| 1. |
- Lysiak, Malgorzata, 1989-
(författare)
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Biomarkers In Brain Tumors With Focus On Glioblastoma
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The primary brain tumors, gliomas, are not very common but they are deadly. Each year in Sweden around 500 patients will be diagnosed with a glioma and unfortunately most of them will have the most aggressive type, glioblastoma (GBM). Median survival, even if treated, is poor (14-17 months). Males are diagnosed up to 60% more often than females and they often have a worse prognosis. GBM affects mainly older patients and treatment includes radiochemotherapy with temozolomide (TMZ). The only known predictive biomarker for TMZ treatment is methylation of the O6-methylguanine DNA methyltransferase (MGMT) promoter and patients with methylated MGMT have better outcomes. There is a great need for biomarkers to decipher existing sex differences and others that identify patients that will benefit from radiotherapy (RT) or TMZ despite of unmethylated MGMT. Papers I-III are focused on investigating sex differences in GBM and in Paper IV we examined the methylation-based biomarkers used in diagnostics, on patients from the Nordic trial with exceptionally good and poor survival when treated with TMZ or RT. Loss of the Y chromosome (LOY) in male’s blood cells is associated with aging and, among other diseases, with cancer. We looked at 10 genes located on chromosome Y in 105 males with GBM treated with TMZ concomitant with RT and found that they are often deleted. Detected LOY, as well as deletion of the sex determining region Y (SRY) gene were associated with shorter overall survival. Low SRY gene expression analyzed in an additional cohort of 219 samples from The Cancer Genome Atlas (TCGA) was also associated with a shorter survival.In Paper II we re-analyzed data from three cohorts to compare the frequency of MGMT methylated tumors in males and females and investigated whether sex is an important factor associated with patient’s survival. This was done in a GBM cohort from the randomized, phase 3 Nordic trial, which included patients 60 years or older, treated with standard RT (60Gy) vs. hypofractionated RT vs. TMZ given in up to six 4 weekly cycles; in a population-based cohort, treated with TMZ concomitant with RT and an excerpt of the TCGA cohort of patients treated with different modalities. In all three cohorts there was a higher fraction of MGMT methylated tumors in females and MGMT methylation was predictive of longer survival for those treated with an alkylating agent, such as TMZ.The third study investigated the androgen receptor (AR), located on chromosome X as a potential sex susceptibility factor for GBM. We found that the gene encoding for AR can be amplified or deleted in GBM, and these changes are more common in females. The AR gene expression was enhanced in GBM but did not differ between sexes. At the same time, in a separate analysis for males and females, we found that high AR expression is associated with shorter survival in females and longer survival in males Also, the methylation sites in the AR promoter that correlated with gene expression are sex specific. In Paper IV we included 59 patients from the Nordic trial, equally divided by the treatment arms and MGMT methylation status, with good prognostic factors and with long or short survival. We performed genome-wide methylation analysis and identified differentially methylated sites between those with long and short survival for the TMZ treated, MGMT methylated samples, as well as the 60Gy, MGMT unmethylated and 34Gy MGMT methylated samples. This small pilot study was unable to discern any differentially methylated sites in TMZ treated samples with unmethylated MGMT, associated with long or short survival. By using a methylation-based diagnostic classifier, we were able to detect a misclassified sample that was not a GBM. Lastly, we calculated so called ‘epigenetic age’ of the tumor tissue based on the methylation data and using three different algorithms and found that in all treatment groups short-term survivors tended to have lower epigenetic age, though these results were not significant and need verification in a larger cohort.In summary, this thesis advances our knowledge on the molecular differences between male and female GBM and the association between these alterations and patients’ survival. Our results also suggest that there are potential methylation-based biomarkers apart from the MGMT promoter methylation, that can be used to distinguish between patients with good and poor prognosis, for instance, the epigenetic age.
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| 2. |
- Lysiak, Malgorzata, et al.
(författare)
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Deletions on Chromosome Y and Downregulation of the SRY Gene in Tumor Tissue Are Associated with Worse Survival of Glioblastoma Patients
- 2021
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Ingår i: Cancers. - : MDPI. - 2072-6694. ; 13:7
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Biological causes of sex disparity seen in the prevalence of cancer, including glioblastoma (GBM), remain poorly understood. One of the considered aspects is the involvement of the sex chromosomes, especially loss of chromosome Y (LOY).METHODS: Tumors from 105 isocitrate dehydrogenase (IDH) wild type male GBM patients were tested with droplet digital PCR for copy number changes of ten genes on chromosome Y. Decreased gene expression, a proxy of gene loss, was then analyzed in 225 IDH wild type GBM derived from TCGA and overall survival in both cohorts was tested with Kaplan-Meier log-rank analysis and maximally selected rank statistics for cut-off determination.RESULTS: LOY was associated with significantly shorter overall survival (7 vs. 14.6 months, p = 0.0016), and among investigated individual genes survival correlated most prominently with loss of the sex-determining region Y gene (SRY) (10.8 vs. 14.8 months, p = 0.0031). Gene set enrichment analysis revealed that epidermal growth factor receptor, platelet-derived growth factor receptor, and MYC proto-oncogene signaling pathways are associated with low SRY expression.CONCLUSION: Our data show that deletions and reduced gene expression of chromosome Y genes, especially SRY, are associated with reduced survival of male GBM patients and connected to major susceptibility pathways of gliomagenesis.
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| 3. |
- Malmström, Annika, 1957-, et al.
(författare)
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Do we really know who has an MGMT methylated glioma? : results of an international survey regarding use of MGMT analyses for glioma
- 2020
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Ingår i: Neuro-Oncology Practice. - Oxford : Oxford University Press. - 2054-2577 .- 2054-2585. ; 7:1, s. 68-76
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Tidskriftsartikel (refereegranskat)abstract
- Background: Glioma O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation status informs clinical decision making. Worldwide different methods and cutoff levels are used, which can lead to discordant methylation results.Methods: We conducted an international survey to clarify which methods are regularly used and why. We also explored opinions regarding international consensus on methods and cutoff.Results: The survey had 152 respondents from 25 countries. MGMT methylation status is determined for all glioblastomas in 37% of laboratories. The most common methods are methylation-specific polymerase chain reaction (msPCR) (37%) and pyrosequencing (34%). A method is selected for simplicity (56%), cost-effectiveness (50%), and reproducibility of results (52%). For sequencing, the number of CpG sites analyzed varies from 1–3 up to more than 16. For 50% of laboratories, the company producing the kit determines which CpG sites are examined, whereas 33% select the sites themselves. Selection of cutoff is equally distributed among a cutoff defined in the literature, by the local laboratory, or by the outside laboratory performing the analysis. This cutoff varies, reported from 1% to 30%, and in 1 laboratory tumor is determined as methylated in case of 1 methylated CpG site of 17 analyzed. Some report tumors as unmethylated or weakly vs highly methylated. An international consensus on MGMT methylation method and cutoff is warranted by 66% and 76% of respondents, respectively. The method preferred would be msPCR (45%) or pyrosequencing (42%), whereas 18% suggest next-generation sequencing.Conclusion: Although analysis of MGMT methylation status is routine, there is controversy regarding laboratory methods and cutoff level. Most respondents favor development of international consensus guidelines.
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| 4. |
- Tabebi, Mouna, et al.
(författare)
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Genetic Alterations in Mitochondrial DNA Are Complementary to Nuclear DNA Mutations in Pheochromocytomas
- 2022
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Ingår i: Cancers. - : MDPI. - 2072-6694. ; 14:2
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Tidskriftsartikel (refereegranskat)abstract
- Background: Somatic mutations, copy-number variations, and genome instability of mitochondrial DNA (mtDNA) have been reported in different types of cancers and are suggested to play important roles in cancer development and metastasis. However, there is scarce information about pheochromocytomas and paragangliomas (PCCs/PGLs) formation.Material: To determine the potential roles of mtDNA alterations in sporadic PCCs/PGLs, we analyzed a panel of 26 nuclear susceptibility genes and the entire mtDNA sequence of seventy-seven human tumors, using next-generation sequencing, and compared the results with normal adrenal medulla tissues. We also performed an analysis of copy-number alterations, large mtDNA deletion, and gene and protein expression.Results: Our results revealed that 53.2% of the tumors harbor a mutation in at least one of the targeted susceptibility genes, and 16.9% harbor complementary mitochondrial mutations. More than 50% of the mitochondrial mutations were novel and predicted pathogenic, affecting mitochondrial oxidative phosphorylation. Large deletions were found in 26% of tumors, and depletion of mtDNA occurred in more than 87% of PCCs/PGLs. The reduction of the mitochondrial number was accompanied by a reduced expression of the regulators that promote mitochondrial biogenesis (PCG1α, NRF1, and TFAM). Further, P62 and LC3a gene expression suggested increased mitophagy, which is linked to mitochondrial dysfunction.Conclusion: The pathogenic role of these finding remains to be shown, but we suggest a complementarity and a potential contributing role in PCCs/PGLs tumorigenesis.
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| 5. |
- Welander, Jenny, et al.
(författare)
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Activating FGFR1 mutations in sporadic pheochromocytoma
- 2018
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Ingår i: World Journal of Surgery. - : Springer. - 0364-2313 .- 1432-2323. ; 42:2, s. 482-489
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Tidskriftsartikel (refereegranskat)abstract
- Pheochromocytomas are neuroendocrine tumors of the adrenal glands that cause hypertension. More than a third of the cases are associated with hereditary mutations in a growing list of susceptibility genes, some of which are also somatically altered in sporadic pheochromocytomas. However, for the majority of sporadic pheochromocytomas, a genetic explanation is still lacking. Here we investigated the genomic landscape of sporadic pheochromocytomas with whole-exome sequencing of 16 paired tumor and normal DNA samples, and discovered on average 33 non-silent somatic mutations per tumor. One of the recurrently mutated genes was FGFR1, encoding the fibroblast growth factor receptor 1, which was recently revealed as an oncogene in pilocytic astrocytoma and childhood glioblastoma. Including a subsequent analysis of a larger cohort, activating FGFR1 mutations were detected in three of 80 sporadic pheochromocytomas (3.8%). Gene expression microarray profiling showed that these tumors clustered with NF1- RET- and HRAS-mutated pheochromocytomas, indicating activation of the MAPK and PI3K-AKT signal transduction pathways. The results advance our biological understanding of pheochromocytoma and suggest that somatic FGFR1 activation is an important event in a subset of these tumors.
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