FORGE Canada Consortium: Outcomes of a 2-Year National Rare-Disease Gene-Discovery Project

Inherited monogenic disease has an enormous impact on the well-being of children and their families. Over half of the children living with one of these conditions are without a molecular diagnosis because of the rarity of the disease, the marked clinical heterogeneity, and the reality that there are thousands of rare diseases for which causative mutations have yet to be identified. It is in this context that in 2010 a Canadian consortium was formed to rapidly identify mutations causing a wide spectrum of pediatric-onset rare diseases by using whole-exome sequencing. The FORGE (Finding of Rare Disease Genes) Canada Consortium brought together clinicians and scientists from 21 genetics centers and three science and technology innovation centers from across Canada. From nation-wide requests for proposals, 264 disorders were selected for study from the 371 submitted; disease-causing variants (including in 67 genes not previously associated with human disease; 41 of these have been genetically or functionally validated, and 26 are currently under study) were identified for 146 disorders over a 2-year period. Here, we present our experience with four strategies employed for gene discovery and discuss FORGE’s impact in a number of realms, from clinical diagnostics to the broadening of the phenotypic spectrum of many diseases to the biological insight gained into both disease states and normal human development. Lastly, on the basis of this experience, we discuss the way forward for rare-disease genetic discovery both in Canada and internationally.     

Evaluation of desialylation during 2-amino benzamide labeling of asparagine-linked oligosaccharides

Labeling of released asparagine-linked (N-linked) oligosaccharides from glycoproteins is commonly performed to aid in the separation and detection of the oligosaccharide. Of the many available oligosaccharide labels, 2-amino benzamide (2-AB) is a popular choice for providing a fluorescent product. The derivatization conditions can potentially lead to oligosaccharide desialylation. This work evaluated the extent of sialic acid loss during 2-AB labeling of N-linked oligosaccharides released from bovine fetuin, polyclonal human serum immunoglobulin G (IgG), and human α₁-acid glycoprotein (AGP) as well as of sialylated oligosaccharide reference standards and found that for more highly sialylated oligosaccharides the loss is greater than the <2% value commonly cited. Manufacturers of glycoprotein biotherapeutics need to produce products with a consistent state of sialylation and, therefore, require an accurate assessment of glycoprotein sialylation.     

Trophic niche partitioning in communities of African annual fish: evidence from stable isotopes

Annual killifish of the genus Nothobranchius often co-occur in temporary savannah pools. Their space- and time-limited environment does not allow for any substantial habitat or temporal segregation. Coexisting species are therefore predicted to have well separated trophic niches to avoid intense food competition. Although in a previous “snapshot” study using stomach content analysis (SCA), the trophic niches of three sympatric species (N. furzeri, N. orthonotus, and N. pienaari) were found to vary among species, the difference was relatively weak and inconsistent across different sites. Here, we used the time-integrative capacity of stable isotope analysis to test whether the trophic niches of sympatric Mozambican Nothobranchius are more distinct over a long-term period. Analysis of carbon and nitrogen stable isotopes separated the trophic niche and trophic position of N. pienaari but failed to find any difference between N. furzeri/N. kadleci and N. orthonotus. No segregation was found at the sites with low prey diversity. In contrast, SCA identified N. orthonotus as the species with the most distinct trophic niche. We discuss the effect of prey diversity and different sensitivities of stomach content and stable isotope analysis in general and conclude that the trophic niches of the three sympatric Nothobranchius species are well separated.     

C-type natriuretic peptide (CNP) signal peptide fragments are present in the human circulation

Background

Signal peptides may be novel biomarkers in cardiovascular diseases.

Methods

We developed a novel immunoassay to the signal peptide of preproCNP (CNPsp) and used this to document circulating venous concentrations of CNPsp in normal healthy volunteers (n = 109), regional plasma CNPsp concentrations in patients undergoing clinically indicated catheterisation (n = 24) and temporal CNPsp concentrations in patients with ST-elevation myocardial infarction (STEMI) <4 h after symptom onset (n = 8). The structure/sequence of circulating CNPsp was confirmed by tandem mass spectrometry (MS/MS).

Results

In normal human plasma, CNPsp was detectable at levels higher than NT-proCNP (74 ± 17 vs. 20 ± 5.5 pmol/L). There was no correlation between NTproCNP and CNPsp, but plasma concentrations of sibling signal peptides – CNPsp and BNPsp – were strongly correlated (r = 0.532, P < 0.001). In patients undergoing catheterisation, there were significant arterio-venous step-ups in CNPsp concentrations across the heart (P < 0.01) and kidney (P < 0.01). Arterial concentrations of CNPsp significantly correlated with heart rate (r = 0.446, P < 0.05). In STEMI patients, plasma concentrations of CNPsp showed a biphasic elevation pattern between 6 and 12 h after symptom onset, with 12 h values significantly elevated (∼3-fold) compared with levels at presentation (P < 0.05). MS/MS verified circulating CNPsp to be preproCNP(14–23) and preproCNP(16–23) peptides.

Conclusions

This is the first report of a circulating preproCNP derived signal peptide. Given the clear cardiac and renal secretion profiles of CNPsp and its response in STEMI patients, further studies on potential biological functions and biomarker applications of CNPsp in cardiovascular disease are warranted.     

Physiological and molecular analysis of the interactive effects of feeding and high environmental ammonia on branchial ammonia excretion and Na+ uptake in freshwater rainbow trout

Recently, a “Na⁺/NH₄ ⁺ exchange complex” model has been proposed for ammonia excretion in freshwater fish. The model suggests that ammonia transport occurs via Rhesus (Rh) glycoproteins and is facilitated by gill boundary layer acidification attributable to the hydration of CO₂ and H⁺ efflux by Na⁺/H⁺ exchanger (NHE-2) and H⁺-ATPase. The latter two mechanisms of boundary layer acidification would occur in conjunction with Na⁺ influx (through a Na⁺ channel energized by H⁺-ATPase and directly via NHE-2). Here, we show that natural ammonia loading via feeding increases branchial mRNA expression of Rh genes, NHE-2, and H⁺-ATPase, as well as H⁺-ATPase activity in juvenile trout, similar to previous findings with ammonium salt infusions and high environmental ammonia (HEA) exposure. The associated increase in ammonia excretion occurs in conjunction with a fourfold increase in Na⁺ influx after a meal. When exposed to HEA (1.5 mmol/l NH₄HCO₃ at pH 8.0), both unfed and fed trout showed differential increases in mRNA expression of Rhcg2, NHE-2, and H⁺-ATPase, but H⁺-ATPase activity remained at control levels. Unfed fish exposed to HEA displayed a characteristic reversal of ammonia excretion, initially uptaking ammonia, whereas fed fish (4 h after the meal) did not show this reversal, being able to immediately excrete ammonia against the gradient imposed by HEA. Exposure to HEA also led to a depression of Na⁺ influx, demonstrating that ammonia excretion can be uncoupled from Na⁺ influx. We suggest that the efflux of H⁺, rather than Na⁺ influx itself, is critical to the facilitation of ammonia excretion.     

Chemical changes in soil and soil solution after calcium silicate addition to a northern hardwood forest

Liming has been used to mitigate effects of acidic deposition in forest ecosystems. This study was designed to examine the effects of calcium (Ca) supply on the spatial patterns and the relations between soil and soil solution chemistry in a base-poor forest watershed. Watershed 1 at the Hubbard Brook Experimental Forest in New Hampshire, USA was experimentally treated with wollastonite (CaSiO₃) in October, 1999. Exchangeable Ca (Ex-Ca), soil pH_s (in 0.01 M CaCl₂), effective cation exchange capacity (CEC_e), and effective base saturation (BS_e) increased, while exchangeable acidity (Ex-Acid) decreased in organic soil horizons in 2000 and 2002. Mineral soils experienced either small increases in Ex-Ca, pH_s, CEC_e, BS_e, small decreases in Ex-Acid or no changes. Thus, most of the added Ca remained in the forest floor during the study period. Prior to the treatment the BS_e decreased with increasing elevation in organic and mineral soil horizons. This spatial pattern changed significantly in the forest floor after the treatment, suggesting that soils at higher elevations were more responsive to the chemical addition than at lower elevations. Soil solutions draining the forest floor responded to the treatment by increases in concentrations of Ca, dissolved silica, pH, and acid neutralizing capacity (ANC), and a decrease in inorganic monomeric Al (Al_i). Treatment effects diminished with increasing soil depth and decreasing elevation. Positive correlations between Ca/total monomeric Al (Al_m) in soil solution and Ex-Ca/Ex-Al ratios in soil indicated that changes in the chemistry of soils significantly influenced the chemistry of soil water, and that Ca derived from the dissolution of wollastonite mitigated the mobilization of Al within the experimental watershed.     

Linking monitoring and modelling: can long-term datasets be used more effectively as a basis for large-scale prediction?

Data from long-term monitoring sites are vital for biogeochemical process understanding, and for model development. Implicitly or explicitly, information provided by both monitoring and modelling must be extrapolated in order to have wider scientific and policy utility. In many cases, large-scale modelling utilises little of the data available from long-term monitoring, instead relying on simplified models and limited, often highly uncertain, data for parameterisation. Here, we propose a new approach whereby outputs from model applications to long-term monitoring sites are upscaled to the wider landscape using a simple statistical method. For the 22 lakes and streams of the UK Acid Waters Monitoring Network (AWMN), standardised concentrations (Z scores) for Acid Neutralising Capacity (ANC), dissolved organic carbon, nitrate and sulphate show high temporal coherence among sites. This coherence permits annual mean solute concentrations at a new site to be predicted by back-transforming Z scores derived from observations or model applications at other sites. The approach requires limited observational data for the new site, such as annual mean estimates from two synoptic surveys. Several illustrative applications of the method suggest that it is effective at predicting long-term ANC change in upland surface waters, and may have wider application. Because it is possible to parameterise and constrain more sophisticated models with data from intensively monitored sites, the extrapolation of model outputs to policy relevant scales using this approach could provide a more robust, and less computationally demanding, alternative to the application of simple generalised models using extrapolated input data.     

Calculations of binding affinity between C8-substituted GTP analogs and the bacterial cell-division protein FtsZ

The FtsZ protein is a self-polymerizing GTPase that plays a central role in bacterial cell division. Several C8-substituted GTP analogs are known to inhibit the polymerization of FtsZ by competing for the same binding site as its endogenous activating ligand GTP. Free energy calculations of the relative binding affinities to FtsZ for a set of five C8-substituted GTP analogs were performed. The calculated values agree well with the available experimental data, and the main contribution to the free energy differences is determined to be the conformational restriction of the ligands. The dihedral angle distributions around the glycosidic bond of these compounds in water are known to vary considerably depending on the physicochemical properties of the substituent at C8. However, within the FtsZ protein, this substitution has a negligible influence on the dihedral angle distributions, which fall within the narrow range of −140° to −90° for all investigated compounds. The corresponding ensemble average of the coupling constants ³ J(C4,H1′) is calculated to be 2.95 ± 0.1 Hz. The contribution of the conformational selection of the GTP analogs upon binding was quantified from the corresponding populations. The obtained restraining free energy values follow the same trend as the relative binding affinities to FtsZ, indicating their dominant contribution.