Biology subjects

Korshunov, A.

Publications and source records attributed to Korshunov, A..

16 recordsLinked to original sources

bioRxiv2024

Transcriptomic landscape identifies two unrecognized ependymoma subtypes and novel pathways in medulloblastoma

Medulloblastoma and ependymoma are common pediatric central nervous system tumors with significant molecular and clinical heterogeneity. We collected bulk RNA sequencing data from 888 medulloblastoma and 370 ependymoma tumors to establish a comprehensive reference landscape. Following rigorous batch effect correction, normalization, and dimensionality reduction, we constructed a unified landscape to explore gene expression, signaling pathways, RNA fusions, and copy number variations. Our analysis revealed distinct clustering patterns, including two primary ependymoma compartments, EPN-E1 and EPN-E2, each with specific RNA fusions and molecular signatures. In medulloblastoma, we observed precise stratification of Group 3/4 tumors by subtype and in SHH tumors by patient age. This landscape serves as a vital resource for identifying biomarkers, refining diagnoses, and enables the mapping of new patients bulk RNA-seq data onto the reference framework to predict biology and outcome from nearest neighbor analysis facilitate accurate disease subtype identification. The landscape is accessible via Oncoscape, an interactive platform, empowering global exploration and application. One Sentence SummaryA landscape built using only Transcriptomic analysis for medulloblastoma and ependymoma reveals novel insights about subtype-specific biology.

bioinformatics↗

bioRxiv2024

Medulloblastoma oncogene aberrations are not involved in tumor initiation, but essential for disease progression and therapy resistance

Despite recent advances in understanding disease biology, treatment of Group 3/4 medulloblastoma remains a therapeutic challenge in pediatric neuro-oncology. Bulk-omics approaches have identified considerable intertumoral heterogeneity in Group 3/4 medulloblastoma, including the presence of clear single-gene oncogenic drivers in only a subset of cases, whereas in the majority of cases, large-scale copy-number aberrations prevail. However, intratumoral heterogeneity, the role of oncogene aberrations, and broad CNVs in tumor evolution and treatment resistance remain poorly understood. To dissect this interplay, we used single-cell technologies (snRNA-seq, snATAC-seq, spatial transcriptomics) on a cohort of Group 3/4 medulloblastoma with known alterations in the oncogenes MYC, MYCN, and PRDM6. We show that large-scale chromosomal aberrations are early tumor initiating events, while the single-gene oncogenic events arise late and are typically sub-clonal, but MYC can become clonal upon disease progression to drive further tumor development and therapy resistance. We identify that the subclones are mostly interspersed across tumor tissue using spatial transcriptomics, but clear segregation is also present. Using a population genetics model, we estimate medulloblastoma initiation in the cerebellar unipolar brush cell-lineage starting from the first gestational trimester. Our findings demonstrate how single-cell technologies can be applied for early detection and diagnosis of this fatal disease.

cancer biology↗

bioRxiv2024

Gene regulatory network landscape of Group 3/4 medulloblastoma

Cellular heterogeneity in Group 3 and Group 4 medulloblastomas is a major driver of therapeutic intractability. Here, we describe transcription factor-driven mechanisms underlying cellular diversity in these tumors using a comprehensive single-nucleus multi-omics atlas. Our analysis reveals that rather than fixed entities, these tumors exist along a continuum of cell states defined by four molecular identity axes. We show that perturbing transcription factor activity drives cellular plasticity, a key contributor to tumor heterogeneity. Strikingly, modulation of the lineage determinant PAX6 redirects tumor cells along both Group 3- and Group 4-like differentiation trajectories, modeling a bi-lineage medulloblastoma, and reduces aggressiveness of MYC-driven tumor models. Together, our findings reveal how oncogenic signals co-opt cerebellar unipolar brush cell programs to rewire tumor cell states and identify cellular plasticity as a potential targetable vulnerability in medulloblastoma.

cancer biology↗

bioRxiv2023

Spatial and temporal transcriptomics of SHH-medulloblastoma with chromothripsis identifies multiple genetic clones that resist to treatment and lead to relapse

Paediatric medulloblastomas with chromothripsis are characterised by high genomic instability and are among the tumours with the worst prognosis. However, the determinants of their aggressiveness and the molecular makeup of chromothriptic medulloblastoma are not well understood. Here, we applied spatial transcriptomics to profile a cohort of 13 chromothriptic and non-chromothriptic medulloblastomas from the same molecular subgroup. Our data reveal a higher extent of spatial intra-tumour heterogeneity in chromothriptic medulloblastomas, which is associated with increased proliferation and stemness, but lower immune infiltration and differentiation. Spatial mapping of genetic subclones of the same tumour identify a regionally distinct architecture and clone-specific phenotypic features, with distinct degrees of differentiation, proliferation and immune infiltration between clones. We conducted temporal profiling of 11 patient-derived xenografts from chromothriptic medulloblastomas, covering the transition from the minimal residual disease stage to treatment-resistant regrown tumours. In chromothriptic medulloblastoma, an ecosystem of cells from multiple genetic clones resisting treatment and leading to relapse highlighted the importance of multi-clone interplay. Finally, we identified a potential role for tumour microtubes in treatment resistance in chromothriptic medulloblastoma, suggesting cell network communication as a putative target. HighlightsO_ST_ABSBiological insightsC_ST_ABSO_LIMedulloblastomas with chromothripsis are characterised by higher spatial intra-tumour heterogeneity, proliferation and stemness, but lower immune infiltration and differentiation, as compared with non-chromothriptic medulloblastomas C_LIO_LISpatially aware genetic clone assignment identifies phenotypic features such as degree of differentiation, proliferation and immune infiltration enriched in specific clones C_LIO_LICells from distinct genetic clones resist to treatment and give rise to relapse in patient-derived xenografts of medulloblastoma with chromothripsis C_LIO_LITumour microtubes point to putative molecular processes implicated in treatment resistance in chromothriptic medulloblastoma C_LI Technological advancesO_LIValidation of the spatial representation of patient-derived xenograft models, providing novel insights into the faithfulness of such models to study cancer C_LIO_LISpatial mapping of clones based on spatial transcriptomics and copy-number variant profiling C_LI

cancer biology↗

bioRxiv2023

Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level

Medulloblastomas (MBs) are malignant pediatric brain tumors that are molecularly and clinically very heterogenous. To unravel phenotypically relevant MB subtypes, we compiled a harmonized proteome dataset of 167 MBs and integrated findings with DNA methylation and N-glycome data. Six proteome MB subtypes emerged, that could be assigned to two main molecular programs: transcription/translation (pSHHt, pWNT and pGroup3-Myc), and synapses/immunological processes (pSHHs, pGroup3 and pGroup4). Multiomic analysis revealed different conservation levels of proteome features across MB subtypes at the DNA-methylation level. Aggressive pGroup3-Myc MBs and favorable pWNT MBs were most similar in cluster hierarchies concerning overall proteome patterns but showed different protein abundances of the vincristine resistance associated multiprotein complex TriC/CCT and of N-glycan turnover associated factors. The N-glycome reflected proteome subtypes and complex-bisecting N-glycans characterized pGroup3-Myc tumors. Our results shed light on new targetable alterations in MB and set a foundation for potential immunotherapies targeting glycan structures. SignificanceWhereas the application of omics technologies has significantly improved MB tumor classification and treatment stratification, it is still of debate, which features predict best clinical outcome. Moreover, treatment options - especially for high-risk groups - are still unsatisfactory. In contrast to nucleic acids, the proteome and their N-glycans may reflect the phenotype of a tumor in a more direct way and thus hold the potential to discover clinically relevant phenotypes and potentially targetable pathways. We show that these analyses are feasible on formalin fixed and paraffine embedded tissue. Compiling a comprehensive MB dataset, we detected new biomarkers and characteristics for high- and low-risk MB subtypes that were not reflected by other omic data modalities before. Specifically, we identified subtype specific abundance differences in proteins of the vincristine resistance associated multiprotein complex TriC/CCT and in proteins involved in N-glycan turnover. Changes in the N-glycans are considered as potential hallmarks of cancer and we show that N-glycan profiles can distinguish MB subtypes. These tumor-specific N-glycan structures hold a strong potential as new biomarkers, as well as immunotherapy targets. Highlights- Integration of in-house proteome data on formalin fixated paraffine embedded medulloblastoma (MB) and publicly available datasets enables large scale proteome analysis of MB - Six proteome MB subtypes can be assigned to two main molecular programs: replication/ translation versus synapse/immune system - Identification and validation of IHC compatible protein-biomarkers for high and low risk MB subtypes, such as TNC and PALMD. - Subtype specific correlation of the DNA methylome and the proteome reveals different conserved molecular characteristics across MB subtypes. - pGroup3-Myc subtype MBs are associated with high-risk features including high abundances of vincristine resistance associated TriC/CCT member proteins - Proteome MB subtypes show differential N-glycosylation patterns, revealing complex-bisecting glycans as potentially immunotargetable hallmarks of the high risk pGroup3-Myc subtype.

cancer biology↗

bioRxiv2022

Compartments in medulloblastoma with extensive nodularity are connected through differentiation along the granular precursor lineage

Medulloblastoma with extensive nodularity (MBEN) are cerebellar tumors with two histologically distinct compartments and varying disease course. In some children MBEN progresses, while others show spontaneous differentiation into more benign tumors. However, the mechanisms that control the tug-of-war between proliferation and differentiation are not well understood. Here, we dissected this process with a multi-modal single cell transcriptome analysis. We found that the internodular MBEN compartment comprised proliferating early cerebellar granular neuronal precursors (CGNP)-like tumor cells as well as stromal, vascular, and immune cells. In contrast, the nodular compartment consisted of postmitotic, neuronally differentiated MBEN cells. Both compartments were connected through an intermediate cell stage of actively migrating CGNPs. Furthermore, astrocyte-like tumor cells were identified that had branched off the main CGNP developmental trajectory. Cells with an astroglial phenotype were found in close proximity to migrating, late CGNP-like and postmitotic neuronally differentiated cells. Our study reveals how the spatial tissue organization is linked to the developmental trajectory of proliferating tumor cells through a migrating precursor stage into differentiated tumor cells with a more benign phenotype. We anticipate that our framework for integrating single nucleus RNA-sequencing and spatial transcriptomics will help to uncover intercompartmental interactions also in other cancers with varying histology.

cancer biology↗

bioRxiv2022

Developmental Basis of SHH Medulloblastoma Heterogeneity

Medulloblastoma (MB) is one of the most common malignant pediatric brain tumors. The sonic hedgehog (SHH) subtype accounts for 30% of MB cases and likely arises from mutations in granule cell precursors (GCPs), neuronal progenitors of the cerebellar cortex that differentiate into granule neurons. SHH MB is extremely heterogeneous, but it is unknown whether this heterogeneity relates to the tumors developmental origins. To investigate this question, we performed single-nucleus RNA-Sequencing on seven highly differentiated SHH MB with extensively nodular histology and observed malignant cells resembling each stage of granule neuron development. Using novel computational approaches, we connected these results to published datasets and found that established molecular subtypes of SHH MB are enriched for specific developmental cell types. Additionally, some genomic copy number variations are associated with certain developmental stages, and we observed distinct metabolic and histological profiles for tumors containing cells resembling late-stage granule neurons. This work details computational and experimental approaches that can be repurposed for analysis of tumor cell differentiation in other cancers.

cancer biology↗

bioRxiv2021

Mapping pediatric brain tumors to their origins in the developing cerebellum

Understanding the cellular origins of childhood brain tumors is key for discovering novel tumor-specific therapeutic targets. Previous strategies mapping cellular origins typically involved comparing human tumors to murine embryonal tissues1,2, a potentially imperfect approach due to spatio-temporal gene expression differences between species3. Here we use an unprecedented single-nucleus atlas of the developing human cerebellum (Sepp, Leiss, et al) and extensive bulk and single-cell transcriptome tumor data to map their cellular origins with focus on three most common pediatric brain tumors - pilocytic astrocytoma, ependymoma, and medulloblastoma. Using custom bioinformatics approaches, we postulate the astroglial and glial lineages as the origins for posterior fossa ependymomas and radiation-induced gliomas (secondary tumors after medulloblastoma treatment), respectively. Moreover, we confirm that SHH, Group3 and Group4 medulloblastomas stem from granule cell/unipolar brush cell lineages, whereas we propose pilocytic astrocytoma to originate from the oligodendrocyte lineage. We also identify genes shared between the cerebellar lineage of origin and corresponding tumors, and genes that are tumor specific; both gene sets represent promising therapeutic targets. As a common feature among most cerebellar tumors, we observed compositional heterogeneity in terms of similarity to normal cells, suggesting that tumors arise from or differentiate into multiple points along the cerebellar "lineage of origin".

cancer biology↗

bioRxiv2021

Single cell multi-omics analysis of chromothriptic medulloblastoma highlights genomic and transcriptomic consequences of genome instability

Chromothripsis is a form of genome instability, whereby a presumably single catastrophic event generates extensive genomic rearrangements of one or few chromosome(s). However, little is known about the heterogeneity of chromothripsis across different clones from the same tumor, as well as changes in response to treatment. We analyzed single-cell genomic and transcriptomic alterations linked with chromothripsis in human p53-deficient medulloblastoma (n=7). We reconstructed the order of somatic events, identified early alterations likely linked to chromothripsis and depicted the contribution of chromothripsis to malignancy. We characterized subclonal variation of chromothripsis and its effects on double-minute chromosomes, cancer drivers and putatively druggable targets. Furthermore, we highlighted the causative role and the fitness consequences of specific rearrangements in neural progenitors. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=85 SRC="FIGDIR/small/449944v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@9d30e4org.highwire.dtl.DTLVardef@1f4d34eorg.highwire.dtl.DTLVardef@5cd50corg.highwire.dtl.DTLVardef@a71a81_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2021

Distribution of GOPC:ROS1 and other ROS1 fusions in glioma types

The ROS proto-oncogene 1 (ROS1) gene is rearranged in various cancers. The translated fusion protein presents an attractive therapeutic target, since specific inhibitors have been approved for several tumor types. In glioma, ROS1 fusions are frequent within infantile hemispheric glioma, and single case reports on occurrences in other glioma types exist. However, a comprehensive analysis spanning the full width of glioma types and subtypes is lacking. We here assessed the spectrum and distribution of ROS1 fusions by screening >20,000 glioma cases for typical chromosomal alterations, with subsequent RNA-sequencing for confirmation of candidate cases. ROS1 fusions were identified in 16 cases, from low grade pilocytic astrocytoma WHO grade 1 to glioblastoma, IDH wildtype WHO grade 4. Thus, despite being enriched in some tumor types, ROS1 fusions are not pathognomonic for specific glioma types and may consitute a relevant target in a variety of cases.

genomics↗

bioRxiv2020

A subset of pediatric thalamic gliomas share a distinct DNA methylation profile, H3K27me3 loss and frequent alteration of EGFR

BackgroundMalignant astrocytic gliomas in children show a remarkable biological and clinical diversity. Small in-frame insertions or missense mutations in the EGFR gene have recently been identified in a distinct subset of pediatric bithalamic gliomas with a unique DNA methylation pattern. MethodsHere, we investigated an epigenetically homogeneous cohort of malignant gliomas (n=58) distinct from other subtypes and enriched for pediatric cases and thalamic location, in order to elucidate the overlap with this recently identified subtype of pediatric bithalamic gliomas. ResultsEGFR gene amplification was detected in 16/58 (27%) tumors, and missense mutations or small in-frame insertions in EGFR were found in 20/30 tumors with available sequencing data (67%; five of them co-occurring with EGFR amplification). Additionally, eight of the 30 tumors (27%) harbored an H3.1 or H3.3 K27M mutation (six of them with a concomitant EGFR alteration). All tumors tested showed loss of H3K27me3 staining, with evidence of EZHIP overexpression in the H3 wildtype cases. Although some tumors indeed showed a bithalamic growth pattern, a significant proportion of tumors occurred in the unilateral thalamus or in other (predominantly midline) locations. ConclusionsOur findings present a distinct molecular class of pediatric malignant gliomas largely overlapping with the recently reported bithalamic gliomas characterized by EGFR alteration, but additionally showing a broader spectrum of EGFR alterations and tumor localization. Global H3K27me3 loss in this group appears to be mediated by either H3 K27 mutation or EZHIP overexpression. EGFR inhibition may represent a potential therapeutic strategy in these highly aggressive gliomas. Key pointsO_LIThis study confirms a distinct new subset of pediatric diffuse midline glioma with H3K27me3 loss, with or without H3 K27 mutation C_LIO_LIThe poor outcome of these tumors is in line with the broader family of pediatric diffuse midline gliomas with H3 K27 mutation or EZHIP overexpression C_LIO_LIFrequent EGFR alterations in these tumors may represent a therapeutic target in this subset C_LI Importance of the StudyMalignant astrocytic gliomas in children show a remarkable biological and clinical diversity. Here, we highlight a distinct molecular class of pediatric malignant gliomas characterized by EGFR alteration and global H3K27me3 loss that appears to be mediated by either H3 K27 mutation or EZHIP overexpression. EGFR inhibition may represent a potential therapeutic strategy in these highly aggressive gliomas.

cancer biology↗

bioRxiv2020

Mosaic trisomy of chromosome 1q in human brain tissue associates with unilateral polymicrogyria, very early-onset focal epilepsy, and severe developmental delay

Polymicrogyria (PMG) is a developmental cortical malformation characterized by an excess of small and frustrane gyration and abnormal cortical lamination. PMG frequently associates with seizures. The molecular pathomechanisms underlying PMG development are not yet understood. About 40 genes have been associated with PMG, and small copy number variations have also been described in selected patients. We recently provided evidence that epilepsy-associated structural brain lesions can be classified based on genomic DNA methylation patterns. Here we analyzed 26 PMG patients employing array-based DNA-methylation profiling on formalin-fixed paraffin-embedded material. A series of 62 well-characterized non-PMG cortical malformations (focal cortical dysplasia type 2a/b and hemimegalencephaly), temporal lobe epilepsy, and non-epilepsy autopsy controls was used as reference cohort. Unsupervised dimensionality reduction and hierarchical cluster analysis of DNA methylation profiles showed that PMG formed a distinct DNA methylation class. Copy number profiling from DNA methylation data identified a uniform duplication spanning the entire long arm of chromosome 1 in 7 out of 26 PMG patients, which was verified by additional fluorescence in situ hybridization analysis. In respective cases about 50% of nuclei in the center of the PMG lesion were 1q triploid. No chromosomal imbalance was seen in adjacent, architecturally normal-appearing tissue indicating mosaicism. Clinically, PMG 1q patients presented with a unilateral frontal or hemispheric PMG without hemimegalencephaly, a severe form of intractable epilepsy with seizure onset in the first months of life, and severe developmental delay. Our results show that PMG can be classified among other structural brain lesions according to their DNA methylation profile. One subset of PMG with distinct clinical features exhibits a duplication of chromosomal arm 1q.

neuroscience↗

bioRxiv2020

A novel neural stem cell-derived immunocompetent mouse model of glioblastoma for preclinical studies

Glioblastomas are the most lethal tumors affecting the central nervous system in adults. Simple and inexpensive syngeneic in vivo models that closely mirror human glioblastoma, including interactions between tumor and immune cells, are urgently needed for deciphering glioma biology and developing more effective treatments. Here, we generated glioblastoma cell lines by repeated in-vivo passaging of cells isolated from a neural stem cell-specific Pten/p53 double-knockout genetic mouse brain tumor model. Transcriptome and genome analyses of the cell lines revealed molecular heterogeneity comparable to that observed in human glioblastoma. Upon orthotopic transplantation into syngeneic hosts they formed high-grade gliomas that faithfully recapitulated the histopathological features, invasiveness and myeloid cell infiltration characteristic of human glioblastoma. These features make our cell lines unique and useful tools to study multiple aspects of glioblastoma pathomechanism and test novel treatments, especially immunotherapies in syngeneic preclinical models.

cancer biology↗

bioRxiv2020

Functional loss of a non-canonical BCOR-PRC1.1 complex accelerates SHH-driven medulloblastoma formation

Medulloblastoma is a childhood brain tumor arising from the developing cerebellum. In Sonic Hedgehog (SHH)-subgroup medulloblastoma, aberrant activation of SHH signaling causes increased proliferation of granule neuron progenitors (GNPs) and predisposes these cells to tumorigenesis. A second, cooperating genetic hit is often required to push these hyperplastic cells to malignancy and confer mutation-specific characteristics associated with oncogenic signaling. Somatic loss-of-function mutations of the transcriptional co-repressor BCOR are recurrent and highly enriched in SHH-medulloblastoma. To investigate BCOR as a putative tumor suppressor, we used a germline genetically engineered mouse model to delete exons 9/10 of Bcor (Bcor{Delta}E9-10) in GNPs during development. This leads to reduced expression of C-terminally truncated BCOR (BCOR{Delta}E9-10). While Bcor{Delta}E9-10 alone did not promote tumorigenesis or affect GNP differentiation, Bcor{Delta}E9-10 combined with loss of the SHH-receptor gene Ptch1 resulted in highly penetrant medulloblastomas. In Ptch1+/-;Bcor{Delta}E9-10 tumors, the growth factor gene Igf2 was aberrantly upregulated, and ectopic Igf2 overexpression was sufficient to drive tumorigenesis in Ptch1+/- GNPs. BCOR directly regulates Igf2, likely through the PRC1.1 complex; the repressive histone mark H2AK119Ub is decreased at the Igf2 promoter in Ptch1+/-;Bcor{Delta}E9-10 tumors. Overall, our data suggests that BCOR-PRC1.1 disruption leads to Igf2 overexpression, which transforms preneoplastic cells to malignant tumors.

cancer biology↗

bioRxiv2018

Defective DNA damage repair leads to frequent catastrophic genomic events in murine and human tumors

Chromothripsis and chromoanasynthesis are catastrophic events leading to clustered genomic rearrangements. Whole-genome sequencing revealed frequent chromothripsis or chromoanasynthesis (n= 16/26) in brain tumors developing in mice deficient for factors involved in homologous-recombination-repair or non-homologous-end-joining. Catastrophic events were tightly linked to Myc/Mycn amplification, with increased DNA damage and inefficient apoptotic response already observable at early postnatal stages. Inhibition of repair processes and comparison of the mouse tumors with human medulloblastomas (n=68) and glioblastomas (n=32) identified chromothripsis as associated with MYC/MYCN gains and with DNA repair deficiencies, pointing towards therapeutic opportunities to target DNA repair defects in tumors with complex genomic rearrangements.

cancer biology↗

bioRxiv2017

Dissecting telomere maintenance mechanisms in pediatric glioblastoma

Pediatric glioblastoma (pedGBM) represent a highly malignant primary brain tumor with recurrent mutations in the chromatin remodeler ATRX and the histone variant H3.3 that is typically associated with a fatal outcome. ATRX acts as suppressor of the alternative lengthening of telomeres (ALT) pathway, which is frequently activated in pedGBM. However, telomere features of pedGBMs have not been studied in detail, and ALT-positive model cell lines are lacking. Here, we systematically characterized a panel of pedGBM models that carry a representative set of recurrent genomic mutations for a variety of telomere features. These included the presence of ALT-associated promyelocytic leukemia nuclear bodies and C-circles, a specific type of extrachromosomal telomeric repeats, the telomere repeat content, and phosphorylation of histone H3.3 at serine 31. From an integrated analysis of seven pedGBM cell lines and 57 primary tumor samples we identified cell lines and tumors that represent the different telomere maintenance mechanisms and conclude the following: (i) A positive signal in the C-circle assay is a reliable ALT marker. (ii) ALT features occur heterogeneously and one pedGBM subgroup uses a non-canonical ALT mechanism in the presence of wild-type ATRX. (iii) The spreading of H3.3S31 phosphorylation during mitosis is associated with loss of ATRX but not with ALT per se. (iv) In contrast to a previous study in glioma stem cells, we did not find a hypersensitivity of ALT cells towards the ATR inhibitor VE-821. (v) ALT-positive pedGBMs can be reliably identified from a classification scheme developed here that evaluates various combinations of cytogenetic and/or genomic data. Thus, our findings elucidate further details of the ALT pathway in pedGBMs, provide valuable models for evaluating ALT targeted therapies in a preclinical setting, and introduce an ALT classification scheme for primary tumor samples.

cancer biology↗