Hormones and the Intestinal Absorption of Calcium and Phosphate in Man

The landscape of GWAS validation; systematic review identifying 309 validated non-coding variants across 130 human diseases

Background

The remarkable growth of genome-wide association studies (GWAS) has created a critical need to experimentally validate the disease-associated variants, 90% of which involve non-coding variants.

Methods

To determine how the field is addressing this urgent need, we performed a comprehensive literature review identifying 36,676 articles. These were reduced to 1454 articles through a set of filters using natural language processing and ontology-based text-mining. This was followed by manual curation and cross-referencing against the GWAS catalog, yielding a final set of 286 articles.

Results

We identified 309 experimentally validated non-coding GWAS variants, regulating 252 genes across 130 human disease traits. These variants covered a variety of regulatory mechanisms. Interestingly, 70% (215/309) acted through cis-regulatory elements, with the remaining through promoters (22%, 70/309) or non-coding RNAs (8%, 24/309). Several validation approaches were utilized in these studies, including gene expression (n = 272), transcription factor binding (n = 175), reporter assays (n = 171), in vivo models (n = 104), genome editing (n = 96) and chromatin interaction (n = 33).

Conclusions

This review of the literature is the first to systematically evaluate the status and the landscape of experimentation being used to validate non-coding GWAS-identified variants. Our results clearly underscore the multifaceted approach needed for experimental validation, have practical implications on variant prioritization and considerations of target gene nomination. While the field has a long way to go to validate the thousands of GWAS associations, we show that progress is being made and provide exemplars of validation studies covering a wide variety of mechanisms, target genes, and disease areas.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12920-022-01216-w.

Bone involvement in exogenous hypercortisolism

Corticosteroids remain a key component in the management of many disorders. Bone loss resulting from long-term administration of these drugs is common and osteoporosis induced by corticosteroids is the most frequent cause of secondary osteoporosis in nearly 50% of individuals on chronic corticosteroid therapy suffering from an osteoporotic fracture at some point. This article reviews the epidemiology and pathogenesis of glucocorticoid-induced osteoporosis.

Effects of high doses of corticosteroids on bone metabolism

The effects of a chronic treatment with corticosteroids on bone are well known, but few data are available regarding the acute effect of these drugs on bone turnover. This study was aimed at evaluating the effects of high doses of corticosteroids administered for a short period on bone metabolism. We assessed 23 subjects (15 women and 8 men) suffering from multiple sclerosis and treated with methylprednisolone (1 g i.v. for 10 days) followed by oral prednisone for 9 days; patients affected by diseases involving bone or treated during the previous 6 months with drugs influencing bone metabolism were excluded. We observed a significant decrease of ALP and bone glia protein (BGP), in these subjects, and a significant sudden increase of urinary calcium/creatinine and urinary cross-laps after 3 days of treatment. All of these parameters, except urinary calcium/creatinine, returned to basal levels after 30 days from the beginning of treatment (11 days after the interruption of corticosteroids administration). Serum phosphorus showed a significant decrease after 3 days of treatment, but returned to basal levels after 10 days. These data suggest that high doses of corticosteroids administered for a short period are able to induce an increase of bone resorption and a decrease of bone formation; moreover, bone turnover returns to basal levels when the treatment is stopped.