Correction: Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

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Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

PurposeThe 2015 American College of Medical Genetics and Genomics-Association for Molecular Pathology (ACMG-AMP) guidelines were a major step toward establishing a common framework for variant classification. In practice, however, several aspects of the guidelines lack specificity, are subject to varied interpretations, or fail to capture relevant aspects of clinical molecular genetics. A simple implementation of the guidelines in their current form is insufficient for consistent and comprehensive variant classification.MethodsWe undertook an iterative process of refining the ACMG-AMP guidelines. We used the guidelines to classify more than 40,000 clinically observed variants, assessed the outcome, and refined the classification criteria to capture exceptions and edge cases. During this process, the criteria evolved through eight major and minor revisions.ResultsOur implementation: (i) separated ambiguous ACMG-AMP criteria into a set of discrete but related rules with refined weights; (ii) grouped certain criteria to protect against the overcounting of conceptually related evidence; and (iii) replaced the "clinical criteria" style of the guidelines with additive, semiquantitative criteria.ConclusionSherloc builds on the strong framework of 33 rules established by the ACMG-AMP guidelines and introduces 108 detailed refinements, which support a more consistent and transparent approach to variant classification.

Domain-dependent clustering and genotype-phenotype analysis of LGI1 mutations in ADPEAF.

OBJECTIVE: In families with autosomal dominant partial epilepsy with auditory features (ADPEAF) with mutations in the LGI1 gene, we evaluated clustering of mutations within the gene and associations of penetrance and phenotypic features with mutation location and predicted effect (truncation or missense). METHODS: We abstracted clinical and molecular information from the literature for all 36 previously published ADPEAF families with LGI1 mutations. We used a sliding window approach to analyze mutation clustering within the gene. Each mutation was mapped to one of the gene's 2 major functional domains, N-terminal leucine-rich repeats (LRRs) and C-terminal epitempin (EPTP) repeats, and classified according to predicted effect on the encoded protein (truncation vs missense). Analyses of phenotypic features (age at onset and occurrence of auditory symptoms) in relation to mutation site and predicted effect included 160 patients with idiopathic focal unprovoked seizures from the 36 families. RESULTS: ADPEAF-causing mutations clustered significantly in the LRR domain (exons 3-5) of LGI1 (p = 0.026). Auditory symptoms were less frequent in individuals with truncation mutations in the EPTP domain than in those with other mutation type/domain combinations (58% vs 80%, p = 0.018). CONCLUSION: The LRR region of the LGI1 gene is likely to play a major role in pathogenesis of ADPEAF.

APOE genotype-function relationship: evidence of -491 A/T promoter polymorphism modifying transcription control but not type 2 diabetes risk.

BACKGROUND: The apolipoprotein E gene (APOE) coding polymorphism modifies the risks of Alzheimer's disease, type 2 diabetes, and coronary heart disease. Aside from the coding variants, single nucleotide polymorphism (SNP) of the APOE promoter has also been shown to modify the risk of Alzheimer's disease. METHODOLOGY/PRINCIPAL FINDINGS: In this study we investigate the genotype-function relationship of APOE promoter polymorphism at molecular level and at physiological level: i.e., in transcription control of the gene and in the risk of type 2 diabetes. In molecular studies, the effect of the APOE -491A/T (rs449647) polymorphism on gene transcription was accessed by dual-luciferase reporter gene assays. The -491 A to T substitution decreased the activity (p<0.05) of the cloned APOE promoter (-1017 to +406). Using the -501 to -481 nucleotide sequence of the APOE promoter as a 'bait' to screen the human brain cDNA library by yeast one-hybrid system yielded ATF4, an endoplasmic reticulum stress response gene, as one of the interacting factors. Electrophoretic-mobility-shift assays (EMSA) and chromatin immuno-precipitation (ChIP) analyses further substantiated the physical interaction between ATF4 and the APOE promoter. Over-expression of ATF4 stimulated APOE expression whereas siRNA against ATF4 suppressed the expression of the gene. However, interaction between APOE promoter and ATF4 was not -491A/T-specific. At physiological level, the genotype-function relationship of APOE promoter polymorphism was studied in type 2 diabetes. In 630 cases and 595 controls, three APOE promoter SNPs -491A/T, -219G/T (rs405509), and +113G/C (rs440446) were genotyped and tested for association with type 2 diabetes in Hong Kong Chinese. No SNP or haplotype association with type 2 diabetes was detected. CONCLUSIONS/SIGNIFICANCE: At molecular level, polymorphism -491A/T and ATF4 elicit independent control of APOE gene expression. At physiological level, no genotype-risk association was detected between the studied APOE promoter SNPs and type 2 diabetes in Hong Kong Chinese.

Apolipoprotein M gene (APOM) polymorphism modifies metabolic and disease traits in type 2 diabetes.

This study aimed at substantiating the associations of the apolipoproein M gene (APOM) with type 2 diabetes (T2D) as well as with metabolic traits in Hong Kong Chinese. In addition, APOM gene function was further characterized to elucidate its activity in cholesterol metabolism. Seventeen APOM SNPs documented in the NCBI database were genotyped. Five SNPs were confirmed in our study cohort of 1234 T2D and 606 control participants. Three of the five SNPs rs707921(C+1871A), rs707922(G+1837T) and rs805264(G+203A) were in linkage disequilibrium (LD). We chose rs707922 to tag this LD region for down stream association analyses and characterized the function of this SNP at molecular level. No association between APOM and T2D susceptibility was detected in our Hong Kong Chinese cohort. Interestingly, the C allele of rs805297 was significantly associated with T2D duration of longer than 10 years (OR = 1.245, p = 0.015). The rs707922 TT genotype was significantly associated with elevated plasma total- and LDL- cholesterol levels (p = 0.006 and p = 0.009, respectively) in T2D patients. Molecular analyses of rs707922 lead to the discoveries of a novel transcript APOM5 as well as the cryptic nature of exon 5 of the gene. Ectopic expression of APOM5 transcript confirmed rs707922 allele-dependent activity of the transcript in modifying cholesterol homeostasis in vitro. In conclusion, the results here did not support APOM as a T2D susceptibility gene in Hong Kong Chinese. However, in T2D patients, a subset of APOM SNPs was associated with disease duration and metabolic traits. Further molecular analysis proved the functional activity of rs707922 in APOM expression and in regulation of cellular cholesterol content.

First report of GLUT1 deficiency syndrome in Chinese patients with novel and hot spot mutations in SLC2A1 gene.

Glucose transporter type 1 deficiency syndrome (GLUT1DS) is increasingly recognized as a cause of various neurological disorders but a high index of suspicion is important to make the diagnosis. We report two Chinese patients with GLUT1DS, one of which had a novel mutation in the SLC2A1 gene.

T295M-associated Glut1 deficiency syndrome with normal erythrocyte 3-OMG uptake.

PURPOSE: Glucose transporter type 1 (Glut1) is expressed in vascular endothelial cells comprising blood-brain barrier. Glut1 deficiency syndrome is characterized by low cerebrospinal fluid (CSF) concentration of glucose with normoglycemia, infantile seizure, acquired microcephaly, developmental delay and ataxia. As Glut1 is also expressed in erythrocytes, the diagnosis is confirmed by a decreased uptake of 3-O-methylglucose (3-OMG) into erythrocytes. However, patients with T295M mutation in the Glut1 gene show normal 3-OMG uptake. An in vitro study has proved that the T295M affects efflux rather than influx of glucose, explaining the discrepancy. However, the normal 3-OMG uptake in erythrocytes still indicates a possibility that the phenotype associated with this particular mutation may be milder. We compared the phenotype of three T295M-associated patients with that of other Glut1-deficient patients. PATIENTS AND METHODS: Two patients are from our clinic and one is a patient reported elsewhere. The phenotype and biochemical data of patients with mutations other than T295M were obtained from a review and our previous report. RESULTS: Despite the normal 3-OMG uptake into erythrocytes, all patients with T295M showed decreased glucose levels in CSF (33, 31 and 38mg/dl, respectively). The levels were comparable to those in patients with mutations other than T295M (31±4.3mg/dl (n=45)). All patients had convulsion, ataxia, speech delay, microcephaly and spasticity. CONCLUSION: Despite the normal 3-OMG uptake in erythrocytes, phenotype of T295M-associated Glut1 deficiency was not significantly different from that of patients with a deficient 3-OMG uptake, indicating that T295M affects the glucose transport at the blood-brain barrier as much as other mutations.

n-3, but not n-6 lipid particle uptake requires cell surface anchoring.

Omega-3 (n-3) fatty acids are emerging as bioactive agents protective against cardiovascular disease. However, their cellular delivery pathways are poorly defined. Here we questioned whether the uptake of n-3 triglyceride-rich particles (TGRP) is mediated by cell surface proteoglycans (PG) using LDL receptor (LDLR)+/+ and LDLR-/- cell models. LDLR+/+ but not LDLR-/- cells showed higher n-6 over n-3 TGRP uptake. Removal of cell surface proteins and receptors by pronase markedly enhanced the uptake of n-3 but not n-6 TGRP. Lactoferrin blockage of apoE-mediated pathways decreased the uptake of n-6 TGRP by up to 85% (p<0.05) but had insignificant effect on n-3 TGRP uptake. PG removal by sodium chlorate in LDLR+/+ cells substantially reduced n-3 TGRP uptake but had little effect on n-6 TGRP uptake. Thus, while n-6 TGRP uptake is preferentially mediated by LDLR-dependent pathways, the uptake of n-3 TGRP depends more on PG and non-LDLR cell surface anchoring.

Disturbance of cellular glucose transport by two prevalently used fluoroquinolone antibiotics ciprofloxacin and levofloxacin involves glucose transporter type 1.

Dysglycemia and central nervous system (CNS) complications are the known adverse effects of fluoroquinolone antibiotics. Ciprofloxacin and levofloxacin are among the most prescribed antibiotics. In this study we demonstrate that ciprofloxacin and levofloxacin disturb glucose transport into HepG2 cells and such inhibition is associated with inhibited glucose transporter type 1 (GLUT1) function. When exposed to ciprofloxacin or levofloxacin at maximum plasma concentrations (C(max)) and 5x of C(max) concentrations, GLUT1 mRNA expression, cell surface GLUT1 protein expression and glucose uptake were significantly reduced. These findings imply that disturbed cellular glucose transport and GLUT1 function may underlie the dysglycemic and CNS effects of ciprofloxacin and levofloxacin.

Gatifloxacin affects GLUT1 gene expression and disturbs glucose homeostasis in vitro.

Gatifloxacin may induce life-threatening dysglycemia. The facilitated glucose transporter type 1 (GLUT1) protein is ubiquitously expressed in many tissues. Disturbed GLUT1 protein function weakens the systemic glycemic control and may cause dysglycemia. In this study we demonstrate that gatifloxacin modulates the transcription and reduces the expression and function of GLUT1 gene in HepG2 cells. When treated with gatifloxacin at concentrations of 3.4 mug/ml (8.4 muM) and 17 mug/ml (42 muM), GLUT1 promoter activity was stimulated by 2.8 and 3.8 folds, GLUT1 mRNA expression was decreased by 41% and 31%, and glucose uptake was decreased by 41% and 52%, respectively. Our findings imply that disturbed GLUT1 gene expression and protein function may underlie the dysglycemic effect of gatifloxacin.

Apoprotein E isoform-dependent expression and secretion of pro-inflammatory cytokines TNF-alpha and IL-6 in macrophages.

The anti-atherogenic properties of human apoprotein E-associated lipoproteins have been partially attributed to its anti-inflammatory properties. We studied if endogenously expressed apoprotein E (apoE) elicits isoform-dependent effects on pro-inflammatory cytokine expression and secretion. Mouse J774A.1 peritoneal macrophages without native expression of apoE were used to establish cell lines with stable expression of the three human apoE isoforms, apoE2, apoE3 and apoE4. In the presence of lipopolysaccharide (LPS), expression and secretion of TNF-alpha and IL-6 in cells expressing different apoE isoforms were determined by RT-PCR, immunoblotting and ELISA assays. ApoE3-expressing cells have significantly lower expression and secretion levels of the two cytokines as compared to cells with apoE2 and apoE4 expression. Such observations were accompanied with the lowest ERK1/2 activity in apoE3-expressing cells. Further study shows that the apoE isoform-dependent variations of TNF-alpha and IL-6 expression/secretion in macrophages are diminished in the presence of ERK1/2 inhibitor U0126. In conclusion, apoE elicits isoform-dependent effects on macrophage TNF-alpha and IL-6 expression as well as secretion. The ERK1/2 signaling pathways are involved in mediating such apoE isoform-dependent effects.

Three Japanese patients with glucose transporter type 1 deficiency syndrome.

We report three Japanese patients with glucose transporter type 1 deficiency syndrome (Glut1DS). Two patients had a normal erythrocyte 3-O-methylglucose (3OMG) uptake, one with a previously reported T295M substitution and the other with a novel 12-bp insertion at nt 1034-1035, ins CAGCAGCTGTCT. The third patient, with deficient 3OMG uptake, had a previously reported hot-spot mutation, R333W. All three patients responded to a ketogenic diet. All patients showed a significant improvement in ataxia, with blood beta-hydroxybutyrate (BOHB) levels ranging from 0.1 to 3mM. BOHB levels of at least 3mM were necessary to control seizures, and higher ketone levels are recommended to meet brain energy needs during development. FDG-PET scan, performed before and after a ketogenic diet in the R333W patient, did not change despite a clinical improvement. This clinical condition is treatable and early diagnosis is important.

Inhibition of cell proliferation by apolipoprotein E isoform expression.

The anti-atherogenic effects of human apolipoprotein E3 (apoE3) have been partially attributed to its anti-proliferation properties. We studied if endogenously expressed apoE elicits isoform-dependent effects on cell proliferation. Rat F111 fibroblasts without native expression of apoE were used to establish cell lines with stable expression of the three human apoE isoforms. Cell growth curve studies showed that expression of apoE isoforms prolonged cell population doubling time in an isoform-dependent manner with apoE3 showing the most potent effect followed by apoE2 and apoE4 exhibiting comparable effects. Interestingly, saturation density of cell population was significantly reduced by the expression of apoE4 isofom. Further analyses revealed that all three apoE isoforms significantly lengthened G0/G1 phase (p < 0.05) of the cell cycle and were associated with the suppression of ERK1/2 activities. However, these changes were not sufficient to explain the isoform-dependent effects of apoE expression on cell population doubling time and saturation density.

Expression and functional characterization of the putative protein 8b of the severe acute respiratory syndrome-associated coronavirus.

SARS 8b is one of the putative accessory proteins of the severe acute respiratory syndrome-associated coronavirus (SARS-CoV) with unknown functions. In this study, the cellular localization and activity of this estimated 9.6 kDa protein were examined. Confocal microscopy results indicated that SARS 8b is localized in both nucleus and cytoplasm of mammalian cells. Functional study revealed that overexpression of SARS 8b induced DNA synthesis. Coexpression of SARS 8b and SARS 6, a previously characterized SARS-CoV accessory protein, did not elicit synergistic effects on DNA synthesis.

The putative protein 6 of the severe acute respiratory syndrome-associated coronavirus: expression and functional characterization.

The SARS-CoV open reading frame 6 (ORF6) is transcribed into mRNA6 and encodes a putative 7.5 kDa accessory protein, SARS 6, with unknown function. In this study, we have confirmed the SARS 6 protein expression in lung and intestine tissues of the SARS patients and in SARS-CoV infected Vero E6 cells by immunohistochemistry. Further studies by immunoblot and confocal microscopy analyses revealed the expression and the endoplasmic reticulum (ER) localization of the recombinant SARS 6 protein in mammalian cells. Expression of SARS 6 protein in mammalian cells elicits biological activity of stimulating cellular DNA synthesis.

Sodium valproate inhibits glucose transport and exacerbates Glut1-deficiency in vitro.

Anticonvulsant sodium valproate interferes with brain glucose metabolism. The mechanism underlying such metabolic disturbance is unclear. We tested the hypothesis that sodium valproate interferes with cellular glucose transport with a focus on Glut1 since glucose transport across the blood-brain barrier relies on this transporter. Cell types enriched with Glut1 expression including human erythrocytes, human skin fibroblasts, and rat astrocytes were used to study the effects of sodium valproate on glucose transport. Sodium valproate significantly inhibited Glut1 activity in normal and Glut1-deficient erythrocytes by 20%-30%, causing a corresponding reduction of Vmax of glucose transport. Similarly, in primary astrocytes as well as in normal and Glut1-deficient fibroblasts, sodium valproate inhibited glucose transport by 20%-40% (P < 0.05), accompanied by an up to 60% downregulation of GLUT1 mRNA expression (P < 0.05). In conclusion, sodium valproate inhibits glucose transport and exacerbates Glut1 deficiency in vitro. Our findings imply the importance of prudent use of sodium valproate for patients with compromised Glut1 function.

The effects of phenytoin and its metabolite 5-(4-hydroxyphenyl)-5-phenylhydantoin on cellular glucose transport.

Glucose is the principal fuel for brain metabolism and its movement across the blood-brain barrier depends on Glut1. Impaired glucose transport to the brain may have deleterious consequences. For example, Glut1 deficiency syndrome (Glut1DS) is the result of heterozygous loss of function Glut1 mutation leading to energy failure of the brain and subsequently, epileptic encephalopathy. To preserve the integrity of the energy supply to the brain in patients with compromised glucose transport function, consumption of compounds with glucose transport inhibiting properties should be avoided. Phenytoin is a widely used anticonvulsant that affects carbohydrate metabolism. In this study, the hypothesis that phenytoin and its metabolite 5-(4-hydroxyphenyl)-5-phenylhydantoin (HPPH) affect cellular glucose transport was tested. With a focus on Glut1, the effects of phenytoin and HPPH on cellular glucose transport were studied. Glucose uptake assay measuring the zero-trans influx of radioactive-labeled glucose analogues showed that phenytoin and HPPH did not exert immediate effects on erythrocyte Glut1 activity or glucose transport in Hs68 control fibroblasts, Glut1DS primary fibroblasts isolated from two patients, or in rat primary astrocytes. Prolonged exposure to the two compounds could stimulate glucose transport by up to 30-60% over the control level (p <0.05) in Hs68 and Glut1DS fibroblasts as well as in rat astrocytes. The stimulation of glucose transport by HPPH was dose-dependent and accompanied by an up-regulation of GLUT1 mRNA expression (p <0.05). In conclusion, phenytoin and HPPH do not compromise cellular glucose transport. Prolonged exposure to these compounds can modify carbohydrate homeostasis by up-regulating glucose transport in both normal and Glut1DS conditions in vitro.