Whole exome sequencing reveals novel candidate variants for endometriosis utilizing multiple affected members in a single family

BACKGROUND

Endometriosis is an estrogen-dependent, chronic inflammatory disease that affects 10% of women during the reproductive ages. Despite the estimated 50% heritability for the condition, only 26% was associated with common genetic variants. Thus, necessity of identifying rare variants for the missing heritability is implicated in the literature. Therefore, our study aimed to identify novel rare genetic variants involved in the pathogenesis of endometriosis utilizing a family of multiple affected members.

METHODS

A family composed of four affected women along with their two unaffected mothers were recruited at a single gynecology and infertility clinic specialized in endometriosis. All patients presented with endometriomas, which was visualized by transvaginal ultrasonography. Two affected individuals had received laparoscopic endometrioma excision and therefore were diagnosed with recurrent disease. One mother had a history of endometrial serous adenocarcinoma (ESC) for which she underwent hysterectomy with bilateral oophorectomy. Three endometriosis cases were whole exome sequenced on Illumina NextSeq 550 platform with an average of 90% coverage. Candidate genes were confirmed by Sanger sequencing and followed-up with family segregation.

RESULTS

Novel rare variants were identified in TNFRSF1B (NM_001066.3: c.1072G>A, p.(Ala358Thr)) and GEN1 (NM_001130009.3: c.1574C>T, p.(Ser525Leu)) as possible genetic causes of endometriosis. A third novel rare variant was identified in CRABP1 (NM_004378.3:c.54G>C, p.(Glu18Asp)) only on the mother with ESC history and her daughters.

CONCLUSION

Novel candidate genetic variants that might contribute to endometriosis were suggested that need replication through independent cohorts or validation by functional studies. The family has also received genetic counseling and that the affected daughters are on clinical follow-up, accordingly.

Biallelic loss of EEF1D function links heat shock response pathway to autosomal recessive intellectual disability

Intellectual disability (ID) is a genetically heterogeneous neurodevelopmental disorder characterised by significantly impaired intellectual and adaptive functioning. ID is commonly syndromic and associated with developmental, metabolic and/or neurological findings. Autosomal recessive ID (ARID) is a significant component of ID especially in the presence of parental consanguinity. Several ultra rare ARID associated variants in numerous genes specific almost to single families have been identified by unbiased next generation sequencing technologies. However, most of these new candidate ARID genes have not been replicated in new families due to the rarity of associated alleles in this highly heterogeneous condition. To determine the genetic component of ARID in a consanguineous family from Turkey, we have performed SNP-based linkage analysis in the family along with whole exome sequencing (WES) in an affected sibling. Eventually, we have identified a novel pathogenic variant in EEF1D, which has recently been recognised as a novel candidate gene for ARID in a single family. EEF1D encodes a ubiquitously expressed translational elongation factor functioning in the cytoplasm. Herein, we suggest that the loss of function variants exclusively targeting the long EEF1D isoform may explicate the ARID phenotype through the heat shock response pathway, rather than interfering with the canonical translational elongation.

Three Novel MEN1 Variants in AIP-Negative Familial Isolated Pituitary Adenoma Patients

OBJECTIVES

Pituitary adenomas (PAs) may rarely occur in well-defined hereditary conditions, like multiple endocrine neoplasia type 1 (MEN1) syndrome and familial isolated pituitary adenoma (FIPA) associated with germline mutations in MEN1 and AIP, respectively. This study aimed to assess MEN1 genetic abnormalities in AIP mutation-negative FIPA patients, not associated with MEN1 components.

METHODS

Among 20 patients evaluated in 13 FIPA families, 12 were previously reported as AIP mutation-negative. In this study, 6 new families with 8 patients were recruited. All patients were subjected to multiplex ligation-dependent probe amplification to detect copy number variations in AIP and MEN1, and AIP sequencing was performed in additional patients. AIP mutation-negative patients were subjected to MEN1 sequencing.

RESULTS

Our cohort revealed only 3 novel heterozygous MEN1 variants including c.1846T>A p.(*616Argext*21), rs778272737:T>C, and rs972128957:C>T in 2 families, with patients diagnosed with Cushing disease, nonfunction al adenoma, and acromegaly, respectively. Among them, c.1846T>A p. (*616Argext*21) is a stop codon read-through, whereas the others are 3'UTR variations. MEN1 variation frequency was detected as 15%.

CONCLUSIONS

MEN1 alterations can be of significance in FIPA patients and screening could be offered to AIP mutation-negative patients without MEN1 features. Further studies are needed to clarify the role of MEN1 in FIPA patients.

Screening of AIP Gene Variations in a Cohort of Turkish Patients with Young-Onset Sporadic Hormone-Secreting Pituitary Adenomas

Aims: Aryl hydrocarbon receptor-interacting protein (AIP) gene mutations have long been associated with apparently sporadic pituitary adenomas (PAs) with a prevalence range of 0-12%. The aim of this study was to evaluate the frequency of germline AIP variations in a large cohort of apparently sporadic PAs diagnosed before the age of 40 years, who did not exhibit hypercalcemia and/or MEN1 syndrome components during long-term follow-up. Materials and Methods: A total of 97 patients, diagnosed with functional PAs ≤40 years old, composed of somatotropinoma (n = 55), prolactinoma (n = 25), and corticotrophinoma (n = 17), were recruited for this study. Fifty-one of these patients [somatotropinoma (n = 30), prolactinoma (n = 15), and corticotrophinoma (n = 11)] were previously reported as AIP mutation-negative by Sanger sequencing. The entire coding sequence of the AIP gene, along with exon/intron boundaries and the untranslated regions of 41 newly recruited patients, were sequenced for germline variations. In addition, all patients were subjected to multiplex ligation-dependent probe amplification to detect copy number variations in the AIP gene. Results: The AIP c.911G>A: p.Arg304Gln (rs104894190) variant was detected in only two patients with functional PA: one with somatotropinoma [in 1/55 (1.8%)] and one with prolactinoma [in 1/25 (4%)]. None of the corticotrophinomas revealed AIP gene alterations. Thus, the overall prevalence of AIP variation was 2.1% in our cohort. Conclusions: Germline AIP gene variations among Turkish patients with apparently sporadic PAs are relatively rare among patients ≤40 years old. None of the patients in our cohort revealed any obviously pathogenic AIP variants.

A novel homozygous GALC variant has been associated with Krabbe disease in a consanguineous family

Krabbe disease (KD) or globoid cell leukodystrophy is an autosomal recessive lysosomal storage disorder involving the white matter of the peripheral and the central nervous systems. It is caused by a deficiency of galactocerebrosidase enzyme activity. The most common manifestation is the classical early onset KD that leads to patient's loss before the age of 2. Herein, we report the evaluation of a consanguineous family with three affected children manifesting severe neurological findings that ended with death before the age of 2, in an attempt to provide genetic diagnosis to the family. One of the children underwent detailed physical and neurological examinations, including brain magnetic resonance imaging (MRI) and scalp electroencephalography (EEG) evaluations. GALC genetic testing on this child enabled identification of a novel homozygous variant (NM_000153.3: c.1394C>T; p.(Thr465Ile)), which confirmed diagnosis as KD. Familial segregation of this variant was performed by PCR amplification and Sanger sequencing that revealed the parents as heterozygous carriers. We believe this novel GALC variant will not only help in genetic counseling to this family but will also aid in identification of future KD cases.

A case of L-2 hydroxyglutaric aciduria presenting as febrile seizure

L-2 hydroxyglutaric aciduria (L2HGA) is a rare, infantile-onset, autosomal recessive organic aciduria affecting exclusively the central nervous system. A case is reported here of L2HGA presenting with macrocephaly and febrile seizure. Although there have been reports of epilepsy associated with L2HGA, to the best of our knowledge this is the second case in literature of febrile seizure in a patient with L2HGA. This report suggests that detailed neurological evaluation of macrocephalic children with febrile convulsion is important. Moreover, metabolic and genetic investigations may be necessary for these kinds of patients.

Identifying SNP targeted pathways in partial epilepsies with genome-wide association study data

PURPOSE

In a recent genome-wide association study for partial epilepsies in the European population, a common genetic variation has been reported to affect partial epilepsy only modestly. However, in complex diseases such as partial epilepsy, multiple factors (e.g. single nucleotide polymorphisms, microRNAs, metabolic and epigenetic factors) may target different sets of genes in the same pathway, affecting its function and thus causing the disease development. In this regard, we hypothesize that the pathways are critical for elucidating the mechanisms underlying partial epilepsy.

METHODS

Previously we had developed a novel methodology with the aim of identifying the disease-related pathways. We had combined evidence of genetic association with current knowledge of (i) biochemical pathways, (ii) protein-protein interaction networks, and (iii) the functional information of selected single nucleotide polymorphisms. In our present study, we apply this methodology to a data set on partial epilepsy, including 3445 cases and 6935 controls of European ancestry.

RESULTS

We have identified 30 overrepresented pathways with corrected p-values smaller than 10(-12). These pathways include complement and coagulation cascades, cell cycle, focal adhesion, extra cellular matrix-receptor interaction, JAK-STAT signaling pathway, MAPK signaling pathway, proteasome, ribosome, calcium signaling and regulation of actin cytoskeleton pathways. Most of these pathways have growing scientific support in the literature as being associated with partial epilepsy. We also demonstrate that different factors affect distinct parts of the pathways, as shown here on complement and coagulation cascades pathway with a comparison of gene expression vs. genome-wide association study.

CONCLUSIONS

Traditional studies on genome-wide association have not revealed strong associations in epilepsies, since these single nucleotide polymorphisms are not shared by most of the patients. Our results suggest that it is more effective to incorporate the functional effect of a single nucleotide polymorphism on the gene product, protein-protein interaction networks and functional enrichment tools into genome-wide association studies. These can then be used to determine leading molecular pathways, which cannot be detected through traditional analyses. We hope that this type of analysis brings the research community one step closer to unraveling the complex genetic structure of epilepsies.