Ultra-Rare Genetic Variation in the Epilepsies: A Whole-Exome Sequencing Study of 17,606 Individuals

Sequencing-based studies have identified novel risk genes associated with severe epilepsies and revealed an excess of rare deleterious variation in less-severe forms of epilepsy. To identify the shared and distinct ultra-rare genetic risk factors for different types of epilepsies, we performed a whole-exome sequencing (WES) analysis of 9,170 epilepsy-affected individuals and 8,436 controls of European ancestry. We focused on three phenotypic groups: severe developmental and epileptic encephalopathies (DEEs), genetic generalized epilepsy (GGE), and non-acquired focal epilepsy (NAFE). We observed that compared to controls, individuals with any type of epilepsy carried an excess of ultra-rare, deleterious variants in constrained genes and in genes previously associated with epilepsy; we saw the strongest enrichment in individuals with DEEs and the least strong in individuals with NAFE. Moreover, we found that inhibitory GABA_A receptor genes were enriched for missense variants across all three classes of epilepsy, whereas no enrichment was seen in excitatory receptor genes. The larger gene groups for the GABAergic pathway or cation channels also showed a significant mutational burden in DEEs and GGE. Although no single gene surpassed exome-wide significance among individuals with GGE or NAFE, highly constrained genes and genes encoding ion channels were among the lead associations; such genes included CACNA1G, EEF1A2, and GABRG2 for GGE and LGI1, TRIM3, and GABRG2 for NAFE. Our study, the largest epilepsy WES study to date, confirms a convergence in the genetics of severe and less-severe epilepsies associated with ultra-rare coding variation, and it highlights a ubiquitous role for GABAergic inhibition in epilepsy etiology.

Modulation of mtDNA copy number ameliorates the pathological consequences of a heteroplasmic mtDNA mutation in the mouse

Heteroplasmic mtDNA mutations typically act in a recessive way and cause mitochondrial disease only if present above a certain threshold level. We have experimentally investigated to what extent the absolute levels of wild-type (WT) mtDNA influence disease manifestations by manipulating TFAM levels in mice with a heteroplasmic mtDNA mutation in the tRNA^Ala gene. Increase of total mtDNA levels ameliorated pathology in multiple tissues, although the levels of heteroplasmy remained the same. A reduction in mtDNA levels worsened the phenotype in postmitotic tissues, such as heart, whereas there was an unexpected beneficial effect in rapidly proliferating tissues, such as colon, because of enhanced clonal expansion and selective elimination of mutated mtDNA. The absolute levels of WT mtDNA are thus an important determinant of the pathological manifestations, suggesting that pharmacological or gene therapy approaches to selectively increase mtDNA copy number provide a potential treatment strategy for human mtDNA mutation disease.

Return of individual results in epilepsy genomic research: A view from the field

Genomic findings are emerging rapidly in 2 large, closely related epilepsy research consortia: the Epilepsy Phenome/Genome Project and Epi4K. Disclosure of individual results to participants in genomic research is increasingly viewed as an ethical obligation, but strategies for return of results were not included in the design of these consortia, raising complexities in establishing criteria for which results to offer, determining participant preferences, managing the large number of sites involved, and covering associated costs. Here, we describe the challenges faced, alternative approaches considered, and progress to date. Experience from these 2 consortia illustrates the importance, for genomic research in epilepsy and other disorders, of including a specific plan for return of results in the study design, with financial support for obtaining clinical confirmation and providing ongoing support for participants. Participant preferences for return of results should be established at the time of enrollment, and methods for allowing future contacts with participants should be included. In addition, methods should be developed for summarizing meaningful, comprehensible information about findings in the aggregate that participants can access in an ongoing way.

Heterozygous HNRNPU variants cause early onset epilepsy and severe intellectual disability

Pathogenic variants in genes encoding subunits of the spliceosome are the cause of several human diseases, such as neurodegenerative diseases. The RNA splicing process is facilitated by the spliceosome, a large RNA-protein complex consisting of small nuclear ribonucleoproteins (snRNPs), and many other proteins, such as heterogeneous nuclear ribonucleoproteins (hnRNPs). The HNRNPU gene (OMIM *602869) encodes the heterogeneous nuclear ribonucleoprotein U, which plays a crucial role in mammalian development. HNRNPU is expressed in the fetal brain and adult heart, kidney, liver, brain, and cerebellum. Microdeletions in the 1q44 region encompassing HNRNPU have been described in patients with intellectual disability (ID) and other clinical features, such as seizures, corpus callosum abnormalities (CCA), and microcephaly. Recently, pathogenic HNRNPU variants were identified in large ID and epileptic encephalopathy cohorts. In this study, we provide detailed clinical information of five novels and review two of the previously published individuals with (likely) pathogenic de novo variants in the HNRNPU gene including three non-sense and two missense variants, one small intragenic deletion, and one duplication. The phenotype in individuals with variants in HNRNPU is characterized by early onset seizures (6/7), severe ID (6/6), severe speech impairment (6/6), hypotonia (6/7), and central nervous system (CNS) (5/6), cardiac (4/6), and renal abnormalities (3/4). In this study, we broaden the clinical and mutational HNRNPU-associated spectrum, and demonstrate that heterozygous HNRNPU variants cause epilepsy, severe ID with striking speech impairment and variable CNS, cardiac, and renal anomalies.

Expression of cancer-testis antigens (MAGE-A1, MAGE-A3/6, MAGE-A4, MAGE-C1 and NY-ESO-1) in primary human uveal and conjunctival melanoma

AIM

Metastatic disease in ocular melanoma remains untreatable, is associated with late detection and is resistant to conventional systemic therapies. Many tumours including cutaneous melanoma express specific cancer-testis (CT) antigens and vaccines targeting these antigens can induce T-cell-mediated and humoural immune responses. The authors examined primary uveal and conjunctival melanomas for expression of CT antigens to assess their potential as targets for ocular melanoma immunotherapy.

METHODS

Paraffin-embedded uveal (n=32) and conjunctival (n=15) melanomas were assessed by immunohistochemistry for melanocyte differentiation antigens (gp100, Melan-A/MART-1 and tyrosinase), and CT antigens (MAGE-A1, MAGE-A3/6, MAGE-A4, MAGE-C1 and NY-ESO-1).

RESULTS

Melanoma differentiation antigens, gp100, Melan-A/MART1 and tyrosinase, were expressed in >75% of tumour cells in all uveal and conjunctival melanomas tested. Expression of all five CT antigens tested was low in uveal melanomas, and when present, stained <25% of the tumour cells. MAGE-A1, MAGE-A4 and NY-ESO-1 were expressed in <10% of tumour cells in conjunctival melanomas, while MAGE-C1 and MAGE-A3/6 were expressed in ∼20% and ∼35% of tumour cells in this malignancy, respectively, with variable expression levels.

CONCLUSIONS

Uveal and conjunctival melanomas consistently expressed high levels of the differentiation antigens (gp100, Melan-A/MART1 and tyrosinase). However, compared with other tumours, including cutaneous melanoma, only low levels of CT antigens were found in ocular melanomas. These observations suggest that immunotherapy directly targeting the CT antigens studied may not be effective for ocular melanoma.

054. TROPHOBLAST, PLACENTA AND EARLY EMBRYO: HOW THE MARSUPIAL DEVELOPS

In marsupials, the blastocyst forms as a single cell layer of cells. The marsupial blastocyst has no inner cell mass, so the 80–100 cell tammar embryo remains in diapause as a unilaminar blastocyst. All marsupials have a unilaminar stage, but what is unusual is that in the tammar the total cessation of cell division and cell metabolism lasts for 11 months each year. Marsupials are placental mammals. The yolk sac forms the definitive placenta up to birth. Only very few marsupials, such as the bandicoot, have a chorio-allantoic placenta, which supplements the placental functions of the yolk sac. However, the understanding how the unilaminar layer of trophoblast cells of the diapausing blastocyst become specified into placental and embryonic tissues has been an ongoing puzzle. To identify genes that do become differentially expressed in tammar development, we targeted the stage of the earliest appearance of the embryonic disc, at which the remainder of the blastocyst is then defined as trophoblast, as well as early cleavage stages. Intriguingly, we found no evidence for early differential expression of the canonical pluripotency genes POU5F1, SOX2 and NANOG, or of CDX2. By contrast, we found overt differential expression of GATA3, the closely related gene GATA2, and FGF4. This expression profile suggests that in the tammar, mechanisms regulating trophoblast- and pluriblast-specific expression of POU5F1, SOX2, NANOG and CDX2 are temporally secondary to those regulating GATA2 & -3 and FGF4 expression. Together, our results may signify the evolution of alternative mechanisms of early lineage specification in marsupials, or alternatively reveal a general hierarchy of signalling mechanisms that are masked in the relatively rapid and ‘compressed’ development of mice. The results of our ongoing study have important implications for understanding not only marsupial stem cells but the early development of all therian mammals.

Pro-protein convertases (PCs) other than PC6 are not tightly regulated for implantation in the human endometrium

Pro-protein convertases (PCs) are a family of serine proteases (furin, PC1/3, PC2, PACE4, PC4, PC5/6, PC7/8) responsible for post-translational processing and activation of inactive precursors of many regulatory proteins. Endometrial PC6 is critical for implantation in mice and for decidualization of human endometrial stromal cells (ESCs). This study investigated the endometrial expression of other PCs during the menstrual cycle and early pregnancy to elucidate potential redundancies. Furin, PC4, PACE4, and PC7 along with PC6 transcripts were detected in total endometrial RNA, whereas PC1 and PC2 transcription levels were negligible. Quantitative RT-PCR demonstrated highest levels of furin mRNA during menstruation and lowest levels during the proliferative phase. Furin protein was immunolocalized in endometrial luminal and glandular epithelia, stromal fibroblasts, endothelia, and leukocytes. PACE4 and PC7 proteins were also immunodetected in endometrial stroma and glands. Total furin, PC7, and PACE4 proteins were constitutive in both stromal and glandular compartments throughout the cycle and during first trimester pregnancy. Furthermore, Furin and PC7 transcription was unaltered during decidualization of ESCsin vitroin contrast to PC6 which is significantly up-regulated during decidualization. Thus, whereas PC6 is tightly regulated during endometrial preparation for implantation, furin, PACE4, and PC7 are constitutively expressed in human endometrium, but must be considered if PC6 is to be targeted for manipulation of fertility.

Placental Function in Two Distantly Related Marsupials

The biochemical composition of uterine and fetal fluids during pregnancy of the grey short-tailed opossum was compared with new and published data on the tammar wallaby. In the grey short-tailed opossum, there are three main phases of embryonic nourishment. During the first phase, the embryo obtains nutrients from uterine secretion transferred into the yolk sac. The amount of uterine secretion declines during the second phase up to the time of shell coat rupture. As a result, the protein concentration in yolk sac fluid also declines. During phase three, which begins with shell coat rupture, nutrients are predominantly available from the maternal blood. In the grey short-tailed opossum that lacks a vesicular, fluid-filled allantois, waste products such as urea are apparently stored in the yolk sac and from there pass into the maternal circulation across the invasive yolk sac placenta. In contrast, in the tammar wallaby, the main source of nutrients available to the late term fetus is glandular secretion that is complemented by substances from the maternal circulation via the chorio-vitelline placenta, and waste products are stored in the large, fluid-filled allantois.

240. Spatial and temporal expression pattern of furin in the human endometrium

Furin is a proprotein convertase (PC) implicated in the endoproteolytic maturation of inactive protein precursors of growth factors, hormones, receptors, and viral envelope glycoproteins.1 Two functionally active forms of furin, one membrane-bound containing a C-terminal transmembrane domain (TD) and a cytoplasmic tail (CT), and one soluble without the TD and CT, have been characterised. We have previously shown that PC6, one of the PCs closely related to furin, is expressed in the human endometrium and is closely associated with decidualization of stromal cells during implantation.2 Although furin is ubiquitously expressed, its expression in the human endometrium is unknown. In this study, we investigated the spatial and temporal expression pattern of furin in the human endometrium using RT-PCR and immunohistochemistry. While furin expression is detected throughout the menstrual cycle and during early pregnancy, lowest mRNA levels are seen during the proliferative phase. Using an antibody directed against the C-terminus of the membrane bound form, furin is detected in the stroma, glandular and luminal epithelium, as well as in endothelia and neutrophils throughout the menstrual cycle and during early pregnancy. In the stroma, highest levels of furin are present during menstruation (n = 3), they are also high during the proliferative phase (n = 4), but significantly lower levels are detected during the secretory phase (n = 10, P < 0.05, Tukey HSD). In the first trimester decidua, furin is present in well decidualised stromal cells. The overall expression pattern of furin is different to that of PC6; in particular, furin expression is associated only with well decidualized stromal cells whereas PC6 is involved in the initial stages of decidualization. These data suggest that furin and PC6 play different roles in the human endometrium, especially during embryo implantation. (1)Nakayama K. (1997). Biochem. J. 327, 625–635.(2)Nie et al. (2005). Biol. Reprod. 72, 1029–1036.

The influence of intravenous L-tryptophan on plasma melatonin and sleep in men

The sleep-inducing mechanisms of L-Tryptophan (L-Trp) are generally thought to be mediated by a central serotonergic activation. Evidence is presented that some effects of L-Trp on sleep may be mediated by melatonin, a Trp-metabolite with sedative properties. Trp effects on vigilance, sleep, and plasma-melatonin concentrations were measured after double-blind application of 0, 1, 3, and 5 g L-Trp in nine and five healthy probands during daytime and nighttime, respectively. A significant sleep-inducing effect was observed after L-Trp administration during daytime and nighttime. The infusions of L-Trp caused a massive elevation of plasma melatonin levels. This effect was significant both during the night and the day, indicating that the increment of circulating melatonin may be of extrapineal origin.