Recent CIG publications Archive

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Methods Mol Biol.: auth.: group Dion

 2020;2056:255-268. doi: 10.1007/978-1-4939-9784-8_16.

GFP Reporters to Monitor Instability and Expression of Expanded CAG/CTG Repeats.

Abstract

Expanded CAG/CTG repeats are genetically unstable and, upon expression, cause neurological and neuromuscular diseases. The molecular mechanisms of repeat instability and expression remain poorly understood despite their importance for the pathogenesis of a family of 14 devastating human diseases. This is in part because conventional assays are tedious and time-consuming. Recently, however, GFP-based reporters have been designed to provide a rapid and reliable means of assessing these parameters. Here we provide protocols for quantifying repeat instability and expression using a GFP-based chromosomal reporter and the newly developed ParB/ANCHOR-mediated Inducible Targeting (PInT) and how to validate the results.

KEYWORDS:

DNA repair; Expanded CAG/CTG repeat diseases; GFP reporters; Gene expression; Genome stability

PMID: 31586353

 

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PLoS Genet.: auth.: group Hamaratoglu

 2019 Sep 30;15(9):e1008396. doi: 10.1371/journal.pgen.1008396. eCollection 2019 Sep.

Ferritin heavy chain protects the developing wing from reactive oxygen species and ferroptosis.

Abstract

The interplay between signalling pathways and metabolism is crucial for tissue growth. Yet, it remains poorly understood. Here, we studied the consequences of modulating iron metabolism on the growth of Drosophila imaginal discs. We find that reducing the levels of the ferritin heavy chain in the larval wing discs leads to drastic growth defects, whereas light chain depletion causes only minor defects. Mutant cell clones for the heavy chain lack the ability to compete against Minute mutant cells. Reactive oxygen species (ROS) accumulate in wing discs with reduced heavy chain levels, causing severe mitochondrial defects and ferroptosis. Preventing ROS accumulation alleviates some of the growth defects. We propose that the increased expression of ferritin in hippo mutant cells may protect against ROS accumulation.

PMID: 31568497

 

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Genes (Basel): auth.: group Gambetta

 2019 Sep 28;10(10). pii: E767. doi: 10.3390/genes10100767.

The Role of Insulation in Patterning Gene Expression.

Abstract

Development is orchestrated by regulatory elements that turn genes ON or OFF in precise spatial and temporal patterns. Many safety mechanisms prevent inappropriate action of a regulatory element on the wrong gene promoter. In flies and mammals, dedicated DNA elements (insulators) recruit protein factors (insulator binding proteins, or IBPs) to shield promoters from regulatory elements. In mammals, a single IBP called CCCTC-binding factor (CTCF) is known, whereas genetic and biochemical analyses in Drosophila have identified a larger repertoire of IBPs. How insulators function at the molecular level is not fully understood, but it is currently thought that they fold chromosomes into conformations that affect regulatory element-promoter communication. Here, we review the discovery of insulators and describe their properties. We discuss recent genetic studies in flies and mice to address the question: Is gene insulation important for animal development? Comparing and contrasting observations in these two species reveal that they have different requirements for insulation, but that insulation is a conserved and critical gene regulation strategy.

KEYWORDS:

CTCF; Drosophila; IBP; gene insulation; gene regulation; genome topology; insulator; mouse

PMID: 31569427

 

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Mol Metab.: auth.: group Thorens

 2019 Sep;27S:S147-S154. doi: 10.1016/j.molmet.2019.06.008.

Use of preclinical models to identify markers of type 2 diabetes susceptibility and novel regulators of insulin secretion – A step towards precision medicine.

Abstract

BACKGROUND:

Progression from pre-diabetes to type 2 diabetes (T2D) and from T2D to insulin requirement proceeds at very heterogenous rates among patient populations, and the risk of developing different types of secondary complications is also different between patients. The diagnosis of pre-diabetes and T2D solely based on blood glucose measurements cannot capture this heterogeneity, thereby preventing proposition of therapeutic strategies adapted to individual needs and pathogenetic mechanisms. There is, thus, a need to identify novel means to stratify patient populations based on a molecular knowledge of the diverse underlying causes of the disease. Such knowledge would form the basis for a precision medicine approach to preventing and treating T2D according to the need of identified patient subgroups as well as allowing better follow up of pharmacological treatment.

SCOPE OF REVIEW:

Here, we review a systems biology approach that aims at identifying novel biomarkers for T2D susceptibility and identifying novel beta-cell and insulin target tissue genes that link the selected plasma biomarkers with insulin secretion and insulin action. This work was performed as part of two Innovative Medicine Initiative projects. The focus of the review will be on the use of preclinical models to find biomarker candidates for T2D prediction and novel regulators of beta-cell function. We will demonstrate that the study of mice with different genetic architecture and widely different adaptation to metabolic stress can be a powerful approach to identify biomarkers of T2D susceptibility in humans or for the identification of so far unrecognized genes controlling beta-cell function.

MAJOR CONCLUSIONS:

The examples developed in this review will highlight the power of the systems biology approach, in particular as it allowed the discovery of dihydroceramide as a T2D biomarker candidate in mice and humans and the identification and characterization of novel regulators of beta-cell function.

KEYWORDS:

Beta-cells; Biomarkers; Ceramides; Elongase; Insulin secretion; Pancreatic islets; Sphingolipids; Type 2 diabetes

PMID: 31500826

 

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Mol Metab.: auth.: group Thorens

 2019 Sep;27S:S147-S154. doi: 10.1016/j.molmet.2019.06.008.

Use of preclinical models to identify markers of type 2 diabetes susceptibility and novel regulators of insulin secretion – A step towards precision medicine.

Abstract

BACKGROUND:

Progression from pre-diabetes to type 2 diabetes (T2D) and from T2D to insulin requirement proceeds at very heterogenous rates among patient populations, and the risk of developing different types of secondary complications is also different between patients. The diagnosis of pre-diabetes and T2D solely based on blood glucose measurements cannot capture this heterogeneity, thereby preventing proposition of therapeutic strategies adapted to individual needs and pathogenetic mechanisms. There is, thus, a need to identify novel means to stratify patient populations based on a molecular knowledge of the diverse underlying causes of the disease. Such knowledge would form the basis for a precision medicine approach to preventing and treating T2D according to the need of identified patient subgroups as well as allowing better follow up of pharmacological treatment.

SCOPE OF REVIEW:

Here, we review a systems biology approach that aims at identifying novel biomarkers for T2D susceptibility and identifying novel beta-cell and insulin target tissue genes that link the selected plasma biomarkers with insulin secretion and insulin action. This work was performed as part of two Innovative Medicine Initiative projects. The focus of the review will be on the use of preclinical models to find biomarker candidates for T2D prediction and novel regulators of beta-cell function. We will demonstrate that the study of mice with different genetic architecture and widely different adaptation to metabolic stress can be a powerful approach to identify biomarkers of T2D susceptibility in humans or for the identification of so far unrecognized genes controlling beta-cell function.

MAJOR CONCLUSIONS:

The examples developed in this review will highlight the power of the systems biology approach, in particular as it allowed the discovery of dihydroceramide as a T2D biomarker candidate in mice and humans and the identification and characterization of novel regulators of beta-cell function.

KEYWORDS:

Beta-cells; Biomarkers; Ceramides; Elongase; Insulin secretion; Pancreatic islets; Sphingolipids; Type 2 diabetes

PMID: 31500826

 

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Neuroimage.: co-auth.: A.Reymond

 2019 Sep 5:116155. doi: 10.1016/j.neuroimage.2019.116155. [Epub ahead of print]

Developmental trajectories of neuroanatomical alterations associated with the 16p11.2 Copy Number Variations.

Abstract

Most of human genome is present in two copies (maternal and paternal). However, segments of the genome can be deleted or duplicated, and many of these genomic variations (known as Copy Number Variants) are associated with psychiatric disorders. 16p11.2 copy number variants (breakpoint 4-5) confer high risk for neurodevelopmental disorders and are associated with structural brain alterations of large effect-size. Methods used in previous studies were unable to investigate the onset of these alterations and whether they evolve with age. In this study, we aim at characterizing age-related effects of 16p11.2 copy number variants by analyzing a group with a broad age range including younger individuals. A large normative developmental dataset was used to accurately adjust for effects of age. We normalized volumes of segmented brain regions as well as volumes of each voxel defined by tensor-based morphometry. Results show that the total intracranial volumes, the global gray and white matter volumes are respectively higher and lower in deletion and duplication carriers compared to control subjects at 4.5 years of age. These differences remain stable through childhood, adolescence and adulthood until 23 years of age (range: 0.5 to 1.0 Z-score). Voxel-based results are consistent with previous findings in 16p11.2 copy number variant carriers, including increased volume in the calcarine cortex and insula in deletions, compared to controls, with an inverse effect in duplication carriers (1.0 Z-score). All large effect-size voxel-based differences are present at 4.5 years and seem to remain stable until the age of 23. Our results highlight the stability of a neuroimaging endophenotype over 2 decades during which neurodevelopmental symptoms evolve at a rapid pace.

KEYWORDS:

16p11.2 Copy number variants; Brain development; Genetics; Imaging; Neurodevelopmental disorders; Normative growth trajectories

PMID: 31494251