Purpose Mutation in isocitrate dehydrogenase 1 (IDH1) at R132 (IDH1R132MUT) is frequent in low-grade diffuse gliomas and, within glioblastoma (GBM), has been proposed as a marker for GBMs that arise by transformation from lower-grade gliomas, regardless of clinical history. To determine how GBMs arising with IDH1R132MUT differ from other GBMs, we undertook a comprehensive comparison of patients presenting clinically with primary GBM as a function of IDH1R132 mutation status. Patients and Methods In all, 618 treatment-naive primary GBMs and 235 lower-grade diffuse gliomas were sequenced for IDH1R132 and analyzed for demographic, radiographic, anatomic, histologic, genomic, epigenetic, and transcriptional characteristics. Results Investigation revealed a constellation of features that distinguishes IDH1R132MUT GBMs from other GBMs (including frontal location and lesser extent of contrast enhancement and necrosis), relates them to lower-grade IDH1R132MUT gliomas, and supports the concept that IDH1R132MUT gliomas arise from a neural precursor population that is spatially and temporally restricted in the brain. The observed patterns of DNA sequence, methylation, and copy number alterations support a model of ordered molecular evolution of IDH1R132MUT GBM in which the appearance of mutant IDH1 protein is an initial event, followed by production of p53 mutant protein, and finally by copy number alterations of PTEN and EGFR. Conclusion Although histologically similar, GBMs arising with and without IDH1R132MUT appear to represent distinct disease entities that arise from separate cell types of origin as the result of largely nonoverlapping sets of molecular events. Optimal clinical management should account for the distinction between these GBM disease subtypes.

The crystal structure based model of the catalytic center of Ago2 revealed that the siRNA and the mRNA must be able to form an A-helix for correct positing of the scissile phosphate bond for cleavage in RNAi. This suggests that base pairing of the target mRNA with itself, i.e. secondary structure, must be removed before cleavage. Early on in the siRNA design, GC-rich target sites were avoided because of their potential to be involved in strong secondary structure. It is still unclear how important a factor mRNA secondary structure is in RNAi. However, it has been established that a difference in the thermostability of the ends of an siRNA duplex dictate which strand is loaded into the RNA-induced silencing complex. Here, we use a novel secondary structure prediction method and duplex-end differential calculations to investigate the importance of a secondary structure in the siRNA design. We found that the differential duplex-end stabilities alone account for functional prediction of 60% of the 80 siRNA sites examined, and that secondary structure predictions improve the prediction of site efficacy. A total of 80% of the non-functional sites can be eliminated using secondary structure predictions and duplex-end differential.

Monoallelic expression is an integral component of regulation of a number of essential genes and gene families. To probe for allele-specific expression in cells of CNS origin, we used next-generation sequencing (RNA-seq) to analyze four clonal neural stem cell (NSC) lines derived from Mus musculus C57BL/6 (B6)×Mus musculus molossinus (JF1) adult female mice. We established a JF1 cSNP library, then ascertained transcriptome-wide expression from B6 vs. JF1 alleles in the NSC lines. Validating the assay, we found that 262 of 268 X-linked genes evaluable in at least one cell line showed monoallelic expression (at least 85% expression of the predominant allele, p-value<0.05). For autosomal genes 170 of 7,198 genes (2.4% of the total) showed monoallelic expression in at least 2 evaluable cell lines. The group included eight known imprinted genes with the expected pattern of allele-specific expression. Among the other autosomal genes with monoallelic expression were five members of the glutathione transferase gene superfamily, which processes xenobiotic compounds as well as carcinogens and cancer therapeutic agents. Monoallelic expression within this superfamily thus may play a functional role in the response to diverse and potentially lethal exogenous factors, as is the case for the immunoglobulin and olfactory receptor superfamilies. Other genes and gene families showing monoallelic expression include the annexin gene family and the Thy1 gene, both linked to inflammation and cancer, as well as genes linked to alcohol dependence (Gabrg1) and epilepsy (Kcnma1). The annotated set of genes will provide a resource for investigation of mechanisms underlying certain cases of these and other major disorders.

Horseradish peroxidase (HRP) was used to determine whether neurons in the rat superior cervical ganglion (SCG) are localized in regions of the ganglion as a function of the postganglionic trunk they utilize. In separate experiments, each of the two major postganglionic trunks was cut 1-3 mm from the SCG and solid HRP was applied to the cut end proximal to the ganglion. The results demonstrated that the cell bodies of neurons whose axons project out the internal carotid nerve (ICN) were located primarily in the rostral part of the ganglion. Cell bodies of neurons whose axons project out the external carotid nerve (ECN) were located primarily in the caudal part. The total percentages of neuronc with axons in the ICN and ECN were about 35% and 45%, respectively. When HRP was applied to both these trunks, 73% of the neurons in the SCG were labeled. In the caudal portion of the ganglion, an additional group of neurons was observed whose axons project into the cervical sympathetic trunk. Control studies indicated that the neuronal labeling observed in our experiments was due to retrograde axonal transport rather than the direct uptake of HRP by neuronal cell bodies. Thus, neuronal subpopulations exist in specific regions of the rat SCG. The significance of these results to biochemical and electrophysiological studies is discussed.

Horseradish peroxidase (HRP) was used to determine the location in the spinal cord of neurons projecting to the superior cervical ganglion of the rat. HRP was applied to the proximal cut end of the cervical sympathetic trunk, close to its entry into the superior cervical ganglion. After survival times of 3, 6, or 9 days, the animals were sacrificed and their spinal cords were processed to visualize HRP using diaminobenzidine, benzidine dihydrochloride, or tetramethylbenzidine. Labeled neurons were found only ipsilateral to the site of HRP application and were restricted to spinal segments C8-T5. Ninety percent of these neurons were located in segments T1-T3. Similar numbers of labeled neurons were found at survival times of 3 and 6 days and the mean number +/- S.E.M. for 11 experiments at these two survival times was 1575 +/- 89. Nine days after application of HRP the mean number of labeled cells and the density of label per cell were reduced. Labeled neurons were found in four regions of the spinal cord: the intermediolateral nucleus (75%), the lateral funiculus (23%), the central autonomic area (1%), and the intercalated region (1%). The cells of the intermediolateral nucleus did not form a continuous column along the rostrocaudal axis of the spinal cord, but instead were often found in clusters, several clusters being present per spinal segment.