Successful treatment of a TSC2-mutant glioblastoma with everolimus

A 14-year-old boy with familial Li-Fraumeni syndrome presented with diplopia. Brain MRI revealed a right temporoparietal rim-enhancing mass. Following surgical resection and diagnosis of a gigantocellular-type glioblastoma multiforme (GBM), his family wished to avoid cytotoxic chemotherapy given the amplified risk of secondary malignancy. As such, we performed whole exome and transcriptome sequencing, which revealed germline TP53 and somatic TSC2 mutations. On completion of adjuvant radiotherapy, he was started on maintenance therapy with everolimus per recommendations from our multi-institutional brain tumour precision medicine tumour board. He has achieved a complete remission with resolution of visual symptoms and remains on everolimus therapy with concurrent electromagnetic field therapy, now 33 months from diagnosis. Our data highlight the benefit of precision medicine in children with GBM and offer insight into a targetable pathway that may be involved in similar cases.

Pediatric Thalamic Gliomas: An Updated Review

CONTEXT

- Neoplasms originating in the thalamus are rare overall (1% of all brain tumors); however, they comprise approximately 5% of pediatric intracranial tumors and approach 15% of all malignant pediatric intracranial tumors in some series.

OBJECTIVE

- To update readers about the current understanding of the diverse histology, biology, and behavior of pediatric thalamic tumors. Histologic verification is now thought to be critical for planning treatment, and, as a result, biopsy and total/subtotal resections are much more common today than in the past.

DATA SOURCES

- A PubMed search using the keywords "pediatric + thalamic + glioma" yielded 45 publications with a total of 445 cases of thalamic gliomas in patients less than 18 years of age. We found only 9 substantial institutional series tabulating all encountered thalamic histologic types in children. This survey confirmed a high proportion of astrocytomas, 81% (214 of 265), of which approximately two-thirds were diffuse astrocytomas (146 of 214) and one-third were pilocytic astrocytomas (68 of 214). Of the diffuse astrocytomas, 34% (49 of 146) were low grade (World Health Organization grade II) and 55% (81 of 146) were high grade (World Health Organization grade III or IV), making the latter subgroup the largest single category of all pediatric thalamic tumors. Oligodendrogliomas and ependymomas (mostly anaplastic in both cases) comprised 10% and 3% of all pediatric thalamic tumors, respectively.

CONCLUSIONS

- Tissue diagnosis is now thought crucial for prognostication and treatment, particularly as more potentially therapeutic molecular targets are discovered. Secure diagnosis allows identification of tumors for which resection is more feasible and beneficial.

Blood-brain barrier-adapted precision medicine therapy for pediatric brain tumors

Targeted chemotherapeutics provide a promising new treatment option in neuro-oncology. The ability of these compounds to penetrate the blood-brain barrier is crucial for their successful incorporation into patient care. "CNS Targeted Agent Prediction" (CNS-TAP) is a multi-institutional and multidisciplinary translational program established at the University of Michigan for evaluating the central nervous system (CNS) activity of targeted therapies in neuro-oncology. In this report, we present the methodology of CNS-TAP in a series of pediatric and adolescent patients with high-risk brain tumors, for which molecular profiling (academic and commercial) was sought and targeted agents were incorporated. Four of five of the patients had potential clinical benefit (partial response or stable disease greater than 6 months on therapy). We further describe the specific drug properties of each agent chosen and discuss characteristics relevant in their evaluation for therapeutic suitability. Finally, we summarize both tumor and drug characteristics that impact the ability to successfully incorporate targeted therapies into CNS malignancy management.

DAWN: a framework to identify autism genes and subnetworks using gene expression and genetics

BACKGROUND

De novo loss-of-function (dnLoF) mutations are found twofold more often in autism spectrum disorder (ASD) probands than their unaffected siblings. Multiple independent dnLoF mutations in the same gene implicate the gene in risk and hence provide a systematic, albeit arduous, path forward for ASD genetics. It is likely that using additional non-genetic data will enhance the ability to identify ASD genes.

METHODS

To accelerate the search for ASD genes, we developed a novel algorithm, DAWN, to model two kinds of data: rare variations from exome sequencing and gene co-expression in the mid-fetal prefrontal and motor-somatosensory neocortex, a critical nexus for risk. The algorithm casts the ensemble data as a hidden Markov random field in which the graph structure is determined by gene co-expression and it combines these interrelationships with node-specific observations, namely gene identity, expression, genetic data and the estimated effect on risk.

RESULTS

Using currently available genetic data and a specific developmental time period for gene co-expression, DAWN identified 127 genes that plausibly affect risk, and a set of likely ASD subnetworks. Validation experiments making use of published targeted resequencing results demonstrate its efficacy in reliably predicting ASD genes. DAWN also successfully predicts known ASD genes, not included in the genetic data used to create the model.

CONCLUSIONS

Validation studies demonstrate that DAWN is effective in predicting ASD genes and subnetworks by leveraging genetic and gene expression data. The findings reported here implicate neurite extension and neuronal arborization as risks for ASD. Using DAWN on emerging ASD sequence data and gene expression data from other brain regions and tissues would likely identify novel ASD genes. DAWN can also be used for other complex disorders to identify genes and subnetworks in those disorders.

Ectopic bone morphogenetic proteins 5 and 4 in the chicken forebrain lead to cyclopia and holoprosencephaly

Proper dorsal-ventral patterning in the developing central nervous system requires signals from both the dorsal and ventral portions of the neural tube. Data from multiple studies have demonstrated that bone morphogenetic proteins (BMPs) and Sonic hedgehog protein are secreted factors that regulate dorsal and ventral specification, respectively, within the caudal neural tube. In the developing rostral central nervous system Sonic hedgehog protein also participates in ventral regionalization; however, the roles of BMPs in the developing brain are less clear. We hypothesized that BMPs also play a role in dorsal specification of the vertebrate forebrain. To test our hypothesis we implanted beads soaked in recombinant BMP5 or BMP4 into the neural tube of the chicken forebrain. Experimental embryos showed a loss of the basal telencephalon that resulted in holoprosencephaly (a single cerebral hemisphere), cyclopia (a single midline eye), and loss of ventral midline structures. In situ hybridization using a panel of probes to genes expressed in the dorsal and ventral forebrain revealed the loss of ventral markers with the maintenance of dorsal markers. Furthermore, we found that the loss of the basal telencephalon was the result of excessive cell death and not a change in cell fates. These data provide evidence that BMP signaling participates in dorsal-ventral patterning of the developing brain in vivo, and disturbances in dorsal-ventral signaling result in specific malformations of the forebrain.

Comparison of Vero cell assay and PCR as indicators of the presence of verocytotoxigenic Escherichia coli in bovine and human fecal samples

Comparisons were made between Vero cell assay (VCA) and PCR as indicators for the detection of verocytotoxigenic Escherichia coli (VTEC; also known as Shiga-like toxin-producing E. coli) and as predictors of VTEC isolation from bovine and human fecal samples. Fecal samples were collected as part of a survey on the prevalence of VTEC on dairy farms in southern Ontario (J. B. Wilson et al., J. Infect. Dis., 174:1021-1027, 1996). A total of 2,655 samples were examined by VCA and PCR, 2,153 originating from cattle and 502 originating from humans. Overall, 36.2% of the samples were positive in the VCA and 38.7% were positive by PCR. Of the VCA-positive samples screened, 41.6% yielded a VTEC isolate. For both human and bovine samples, a significant positive association between PCR result and VCA titer (P = 0.0001) was found. In addition, there was a significant positive association between the PCR result and VTEC isolation from VCA-positive samples for cattle (odds ratio = 9.1, P < 0.0001). For bovine samples positive in the VCA, VCA titer was significantly associated with the probability of obtaining a VTEC isolate. Agreement between VCA and PCR was good for both bovine and human samples (kappa = 0.69 and 0.64, respectively). The sensitivity and specificity of the PCR with respect to the VCA for bovine samples were 82.0 and 86.5%, respectively, and those for human samples were 59.3 and 98.1%, respectively. Although correlation between VCA and PCR results was not absolute, when used in conjunction, these tests complemented one another as predictors of VTEC isolation.

Drug resistance, plasmids, biotypes and susceptibility to bacteriophages of Salmonella isolated from poultry in Canada

Salmonella isolates from 295 layer and 294 broiler flocks in Canada were examined to determine resistance to antimicrobial agents, plasmid profiles, biochemical properties, and susceptibility to polyvalent bacteriophages. Except for the high number of strains resistant to spectinomycin (97.8%), the frequency of drug resistance of Salmonella isolates from layer flocks was low. None of 457 isolates from layer flocks was resistant to amikacin or ciprofloxacin, and less than 2% of the strains were resistant to cephalothin, chloramphenicol, cotrimoxazole, gentamicin, kanamycin, neomycin, nitrofurantoin, and/or polymyxin B. About 3% of the strains were resistant to ampicillin, carbenicillin and/or tetracycline, whereas 8% of the strains were resistant to sulfisoxazole. Salmonella anatum var. O15+ and S. typhimurium var. copenhagen strains were resistant to multiple antimicrobial agents. None of 1159 Salmonella strains from broiler flocks was resistant to amikacin, cephalothin, ciprofloxacin or polymyxin B, less than 1% of the strains were resistant to chloramphenicol, 2% were resistant to ampicillin, carbenicillin and/or chloramphenicol; 5-7% were resistant to the aminoglycosides gentamicin, kanamycin and/or neomycin; 6% were resistant to nitrofurantoin; 10% to tetracycline; 14% to sulfisoxazole; and 99% to spectinomycin. A high percentage of S. binza, S. anatum var. O15+, S. schwarzengrund and S. heidelberg strains were resistant to antimicrobial agents. Some of the single or multiple resistances were encoded by conjugative plasmids or by plasmids that were thermosensitive for transfer. Eight percent of S. heidelberg strains did not produce hydrogen sulfide. Ninety-seven percent of the Salmonella strains were susceptible to the lytic effect of polyvalent bacteriophages.

Characterization of Salmonella enteritidis strains

A study was conducted to characterize 318 Salmonella enteritidis strains that were mainly isolated from poultry and their environment in Canada. Biotype, phagetype (PT), plasmid profile (PP), hybridization with a plasmid-derived virulence sequence probe, antibiotic resistance, outer membrane proteins (OMPs), and lipopolysaccharide (LPS) profiles were determined. Relationships of these properties to one another, and their diagnostic and pathogenic significance were assessed. Biotyping indicated that failure to ferment rhamnose was sometimes useful as a marker for epidemiologically related strains. Phagetyping was the most effective method for subdividing S. enteritidis; it distinguished 12 PTs. Phagetype 13 was occasionally associated with septicemia and mortality in chickens. The strains belonged to 15 PPs. A 36 megadalton (MDa) plasmid was found in 97% of the strains. Only the 36 MDa plasmid hybridized with the probe. Seventeen percent of the strains were drug resistant; all strains were sensitive to ciprofloxacin. Thirty-five of 36 strains possessed the same OMP profile, and 36 of 41 strains contained smooth LPS.