Cytogenetic prognostication within medulloblastoma subgroups

PURPOSE

Medulloblastoma comprises four distinct molecular subgroups: WNT, SHH, Group 3, and Group 4. Current medulloblastoma protocols stratify patients based on clinical features: patient age, metastatic stage, extent of resection, and histologic variant. Stark prognostic and genetic differences among the four subgroups suggest that subgroup-specific molecular biomarkers could improve patient prognostication.

PATIENTS AND METHODS

Molecular biomarkers were identified from a discovery set of 673 medulloblastomas from 43 cities around the world. Combined risk stratification models were designed based on clinical and cytogenetic biomarkers identified by multivariable Cox proportional hazards analyses. Identified biomarkers were tested using fluorescent in situ hybridization (FISH) on a nonoverlapping medulloblastoma tissue microarray (n = 453), with subsequent validation of the risk stratification models.

RESULTS

Subgroup information improves the predictive accuracy of a multivariable survival model compared with clinical biomarkers alone. Most previously published cytogenetic biomarkers are only prognostic within a single medulloblastoma subgroup. Profiling six FISH biomarkers (GLI2, MYC, chromosome 11 [chr11], chr14, 17p, and 17q) on formalin-fixed paraffin-embedded tissues, we can reliably and reproducibly identify very low-risk and very high-risk patients within SHH, Group 3, and Group 4 medulloblastomas.

CONCLUSION

Combining subgroup and cytogenetic biomarkers with established clinical biomarkers substantially improves patient prognostication, even in the context of heterogeneous clinical therapies. The prognostic significance of most molecular biomarkers is restricted to a specific subgroup. We have identified a small panel of cytogenetic biomarkers that reliably identifies very high-risk and very low-risk groups of patients, making it an excellent tool for selecting patients for therapy intensification and therapy de-escalation in future clinical trials.

Subgroup-specific structural variation across 1,000 medulloblastoma genomes

Medulloblastoma, the most common malignant paediatric brain tumour, is currently treated with nonspecific cytotoxic therapies including surgery, whole-brain radiation, and aggressive chemotherapy. As medulloblastoma exhibits marked intertumoural heterogeneity, with at least four distinct molecular variants, previous attempts to identify targets for therapy have been underpowered because of small samples sizes. Here we report somatic copy number aberrations (SCNAs) in 1,087 unique medulloblastomas. SCNAs are common in medulloblastoma, and are predominantly subgroup-enriched. The most common region of focal copy number gain is a tandem duplication of SNCAIP, a gene associated with Parkinson's disease, which is exquisitely restricted to Group 4α. Recurrent translocations of PVT1, including PVT1-MYC and PVT1-NDRG1, that arise through chromothripsis are restricted to Group 3. Numerous targetable SCNAs, including recurrent events targeting TGF-β signalling in Group 3, and NF-κB signalling in Group 4, suggest future avenues for rational, targeted therapy.

An analysis of several variables influencing the efficacy of flash card instruction

We conducted four experiments using an alternating treatments design to assess the influence of several variables on children's acquisition of number facts during one-on-one flash card instruction. In Experiment 1, we manipulated the order of stimulus presentation; in most cases a higher percentage of correct responses occurred, and mastery criterion was reached in somewhat fewer sessions, when a missed problem was re-presented after the next item than when problems were re-presented in a sequential order. In Experiment 2 a comparison of error-contingent reprimands with no reprimands yielded similar results in favor of the former procedure. Experiment 3 indicated that a higher percentage of correct responses and more rapid acquisition occurred when the tutor and student were seated knee-to-knee than when a desk was positioned between them. Experiment 4 compared the rate of learning in the presence and absence of a treatment package consisting of all three variables identified as leading to more rapid learning in the previous three experiments. Children reached criterion in less than half the time when the treatment package was in effect.

Increasing driver yielding and pedestrian signaling with prompting, feedback, and enforcement

The effects of an intervention package on drivers' yielding to pedestrians and on pedestrians' signaling their intention to cross the street were assessed using a multiple baseline design. The intervention, which consisted of publicly posted feedback on the percentage of motorists yielding to pedestrians, small signs prompting pedestrians to engage in appropriate crossing behavior, and an enforcement program involving the use of warning tickets and feedback fliers, was sequentially introduced on two streets. The intervention more than doubled the percentage of motorists yielding to pedestrians and increased the percentage of pedestrians signaling their intention to cross the street to over 13% from a baseline level of less than 1%. Near misses involving pedestrians decreased by more than 50% on the narrower of the two streets.

Regulation of major cellulosomal endoglucanases of Clostridium thermocellum differs from that of a prominent cellulosomal xylanase

The expression of scaffoldin-anchoring genes and one of the major processive endoglucanases (CelS) from the cellulosome of Clostridium thermocellum has been shown to be dependent on the growth rate. For the present work, we studied the gene regulation of selected cellulosomal endoglucanases and a major xylanase in order to examine the previously observed substrate-linked alterations in cellulosome composition. For this purpose, the transcript levels of genes encoding endoglucanases CelB, CelG, and CelD and the family 10 xylanase XynC were determined in batch cultures, grown on either cellobiose or cellulose, and in carbon-limited continuous cultures at different dilution rates. Under all conditions tested, the transcript levels of celB and celG were at least 10-fold higher than that of celD. Like the major processive endoglucanase CelS, the transcript levels of these endoglucanase genes were also dependent on the growth rate. Thus, at a rate of 0.04 h(-1), the levels of celB, celG, and celD were threefold higher than those obtained in cultures grown at maximal rates (0.35 h(-1)) on cellobiose. In contrast, no clear correlation was observed between the transcript level of xynC and the growth rate-the levels remained relatively high, fluctuating between 30 and 50 transcripts per cell. The results suggest that the regulation of C. thermocellum endoglucanases is similar to that of the processive endoglucanase celS but differs from that of a major cellulosomal xylanase in that expression of the latter enzyme is independent of the growth rate.

Regulation of expression of scaffoldin-related genes in Clostridium thermocellum

Clostridium thermocellum produces an extracellular multienzyme complex, termed the cellulosome, that allows efficient solubilization of crystalline cellulose. The complex is organized around a large noncatalytic protein subunit, termed CipA or scaffoldin, and is found either free in the supernatant or cell bound. The binding of the complex to the cell is mediated by three cell surface anchoring proteins, OlpB, Orf2p, and SdbA, that interact with the CipA scaffoldin. The transcriptional level of the olpB, orf2, sdbA, and cipA genes was determined quantitatively by RNase protection assays in batch and continuous cultures, under carbon and nitrogen limitation. The mRNA level of olpB, orf2, and cipA varied with growth rate, reaching 40 to 60 transcripts per cell under carbon limitation at a low growth rate of 0.04 h(-1) and 2 to 10 transcripts per cell at a growth rate of 0.35 h(-1) in batch culture. The mRNA level of sdbA was about three transcripts per cell and was not influenced by growth rate. Primer extension analysis revealed two major transcriptional start sites, at -81 and -50 bp, upstream of the translational start site of the cipA gene. The potential promoters exhibited homology to the known sigma factors sigma(A) and sigma(L) (sigma(54)) of Bacillus subtilis. Transcription from the sigma(L)-like promoter was found under all growth conditions, whereas transcription from the sigma(A)-like promoter was significant only under carbon limitation. The overall expression level obtained in the primer extension analysis was in good agreement with the results of the RNase-protection assays.

Regulation of the cellulosomal CelS (cel48A) gene of Clostridium thermocellum is growth rate dependent

Clostridium thermocellum produces an extracellular multienzyme complex, termed cellulosome, that allows efficient solubilization of crystalline cellulose. One of the major enzymes in this complex is the CelS (Cel48A) exoglucanase. The regulation of CelS at the protein and transcriptional levels was studied using batch and continuous cultures. The results of sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blot analyses indicated that the amount of CelS in the supernatant fluids of cellobiose-grown cultures is lower than that of cellulose-grown cultures. The transcriptional level of celS mRNA was determined quantitatively by RNase protection assays with batch and continuous cultures under carbon and nitrogen limitation. The amount of celS mRNA transcripts per cell was about 180 for cells grown under carbon limitation at growth rates of 0.04 to 0.21 h(-1) and 80 and 30 transcripts per cell for batch cultures at growth rates of 0.23 and 0.35 h(-1), respectively. Under nitrogen limitation, the corresponding levels were 110, 40, and 30 transcripts/cell for growth rates of 0.07, 0.11, and 0.14 h(-1), respectively. Two major transcriptional start sites were detected at positions -140 and -145 bp, upstream of the translational start site of the celS gene. The potential promoters exhibited homology to known sigma factors (i.e., sigma(A) and sigma(B)) of Bacillus subtilis. The relative activity of the two promoters remained constant under the conditions studied and was in agreement with the results of the RNase protection assay, in which the observed transcriptional activity was inversely proportional to the growth rate.

Natural and structured baselines in the treatment of aggression following brain injury

This single-case study describes the importance of presenting relevant baseline conditions in planning and evaluating treatment for aggression in a severely brain injured man 1 year after injury. An artificially low natural baseline resulted from staff reluctance to deliver instructions and corrective feedback needed for rehabilitation of self-care skill because these were frequently followed by aggression. A subsequent structured baseline presented these antecedents at the higher rates that were necessary for progress in the patient's rehabilitation. This resulted in an increase in aggressive behaviour, but also gave a more accurate representation of what his behaviour would be like under effective rehabilitation conditions. Intervention was based on data from the structured baseline, and included providing clear expectations, social reinforcement, and decelerative procedures. After reduction of aggression to zero, regular staff were reintroduced and presented instruction and corrective feedback as required. No further aggressive behaviour was noted, and self-care improved so that only minimal assistance was needed. Six months following reintroduction of regular staff, both baseline conditions were replicated. No aggressive behaviour was observed during either, suggesting that maintenance of gains could not be attributed to an artificially reduced rate caused by staff avoiding trigger antecedents.

The failure of feedback on alcohol impairment to reduce impaired driving

We examined the effects of rules to govern drinking, individual feedback on blood alcohol concentration (BAC), and public posting of group data on impaired driving on the incidence of impaired driving. Level of impairment was determined from breath samples taken from tavern patrons. Following baseline, an intervention package consisting of (a) cards to guide patrons in pacing their drinking to stay under the legal limit, (b) individual feedback on BAC, and (c) posted group feedback on the percentage of patrons driving while impaired the preceding week was introduced in two taverns. Results indicated that the intervention package did not reduce the percentage of impaired drivers departing either tavern. The addition of a brief intensive police enforcement program directed at impaired driving produced a short-term reduction in impaired driving.

The use of a brief movement restriction procedure to eliminate severe inappropriate behavior

The effect of a brief movement restriction (BMR) procedure on the maladaptive behavior of two severely mentally retarded persons was evaluated using a multiple baseline research design. Following a functional analysis of the maladaptive behaviors, baseline data were collected on the frequency of smearing in a six year old boy and the frequency of aggression-destruction and stereotypic behavior in a 24 year old man. Following the baseline period a treatment package that included reinforcement for alternative behavior and BMR were first introduced for feces smearing. After feces smearing had shown a reduction with the first client the treatment package was introduced for aggression and destruction with the second client. After aggression and destruction had been reduced, the treatment package was added for stereotypy. The treatment package completely eliminated each of the target behaviors and they remained absent during a long follow-up period.

Side effects of therapeutic punishment on academic performance and eye contact

The effects of therapeutic punishment delivered following inappropriate behavior on the academic responding and eye-to-face contact of 2 persons with developmental handicaps was examined using a counterbalanced alternating treatment design. Each subject was sequentially taught by two therapists each day. While one of the therapists taught the subject, the second therapist stood in close proximity directly behind the subject. During baseline, neither therapist delivered punishment following inappropriate behavior. During the treatment condition, one of the therapists delivered all punishment regardless of whether she was teaching or standing behind the subject. The therapist who delivered all punishment for 1 subject did not deliver any punishment for the other subject. During the last condition, the therapist delivering all punishment was reversed for 1 of the subjects. The results indicated that the task being taught was mastered by each subject only when the therapist delivering punishment was teaching. Data collected also indicated that each subject made more eye-to-face contact when the therapist delivering all punishment was teaching. Although neither therapist had to deliver punishers often, punishment had to be administered less often when the therapist teaching the subject was also the therapist delivering punishment.

Recreating the scene: an effective way to provide delayed punishment for inappropriate motor behavior

A mediated punishment procedure that involved recreating a behavioral sequence by guiding the subject through the behavior in the situation in which it occurred was used to suppress several severe problem behaviors in two developmentally delayed children. The mediational procedure was first used with a 4-year-old autistic boy for biting and then for foot stomping. Next the procedure was used for stealing and hoarding behavior with a multiply handicapped 17-year-old girl. Results indicated that the procedure was effective and produced relatively rapid results. One advantage of the procedure is that it provides an opportunity for trained personnel to apply restrictive procedures to low frequency behavior that occurs in their absence rather than relying on less qualified staff to implement the procedure immediately after the behavior occurs.

Treatment of constipation-caused encopresis by a negative reinforcement procedure

During a baseline condition soiling and the cumulative number of bowel movements of a child suffering from retentive encopresis were recorded. Following this, a DRO (differential reinforcement of other behavior) alone, a DRO plus overcorrection procedure, and a negative reinforcement procedure were each evaluated using a reversal design. The negative reinforcement procedure, which involved having the child sit on the toilet three times a day for increasing time periods if no bowel movement occurred, suppressed soiling and led to regular unprompted daily bowel movements in a very brief period of time. The DRO alone and DRO plus overcorrection conditions produced only a small decline in soiling.

Large-scale reductions in speeding and accidents in Canada and Israel: a behavioral ecological perspective

We assessed the effects of posted feedback and warning ticket programs on speeding and accidents in two cities. In Experiment 1, speeding feedback signs were effective even when 10 were used in Dartmouth, Nova Scotia, and reductions in speeding were associated with reductions in accidents. The effectiveness of the signs was correlated with the number of intersections and residences within 0.5 km beyond them, and the signs had no effect on untreated streets. In Experiment 2, posted feedback and a warning program reduced speeding and accidents on 14 streets in Haifa, Israel.

Movement suppression time-out for undesirable behavior in psychotic and severely developmentally delayed children

The effects of a movement suppression time-out, which involved punishing any movement or verbalization while a client is in the time-out area, were evaluated in four experiments. The first experiment examined the effects of a DRO procedure and movement suppression plus DRO in suppressing self-injurious behavior in a psychotic child in three different situations. In Experiment 2, the results of the previous experiment were replicated with two dangerous behaviors in a second psychotic child. In a third experiment, movement suppression plus DRO was compared with contingent restraint in reducing inappropriate poking behavior in two settings. The movement suppression procedure eliminated poking whereas contingent restraint had little effect. In the final experiment, movement suppression time-out alone was compared with exclusionary time-out alone and simple corner time-out alone. Self-stimulation occurred at high levels during the exclusionary and simple corner time-out procedures. Self-stimulation was either suppressed or reduced during movement suppression time-out. The movement suppression time-out procedure produced a larger reduction in the target behavior in all three children. The effectiveness of the movement suppression procedure was explained in terms of the suppression of self-stimulation while the time-out procedure was being applied.

The use of response prevention to eliminate nocturnal thumbsucking

The effects of a response prevention strategy consisting of the fading of restraint and the removal of reinforcers on nocturnal thumbsucking behavior was evaluated in four experiments. In the first experiment, nocturnal thumbsucking was restrained for approximately 1 week by having each of two boys wear a boxing glove to bed. Next they wore absorbent cotton over the thumb for 11 nights. During the last phase in this condition, they wore a fingertip bandage over the thumb for 10 to 11 nights. The response prevention package completely eliminated thumbsucking behavior in both boys. In the second experiment, the removal of reinforcers alone for nocturnal thumbsucking had little or no effect on the thumbsucking behavior of three girls whereas the later introduction of the entire package completely suppressed thumbsucking in all three girls. In the third experiment, the package was evaluated in the absence of the glove restraint condition. The results showed that the treatment package was effective in the absence of the glove restraint condition for all three children. The final experiment examined whether the package could be effective if the absorbent cotton condition was abruptly removed without using the fingertip bandage condition. The results showed the treatment to be effective with one of two boys, but not the other.