Els tumors de cervell humans (HBTs) són uns dels càncers més agressius i intractables. El sistema actual de diagnosi i prognosi dels HBTs es basa en l'examinació histològica d'un tall de biòpsia, el qual es considera el sistema de referència ("gold¬standard"). A més de ser invasiva, aquesta tècnica no és prou acurada per a diferenciar els graus de malignitat de determinats HBTs i la correlació amb la resposta del pacient a la teràpia sol ser variable. En aquest context, les signatures gèniques obtingudes a partir de microarrays de DNA poden millorar els resultats del "gold-standard". En aquesta tesi, vaig recollir 333 biòpsies de varis tipus de HBTs. Com un 38% de les mostres tenien l'RNA degradat, vam avaluar si el tipus de HBTs, el contingut aparent de sang de la biòpsia i el medi de recollida de la biòpsia hi afectaven. Com no vam determinar cap relació, hipotetitzo que un temps variable d'isquèmia a temperatura normal del cos abans de l'extracció de la biòpsia podria induir la degradació de l'RNA. Això va ser avaluat en un tumor glial pre-clínic desenvolupat en ratolí. Es va detectar que 30 minuts de temps d'isquèmia afecta la integritat del RNA en tumors no necròtics, però no en els necròtics. Una part crucial de la tesi va ser la demostració com una "prova de principis" de l'habilitat de les signatures gèniques per a predir objectivament els HBTs. Això es va mostrar mitjançant una predicció perfecta de glioblastoma multiforme (Gbm) i meningioma meningotelial (Mm) utilitzant microarrays de cDNA i microchips d'Affymetrix. Els histopatòlegs poden discriminar perfectament aquests dos tipus de tumors, però aquest treball demostra una predicció perfecta utilitzant una fórmula matemàtica objectiva. Un cop es va demostrar això, em vaig sentir confiat per a predir diferents graus de malignitat i possibles subtipus moleculars de tumors glials. En aquest sentit, es va descriure una signatura gènica basada en l'expressió de 59 transcrits, la qual va distingir dos grups de glioblastomes. Finalment, una anàlisi inicial de les dades clíniques associades suggereix que la signatura gènica podria correlacionar amb glioblastomes primaris i secundaris. / Human brain tumours (HBTs) are among the most aggressive and intractable cancers. The current system for diagnosis and prognosis of HBTs is based on the histological examination of a biopsy slice, which is considered the 'gold standard'. Apart from being invasive, this technique is not accurate enough to differentiate malignancy grades of some HBTs and it provides a variable correlation with response to therapy of the patient. In this context, gene signatures from DNA microarray experiments can improve the results of the 'gold standard'. In this thesis, I collected 333 biopsies from various types of HBTs. As 38% of samples displayed degraded RNA, I evaluated whether the HBT type, the apparent blood content and the collection medium of the biopsy could play a role in this. As no relationship was found, I hypothesized that the variable ischaemia time at normal body temperature prior to removal of the biopsy may induce degradation of RNA. This was tested in a preclinical glial tumour model in mice. It was detected that 30 minutes ischaemia time affects the integrity of the RNA in non-necrotic tumours, but not in the necrotic ones. A crucial part of this thesis was the demonstration of proof-of-principle of the ability of gene signatures for objective prediction of HBTs. This was shown by perfect prediction of glioblastoma multiforme (Gbm) and meningothelial meningioma (Mm) using cDNA and Affymetrix microarrays. Histopathologists perfectly discriminates both tumour types, but this work demonstrated perfect prediction using a simple mathematical formula. Once this was demonstrated, I felt confident to predict different malignancy grades and possible molecular subtypes of glial tumours. In this respect, a gene signature based on the expression of 59 transcripts, which distinguished two groups of glioblastomas, was described. Finally, a crude initial analysis of associated clinical data suggests that this gene signature may correlate to primary and secondary glioblastomas.

Brain tumours, even though rare, are one of the deadliest types of cancer. The five year survival rate for the most malignant type of brain tumours is below 5%. Modern medicine provides many options for treating brain cancer such as radiotherapy and chemotherapy. However, one of the most effective ways of fighting the disease is surgical resection. During such a procedure the tumour is partially or completely removed. Unfortunately, even after a complete resection some tumourous tissue is left behind and can grow back or metastasise to a different location in the brain. It has been shown, however, that more aggressive resections lead to longer life expectancy. This does not come without risks. Depending on tumour location, extensive resections can lead to transient or permanent post-operative neurological deficits. Therefore, when planning a procedure, the neurosurgeon needs to find balance between extending patients life and maintaining its quality. Recent developments in Magnetic Resonance Imaging (MRI) fueled by the field of human cognitive neuroscience have led to improved methods of non-invasive imaging of the brain function. Such methods allow the creation of functional brain maps of populations or individual subjects. Adapting this technique to the clinical environment enables the assessment of the risks and to plan surgical procedures. The following work aims at improving the use of functional MRI with a specific clinical goal in mind. The thesis begins with description of etiology, epidemiology and treatment options for brain tumours. This is followed by a description of MRI and related data processing methods, which leads to introduction of a new technique for thresholding statistical maps which improves upon existing solutions by adapting to the nature of the problem at hand. In contrast to methods used in cognitive neuroscience our approach is optimized to work on single subjects and maintain a balance between false positive and false negative errors. This balance is crucial for accurate assessment of the risk of a surgical procedure. Using this method a test-retest reliability study was performed to assess five different behavioural paradigms and scanning parameters. This experiment was performed on healthy controls and was aimed at selecting which paradigms produce reliable results and therefore can be used for presurgical planning. This allowed the creation of a battery of task that was applied to glioma patients. Functional maps created before the surgeries were compared with electrocortical stimulation performed during the surgeries. The final contribution of this work focuses on technical aspects of performing neuroimaging data analysis. A novel data processing framework which provides means for rapid prototyping and easy translation and adaptation of already existing methods taken from cognitive neuroscience field is introduced. The framework enables fully automatic processing of patient data and therefore greatly reduced costs while maintaining quality control. A discussion of future directions and challenges in using functional MRI for presurgical planning concludes the thesis.

No description available.

Thesis (MA)--Stellenbosch University, 2015 / ENGLISH ABSTRACT : Worldwide there are various reports on the prevalence of depression in patients diagnosed with brain tumours. In South Africa, psychological research in relation to psychiatric symptoms among patients with brain tumours is lacking. The aims of this study were to determine the incidence of depression in patients diagnosed with brain tumours and to clarify our understanding of the relationship between depression and tumour localisation, histopathological type of tumour, and participant characteristics. The study sample consisted of 35 patients (11 males and 24 females) aged between 21 and 64 years with a solitary primary brain tumour. The patients were treated at the neurosurgery clinics located at Tygerberg Hospital in the Western Cape and Universitas Hospital in the Free State between mid-2010 and 2013. The major histological subgroup consisted of meningiomas (47%), glioblastomas (22%), astrocytomas (19%), gliomas (9%) and epidiomas (3%). The tumour distribution was as follows: 52% in the left hemisphere, 37% in the right hemisphere, and 11 % in the midline. The psychiatric symptoms of the patients were assessed before treatment by the Beck Depression Inventory and Mini International Neuropsychiatric Interview. In addition, the patients’ neuropsychological functions were evaluated by a short neuropsychological test battery (Mini Mental State Examination, Trail Making Test (Part A), Letter Number Sequencing subtest, Hopkins Verbal Learning Test – Revised, and Brief Visuospatial Memory Test – Revised). Results from the quantitative data, showed the prevalence of mild depression was 26% for men and 43% for women. Overall 37% of the total sample had depressive symptoms. No significant relationship was found between depression and tumour location or between the various neuropsychological characteristics and neurological symptoms and tumour location. The study showed that depression is a common symptom in patients diagnosed with brain tumours and therefore depression symptoms have to be recognised and treated by psycho-educating the patients and their families, pharmacotherapy, or psychotherapy as soon as possible. However, due to the relatively small sample size, the results are of limited generalisability. / AFRIKAANSE OPSOMMING : Wêreldwyd is daar verskeie verslae oor die voorkoms van depressie in pasiënte gediagnoseer met breingewasse. In Suid-Afrika is daar ’n tekort aan sielkundige navorsing met betrekking tot psigiatriese simptome by pasiënte. Die doel van hierdie studie was om die voorkoms van depressie te bepaal in pasiënte gediagnoseer met breingewasse en om duidelikheid te kry oor die verband tussen depressie en die ligging van breingewasse, histopatologiese tipe gewas en karakter eienskappe van die deelnemers. Die steekproef van die studie het bestaan uit 35 pasiënte (11 mans en 24 vroue) tussen die ouderdomme 21 en 64 jaar met ‘n soliede breingewas. Die pasiënte is behandel by die neurochirurgiese klinieke by Tygerberg Hospitaal in die Wes-Kaap en by Universitas Hospitaal in die Vrystaat vanaf middel 2010 tot 2013. Die mees algemene histologiese subgroep het bestaan uit meningiome (47%), glioblastomas (22%), astrocytomas (19%), gliomas (9%) en epidiomas (3%). Die verspreiding van die gewasse was soos volg: 52% in die linkerhemisfeer, 37% in die regterhemisfeer en 11% in die middel. Die psigiatriese simptome van die pasiënte is voor behandeling geëvalueer met behulp van die Beck Depression Inventory en die Mini International Neuropsychiatric Interview. Bykomend is die pasiënte se neurosielkundige funksies geëvalueer met behulp van ‘n neurosielkundige toetsbattery (Mini Mental State Examination, Trail Making Test (Part A), Letter Number Sequencing subtest, Hopkins Verbal Learning Test – Revised en Brief Visuospatial Memory Test – Revised). Die resultate van die kwantitatiewe data het getoon die voorkoms van matige depressie was 26% vir mans en 43% vir vroue. In geheel het 37% van die totale steekproef depressiewe simptome getoon. Daar was geen beduidende verhouding tussen depressie en die ligging van die gewas of tussen die verskeie neurosielkundige eienskappe en die ligging van die gewas nie. Die studie het getoon dat depressie ’n algemene simptoom is in pasiënte gediagnoseer met breingewasse en daarom moet depressiewe simptome herken en so gou as moontlik behandel word deur psigo-opvoeding van die pasiënte en hul familie, farmakoterapie of psigoterapie. As gevolg van die relatiewe klein steekproef grootte het die resultate ’n beperkte veralgemeenbaarheid.

Purpose: To examine the social competence of childhood brain tumour survivors in the context of a group social skills intervention program developed to address documented social deficits among this population and to expand outcomes obtained from a feasibility study, by: conceptualizing social competence as three separate but interrelated constructs including social adjustment, social performance, and social skills; incorporating a control group; eliciting teacher responses; and examining sense of self. Methods: Participants were 23 survivors (10 males; 13 females) aged 7 to 15 years and comprised an intervention (n=15) and control group (n=8). The intervention consisted of 8 2-hour weekly sessions focused on social skills including friendship making. At the level of social adjustment, intervention participants, controls, parents, and teachers (n=6) completed standardized measures of social adjustment including: social skills (SSRS, Gresham & Elliott, 1990); social functioning (Varni, 1999); and social problems (Achenbach, 2001). At the level of social performance, behavioural observations were conducted on intervention participants. At the level of social skills, intervention participants responded to the Social Problem-Solving Measure (SPSM; Vannatta, 1993). Survivors also completed standardized sense of self measures. Results: Outcomes related to social adjustment showed a significant increase from Time 1 to Time 2 for parent reported SSRS within and between groups. Significant improvements were also found for parent reported social problems between groups. Child reported social problems decreased within groups and a borderline effect was found between groups. Teachers reported improved SSRS scores form Time 1 to Time 2. For social performance, significant increases in frequency were found for maintaining facial attention and social conversations with peers over the course of the intervention. At the level of social skills, a borderline significant increase was found for quantity of strategies offered from Time 1 to Time 2. No significant findings were found for sense of self data. Conclusions: Improvements after intervention were noted at each level of social competence, but primarily at the level of social adjustment. Control group and teacher outcomes strengthen findings. This is the first study to explore varying levels of social competence and provides important insight into the source of survivors’ social deficits.

Purpose: To examine the social competence of childhood brain tumour survivors in the context of a group social skills intervention program developed to address documented social deficits among this population and to expand outcomes obtained from a feasibility study, by: conceptualizing social competence as three separate but interrelated constructs including social adjustment, social performance, and social skills; incorporating a control group; eliciting teacher responses; and examining sense of self. Methods: Participants were 23 survivors (10 males; 13 females) aged 7 to 15 years and comprised an intervention (n=15) and control group (n=8). The intervention consisted of 8 2-hour weekly sessions focused on social skills including friendship making. At the level of social adjustment, intervention participants, controls, parents, and teachers (n=6) completed standardized measures of social adjustment including: social skills (SSRS, Gresham & Elliott, 1990); social functioning (Varni, 1999); and social problems (Achenbach, 2001). At the level of social performance, behavioural observations were conducted on intervention participants. At the level of social skills, intervention participants responded to the Social Problem-Solving Measure (SPSM; Vannatta, 1993). Survivors also completed standardized sense of self measures. Results: Outcomes related to social adjustment showed a significant increase from Time 1 to Time 2 for parent reported SSRS within and between groups. Significant improvements were also found for parent reported social problems between groups. Child reported social problems decreased within groups and a borderline effect was found between groups. Teachers reported improved SSRS scores form Time 1 to Time 2. For social performance, significant increases in frequency were found for maintaining facial attention and social conversations with peers over the course of the intervention. At the level of social skills, a borderline significant increase was found for quantity of strategies offered from Time 1 to Time 2. No significant findings were found for sense of self data. Conclusions: Improvements after intervention were noted at each level of social competence, but primarily at the level of social adjustment. Control group and teacher outcomes strengthen findings. This is the first study to explore varying levels of social competence and provides important insight into the source of survivors’ social deficits.

Epidemiology of primary paediatric brain tumours has been studied extensively in developed countries of the west. Such studies are lacking in developing countries especially sub-Saharan Africa. This study seeks to establish the epidemiology of primary brain tumours seen among children that were treated at Chris Hani Baragwanath and Johannesburg Hospitals from April 1995 to April 2005. The records of 252 patients who presented with this condition during the study period were reviewed, for the following details: ● Demographic details such as age, gender and race ● Diagnosis and the date when it was made ● The follow-up period at the hospital(s)/clinic(s) ● The anatomical location of the tumours; supratentorial or infratentorial ● The treatment that was given which included mainly surgery for tumour removal or biopsy, radiotherapy, chemotherapy and others which included ventriculoperitoneal shunt, external ventricular drain insertion. ● The outcome of treatment included: - alive - dead - presumed alive - lost to follow-up It was found: ● That 225 patients had full demographic details of race, gender and age. ● That there was a slight male predominance among children with primary brain tumour. ● That the majority of children with brain tumours were black, followed by whites which is in keeping with the country’s demographics. ● The three most common tumours were astrocytomas, medulloblastomas and brainstem gliomas in the descending order of frequency. ● Medulloblastomas were the commonest tumours in the infratentorial region while craniopharyngiomas were commonest tumours in the supratentorial region. ● More children had infratentorial tumours ● Younger children were more likely to have infratentorial tumours. ● Majority of patients had surgery either for diagnosis or for diagnosis and treatment. ● Few patients were presumptively diagnosed clinically and by imaging modalities ● Combination therapy of surgery, chemotherapy and radiotherapy had the best survival outcome while chemotherapy as the only form of treatment had the worst outcome. ● The overall 5 year survival rate for all the study participants was much lower than that of their counterparts in the literature. ● Children who had craniopharyngiomas and astrocytomas had better survival. ● Mortality incidence was slightly higher for whites than blacks but that could have been skewed by a high number of blacks that was lost to follow-up. ● A higher infratentorial tumour prevalence than in the literature was noted. It was noted that racial prevalence of primary paediatric brain tumours follows population demographics. From the results of this study, there is a need for a better record keeping and improved patients follow-up. There is also a need for a larger epidemiological study in the two hospitals. There is need to establish a specialized paediatric unit which will help start a paediatric team comprising of a paediatric neurosurgeon, paediatric oncologist, paediatric intensivist and neuroradiologist with dedicated neuropaediatric ICU. Such a team given resources will improve survival outcome of children with brain tumours.

Background: A compilation of high quality systematic reviews (SRs) on lifestyle factors associated with adult glioma and meningioma was developed. Methods and Materials: Phase 1 consisted of a systematic overview of existing SRs. For Phase 2, high quality SRs were incorporated in an update. Moderate or low quality SRs which had not been considered in a high quality review were eligible for a de-novo synthesis. Results: Phase 1 resulted in seven moderate to low quality reviews. From this, in Phase 2, smoking, mobile phone and hair dye use were subjected to de-novo reviews. For smoking, it was suggestive that past smokers had an increased risk. For mobile phone use, there was no overall association, however it was suggestive that ipsilateral and high cumulative call time were associated with slight increased risk. No association was observed for personal hair dye use. Conclusions: Despite these null associations, rigorous SR methods were used providing confidence in conveying these results.

Telomeres are nucleoprotein complexes located at the end of chromosomes. They have an essential role in protecting chromosome ends. Telomerase or ALT (alternative lengthening of telomeres) mechanisms maintain telomeres by compensating natural telomeric loss. We have set up a flow-FISH method and using mouse lymphoma cell lines we identified unexpectedly the presence of subpopulations of cells with different telomere lengths. Subpopulations of cells with different telomere lengths were also observed in a human ALT and non-ALT cell line. Differences in telomere length between subpopulations of cells were significant and we term this phenomenon TELEFLUCS (TElomere LEngth FLUctuations in Cell Subpopulations). By applying flow-FISH we could successfully measure telomere lengths during replicative senescence in human primary fibroblasts with different genetic defects that confer sensitivity to ionising radiation (IR). The results from this study, based on flow-FISH and Southern hybridisation measurements, revealed an accelerated rate of telomere shortening in radiosensitive fibroblasts. We also observed accelerated telomere shortening in murine BRCA1 deficient cells, another defect conferring radiosensitivity, in comparison with a BRCA1 proficient cell line. We transiently depleted BRCA1 by siRNAs in two human mammary epithelial cell lines but could not find changes in telomere length in comparison with control cells. Cytological evidence of telomere dysfunction was observed in all radiosensitive cell lines. These results suggest that mechanisms that confer sensitivity to IR may be linked with mechanisms that cause telomere dysfunction. Furthermore, we have been able to show that human ALT positive cell lines show dysfunctional telomeres as detected by either the presence of DSBs at their telomeres or cytogenetic analysis and usually cells with dysfunctional telomeres are sensitive to IR. Finally, we assessed hTERT mRNA splicing variants and telomerase activity in brain tumours, which exhibit considerable chromosome instability suggesting that DNA repair mechanisms may be impaired. We demonstrated that high levels of hTERT mRNAs and telomerase activity correlate with proliferation rate. The presence of hTERT splice variants did not strictly correlate with absence of telomerase activity but hTERT spliced transcripts were observed in some telomerase negative brain tumours suggesting that hTERT splicing may contribute to activation of ALT mechanisms.

Brain tumours account for the most frequent type of solid tumours among children. Despite advances in surgery and chemotherapy, brain tumours are still the main cause of cancer deaths in children. Furthermore, little is known about DNA methylation changes in paediatric astrocytoma. Recent investigations suggest that many tumours are initiated not only by genetic abnormalities, but also caused by epigenetic changes. DNA methylation is a key epigenetic mechanism that controls the regulation of gene expression. Interestingly, unlike DNA mutations, epigenetic abnormalities are reversible. The reversibility of epigenetic abnormalities upon pharmacological unmasking has prompted interest in developing epigenetic therapy with the crucial goal of restoring the expression of aberrantly silenced genes. The focus of this study was to utilise a combination of different microarray strategies to develop an integrative candidate gene approach to identify several novel frequently methylated genes in a cohort of paediatric HGA (High grade glioma) samples. In addition, to investigate the potential of therapeutic efficacy of a DNA methyltransferase inhibitor, 5-Aza-dC in paediatric HGA. There were 147 genes commonly identified to be potentially methylated in IN699 cells using the two different array strategies integration; re-expression array and Illumina Infinium Human Methylation 450k array. Furthermore, using two complementary microarray strategies including methylation 450k array and expression array, this work identified 55 genes that were both methylated and under-expressed in these HGA cultures. Following validation with CoBRA and RT-PCR coupled with the response of hypermethylated promoters to the demethylating agent 5-Aza-dC, six novel genes (CXCL14, PRR5L, ELTD1, ITGA2, KRT8 and NTM) that are frequently silenced in paediatric astrocytoma were identified. This study suggests that re-expression of ii CXCL14 inhibited the colony formation and cell growth and reduces the migration rate significantly in IN699 short term culture and likely have functional significance in the development of paediatric HGA and an excellent candidate gene for further analysis. In parallel, the efficacy of 5-Aza-dC treatment was examined in paediatric HGA aiming to introduce this epigenetic therapy as a potential mechanism in management of this tumours. This study demonstrated that, relatively low dose of 5-Aza-dC sharply reduced the colony formation and inhibited proliferation and not through the apoptotic effect. It is likely that this reduction in proliferation without cell death is due to using relatively low doses that do not acutely kill cells, thus, allow the sustained alterations in both gene expression patterns and appearance of a new phenotype to emerge. Taken together, this work contributes to a more detailed understanding of the effect of epigenetic silencing on paediatric HGA. This investigation also demonstrated the use of epigenetic drug, 5-aza-dC to reverse the gene silencing for the potential treatment of paediatric HGA.