Biology subjects

Milde, T.

Publications and source records attributed to Milde, T..

7 recordsLinked to original sources

bioRxiv2026

The ITCC-P4 PDX platform of pediatric cancers for preclinical testing

Cancer is the leading cause of disease-related deaths among children in high-income countries. Tumor heterogeneity and lack of mechanism-of-action-based therapeutic options are key challenges to overcome in order to improve pediatric cancer patients survival. Here, we report the EU-IMI-2 funded public-private partnership "ITCC-Pediatric Preclinical Proof-of-Concept Platform" (ITCC-P4), which has built a large repertoire of patient-derived xenograft (PDX) models, representing all major solid pediatric cancer types, for in vivo drug testing. Three-hundred-fifty-three PDX models from diagnostic and relapsed pediatric cancers have been established and molecularly characterized, together with matched germline/tumor samples. As proof-of-concept, we present in vivo drug screening data in neuroblastoma and rhabdomyosarcoma models. PDX data, accessible at http://r2platform.com/itcc-p4, allow the selection of models based on oncogenic drivers and/or potential biomarkers for preclinical testing. Operated by a non-profit entity (www.itccp4.com), this sustainable platform aids academic and industrial researchers in developing and prioritizing innovative therapies for pediatric cancer. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/703023v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@195ba30org.highwire.dtl.DTLVardef@f2c2d9org.highwire.dtl.DTLVardef@1d63f4dorg.highwire.dtl.DTLVardef@d60027_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2026

Standard treatment against paediatric BRAF-V600E glioma promotes senescence and sensitizes tumours to BCL-xL inhibition

BackgroundChemo-, radio-, and targeted therapies can induce senescence in tumour cells, a process called therapy-induced senescence (TIS), which can be exploited therapeutically using compounds that kill senescent cells (senolytics). Children with BRAF-V600E activated brain tumours are commonly treated with Dabrafenib, Trametinib or Vinblastine (alone or in combination) with good responses. However, a subset of patients experiences tumour regrowth upon treatment withdrawal. Here, we explore the role of TIS and senolytic therapies in preclinical models of paediatric BRAF-V600E driven brain tumours. MethodsHuman BT-40 tumour cells derived from pleomorphic xanthoastrocytoma are used in vitro or in vivo orthotopically transplanted into mice and treated with either Dabrafenib, Trametinib or Vinblastine. Senescence is assessed by immunostaining and RNA sequencing. Sensitivity to senolytics is determined in vitro in dose response assays and in vivo. ResultsTrametinib treatment induces a senescent phenotype in BT-40 cells in vivo with activation of a senescence-associated secretory phenotype (SASP) and expansion of IBA-1 microglia. Senescence is induced in BT-40 cells in vitro when treated not only with Trametinib, but also with Dabrafenib and Vinblastine. In vitro testing identifies Navitoclax as a potent senolytic against BT-40 senescent cells, mostly through inhibition of the anti-apoptotic protein BCL-xL. In BT-40 tumour bearing mice, combination of Trametinib and Navitoclax causes the ablation of senescent BT-40 cells with significant reduction in tumour regrowth after treatment withdrawal and increased mouse survival. ConclusionsThis study shows that Navitoclax enhances the anti-tumour efficacy of Trametinib and limits tumour regrowth following treatment withdrawal. Key PointsO_LITrametinib, Dabrafenib and Vinblastine induce senescence in BT-40 cells in vitro C_LIO_LISenescent BT-40 cells are sensitive to BCL-xL inhibition C_LIO_LICombination of Trametinib and Navitoclax reduces rebound tumour growth in vivo C_LI Importance of the StudyChildren with BRAF-V600E activated glioma are frequently treated with Dabrafenib, Trametinib or Vinblastine with good responses. However, a subset of patients shows tumour regrowth when the treatment is stopped. To prevent this rebound growth, patients must continue treatment with potential aggravation in quality of life and risk of malignant progression. Our research demonstrates that these therapies induce BT-40 tumour cells to enter a non-proliferative state that shows features of cellular senescence. We identify that senescent tumour cells can be killed using Navitoclax, and potent inhibitor of the anti-apoptotic protein BCL-xL and a well-studied senolytic. We demonstrate that the combination of Trametinib and Navitoclax reduces tumour regrowth after treatment withdrawal. Our research provides a strong rationale supporting the combined use of senolytics with current conventional and targeted therapies against BRAF-V600E mutated brain tumours.

cancer biology↗

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↗

bioRxiv2021

Integrated phospho-proteogenomic and single-cell transcriptomic analysis of meningiomas establishes robust subtyping and reveals subtype-specific immune invasion

Meningiomas are the most frequent primary intracranial tumors. They can follow a wide clinical spectrum from benign to highly aggressive clinical course. No specific therapy exists for refractory cases or cases not amenable to resection and radiotherapy. Identification of risk of recurrence and malignant transformation for the individual patients is challenging. However, promising molecular markers and prognostic subgrouping by DNA methylation are emerging. Still, the biological underpinnings of these diagnostic subgroups are elusive, and, consequently, no novel therapeutic options arise thereof. Here we establish robust subgroups across the full landscape of meningiomas, consistent through DNA methylation, mutations, the transcriptomic, proteomic and phospho-proteomic level. Pronounced proliferative stress and DNA damage repair signals in malignant cells and in clusters exclusive to recurrent tumors are in line with their higher mitotic activity, but also provide an explanation for the accumulation of genomic instability in anaplastic meningiomas. Although homozygous deletion of CDKN2A/B is a diagnostic marker of high-grade meningioma, the expression of its gene product increased from low to non-deleted high-grade cases. Differences between subgroups in lymphocyte and myeloid cell infiltration, representing a majority of tumor mass in low-grade NF2 tumors, could be assigned to cluster-specific interaction with tumor cells. Activation to a more proinflammatory phenotype and decreased infiltration of myeloid cells in high-grade cases correlated with lower expression of CSF1, located on chromosome arm 1p, whose deletion is known as prognostic marker, with no proposed mechanism before. Our results demonstrate a robust molecular subclassification of a tumor type across multiple layers, provide insight into heterogeneous growth dynamics despite shared pathognomonic mutations, and highlight immune infiltration modulation as a novel target for meningioma therapy.

genomics↗

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↗

bioRxiv2021

A synergistic interaction between HDAC- and PARP inhibitors in childhood tumors with chromothripsis

Chromothripsis is a form of genomic instability characterized by the occurrence of tens to hundreds of clustered DNA double-strand breaks in a one-off catastrophic event. Rearrangements associated with chromothripsis are detectable in numerous tumor entities and linked with poor prognosis in some of these, such as Sonic Hedgehog medulloblastoma, neuroblastoma and osteosarcoma. Hence, there is a need for therapeutic strategies eliminating tumor cells with chromothripsis. Defects in DNA double-strand break repair, and in particular homologous recombination repair, have been linked with chromothripsis. Targeting DNA repair deficiencies by synthetic lethality approaches, we performed a synergy screen using drug libraries (n = 375 compounds, 15 models) combined with either a PARP inhibitor or cisplatin. This revealed a synergistic interaction between the HDAC inhibitor romidepsin and PARP inhibition. Functional assays, transcriptome analyses, and in vivo validation in patient-derived xenograft mouse models confirmed the efficacy of the combinatorial treatment.

cancer biology↗