Biology subjects

Valentine, V.

Publications and source records attributed to Valentine, V..

3 recordsLinked to original sources

bioRxiv2025

Oncogenic Ppm1d mutations deregulate the p53 pathway in primary mouse gliomas

Importance of StudyProtein phosphatase magnesium-dependent 1D (PPM1D) is frequently mutated in diffuse midline gliomas (DMGs). DMGs are rare pediatric brain tumors with limited treatment options. Due to the cancers rapid progression, patients usually survive 12-24 months after diagnosis. This underscores the critical need to better understand the molecular mechanisms driving DMGs. This study describes a novel mouse model that provides a powerful platform to investigate PPM1D-driven tumor biology and offers mechanistic insights into disease development and progression. Furthermore, it serves as a valuable preclinical system for evaluating therapeutic strategies and identifying translational opportunities to target Ppm1d-mutant tumors. BackgroundDiffuse midline gliomas (DMGs) are incurable brain tumors with limited treatment options. Approximately 20% of DMGs harbor truncating mutations in exon 6 of phosphatase PPM1D, which stabilize the protein and deregulate p53 signaling. However, the consequences of these mutations for tumor initiation, progression, and therapy remain unclear. MethodsWe developed a conditional Ppm1d-loxP-exon6-loxP-exon6-E518X-tag mouse allele (Ppm1d-flex-6) that enables lineage-, spatial-, and temporal-specific expression of a DMG-derived truncated Ppm1d protein from its endogenous locus in the presence of Cre-recombinase. Ubiquitous activation of mutant Ppm1d was modeled using the Meox2-Cre driver, and primary gliomas were modeled using the RCAS/tv-a system to introduce Cre and PDGFB co-drivers into Nestin-positive neural stem cells. Complementary studies were performed in mouse embryonic fibroblasts (MEFs) expressing truncated Ppm1d following Cre recombination. ResultsWhile Meox2-Cre-driven ubiquitous recombination of Ppm1d-flex-6 produced muted phenotypes, Ppm1d-flex-6 recombination in Nestin+ neural stem cells accelerated gliomagenesis. Its oncogenic effect was weaker than complete p53 loss, and it did not accelerate tumorigenesis further in p53-null tumors. Single-cell RNA-sequencing revealed that Ppm1d-flex-6 gliomas adopt more progenitor-like transcriptional states and upregulate p53- and cell cycle associated pathways. In MEFs, Ppm1d-flex-6 enhanced proliferation and shifted transcriptomic programs toward MAPK and PI3K-Akt signaling, while impairing DNA damage responses, including reduced {gamma}-H2AX induction after irradiation. These defects sensitized cells to radiation and decreased clonogenic survival after ionizing radiation and PARP inhibition. ConclusionsPpm1d mutations confer intermediate suppression of the p53 pathway, consistent with the clinical features of PPM1D-mutant DMGs and are associated with radiosensitivity and PARP inhibitor vulnerability.

genetics↗

bioRxiv2025

Seq2Karyotype (S2K): A Method for in-silico Karyotyping Using Single-Sample Whole-Genome Sequencing Data

DNA abnormalities characterized by cytogenetic imaging at the single cell resolution, i.e. karyotyping, have long served as cancer diagnostic and prognostic biomarkers. To enable in-silico karyotyping using unpaired whole-genome sequencing data, we developed Seq2Karyotype (S2K), a tool that fits karyotype models with clonality estimation based on read-depth and allelic imbalance in a bulk sample and supports visualization-guided refinement. Analysis on 19 adult and pediatric cancer cell lines revealed unexpected intratumoral heterogeneity involving multiple copy number variation (CNV) states including whole-genome duplication, which were validated by imaging and single-cell omics profiling. Analyses on patient samples showed high concordance with clinical cytogenetic reports for acute myeloid leukemia, and revealed evolutionary trajectories from multi-region metastatic neuroblastomas implicating reversion. These findings highlight extensive and dynamic intratumoral heterogeneity contributed by CNV in both cell line models and patient samples, which may inform future research on tumor evolution under selective pressure such as drug exposure.

bioinformatics↗

bioRxiv2024

Topology-informed regulatory element collections coordinate cell identity gene expression programs

Transcription proteins are concentrated at nuclear transcriptional condensates. These condensates contain cis-regulatory elements (CREs), including enhancers and promoters, that are thought to regulate genes in the same condensate. The roles of condensates are of great current interest, but research into their function is limited by an inability to comprehensively identify their associated CREs. Here, we present a conceptual framework and algorithm, BOUQUET, for integrating genome topology, chromatin occupancy, and graph theory to associate CREs and transcription protein machinery with target genes and identify exceptionally protein-rich communities that interact with condensates. BOUQUET uncovers surprising quantitative correlations between community protein accumulation and gene expression phenotypes by combining accurate CRE-gene assignment with co-activator binding profiles. A small subset of communities, which we call "3D-super-enhancers," is exceptionally protein-rich. BOUQUET-predicted 3D-SEs are comparable in number to co-activator nuclear puncta, and all genes known to interact with co-activator condensates in embryonic stem cells are within 3D-SEs. 3D-SEs are enriched for association with cell identity genes across mammalian tissues. Microscopy analyses show frequent co-localization and co-expression of genes from the same 3D-SE within a single co-activator punctum, suggesting 3D-SE components interact with co-activator condensates. Thus 3D-SEs correspond to co-activator puncta, which nominates additional condensate-associated genes and CREs.

molecular biology↗