Somatic uniparental disomy of Chromosome 16p in hemimegalencephaly

Hemimegalencephaly (HME) is a heterogeneous cortical malformation characterized by enlargement of one cerebral hemisphere. Somatic variants in mammalian target of rapamycin (mTOR) regulatory genes have been implicated in some HME cases; however, ∼70% have no identified genetic etiology. Here, we screened two HME patients to identify disease-causing somatic variants. DNA from leukocytes, buccal swabs, and surgically resected brain tissue from two HME patients were screened for somatic variants using genome-wide genotyping arrays or sequencing of the protein-coding regions of the genome. Functional studies were performed to evaluate the molecular consequences of candidate disease-causing variants. Both HME patients evaluated were found to have likely disease-causing variants in DNA extracted from brain tissue but not in buccal swab or leukocyte DNA, consistent with a somatic mutational mechanism. In the first case, a previously identified disease-causing somatic single nucleotide in MTOR was identified. In the second case, we detected an overrepresentation of the alleles inherited from the mother on Chromosome 16 in brain tissue DNA only, indicative of somatic uniparental disomy (UPD) of the p-arm of Chromosome 16. Using methylation analyses, an imprinted locus on 16p spanning ZNF597 was identified, which results in increased expression of ZNF597 mRNA and protein in the brain tissue of the second case. Enhanced mTOR signaling was observed in tissue specimens from both patients. We speculate that overexpression of maternally expressed ZNF597 led to aberrant hemispheric development in the patient with somatic UPD of Chromosome 16p possibly through modulation of mTOR signaling.

Differential gene expression in dentate granule cells in mesial temporal lobe epilepsy with and without hippocampal sclerosis

OBJECTIVE

Hippocampal sclerosis is the most common neuropathologic finding in cases of medically intractable mesial temporal lobe epilepsy. In this study, we analyzed the gene expression profiles of dentate granule cells of patients with mesial temporal lobe epilepsy with and without hippocampal sclerosis to show that next-generation sequencing methods can produce interpretable genomic data from RNA collected from small homogenous cell populations, and to shed light on the transcriptional changes associated with hippocampal sclerosis.

METHODS

RNA was extracted, and complementary DNA (cDNA) was prepared and amplified from dentate granule cells that had been harvested by laser capture microdissection from surgically resected hippocampi from patients with mesial temporal lobe epilepsy with and without hippocampal sclerosis. Sequencing libraries were sequenced, and the resulting sequencing reads were aligned to the reference genome. Differential expression analysis was used to ascertain expression differences between patients with and without hippocampal sclerosis.

RESULTS

Greater than 90% of the RNA-Seq reads aligned to the reference. There was high concordance between transcriptional profiles obtained for duplicate samples. Principal component analysis revealed that the presence or absence of hippocampal sclerosis was the main determinant of the variance within the data. Among the genes up-regulated in the hippocampal sclerosis samples, there was significant enrichment for genes involved in oxidative phosphorylation.

SIGNIFICANCE

By analyzing the gene expression profiles of dentate granule cells from surgically resected hippocampal specimens from patients with mesial temporal lobe epilepsy with and without hippocampal sclerosis, we have demonstrated the utility of next-generation sequencing methods for producing biologically relevant results from small populations of homogeneous cells, and have provided insight on the transcriptional changes associated with this pathology.

IL28B genotype is associated with differential expression of intrahepatic interferon-stimulated genes in patients with chronic hepatitis C

Genetic variation in the IL28B (interleukin 28B; interferon lambda 3) region has been associated with sustained virological response (SVR) rates in patients with chronic hepatitis C (CHC) who were treated with peginterferon-α and ribavirin. We hypothesized that IL28B polymorphism is associated with intrahepatic expression of interferon-stimulated genes (ISGs), known to influence treatment outcome. IL28B genotyping (rs12979860) and whole-genome RNA expression were performed using liver biopsies from 61 North American patients with CHC. After correction for multiple testing (false discovery rate < 0.10), 164 transcripts were found to be differentially expressed by IL28B-type. The interferon signaling pathway was the most enriched canonical pathway differentially expressed by IL28B-type (P < 10(-5)), with most genes showing higher expression in livers of individuals carrying the poor-response IL28B-type. In 25 patients for which treatment response data were available, IL28B-type was associated with SVR (P = 0.0054). ISG expression was also associated with SVR; however, this was not independent of IL28B-type. Analysis of miR-122 expression in liver biopsies showed reduced miR-122 levels associated with poorer treatment outcome, independently of IL28B-type. No association was observed between IL28B-type and levels of liver IL28B or IL28A messenger RNA expression. IL28B protein sequence variants associated with rs12979860 were therefore investigated in vitro: no differences in ISG induction or inhibition of HCV replication were observed in Huh7.5 cells.

CONCLUSION

The good response IL28B variant was strongly associated with lower level ISG expression. The results suggest that IL28B genotype may explain the relationship between hepatic ISG expression and HCV treatment outcome, and this is independent of miR-122 expression. IL28B-type was not associated with intrahepatic IL28B messenger RNA expression in vivo. Further investigation of the precise molecular mechanism(s) by which IL28B genetic variation influences HCV outcomes is warranted.

Rare deletions at 16p13.11 predispose to a diverse spectrum of sporadic epilepsy syndromes

Deletions at 16p13.11 are associated with schizophrenia, mental retardation, and most recently idiopathic generalized epilepsy. To evaluate the role of 16p13.11 deletions, as well as other structural variation, in epilepsy disorders, we used genome-wide screens to identify copy number variation in 3812 patients with a diverse spectrum of epilepsy syndromes and in 1299 neurologically-normal controls. Large deletions (> 100 kb) at 16p13.11 were observed in 23 patients, whereas no control had a deletion greater than 16 kb. Patients, even those with identically sized 16p13.11 deletions, presented with highly variable epilepsy phenotypes. For a subset of patients with a 16p13.11 deletion, we show a consistent reduction of expression for included genes, suggesting that haploinsufficiency might contribute to pathogenicity. We also investigated another possible mechanism of pathogenicity by using hybridization-based capture and next-generation sequencing of the homologous chromosome for ten 16p13.11-deletion patients to look for unmasked recessive mutations. Follow-up genotyping of suggestive polymorphisms failed to identify any convincing recessive-acting mutations in the homologous interval corresponding to the deletion. The observation that two of the 16p13.11 deletions were larger than 2 Mb in size led us to screen for other large deletions. We found 12 additional genomic regions harboring deletions > 2 Mb in epilepsy patients, and none in controls. Additional evaluation is needed to characterize the role of these exceedingly large, non-locus-specific deletions in epilepsy. Collectively, these data implicate 16p13.11 and possibly other large deletions as risk factors for a wide range of epilepsy disorders, and they appear to point toward haploinsufficiency as a contributor to the pathogenicity of deletions.

Host determinants of HIV-1 control in African Americans

We performed a whole-genome association study of human immunodeficiency virus type 1 (HIV-1) set point among a cohort of African Americans (n = 515), and an intronic single-nucleotide polymorphism (SNP) in the HLA-B gene showed one of the strongest associations. We use a subset of patients to demonstrate that this SNP reflects the effect of the HLA-B*5703 allele, which shows a genome-wide statistically significant association with viral load set point (P = 5.6 x 10(-10)). These analyses therefore confirm a member of the HLA-B*57 group of alleles as the most important common variant that influences viral load variation in African Americans, which is consistent with what has been observed for individuals of European ancestry, among whom the most important common variant is HLA-B*5701.

Genetic regulation of alpha-synuclein mRNA expression in various human brain tissues

Genetic variability across the SNCA locus has been repeatedly associated with susceptibility to sporadic Parkinson's disease (PD). Accumulated evidence emphasizes the importance of SNCA dosage and expression levels in PD pathogenesis. However whether genetic variability in the SNCA gene modulates the risk to develop sporadic PD via regulation of SNCA expression remained elusive. We studied the effect of PD risk-associated variants at SNCA 5' and 3'regions on SNCA-mRNA levels in vivo in 228 human brain samples from three structures differentially vulnerable to PD pathology (substantia-nigra, temporal- and frontal-cortex) obtained from 144 neurologically normal cadavers. The extensively characterized PD-associated promoter polymorphism, Rep1, had an effect on SNCA-mRNA levels. Homozygous genotype of the 'protective', Rep1-259 bp allele, was associated with lower levels of SNCA-mRNA relative to individuals that carried at least one copy of the PD-risk associated alleles, amounting to an average decrease of approximately 40% and >50% in temporal-cortex and substantia-nigra, respectively. Furthermore, SNPs tagging the SNCA 3'-untranslated-region also showed effects on SNCA-mRNA levels in both the temporal-cortex and the substantia-nigra, although, in contrast to Rep1, the 'decreased-risk' alleles were correlated with increased SNCA-mRNA levels. Similar to Rep1 findings, no difference in SNCA-mRNA level was seen with different SNCA 3'SNP alleles in the frontal-cortex, indicating there is brain-region specificity of the genetic regulation of SNCA expression. We provide evidence for functional consequences of PD-associated SNCA gene variants in disease relevant brain tissues, suggesting that genetic regulation of SNCA expression plays an important role in the development of the disease.

Expansion of the Parkinson disease-associated SNCA-Rep1 allele upregulates human alpha-synuclein in transgenic mouse brain

α-Synuclein (SNCA) gene has been implicated in the development of rare forms of familial Parkinson disease (PD). Recently, it was shown that an increase in SNCA copy numbers leads to elevated levels of wild-type SNCA-mRNA and protein and is sufficient to cause early-onset, familial PD. A critical question concerning the molecular pathogenesis of PD is what contributory role, if any, is played by the SNCA gene in sporadic PD. The expansion of SNCA-Rep1, an upstream, polymorphic microsatellite of the SNCA gene, is associated with elevated risk for sporadic PD. However, whether SNCA-Rep1 is the causal variant and the underlying mechanism with which its effect is mediated by remained elusive. We report here the effects of three distinct SNCA-Rep1 variants in the brains of 72 mice transgenic for the entire human SNCA locus. Human SNCA-mRNA and protein levels were increased 1.7- and 1.25-fold, respectively, in homozygotes for the expanded, PD risk-conferring allele compared with homozygotes for the shorter, protective allele. When adjusting for the total SNCA-protein concentration (endogenous mouse and transgenic human) expressed in each brain, the expanded risk allele contributed 2.6-fold more to the SNCA steady-state than the shorter allele. Furthermore, targeted deletion of Rep1 resulted in the lowest human SNCA-mRNA and protein concentrations in murine brain. In contrast, the Rep1 effect was not observed in blood lysates from the same mice. These results demonstrate that Rep1 regulates human SNCA expression by enhancing its transcription in the adult nervous system and suggest that homozygosity for the expanded Rep1 allele may mimic locus multiplication, thereby elevating PD risk.

Gamma protocadherin expression in the embryonic chick nervous system

Protocadherin γ (pcdh-γ) family expression was examined in the embryonic chick central nervous system by in situ hybridization. Transcripts were visualized in discrete regions of fore-, mid-, and hindbrain at stages 23 and 25 and in spinal cord and optic lobe at stages 27 and 43, respectively. Results suggest that pcdh-γ may function cooperatively with other cell adhesion molecules in neuronal differentiation and establishment of neural networks in several areas of the developing brain, particularly regions involved in visual processing.

Arterial lignocaine concentrations following cervical plexus blockade for carotid endarterectomy

Arterial lignocaine concentrations were measured in twenty-six patients who had carotid endarterectomy performed under deep and superficial cervical plexus blockade. A dose of 6 mg/kg of 1.5% lignocaine with 1:200,000 adrenaline was used, as well as additional supplementation by the surgeons when required. Concentrations obtained produced a mean peak of 5 micrograms/ml and were similar to those previously reported from multiple bilateral intercostal blockade, which is the regional technique widely considered to produce the highest systemic levels of local anaesthetic. Apart from one peak concentration of 16.9 micrograms/ml, levels were well below the convulsion threshold. We find the technique acceptable and safe for carotid surgery and lignocaine toxicity is not identified as a problem.

Carotid endarterectomy under cervical plexus block--a prospective clinical audit

One hundred and twenty-eight patients having carotid endarterectomy under superficial and deep cervical plexus blocks were prospectively audited. The aim of the audit was to determine the incidence of intra-operative and postoperative neurological and cardiovascular complications and to establish patient acceptance of the technique. Twenty-seven patients who had intra-operative neurological changes following carotid artery clamping responded to shunt insertion. Six patients had transient neurological changes after the operation but there were no permanent neurological complications. Tachycardia (55%) and hypertension (67%) were the most common intra-operative cardiovascular changes and there was one clinical postoperative myocardial infarction. Ninety-two per cent of patients who could be adequately assessed preferred to have the same method of anaesthesia for future carotid endarterectomy. The authors concluded that carotid endarterectomy under superficial and deep cervical plexus blocks was associated with a high patient acceptance, low neurological complication rate and an acceptable rate of cardiovascular complications.

Pre-bypass myocardial ischaemia in patients undergoing coronary artery surgery

One hundred patients undergoing elective coronary artery surgery were studied to determine the incidence of pre-bypass myocardial ischaemia. Leads II, aVF and V5 of the electrocardiogram (ECG) were recorded at five-minute intervals from arrival in the anaesthetic room until onset of cardiopulmonary bypass. Thirteen patients developed sixteen episodes of significant ST depression on the ECG during the study period. Three patients were diagnosed as having postoperative myocardial infarction by ECG criteria and creatine phosphokinase-MB rise above 80 units. None of these patients had pre-bypass ST depression. Comparisons of these results with similar studies are presented.

EEG monitoring using aperiodic analysis during carotid and open heart surgery

The Cerebral Electrical Activity (CEA) was monitored by Lifescan in 38 patients undergoing carotid surgery under general or regional anaesthesia and another 20 patients during cardiopulmonary bypass undergoing open heart surgery. This monitor uses aperiodic analysis to process the electroencephalogram. Abrupt changes in CEA were observed when blood flow was disrupted due to surgical intervention or administration of thiopentone. Gradual changes in CEA were due to anaesthesia or hypothermia. In one patient a long period of depressed CEA did not result in a neurological deficit and in another patient a neurological event was undetected by the monitor.

Comparison of the processed electroencephalogram and awake neurological assessment during carotid endarterectomy

A processed electroencephalogram (EEG) produced by the Lifescan monitor (Neurometrics), was compared to awake neurological assessment for detecting cerebral ischaemia in seventy patients undergoing carotid endarterectomy under cervical plexus block. Of the six patients demonstrating neurological signs on cross-clamping the carotid, five displayed simultaneous EEG changes, four being detected during surgery, and one being detected after reviewing the EEG postoperatively. Another four patients displayed EEG changes indicative of ischaemia but unassociated with neurological signs. A further patient displayed contralateral intraoperative EEG changes. Hypotension resulted in one EEG change and two cases were associated with technical difficulties with the monitor. The presence of false negatives, possible false positives, technical errors and subjective interpretation associated with the processed EEG make it less reliable than awake neurological assessment for the detection of cerebral ischaemia.

The use of aperiodic analysis of the EEG during carotid artery surgery

A new processed EEG machine, the Lifescan, which uses aperiodic analysis, was used to monitor cerebral activity prospectively in twenty-one patients undergoing carotid artery surgery under general anaesthesia. The machine was easy to apply, use and read. Volatile agents caused a bilateral decrease in high frequency activity. Unilateral changes consistent with cerebral ischaemia at the time of carotid cross-clamping were also seen. One such prolonged change was not associated with neurological deficit. A further patient awoke with neurological deficit without displaying Lifescan evidence of ischaemia. The machine requires further assessment.

An experimental in vivo study of the canine internal mammary artery and its response to vasoactive drugs

The internal mammary artery is clearly the preferred conduit for most patients undergoing coronary artery bypass grafting. However, the hemodynamic responses of this graft to vasoactive agents immediately after bypass have not been documented. We have therefore studied blood flow in the canine internal mammary artery after anastomosis to the left anterior descending artery, and its response to epinephrine, metaraminol, isoproterenol, and calcium chloride. Blood flow in the internal mammary artery clearly paralleled changes in systolic blood pressure with perfusion pressure being of prime importance in maintaining flow in the internal mammary artery. No deleterious effect of systemic vasoconstricting agents was demonstrated. We suggest that the administration of these drugs is safe in patients with internal mammary artery grafts.

Radial artery cannulation--the influence of method on blood flow after decannulation

A prospective randomised study of two hundred patients undergoing open-heart surgery was carried out to determine if the method of radial artery cannulation (direct threading or transfixion) had any influence on the incidence of abnormal flow after decannulation. A standard 20-gauge non-tapered teflon-coated cannula was used and the groups were well matched for age, sex, wrist circumference, duration of cannulation and haematoma formation, all of which have been postulated to influence thrombosis rate. We were unable to demonstrate a statistically significant difference between the two methods of cannulation. The overall abnormal flow rate at five days assessed by Doppler ultrasound was low at 5%.

A prospective randomised trial comparing spinal anaesthesia using hyperbaric cinchocaine with general anaesthesia for lower limb vascular surgery

One hundred and one patients were randomly allocated to have their peripheral vascular surgery performed under general anaesthesia (51 patients) or spinal anaesthesia (50 patients). Intraoperative haemodynamic changes were markedly different between the two groups with a higher incidence of hypotension in the spinal group (72% vs 31%) and a higher incidence of hypertension in the general anaesthesia group (22% vs 0%). Blood loss was significantly less in the spinal group (560, SD 340, ml vs 792, SD 440, ml). Postoperatively three patients from the general anaesthesia group died from causes unrelated to the anaesthesia, and one had a myocardial infarct. Two patients in the spinal group had myocardial infarcts, both had been treated for bradycardia and hypotension intraoperatively, and one died. There was a significantly higher incidence of postoperative chest infection in the general anaesthesia group (33% vs 16%). There was no significant difference between the groups in the incidence of postoperative confusion, or lower limb amputation rate or need for further surgery prior to hospital discharge.

Blood conservation in elective surgery

Blood conservation for elective surgery involves both the reduction of blood loss and the reduction of homologous blood transfusion. Methods of reducing blood loss such as the use of tourniquets, vasoconstrictor drugs, regional anaesthetic supplements and hypotensive anaesthesia are considered briefly. Preoperative and intraoperative techniques of autotransfusion and haemodilution are considered in detail, including a technique of scavenging and reinfusing blood aspirated from the surgical site.

Cardiovascular risk factors in patients for vascular surgery

Various attempts have made been made to quantify the cardiovascular risk factors associated with anaesthesia and surgery. Two such schemes are the "Multifactorial Index of Cardiac Risk" developed by Goldman et al., and the one devised by Cooperman et al. The validity of these two schemes in relation to anaesthesia for vascular surgery was investigated by carrying out a prospective study of 100 patients. Cooperman's scheme was found to be much more accurate than Goldman's scheme in assessing patient risk. The study confirms the impression that the vascular patient falls into a higher risk group than most other surgical patients with regard to cardiovascular complications.

Haemodilution for major vascular surgery--using 3.5% polygeline (Haemaccel)

Intra-operative haemodilution and autotransfusion was carried out in 32 patients having major vascular surgery. The intra-operative blood loss and peri-operative blood replacement was compared with that in 25 patients having similar surgery in whom haemodilution was considered to be contraindicated. Both groups of patients had similar mean intra-operative blood loss measured but homologous blood transfusion requirements were significantly different; 2.6 units (SD 1.9) in the haemodiluted patients compared with 6.0 units (SD 3.5) in the non-diluted patients. There was no mortality in the haemodiluted patients nor was any morbidity attributed to the procedure. Polygeline (haemaccel) was used as the diluent and proved satisfactory for this purpose.

Pulmonary artery catheterisation. An assessment of risks and benefits in 220 surgical patients

The benefits and risks of pulmonary artery catheterisation were assessed in 220 patients having cardiac or vascular surgery. Prior to induction of anaesthesia 20% of patients had pulmonary artery wedge pressure measurements which indicated the need for blood volume support, vasodilator therapy or modification of the anaesthetic induction technique. Of those patients for cardiac surgery, 38% had important changes before cardiopulmonary bypass requiring blood volume support or vasodilator therapy. These changes were not reflected by similar changes in the central venous pressure. The risks of the technique were minimal. Minor complications occurred in 25% of patients (transient arrhythmias) and more serious complications occurred in 3.6% of patients. There was no mortality or long-term sequelae. We conclude that the benefits of pulmonary artery catheterisation outweigh its risks in patients having major cardiac and vascular surgery.

The prevention of hypertension at intubation. A controlled study of intravenous hydrallazine on patients undergoing intracranial surgery

Arterial blood pressure and pulse rate changes following tracheal intubation were studied in 20 patients undergoing intracranial surgery who received a thiopentone/suxamethonium anaesthetic induction sequence. Ten of the patients were pretreated with 0.4 mg/kg of hydrallazine and 10 with saline to determine whether hydrallazine prevents intubation hypertension. The results show that the incidence of intubation hypertension can be reduced using this dose of hydrallazine. Hydrallazine pretreatment is therefore recommended in patients at risk from hypertension following tracheal intubation.

Post carotid endarterectomy hypertension

Blood pressure changes following carotid endarterectomy were studied in 39 patients undergoing 42 carotid endarterectomies, in order to establish the incidence of hypertension and to study the use of hydrallazine for its treatment. Hypertension occurred in 28 cases (66%) and was treated with intravenous hydralazine in a dose of 20 +/- 8 mg; this resulted in a systolic blood pressure fall of 46 +/- 22 mmHg, diastolic blood pressure fall of 24 +/- 12 mmHg, mean blood pressure fall of 31 +/- 15 mmHg, and a pulse rate increase of 7 +/- 9 beats per minute. Hydrallazine is a safe, effective drug for the treatment of intraoperative hypertension.

Assessment of sympathectomy--the skin potential response

Objective assessment of the results of surgical sympathectomy and sympathetic block (both temporary and permanent) are not widely practised. This article comments briefly on the available methods, and describes the use of the abolition of the skin potential response (formerly known as the psychogalvanic reflex) to assess the abolition of sympathetic function. This method of assessment has proved useful in clinical practice.

Intercostal block for post operative pain relief

Intercostal nerve blocks with 0-5 per cent bupivicaine were used for post operative pain relief in 100 patients having upper abdominal operations. The blocks were very effective in 86 patients and had an average duration of 11 hours. Two asymptomatic pneumothoraces occurred.