Unreliability of genotyping arrays for detecting very rare variants in human genetic studies: Example from a recent study of MC4R

Polymorphisms in drug-metabolizing genes and urinary bladder cancer susceptibility and prognosis: Possible impacts and future management

Epidemiological studies have shown the association of genetic variants with risks of occupational and environmentally induced cancers, including bladder (BC). The current review summarizes the effects of variants in genes encoding phase I and II enzymes in well-designed studies to highlight their contribution to BC susceptibility and prognosis. Polymorphisms in genes codifying drug-metabolizing proteins are of particular interest because of their involvement in the metabolism of exogenous genotoxic compounds, such as tobacco and agrochemicals. The prognosis between muscle-invasive and non-muscle-invasive diseases is very different, and it is difficult to predict which will progress worse. Web of Science, PubMed, and Medline were searched to identify studies published between January 1, 2010, and February 2023. We included 73 eligible studies, more than 300 polymorphisms, and 46 genes/loci. The most studied candidate genes/loci of phase I metabolism were CYP1B1, CYP1A1, CYP1A2, CYP3A4, CYP2D6, CYP2A6, CYP3E1, and ALDH2, and those in phase II were GSTM1, GSTT1, NAT2, GSTP1, GSTA1, GSTO1, and UGT1A1. We used the 46 genes to construct a network of proteins and to evaluate their biological functions based on the Reactome and KEGG databases. Lastly, we assessed their expression in different tissues, including normal bladder and BC samples. The drug-metabolizing pathway plays a relevant role in BC, and our review discusses a list of genes that could provide clues for further exploration of susceptibility and prognostic biomarkers.

G protein-coupled receptor (GPCR) gene variants and human genetic disease

Genetic variations in the genes encoding G protein-coupled receptors (GPCRs) can disrupt receptor structure and function, which can result in human genetic diseases. Disease-causing mutations have been reported in at least 55 GPCRs for more than 66 monogenic diseases in humans. The spectrum of pathogenic and likely pathogenic variants includes loss of function variants that decrease receptor signaling on one extreme and gain of function that may result in biased signaling or constitutive activity, originally modeled on prototypical rhodopsin GPCR variants identified in retinitis pigmentosa, on the other. GPCR variants disrupt ligand binding, G protein coupling, accessory protein function, receptor desensitization and receptor recycling. Next generation sequencing has made it possible to identify variants of uncertain significance (VUS). We discuss variants in receptors known to result in disease and in silico strategies for disambiguation of VUS such as sorting intolerant from tolerant and polymorphism phenotyping. Modeling of variants has contributed to drug development and precision medicine, including drugs that target the melanocortin receptor in obesity and interventions that reverse loss of gonadotropin-releasing hormone receptor from the cell surface in idiopathic hypogonadotropic hypogonadism. Activating and inactivating variants of the calcium sensing receptor (CaSR) gene that are pathogenic in familial hypocalciuric hypercalcemia and autosomal dominant hypocalcemia have enabled the development of calcimimetics and calcilytics. Next generation sequencing has continued to identify variants in GPCR genes, including orphan receptors, that contribute to human phenotypes and may have therapeutic potential. Variants of the CaSR gene, some encoding an arginine-rich region that promotes receptor phosphorylation and intracellular retention, have been linked to an idiopathic epilepsy syndrome. Agnostic strategies have identified variants of the pyroglutamylated RF amide peptide receptor gene in intellectual disability and G protein-coupled receptor 39 identified in psoriatic arthropathy. Coding variants of the G protein-coupled receptor L1 (GPR37L1) orphan receptor gene have been identified in a rare familial progressive myoclonus epilepsy. The study of the role of GPCR variants in monogenic, Mendelian phenotypes has provided the basis of modeling the significance of more common variants of pharmacogenetic significance.

Recommendations for risk allele evidence curation, classification, and reporting from the ClinGen Low Penetrance/Risk Allele Working Group

PURPOSE

Genetic variants at the low end of the penetrance spectrum have historically been challenging to interpret because their high population frequencies exceed the disease prevalence of the associated condition, leading to a lack of clear segregation between the variant and disease. There is currently substantial variation in the classification of these variants, and no formal classification framework has been widely adopted. The Clinical Genome Resource Low Penetrance/Risk Allele Working Group was formed to address these challenges and promote harmonization within the clinical community.

METHODS

The work presented here is the product of internal and community Likert-scaled surveys in combination with expert consensus within the Working Group.

RESULTS

We formally recognize risk alleles and low-penetrance variants as distinct variant classes from those causing highly penetrant disease that require special considerations regarding their clinical classification and reporting. First, we provide a preferred terminology for these variants. Second, we focus on risk alleles and detail considerations for reviewing relevant studies and present a framework for the classification these variants. Finally, we discuss considerations for clinical reporting of risk alleles.

CONCLUSION

These recommendations support harmonized interpretation, classification, and reporting of variants at the low end of the penetrance spectrum.

Array genotyping as diagnostic approach in medical genetics

Genotyping arrays are by far the most widely used genetic tests but are not generally utilized for diagnostic purposes in a medical context. In the present study, we examined the diagnostic value of a standard genotyping array (Illumina Global Screening Array) for a range of indications. Applications included stand‐alone testing for specific variants (32 variants in 10 genes), first‐tier array variant screening for monogenic conditions (10 different autosomal recessive metabolic diseases), and diagnostic workup for specific conditions caused by variants in multiple genes (suspected familial breast and ovarian cancer, and hypercholesterolemia). Our analyses showed a high analytical sensitivity and specificity of array‐based analyses for validated and non‐validated variants, and identified pitfalls that require attention. Ethical‐legal assessment highlighted the need for a software solution that allows for individual indication‐based consent and the reliable exclusion of non‐consented results. Cost/time assessment revealed excellent performance of diagnostic array analyses, depending on indication, proband data, and array design. We have implemented some analyses in our diagnostic portfolio, but array optimization is required for the implementation of other indications.

Islet MC4R Regulates PC1/3 to Improve Insulin Secretion in T2DM Mice via the cAMP and β-arrestin-1 Pathways

Melanocortin-4 receptor (MC4R) plays an important role in energy balance regulation and insulin secretion. It has been demonstrated that in the pancreas, it is expressed in islet α and β cells, wherein it is significantly correlated with insulin and glucagon-like peptide-1 (GLP-1) secretion. However, the molecular mechanism by which it regulates islet function is still unclear. Therefore, in this study, our aim was to clarify the signaling and target genes involved in the regulation of insulin and GLP-1 secretion by islet MC4R. The results obtained showed that in islet cells, the expression of prohormone convertase 1/3 (PC1/3), which is correlated with islet GLP-1 and insulin secretion, increased significantly under the action of the MC4R agonist, NDP-α-MSH, but decreased under the action of the MC4R antagonist, AgRP. Additionally, we observed that to exert their regulatory functions in the islets, cAMP and β-arrestin-1 acted as important signaling mediators of MC4R, and compared with control islets, the cAMP, PKA, and β-arrestin-1 levels corresponding to NDP-α-MSH-treated islets were significantly elevated; however, in AgRP-treated islets, their levels decreased significantly. Islets treated with the PKA inhibitor, H89, and the ERK1/2 inhibitor, PD98059, also showed significant decreases in PC1/3 expression level, indicating that the cAMP and β-arrestin-1 pathways are significantly correlated with PC1/3 expression. These findings suggest that islet MC4R possibly affects PC1/3 expression via the cAMP and β-arrestin-1 pathways to regulate GLP-1 and insulin secretion. These results provide a new theoretical basis for targeting the molecular mechanism of type 2 diabetes mellitus.