Post genome-wide association studies of novel genes associated with type 2 diabetes show gene-gene interaction and high predictive value

Background

Recently, several Genome Wide Association (GWA) studies in populations of European descent have identified and validated novel single nucleotide polymorphisms (SNPs), highly associated with type 2 diabetes (T2D). Our aims were to validate these markers in other European and non-European populations, then to assess their combined effect in a large French study comparing T2D and normal glucose tolerant (NGT) individuals.

Methodology/Principal Findings

In the same French population analyzed in our previous GWA study (3,295 T2D and 3,595 NGT), strong associations with T2D were found for CDKAL1 (OR_rs7756992 = 1.30[1.19–1.42], P = 2.3×10⁻⁹), CDKN2A/2B (OR_rs10811661 = 0.74[0.66–0.82], P = 3.5×10⁻⁸) and more modestly for IGFBP2 (OR_rs1470579 = 1.17[1.07–1.27], P = 0.0003) SNPs. These results were replicated in both Israeli Ashkenazi (577 T2D and 552 NGT) and Austrian (504 T2D and 753 NGT) populations (except for CDKAL1) but not in the Moroccan population (521 T2D and 423 NGT). In the overall group of French subjects (4,232 T2D and 4,595 NGT), IGFBP2 and CXCR4 synergistically interacted with (LOC38776, SLC30A8, HHEX) and (NGN3, CDKN2A/2B), respectively, encoding for proteins presumably regulating pancreatic endocrine cell development and function. The T2D risk increased strongly when risk alleles, including the previously discovered T2D-associated TCF7L2 rs7903146 SNP, were combined (8.68-fold for the 14% of French individuals carrying 18 to 30 risk alleles with an allelic OR of 1.24). With an area under the ROC curve of 0.86, only 15 novel loci were necessary to discriminate French individuals susceptible to develop T2D.

Conclusions/Significance

In addition to TCF7L2, SLC30A8 and HHEX, initially identified by the French GWA scan, CDKAL1, IGFBP2 and CDKN2A/2B strongly associate with T2D in French individuals, and mostly in populations of Central European descent but not in Moroccan subjects. Genes expressed in the pancreas interact together and their combined effect dramatically increases the risk for T2D, opening avenues for the development of genetic prediction tests.     

Modulation of drought resistance by the abscisic acid receptor PYL5 through inhibition of clade A PP2Cs

Abscisic acid (ABA) is a key phytohormone involved in adaption to environmental stress and regulation of plant development. Clade A protein phosphatases type 2C (PP2Cs), such as HAB1, are key negative regulators of ABA signaling in Arabidopsis. To obtain further insight into regulation of HAB1 function by ABA, we have screened for HAB1‐interacting partners using a yeast two‐hybrid approach. Three proteins were identified, PYL5, PYL6 and PYL8, which belong to a 14‐member subfamily of the Bet v1‐like superfamily. HAB1–PYL5 interaction was confirmed using BiFC and co‐immunoprecipitation assays. PYL5 over‐expression led to a globally enhanced response to ABA, in contrast to the opposite phenotype reported for HAB1‐over‐expressing plants. F₂ plants that over‐expressed both HAB1 and PYL5 showed an enhanced response to ABA, indicating that PYL5 antagonizes HAB1 function. PYL5 and other members of its protein family inhibited HAB1, ABI1 and ABI2 phosphatase activity in an ABA‐dependent manner. Isothermal titration calorimetry revealed saturable binding of (+)ABA to PYL5, with K_d values of 1.1 μm or 38 nm in the absence or presence of the PP2C catalytic core of HAB1, respectively. Our work indicates that PYL5 is a cytosolic and nuclear ABA receptor that activates ABA signaling through direct inhibition of clade A PP2Cs. Moreover, we show that enhanced resistance to drought can be obtained through PYL5‐mediated inhibition of clade A PP2Cs.     

Growth arrest of proadipocytes at a distinct predifferentiation G1 state associated with cytotoxic responsiveness to 8-bromo cyclic AMP

The control of cell proliferation can result from the coupling of growth arrest and differentiation. In this regard, we recently demonstrated that growth arrest which precedes the differentiation of 3T3 T proadipocytes must occur at a distinct state in the G1 phase of the cell cycle (GD). Cells arrested at GD differ in several biological parameters from cells arrested in G1 at other states induced by either serum deprivation (GS) or nutrient deficiency (GN). Specifically, GD-arrested cells can differentiate in the absence of DNA synthesis and GD-arrested cells can be induced to proliferate when stimulated with 1-methyl-3-isobutylxanthine; GS- and GN-arrested cells cannot. In addition, GD-, GS- and GN-arrested cells reside at topographically distinct states in G1. We now report that GD-arrested proadipocytes are also distinct in that they are highly sensitive to a cytotoxic effect of 8-bromocyclic AMP, whereas GS- and GN-arrested cells are not.     

Detection of the elusive Dwarf sperm whale (Kogia sima) using environmental DNA at Malpelo island (Eastern Pacific,Colombia)

1. Monitoring large marine mammals is challenging due to their low abundances in general, an ability to move over large distances and wide geographical range sizes.
2. The distribution of the pygmy (Kogia breviceps) and dwarf (Kogia sima) sperm whales is informed by relatively rare sightings, which does not permit accurate estimates of their distribution ranges. Hence, their conservation status has long remained Data Deficient (DD) in the Red list of the International Union for Conservation of Nature (IUCN), which prevent appropriate conservation measures.
3. Environmental DNA (eDNA) metabarcoding uses DNA traces left by organisms in their environments to detect the presence of targeted taxon, and is here proved to be useful to increase our knowledge on the distribution of rare but emblematic megafauna.
4. Retrieving eDNA from filtered surface water provides the first detection of the Dwarf sperm whale (Kogia sima) around the remote Malpelo island (Colombia).
5. Environmental DNA collected during oceanic missions can generate better knowledge on rare but emblematic animals even in regions that are generally well sampled for other taxa.