Molecular classification of high grade pediatric brain tumors based on gene expression profiling using NanoString technology


Sobocińska, Anna Antonina


Łastowska, Maria Anna (Promotor) ; Matyja, Ewa (Promotor)

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Date issued/created:



Bibliografia zawiera 95 pozycji ; 97 s.: ryc., tabl.; 30 cm.

Degree name:


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Degree discipline :

medical sciences

Degree grantor:

Instytut Medycyny Doświadczalnej i Klinicznej im. M. Mossakowskiego PAN

Subject and Keywords:

Infratentorial brain tumors ; Gene signature ; NanoString


Brain tumors in children are the second most common group of tumors after the leukemias. They represent 20-25% of all pediatric tumors and are still a leading cause of death in this age group. Central nervous system tumors in children can occur in all anatomical localization, although the most common is the posterior fossa region. The main therapeutic problem with tumors localized in the infratentorial region, especially in the case of brainstem tumors with diffuse growth pattern, are limited access totumor site and thus inability to perform complete resection. Routine histopathological analysis is not always an objective prognostic factor, therefore there is a need for more reliable methods that can successfully stratify patients to risk groups, as well as for novel therapeutic approaches for patients that don’t meet the standard criteria for treatment. Until recently, prognostic criteria in brain tumors were based on extension of surgical resection of the tumor and histopathological assessment. In recent years there has been remarkable progress in molecular analysis of brain tumors, which resulted in the actualization of WHO classification in 2021. Genetic and epigenetic profiling of brain tumors had an impact on diagnosis, introducing new molecular subgroups and a novel category of tumors. Nevertheless, most of the molecular biology techniques used in research require a high level quality and integrity of RNA, which is not obtainable in the case of Formalin-Fixed Paraffin-Embedded (FFPE) material, routinely used and available in pathomorphological laboratories. Therefore, this dissertation is focused on an attempt to classify high grade brain tumors in children based on gene expression analysis performed by NanoString technology that allows working with degraded RNA.The main objective of this dissertation was a molecular classification of high grade, infratentorial brain tumors in children. Analyses involved designing and testing of the unique marker gene signatures, specific for molecular types of selected infratentorial tumors, which are characterized by poor prognosis for patients, therefore presenting a great challenge for neuropathologists and pediatric oncologists. Moreover, the further objectives are establishment of biological and clinical correlations in analyzed tumors, comparison of the results to current literature data and an assessment of the utility of nCounter Analysis System for tumor diagnosis. An additional goal was to identify immunohistochemical markers for selected molecular groups of analyzed brain tumors.Results of the dissertation confirm that establishing the unique gene signatures for medulloblastoma, ependymoma, CNS HGNET-BCOR and CNS-HGNET-MN1 tumors, as well as RNA expression profiling of FFPE blocks using the nCounter Analysis System, is an useful technique that allows for identification of molecular groups in pediatric brain tumors. This approach allowed for ependymoma and medulloblastoma molecular group identification and detection of two CNS HGNET-BCOR tumors. After accomplishment of gene expression analysis, biological and clinical correlations were established and the results demonstrated that in ependymoma patients molecular group correlates with clinical features, including rates of survival. The results of immunohistochemical analyses imply that in the case of WNT medulloblastoma, the ALK protein expression may serve as a potential diagnostic marker, whereas, the BCOR protein expression may serve as a surrogate marker for CNS HGNET-BCOR tumors.

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Detailed Resource Type:

PhD Dissertations




IMDiK PAN, sygn. ZS 418



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Creative Commons Attribution BY 4.0 license

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Copyright-protected material. [CC BY 4.0] May be used within the scope specified in Creative Commons Attribution BY 4.0 license, full text available at: ; -

Digitizing institution:

Mossakowski Medical Research Institute PAS

Original in:

Library of the Mossakowski Medical Research Institute PAS

Projects co-financed by:

Operational Program Digital Poland, 2014-2020, Measure 2.3: Digital accessibility and usefulness of public sector information; funds from the European Regional Development Fund and national co-financing from the state budget.





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