as long as 5 min microwave treatment (Newcastle disease virus and avian influenza viruses were not tested). Double microwave treatment of IBV and APV with an interval of 2 to 7 days between was tested. After the second treatment, RT-PCR products were readily detected in all samples. Swabs from the tracheas and cloacas of chicks infected with IBV shown to contain infectious virus were microwaved. Swabs from both sources were positive by RT-PCR. Microwave treatment appears to be a satisfactory method of inactivating virus while preserving nucleic acid for PCR identification.

Abstract 1164: Parallel preparation of targeted resequencing libraries from 480 genomic regions using multiplex PCR on the Access Array system

Next generation sequencing platforms have dramatically reduced sequencing costs. However, it currently remains too expensive to routinely resequence entire human genomes in order to discover genetic variants or somatic mutations underlying tumorigenesis. Therefore, a need exists for multiplexed, targeted amplification methods that allow for the analysis of multiple genomic regions in large cohorts. Available targeted enrichment technologies are either aimed at the capture of regions of interest from a single sample, exhibit uneven representation or require significant amounts of input material. The novel microfluidic platform, the Access Array system, combines 48 samples with 48 primer sets resulting in 2,304 simultaneously occurring PCR amplifications requiring as little as 50ng DNA per sample. PCR products generated on the Access Array system can be used for sequencing on all next-generation sequencing platforms, including 454 GS FLX and Illumina GAII. To increase coverage and throughput, PCR reactions can be multiplexed within Access Array chips generating up to 480 amplicons per sample.

As proof-of-principal experiments, we have carried out multiplexed amplifications of a set of commonly mutated cancer gene exons across 48 genomic DNA samples. In initial experiments, 580 primer pairs were validated in individual PCR reactions in 96-well plates. Each primer pair was designed to include 5’ sequences that allow for the incorporation of 454 and Illumina adapters necessary for subsequent emPCR and cluster generation, respectively. 480 primer pairs that produced a single band of the correct size, as determined on a Caliper LabChip system, were selected for multiplex PCR experiments. Primer pairs yielding amplicons with a similar size were combined in groups of 10 sets, resulting in 48 primer pools of 10 primer pairs each. Multiplex PCR was carried out on Access Array chips, followed by harvesting of the 48 amplicon pools. Each pool was diluted and then subjected to a second round of PCR in standard 96-well plates with barcoded universal primers corresponding to the 454 and Illumina sequences. The resulting products are 48 uniquely barcoded amplicon pools, each comprising 480 amplicons derived from one sample, that are ready for sequencing. We will present sequencing data generated on both 454 and Illumina systems.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1164.

Abstract 1147: High-throughput nanofluidic PCR-based preparation of 454 sequencing libraries for identifying mutations in EGFR and MET

The epidermal growth factor receptor (EGFR) and mesenchymal-epithelial transition factor (MET) play important roles in cancer development and are promising targets for anticancer therapies. Mutations in the EGFR and MET genes are associated with multiple types of cancer and the ability to detect variants in these genes is crucial for a better understanding of disease progression and response to targeted therapeutics. Next-generation sequencers (e.g. 454, Illumina) hold great potential for detecting disease-specific alterations within patient populations for a given cancer type. However, current approaches for targeted resequencing of specific genetic regions are not well suited to studying the hundreds or thousands of patient samples required to assign significance to mutations.

We have developed a novel nanofluidic platform, the Access Array™ system, which enables the robust, simultaneous amplification of 48 PCR products (amplicon) from 48 samples in parallel using only 50ng input DNA per sample. In addition, we have developed a primer design strategy that incorporates sample-specific barcodes and 454 sequencing adaptors into each amplicon, removing the need for library preparation before sequencing. We will present sequencing data collected from amplicon libraries prepared using the Access Array system to amplify 48 exon regions of the EGFR and MET genes from the NCI-60 cell lines. Sequencing data from these libraries demonstrates excellent uniformity in representation between amplicons and across samples. We will present data mapping mutations within these genes across the NCI-60, and discuss the use of Access Array enrichment panels in monitoring mutations across large patient populations.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1147.

Quantifying EGFR Alterations in the Lung Cancer Genome with Nanofluidic Digital PCR Arrays

Background: The EGFR [epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)] gene is known to harbor genomic alterations in advanced lung cancer involving gene amplification and kinase mutations that predict the clinical response to EGFR-targeted inhibitors. Methods for detecting such molecular changes in lung cancer tumors are desirable.

Methods: We used a nanofluidic digital PCR array platform and 16 cell lines and 20 samples of genomic DNA from resected tumors (stages I–III) to quantify the relative numbers of copies of the EGFR gene and to detect mutated EGFR alleles in lung cancer. We assessed the relative number of EGFR gene copies by calculating the ratio of the number of EGFR molecules (measured with a 6-carboxyfluorescein–labeled Scorpion™ assay) to the number of molecules of the single-copy gene RPP30 (ribonuclease P/MRP 30kDa subunit) (measured with a 6-carboxy-X-rhodamine–labeled TaqMan™ assay) in each panel. To assay for the EGFR L858R (exon 21) mutation and exon 19 in-frame deletions, we used the ARMS™ and Scorpion technologies in a DxS/Qiagen EGFR29 Mutation Test Kit for the digital PCR array.

Results: The digital array detected and quantified rare gefitinib/erlotinib-sensitizing EGFR mutations (0.02%–9.26% abundance) that were present in formalin-fixed, paraffin-embedded samples of early-stage resectable lung tumors without an associated increase in gene copy number. Our results also demonstrated the presence of intratumor molecular heterogeneity for the clinically relevant EGFR mutated alleles in these early-stage lung tumors.

Conclusions: The digital PCR array platform allows characterization and quantification of oncogenes, such as EGFR, at the single-molecule level. Use of this nanofluidics platform may provide deeper insight into the specific roles of clinically relevant kinase mutations during different stages of lung tumor progression and may be useful in predicting the clinical response to EGFR-targeted inhibitors.