Detecting potential pleiotropy across cardiovascular and neurological diseases using univariate, bivariate, and multivariate methods on 43,870 individuals from the eMERGE network

The link between cardiovascular diseases and neurological disorders has been widely observed in the aging population. Disease prevention and treatment rely on understanding the potential genetic nexus of multiple diseases in these categories. In this study, we were interested in detecting pleiotropy, or the phenomenon in which a genetic variant influences more than one phenotype. Marker-phenotype association approaches can be grouped into univariate, bivariate, and multivariate categories based on the number of phenotypes considered at one time. Here we applied one statistical method per category followed by an eQTL colocalization analysis to identify potential pleiotropic variants that contribute to the link between cardiovascular and neurological diseases. We performed our analyses on ~530,000 common SNPs coupled with 65 electronic health record (EHR)-based phenotypes in 43,870 unrelated European adults from the Electronic Medical Records and Genomics (eMERGE) network. There were 31 variants identified by all three methods that showed significant associations across late onset cardiac- and neurologic- diseases. We further investigated functional implications of gene expression on the detected "lead SNPs" via colocalization analysis, providing a deeper understanding of the discovered associations. In summary, we present the framework and landscape for detecting potential pleiotropy using univariate, bivariate, multivariate, and colocalization methods. Further exploration of these potentially pleiotropic genetic variants will work toward understanding disease causing mechanisms across cardiovascular and neurological diseases and may assist in considering disease prevention as well as drug repositioning in future research.

Biallelic SCN10A mutations in neuromuscular disease and epileptic encephalopathy

Objectives

Two consanguineous families, one of Sudanese ethnicity presenting progressive neuromuscular disease, severe cognitive impairment, muscle weakness, upper motor neuron lesion, anhydrosis, facial dysmorphism, and recurrent seizures and the other of Egyptian ethnicity presenting with neonatal hypotonia, bradycardia, and recurrent seizures, were evaluated for the causative gene mutation.

Methods and Results

Homozygosity mapping and whole exome sequencing (WES) identified damaging homozygous variants in SCN10A, namely c.4514C>T; p.Thr1505Met in the first family and c.4735C>T; p.Arg1579* in the second family. A third family, of Western European descent, included a child with febrile infection‐related epilepsy syndrome (FIRES) who also had compound heterozygous missense mutations in SCN10A, namely, c.3482T>C; p.Met1161Thr and c.4709C>A; p.Thr1570Lys. A search for SCN10A variants in three consortia datasets (EuroEPINOMICS, Epi4K/EPGP, Autism/dbGaP) identified an additional five individuals with compound heterozygous variants. A Hispanic male with infantile spasms [c.2842G>C; p.Val948Leu and c.1453C>T; p.Arg485Cys], and a Caucasian female with Lennox–Gastaut syndrome [c.1529C>T; p.Pro510Leu and c.4984G>A; p.Gly1662Ser] in the epilepsy databases and three in the autism databases with [c.4009T>A; p.Ser1337Thr and c.1141A>G; p.Ile381Val], [c.2972C>T; p.Pro991Leu and c.2470C>T; p.His824Tyr], and [c.4009T>A; p.Ser1337Thr and c.2052G>A; p.Met684Ile].

Interpretation

SCN10A is a member of the voltage‐gated sodium channel (VGSC) gene family. Sodium channels are responsible for the instigation and proliferation of action potentials in central and peripheral nervous systems. Heterozygous mutations in VGSC genes cause a wide range of epileptic and peripheral nervous system disorders. This report presents autosomal recessive mutations in SCN10A that may be linked to epilepsy‐related phenotypes, Lennox–Gastaut syndrome, infantile spasms, and Autism Spectrum Disorder.

Distributed Cognition and Process Management Enabling Individualized Translational Research: The NIH Undiagnosed Diseases Program Experience

The National Institutes of Health Undiagnosed Diseases Program (NIH UDP) applies translational research systematically to diagnose patients with undiagnosed diseases. The challenge is to implement an information system enabling scalable translational research. The authors hypothesized that similar complex problems are resolvable through process management and the distributed cognition of communities. The team, therefore, built the NIH UDP integrated collaboration system (UDPICS) to form virtual collaborative multidisciplinary research networks or communities. UDPICS supports these communities through integrated process management, ontology-based phenotyping, biospecimen management, cloud-based genomic analysis, and an electronic laboratory notebook. UDPICS provided a mechanism for efficient, transparent, and scalable translational research and thereby addressed many of the complex and diverse research and logistical problems of the NIH UDP. Full definition of the strengths and deficiencies of UDPICS will require formal qualitative and quantitative usability and process improvement measurement.

MED23-associated intellectual disability in a non-consanguineous family

Intellectual disability (ID) is a heterogeneous condition arising from a variety of environmental and genetic factors. Among these causes are defects in transcriptional regulators. Herein, we report on two brothers in a nonconsanguineous family with novel compound heterozygous, disease-segregating mutations (NM_015979.3: [3656A > G];[4006C > T], NP_057063.2: [H1219R];[R1336X]) in MED23. This gene encodes a subunit of the Mediator complex that modulates the expression of RNA polymerase II-dependent genes. These brothers, who had profound ID, spasticity, congenital heart disease, brain abnormalities, and atypical electroencephalography, represent the first case of MED23-associated ID in a non-consanguineous family. They also expand upon the clinical features previously reported for mutations in this gene.

York platelet syndrome is a CRAC channelopathy due to gain-of-function mutations in STIM1

Store-operated Ca(2+) entry is the major route of replenishment of intracellular Ca(2+) in animal cells in response to the depletion of Ca(2+) stores in the endoplasmic reticulum. It is primarily mediated by the Ca(2+)-selective release-activated Ca(2+) (CRAC) channel, which consists of the pore-forming subunits ORAI1-3 and the Ca(2+) sensors, STIM1 and STIM2. Recessive loss-of-function mutations in STIM1 or ORAI1 result in immune deficiency and nonprogressive myopathy. Heterozygous gain-of-function mutations in STIM1 cause non-syndromic myopathies as well as syndromic forms of miosis and myopathy with tubular aggregates and Stormorken syndrome; some of these syndromic forms are associated with thrombocytopenia. Increased concentration of Ca(2+) as a result of store-operated Ca(2+) entry is essential for platelet activation. The York Platelet syndrome (YPS) is characterized by thrombocytopenia, striking ultrastructural platelet abnormalities including giant electron-opaque organelles and massive, multilayered target bodies and deficiency of platelet Ca(2+) storage in delta granules. We present clinical and molecular findings in 7 YPS patients from 4 families, demonstrating that YPS patients have a chronic myopathy associated with rimmed vacuoles and heterozygous gain-of-function STIM1 mutations. These findings expand the phenotypic spectrum of STIM1-related human disorders and define the molecular basis of YPS.

The expression of the testis-specific Dyrk4 kinase is highly restricted to step 8 spermatids but is not required for male fertility in mice

Members of the dual specificity tyrosine phosphorylated and regulated kinase family (Dyrk) were shown to have a highly testis-abundant or testis-restricted expression pattern. Furthermore, for some members of the family an involvement in gene expression regulation by phosphorylating transcription factors has been shown. Since little is known about the complex regulation of germ cell differentiation in spermatogenesis, we analysed the possible involvement of Dyrk kinases in this process. ISH experiments showed specific distribution of Dyrk kinases mainly in postmeiotic germ cell. We identified Dyrk4 as a testis-specific kinase with a very restricted expression to stage VIII postmeiotic spermatids. In vitro and in vivo experiments proved the enzymatic activity and suggested the cytoplasmatic localisation of Dyrk4. Finally, analysis of a Dyrk4 deficient mouse line showed that Dyrk4 is dispensable for male fertility, hence suggesting a functional redundancy of some Dyrk isoforms during spermiogenesis.

Miglustat has no apparent effect on spermatogenesis in normal men

BACKGROUND

In mice, administration of the glycosphingolipid biosynthesis inhibitor miglustat results in reversible infertility, characterized by impaired sperm motility and markedly abnormal sperm morphology. This observation suggested that miglustat might have utility for fertility control in man. To ascertain the impact of miglustat on human spermatogenesis, we conducted a pilot study of miglustat administration in normal men.

METHODS

After a 2-week baseline period, seven normal men were administered miglustat 100 mg, orally, twice daily for 6 weeks. During treatment, subjects had frequent seminal fluid analyses to assess the impact of treatment on sperm concentration, motility and morphology and the ability to undergo the acrosome reaction by in vitro assays.

RESULTS

Five subjects completed all aspects of the study. In these subjects, there was no apparent effect of miglustat on sperm concentration, motility or sperm morphology after 6 weeks of therapy. In addition, no changes in acrosome structure or function were observed with treatment, despite therapeutic concentrations of miglustat in the serum and seminal plasma. All subjects experienced gastrointestinal upset, diarrhoea and mild weight loss during treatment. No other abnormalities in blood counts, serum chemistries, vision or overall health were observed.

CONCLUSION

In contrast to the observations in mice, the oral administration of miglustat does not appear to affect human spermatogenesis. Further elucidation of the mechanism underlying the species specificity of miglustat may improve our understanding of the role of glycosphingolipids in spermatogenesis and result in alternative approaches to male fertility control.

Lack of antifertility properties of novel halogenated glycolytic inhibitors and the urinary excretion and metabolism of 1,6-dichloro-1,6-dideoxy-D-fructofuranose in the male rat

The antifertility action of (R,S)-alpha-chlorohydrin administered orally to male rats was compared with that of several novel chlorinated compounds known to inhibit glycolysis and the kinematics of rat sperm in vitro. Oral gavage of 1,6-dichloro-1,6-dideoxy-D-fructofuranose (dichlorodideoxyfructose, DCF), 1-chloro-3-hydroxypropanone, its dimethylketal and bromopyruvate did not reduce the fertility of male rats below that of controls at the equivalent antifertility dose of (R,S)-alpha-chlorohydrin (5 mg/kg/day) or higher. As anticipated for a compound cleaved to products of (S)-chirality even high doses of DCF (200 mg/kg) showed no effect on renal function. 36Cl-Labelled DCF administered orally to male rats was eliminated only slowly in the urine (16% of the ingested dose excreted in 96 h). In the first 8 h, approximately 50% of DCF was excreted unchanged, 30% was excreted as 3-chlorolactate (BCLA), the oxidation product 3-chlorolactaldehyde and 25% as Cl-. By 24 h little DCF remained and the major metabolite (70%) was BCLA and 20% Cl-. The high rate of dechlorination is most likely responsible for the low antifertility action of DCF.

The effect of (R,S)-ornidazole on the fertility of male mice and the excretion and metabolism of 36Cl-(R,S)-ornidazole and 36Cl-(R,S)-alpha-chlorohydrin in male mice and rats

(R,S)-Ornidazole, an effective antifertility agent for male rats at 400 mg/kg/day, was ineffective at this dose in male mice and at 1000 mg/kg/day caused neural effects. The compound was not excreted unchanged and more polar metabolites and Cl- were detected in 0-8 h urine following a single injection (400 mg/kg). In 8-24 h urine even these metabolites and most Cl ion were absent, indicating rapid metabolism of ornidazole. There was no organ specific accumulation of 36Cl-(R,S)-ornidazole in murine tissues. After injection of 36Cl-(R,S)-alpha-chlorohydrin, another antifertility agent in the rat but not the mouse, there was also no tissue-specific accumulation of radioactivity in the reproductive tract of either species. Urinary excretion rates of alpha-chlorohydrin were twice as rapid in mice as in rats. In mice, alpha-chlorohydrin was the major urinary metabolite, but in the rat metabolites included Cl-, 3-chlorolactate (BCLA) at 5 and 10 h and BCLA only at 24 h. BCLA was the major metabolite detected in most tissues at 10 and 24 h. In the rat cauda (but not caput) epididymidis the glycolytic inhibitor 3-chlorolactaldehyde was present at 5 h (but not 10 h), indicative of early metabolism. These results demonstrate a greater metabolism and excretion of putative antifertility agents in the mouse than the rat, lowering the amount of effective inhibitor circulating in the animal, which may explain why (R,S)-alpha-chlorohydrin and (R,S)-ornidazole are ineffective in this species at the dosages and injection times used, despite their spermatozoa being sensitive to inhibition by (R,S)-alpha-chlorohydrin in vitro.

Susceptibility of glycolytic enzyme activity and motility of spermatozoa from rat, mouse, and human to inhibition by proven and putative chlorinated antifertility compounds in vitro

Nonhormonal contraceptives that act by blocking energy metabolism within sperm have the advantage over spermatogenic inhibitors by their fast onset of infertility and their almost immediate restoration of fertility after withdrawal of the contraceptive agent. This study was done to test new chlorinated compounds for their contraceptive potency on rodent and human sperm in vitro. Cells were incubated in a medium containing glucose as the sole energy source with 1-chloro-3-hydroxypropanone (CHOP) and 1,6-dichloro-1,6-dideoxy-D-fructose (DCDF), chlorinated analogues of glycolytic substrates, as well as racemic (R,S)-alpha-chlorohydrin (ACH). After incubation, enzymatic activity and kinematic parameters were estimated. A dose-dependent inhibition of the glycolytic enzyme, glyceraldehyde 3-phosphate dehydrogenase (GAPDH), of rat and mouse distal cauda epididymidal and human ejaculated sperm by ACH, CHOP, and DCDF was demonstrated. Triosephosphate isomerase (TPI) was inhibited by ACH, but not by CHOP and DCDF, irrespective of species. All compounds inhibited sperm motility and kinematic parameters with increasing concentration. The results confirm that inhibition of glycolytic enzymes of sperm, including those of human, can be effectively brought about by a variety of chloro-compounds that can be converted to (S)-3-chlorolactaldehyde, the stereospecific chloro-derivative of the enzyme's natural substrate, (R)-glyceraldehyde 3-phosphate, and could be developed into contraceptive agents for men.

In vitro inhibition of rat cauda epididymal sperm glycolytic enzymes by ornidazole, alpha-chlorohydrin and 1-chloro-3-hydroxypropanone

Chlorinated antifertility compounds are known to inhibit glycolysis of spermatozoa as they reside in the epididymis but new compounds need to be evaluated that retain antifertility action but do not exhibit side-effects. In this study, two known antifertility agents and a related compound were compared for their inhibition of rat sperm metabolism and motility in vitro. The dose-dependent inhibition in vitro of the glycolytic enzymes glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and triosephosphate isomerase (TPI) of distal cauda epididymal rat spermatozoa by (R)-, (S)- and (R,S)-ornidazole (ORN), (R,S)-alpha-chlorohydrin (ACH) and 1-chloro-3-hydroxypropanone (CHOP) was compared. The direct inhibition of GAPDH by ORN suggests that it inhibits without prior conversion outside the cell but inhibition was not stereo-specific. The GAPDH, but not TPI, activity of spermatozoa incubated with ACH and CHOP was highly correlated with kinematic parameters of spermatozoa incubated in pyruvate- and lactate-free medium. ACH only inhibited the activity of intact spermatozoa and the inhibition was not reversed by washing the particulate sperm fraction after sonication. High concentrations of ACH (100 mmol/L) killed intact rat spermatozoa and decreased the extent of GAPDH inhibition. CHOP, unlike ACH, was an effective inhibitor of both intact and sonicated cells. Pre-CHOP, the dimethylketal precursor of CHOP, and its other hydrolysis product MeOH, were both ineffective in vitro. CHOP and related ketals may be more effective inhibitors of sperm glycolysis than ACH and may prove useful for investigating sperm-specific glycolytic inhibition, a prerequisite for the development of antiglycolytic, post-testicular acting contraceptives.

Effect of ornidazole on fertility of male rats: inhibition of a glycolysis-related motility pattern and zona binding required for fertilization in vitro

The effects of the male antifertility agent ornidazole on glycolysis as a prerequisite for fertilization were investigated in rats. Antifertility doses of ornidazole inhibited glycolysis within mature spermatozoa as determined from the lack of glucose utilization, reduced acidosis under anaerobic conditions and reduced glycolytic enzyme activity. As a consequence, cauda epididymidal spermatozoa from ornidazole-fed rats were unable to fertilize rat oocytes in vitro, with or without cumulus cells, which was not due to transfer of an inhibitor in epididymal fluid with the spermatozoa. Under IVF conditions, binding to the zona pellucida was reduced in spermatozoa from ornidazole-fed males and the spermatozoa did not undergo a change in swimming pattern, which was observed in controls. The block to fertilization could be explained by the disruption of glycolysis-dependent events, since reduced binding to the zona pellucida and a lack of kinematic changes were demonstrated by control spermatozoa in glucose-free media in the presence of respiratory substrates. The importance of glycolysis for binding to, and penetration of, the zona pellucida, and hyperactivation in rats is discussed in relation to the glycolytic production of ATP in the principal piece in which local deprivation of energy may explain the reduced force of spermatozoa from ornidazole-fed males.

Effect of ornidazole on fertility of male rats: inhibition of a glycolysis-related motility pattern and zona binding required for fertilization in vitro

The effects of the male antifertility agent ornidazole on glycolysis as a prerequisite for fertilization were investigated in rats. Antifertility doses of ornidazole inhibited glycolysis within mature spermatozoa as determined from the lack of glucose utilization, reduced acidosis under anaerobic conditions and reduced glycolytic enzyme activity. As a consequence, cauda epididymidal spermatozoa from ornidazole-fed rats were unable to fertilize rat oocytes in vitro, with or without cumulus cells, which was not due to transfer of an inhibitor in epididymal fluid with the spermatozoa. Under IVF conditions, binding to the zona pellucida was reduced in spermatozoa from ornidazole-fed males and the spermatozoa did not undergo a change in swimming pattern, which was observed in controls. The block to fertilization could be explained by the disruption of glycolysis-dependent events, since reduced binding to the zona pellucida and a lack of kinematic changes were demonstrated by control spermatozoa in glucose-free media in the presence of respiratory substrates. The importance of glycolysis for binding to, and penetration of, the zona pellucida, and hyperactivation in rats is discussed in relation to the glycolytic production of ATP in the principal piece in which local deprivation of energy may explain the reduced force of spermatozoa from ornidazole-fed males.

Toxicity of ornidazole and its analogues to rat spermatozoa as reflected in motility parameters

Ornidazole, a 5-nitro-imidazole derivative, has contraceptive properties in rats. As some ornidazole passes through the body unmetabolized after administration, the aim of this study was to investigate if ornidazole itself has a direct effect on sperm motility and whether these effects are limited or potentiated by the epididymal epithelium or structural changes to the molecule. Cauda epididymal spermatozoa or cauda epididymal tubules were incubated with ornidazole or ornidazole analogues, and motility parameters were subsequently measured by means of a computer-assisted sperm analysis (CASA) system. Incubation of spermatozoa in 2.5 mmol/L ornidazole for 4 h reduced their motility significantly, whereas incubation of epididymal tubules for 8 h in 10 mmol/L ornidazole was required to alter the velocity parameters of the enclosed spermatozoa upon release, suggesting that extratubular non-metabolized ornidazole can participate in inhibiting the motility in vivo. The in vitro toxicity of ornidazole derivatives depends on the halogen present and on the position of the nitro-group. The putatively inactive (R)- and the active (S)-ornidazole exhibited equivalent depression of sperm motility by direct incubation. This observation, and the differences between the in vitro and the in vivo efficacies of various ornidazole analogues, indicates distinct mechanisms of motility inhibition in the two experimental systems.