Whole-genome sequencing reveals principles of brain retrotransposition in neurodevelopmental disorders.

Neural progenitor cells undergo somatic retrotransposition events, mainly involving L1 elements, which can be potentially deleterious. Here, we analyze the whole genomes of 20 brain samples and 80 non-brain samples, and characterized the retrotransposition landscape of patients affected by a variety of neurodevelopmental disorders including Rett syndrome, tuberous sclerosis, ataxia-telangiectasia and autism. We report that the number of retrotranspositions in brain tissues is higher than that observed in non-brain samples and even higher in pathologic vs normal brains. The majority of somatic brain retrotransposons integrate into pre-existing repetitive elements, preferentially A/T rich L1 sequences, resulting in nested insertions. Our findings document the fingerprints of encoded endonuclease independent mechanisms in the majority of L1 brain insertion events. The insertions are "non-classical" in that they are truncated at both ends, integrate in the same orientation as the host element, and their target sequences are enriched with a CCATT motif in contrast to the classical endonuclease motif of most other retrotranspositions. We show that L1Hs elements integrate preferentially into genes associated with neural functions and diseases. We propose that pre-existing retrotransposons act as "lightning rods" for novel insertions, which may give fine modulation of gene expression while safeguarding from deleterious events. Overwhelmingly uncontrolled retrotransposition may breach this safeguard mechanism and increase the risk of harmful mutagenesis in neurodevelopmental disorders.

A novel homozygous splice site mutation in NALCN identified in siblings with cachexia, strabismus, severe intellectual disability, epilepsy and abnormal respiratory rhythm.

We studied three siblings, born to consanguineous parents who presented with severe intellectual disability, cachexia, strabismus, seizures and episodes of abnormal respiratory rhythm. Whole exome sequencing led to identification of a novel homozygous splice site mutation, IVS29-1G > A in the NALCN gene, that resulted in aberrant transcript in the patients. NALCN encodes a voltage-independent cation channel, involved in regulation of neuronal excitability. Three homozygous mutations in the NALCN gene were previously identified in only eight patients with severe hypotonia, speech impairment, cognitive delay, constipation and Infantile-Neuroaxonal-dystrophy- like symptoms. Our patients broaden the clinical spectrum associated with recessive mutations in NALCN, featuring also disrupted respiratory rhythm mimicking homozygous Nalcn knockout mice.

Population-based screening for breast and ovarian cancer risk due to BRCA1 and BRCA2.

In the Ashkenazi Jewish (AJ) population of Israel, 11% of breast cancer and 40% of ovarian cancer are due to three inherited founder mutations in the cancer predisposition genes BRCA1 and BRCA2. For carriers of these mutations, risk-reducing salpingo-oophorectomy significantly reduces morbidity and mortality. Population screening for these mutations among AJ women may be justifiable if accurate estimates of cancer risk for mutation carriers can be obtained. We therefore undertook to determine risks of breast and ovarian cancer for BRCA1 and BRCA2 mutation carriers ascertained irrespective of personal or family history of cancer. Families harboring mutations in BRCA1 or BRCA2 were ascertained by identifying mutation carriers among healthy AJ males recruited from health screening centers and outpatient clinics. Female relatives of the carriers were then enrolled and genotyped. Among the female relatives with BRCA1 or BRCA2 mutations, cumulative risk of developing either breast or ovarian cancer by age 60 and 80, respectively, were 0.60 (± 0.07) and 0.83 (± 0.07) for BRCA1 carriers and 0.33 (± 0.09) and 0.76 (± 0.13) for BRCA2 carriers. Risks were higher in recent vs. earlier birth cohorts (P = 0.006). High cancer risks in BRCA1 or BRCA2 mutation carriers identified through healthy males provide an evidence base for initiating a general screening program in the AJ population. General screening would identify many carriers who are not evaluated by genetic testing based on family history criteria. Such a program could serve as a model to investigate implementation and outcomes of population screening for genetic predisposition to cancer in other populations.

Endocrine outcome in long-term survivors of childhood brain tumors.

AIM: To evaluate the rates of endocrine abnormalities in survivors of childhood brain tumors and identify risk factors. METHODS: The medical charts of patients were reviewed for background, disease-related and treatment-related data. Endocrine dysfunction was determined by clinical and laboratory evaluation. RESULTS: The study group included 114 patients with a mean age of 15.57 ± 5.93 years. Mean age at brain tumor diagnosis was 7.07 ± 5.42 years, and mean follow-up was 12.8 ± 6.25 years. Fifty-seven patients (50%) had an endocrine abnormality. The occurrence of several endocrine abnormalities was significantly associated with cranial irradiation and age <16 years at tumor diagnosis. The presence of growth hormone deficiency (n = 40) was associated with cranial or spinal irradiation, younger age and prepubertal stage at tumor diagnosis; the presence of hypogonadotropic hypogonadism (n = 9) was associated with prepubertal stage at diagnosis, and hypothyroidism (n = 23) was associated with cranial irradiation. Hypocortisolism was diagnosed in 9 patients, short stature in 20 patients and obesity in 8 male patients. Patients with early puberty (n = 19) and an abnormal lipid profile (n = 15) were significantly younger at tumor diagnosis than patients without these disorders. CONCLUSIONS: Childhood brain tumor survivors are at increased risk of late endocrine effects, particularly those treated with cranial radiation and diagnosed at a younger age. The frequency of hormonal deficits increases with time, warranting lifelong surveillance.

Molecular analysis expands the spectrum of phenotypes associated with GLI3 mutations.

A range of phenotypes including Greig cephalopolysyndactyly and Pallister-Hall syndromes (GCPS, PHS) are caused by pathogenic mutation of the GLI3 gene. To characterize the clinical variability of GLI3 mutations, we present a subset of a cohort of 174 probands referred for GLI3 analysis. Eighty-one probands with typical GCPS or PHS were previously reported, and we report the remaining 93 probands here. This includes 19 probands (12 mutations) who fulfilled clinical criteria for GCPS or PHS, 48 probands (16 mutations) with features of GCPS or PHS but who did not meet the clinical criteria (sub-GCPS and sub-PHS), 21 probands (6 mutations) with features of PHS or GCPS and oral-facial-digital syndrome, and 5 probands (1 mutation) with nonsyndromic polydactyly. These data support previously identified genotype-phenotype correlations and demonstrate a more variable degree of severity than previously recognized. The finding of GLI3 mutations in patients with features of oral-facial-digital syndrome supports the observation that GLI3 interacts with cilia. We conclude that the phenotypic spectrum of GLI3 mutations is broader than that encompassed by the clinical diagnostic criteria, but the genotype-phenotype correlation persists. Individuals with features of either GCPS or PHS should be screened for mutations in GLI3 even if they do not fulfill clinical criteria.

Egr-1 upregulates the Alzheimer's disease presenilin-2 gene in neuronal cells.

Regulation of the Alzheimer's disease (AD)-related gene, presenilin-2 (PSEN2), was analyzed in neuronal (SK-N-SH) and non-neuronal (human embryonic kidney 293, HEK293) cells. We show that the PSEN2 regulatory region includes two separate promoter elements, each located upstream of multiple transcription start sites in the first and second exons. The stronger upstream promoter, P1, has housekeeping characteristics: it resides in a CpG island, is TATA-less, and up to 83% of PSEN2-P1 activity depends on a stimulating protein 1 (Sp1) site at the most 5' initiation site. However, the downstream promoter P2 includes neuronal-specific elements and two sites for early growth response gene-1 (Egr-1), a transcription factor upregulated in learning paradigms and implicated in neuronal plasticity, in response to injury. We show that Egr-1 binds to PSEN-P2, and that PSEN-P2 activity is increased threefold by overexpression of Egr-1, and by 12-O-tetradecanoylphorbol-13-acetate (TPA), which induces physiological Egr-1 levels. Egr-1 represses PSEN2-P1 activity by 50% in neuronal cells, suggesting it partially shifts promoter usage from PSEN2-P1 to PSEN2-P2. This could lead to a relative increase in shorter exon 2 transcripts, which may be more efficiently translated than exon 1 transcripts. Identification of PSEN2 as an Egr-1 target suggests a link between PSEN2 expression and Egr-1-related processes, which may impact on understanding PSEN-2's physiological function and its role in Alzheimer's disease.