Periodic Reporting for period 3 - BRAIN-MATCH (Matching CNS Lineage Maps with Molecular Brain Tumor Portraits for Translational Exploitation)
Berichtszeitraum: 2022-05-01 bis 2023-10-31
Brain tumors are one of the leading causes of deaths in children, and even with recent advances in diagnosis and classification, intervention therapies still lag behind in improving overall quality of life post-treatment. Common surgical, radiological and chemotherapeutic approaches frequently result in life long cognitive and motor disabilities, and in certain cases, fatal tumor recurrence. Improvement in molecular biology techniques have shed light on the heterogeneity among tumors of a class and interaction with the tumor micro-environment. Similarly, the application of these technologies has also improved our understanding of normal brain development. Comparison of tumor and normal development at single cell resolution has revealed associations that were hidden at the bulk level, but also highlighted the complexity within tumor tissues. Hence, here we proposed to improve understanding of pediatric tumor development by comparing it to normal human brain development. The aims of this project can be summarized as follows:
• improvement of our understanding of the tumor “cell of origin” by investigating tumor and normal brain development at single cell resolution
• identification of the transcriptional regulation shared between tumors and it’s lineage of origin, in addition to identifying genes that distinguishes former from the later
• identification of newer therapeutic targets that could be cell surface-based proteins involved in cell-cell communication, signaling or intracellular regulatory protein that could be targeted by known or putative drugs
• atlasing the hindbrain (cerebellum and lower brainstem) since these are common locations of childhood brain tumors
• improvement of our understanding of the tumor “cell of origin” by investigating tumor and normal brain development at single cell resolution
• identification of the transcriptional regulation shared between tumors and it’s lineage of origin, in addition to identifying genes that distinguishes former from the later
• identification of newer therapeutic targets that could be cell surface-based proteins involved in cell-cell communication, signaling or intracellular regulatory protein that could be targeted by known or putative drugs
• atlasing the hindbrain (cerebellum and lower brainstem) since these are common locations of childhood brain tumors
As of now, we have achieved the following milestones:
1) We have generated and fully annotated a single cell RNA sequencing atlas of the human cerebellum covering its development from the early neurogenesis to adult.
2) We compared the cerebellar tumors to the above generated normal developing cerebellum atlas in order to identify most similar cerebellar cell population associated with specific tumor types. We focused on medulloblastoma, posterior fossa ependymoma, pilocytic astrocytoma and radiation induced glioma (possible relapse tumor type after medulloblatoma treatment) and identified specific cell populations (lineage of origin) that match most to
each of these tumor types.
3) We distinguished tumor-specific genes in association with the cells of origin as well as the unique tumor that could be potentially used in improved therapeutic approaches.
4) We generated a single nucleus RNA sequencing atlas of the human lower brainstem (pons and medulla) covering its development from the early neurogenesis to adult. We have data for 250,00 cells and the analysis is ongoing.
5) We established a single nucleus ATAC sequencing atlas of the mouse cerebellum development (90,000 cells, published) and the human cerebellum development (110,000 cells, analysis ongoing).
1) We have generated and fully annotated a single cell RNA sequencing atlas of the human cerebellum covering its development from the early neurogenesis to adult.
2) We compared the cerebellar tumors to the above generated normal developing cerebellum atlas in order to identify most similar cerebellar cell population associated with specific tumor types. We focused on medulloblastoma, posterior fossa ependymoma, pilocytic astrocytoma and radiation induced glioma (possible relapse tumor type after medulloblatoma treatment) and identified specific cell populations (lineage of origin) that match most to
each of these tumor types.
3) We distinguished tumor-specific genes in association with the cells of origin as well as the unique tumor that could be potentially used in improved therapeutic approaches.
4) We generated a single nucleus RNA sequencing atlas of the human lower brainstem (pons and medulla) covering its development from the early neurogenesis to adult. We have data for 250,00 cells and the analysis is ongoing.
5) We established a single nucleus ATAC sequencing atlas of the mouse cerebellum development (90,000 cells, published) and the human cerebellum development (110,000 cells, analysis ongoing).
We have generated snATAC-seq datasets for cerebellum development in mouse (published, 90,000 cells spanning 11 stages) and human (110,000 cells, analysis ongoing). snATAC-seq data allow investigations of the regulatory basis of development and identification of cis-regulatory elements (enhancers, promoters) active in different cell types and different developmental stages.
We are also developing a single cell methylome protocol. This would allow the comparison of the cell type-specific methylation profiles from normal development to the tumour types (classified by methylation profiles).
We expect these state-of-the-art methods to complement the snRNA-seq atlases (this is what was proposed) that altogether would allow more precise mapping of the tumour classes/types.
We are also developing a single cell methylome protocol. This would allow the comparison of the cell type-specific methylation profiles from normal development to the tumour types (classified by methylation profiles).
We expect these state-of-the-art methods to complement the snRNA-seq atlases (this is what was proposed) that altogether would allow more precise mapping of the tumour classes/types.