Biology subjects

Plaisier, C. L.

Publications and source records attributed to Plaisier, C. L..

8 recordsLinked to original sources

bioRxiv2026

Monocyte-Mimetic Nanoparticle Delivery of Verteporfin Promotes Plaque-Stabilizing Remodeling in Atherosclerosis

Background: Despite advances in lipid-lowering and anti-inflammatory therapies, pharmacological strategies that act directly within established atherosclerotic lesions to suppress plaque progression remain limited. We recently developed a monocyte-mimetic nanoparticle (MoNP) platform that selectively targets inflamed endothelium and delivers Verteporfin (VP), termed MoNP-VP, to suppress YAP/TAZ-associated endothelial activation and plaque development. Here, we extend this biomimetic nanotherapy by defining the pharmacological effects of MoNP-VP within atherosclerotic vessels and evaluating its therapeutic efficacy in pre-existing plaques under distinct lipid burden. Methods: MoNP-VP were formulated by encapsulating VP in polymeric cores followed by cloaking with mouse monocyte membranes. Partial ligation was performed in ApoE-deficient mice, and single-cell RNA sequencing was used to define pharmacodynamic responses in carotid lesions. Proprotein convertase subtilisin/kexin type 9 (PCSK9) gain-of-function was induced in wild-type mice to generate pre-existing aortic lesions, followed by continued high-fat-diet or switching to chow to evaluate MoNP-VP efficacy under persistent hyperlipidemia and lipid-lowering conditions. Results: Single-cell analysis revealed that MoNP-VP remodeled the plaque microenvironment in carotid arteries, selectively reducing foamy macrophage populations while enriching vascular stromal populations associated with fibrotic remodeling. In mice with pre-existing aortic plaques, MoNP-VP suppressed lesion progression and reduced macrophage content under persistent hyperlipidemia. Following diet-induced lipid lowering, MoNP-VP further reduced macrophage accumulation despite no significant change in plaque size. Across both settings, MoNP-VP increased fibroblast-like cell populations and collagen deposition accompanied by activation of TGF{beta} signaling, features consistent with a more stable plaque. Importantly, repeated MoNP-VP administration was well tolerated and elicited no overt systemic toxicity. Conclusion: These findings bridge mechanistic insight and therapeutic efficacy in pre-established plaques by demonstrating that MoNP-VP remodels the inflammatory plaque microenvironment and promotes lesion stabilization, supporting its translational potential as a precision nanotherapy for atherosclerosis.

molecular biology↗

bioRxiv2026

Representation Methods of Transcriptomics with Applications in Neuroimmune Biology

Interpretable representations of gene expression are used to define cellular identities and the molecular programs active within cells, two related, but distinct phenomena. In the case of microglia, a cell type with high transcriptomic, functional, and morphological heterogeneity, the predominant representation of transcriptomic data presumes the adoption of distinct molecular identities, despite a lack of easily separable transcriptional states. Here, we explore alternative transcriptomic representations by comparing two single-cell analysis methods: differential expression analysis for identities and co-expression network analysis for molecular programs. For microglia, co-expression network analysis identifies highly significant functional ontologies not resolved by differential expression analysis. The identified co-expression modules are preserved across transcriptomic datasets and suggest reducible functional programs that activate and modulate depending on context. We conclude that co-expression analysis constitutes a best practice for single cell analysis of an individual cell type and describing microglia function as concurrent molecular programs offers a more parsimonious model of microglia function.

bioinformatics↗

bioRxiv2026

Differential sex-dependent responses of circulating steroid hormones and cortical gene expression in a preclinical traumatic brain injury model

Accumulating evidence supports sex differences in traumatic brain injury (TBI) outcomes, however the underlying processes that lead to sex differences are not well understood. TBI results in the initiation of molecular and cellular responses that facilitate the progression of neurodegeneration. Importantly, little is known about how the circulating hormone profile is altered in response to TBI, and whether sex differences in endocrine responses might shape secondary injury pathologies. Using intact male and female mice in a preclinical TBI model, we assessed changes in plasma hormone concentrations and cortical gene expression at 24 and 72 hours after TBI. We demonstrate that males and females exhibit sex-specific alterations in circulating levels of progesterone, testosterone, androstenedione, estradiol and dehydroepiandrosterone (DHEA) in response to TBI. We also identified sex differences in the expression of genes that are involved in immune responses and tissue remodeling after injury. Moreover, we report divergent circulating hormone and gene expression correlations between sexes.

neuroscience↗

bioRxiv2025

Multi-omics characterization of IDH-mutant astrocytoma-derived cell lines reveals NOTCH-regulated plastic quiescent astrocyte-like state

Diffuse IDH-mutant astrocytomas are brain tumors typically diagnosed as low-grade but capable of progressing to higher grades. They exhibit three cellular states resembling astrocytes, oligodendrocytes, and neural progenitor (NPC) cells. Understanding their biology has been challenging due to the lack of relevant in vitro models. Here we established and extensively characterized four astrocytoma cell lines (LGG275, LGG336, LGG85, LGG349) derived from IDH-mutant astrocytoma at different grades, cultured in defined media and analyzed by multi-omics. These lines display growth rates in vitro and in vivo consistent with tumor grade and recapitulate key molecular alterations observed in patient tumors, including IDH1, ATRX, and TP53 mutations, activation of the alternative lengthening of telomeres (ALT) pathway and, in the most aggressive line, amplification of MET and PDGFRA. Single-cell RNA sequencing showed that the 4 astrocytoma lines maintain the three major cellular states observed in patient tumors. A hallmark of higher-grade-derived lines (LGG85, LGG349) is the persistence of NPC-like populations without growth factors, reflecting tumor progression. The LGG275 line most accurately mirrors slow-growing astrocytomas. Using CD44 and GLAST, we isolated astrocyte-like (CD44+/GLAST+) cells from LGG275 that preferentially adopt a quiescent state yet retain remarkable plasticity, generating oligodendrocyte-like cells (CD44-/GLAST-). Transcriptomic and proteomic analyses revealed that astrocyte-like and oligodendrocyte-like cells populations resemble quiescent and activated neural stem (NSC) cells from the adult subventricular zone (SVZ). Finally, we found that NOTCH signaling regulates the balance between astrocytic and oligodendrocytic states, while DLL3, expressed by oligodendrocyte-like cells, modulates both proliferation and phenotype. These cell lines represent valuable resources for dissecting lineage dynamics, heterogeneity, and progression mechanisms in IDH-mutant astrocytomas. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC="FIGDIR/small/696808v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@953108org.highwire.dtl.DTLVardef@c6234aorg.highwire.dtl.DTLVardef@3703fcorg.highwire.dtl.DTLVardef@1e6c3a9_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightO_LIWe constituted a richly annotated biobank derived from 4 astrocytomas, showing similar characteristics to those found in patients, providing valuable tools to investigate cellular heterogeneity and plasticity, and link with tumor progression. C_LIO_LIscRNA-sequencing revealed three cell states (oligodendrocyte-like, astrocyte-like, and stem cell-like cells) akin to those found in tumors. C_LIO_LIAstrocyte-like cells are quiescent cells, plastic and similar to quiescent neural stem cell (qNSC) from the sub-ventricular zone (SVZ), while oligodendrocyte-like cells are similar to active NSC (aNSC). C_LIO_LIThe Notch pathway plays a role in cell plasticity, enabling a shift towards an astrocyte-like state. C_LI

cancer biology↗

bioRxiv2025

Decoding Gene Responsiveness to Synthetic Chromatin Reader-Actuators with Multi-Modal Epigenomic Profiling

Cell identity is regulated by chromatin states that encode gene regulatory memory and shape responses to new inputs. To investigate how chromatin context influences inducibility in differentiated cells, we employed engineered synthetic reader-actuators (SRAs), fusion proteins containing the polycomb chromodomain (PCD) that binds H3K27me3. In MCF7 breast cancer cells, we mapped PCD-fusion occupancy by ChIP-seq and used RNA-seq to identify temporally resolved gene activation patterns. ChIP-seq profiling and machine learning models (MLM) demonstrated that PCD-fusion binding was predicted by the presence of H3K27me3, H4K20me1, or H3K36me3 enrichment, suggesting selective accessibility at enhancers and chromatin transition zones. Among genes with PCD-fusion enriched enhancers, the SRA-induced subset was distinguished by promoter features including bivalent histone modifications and enrichment of transcriptional repressors REST and MTA1. Collectively, our results demonstrate that SRA responsiveness depends on a specific chromatin signature beyond H3K27me3 alone. This study demonstrates the power of SRAs to dissect inducible chromatin features in their native genomic context, and suggests that epigenetically repressed regions in differentiated cells can retain regulatory plasticity.

synthetic biology↗

bioRxiv2025

Characterization of quiescent subpopulations and proliferative compartments in glioblastoma

Glioblastoma (GBM) quiescent (Q) cell populations are hypothesized to contain cancer stem-like cells (CSC) that drive tumor growth, cellular heterogeneity, and recurrence. However, GBM tumors do not neatly resolve into developmental hierarchies and Q stem-like activities are difficult to assess. Here, we evaluated tumor Q subpopulations in patient-derived GBM xenograft tumors using live cell reporters, DNA label retention assays, and single cell genomics. Compared to adult neural stems cells (NSCs), GBM Q populations contain hybrid transcriptional states composed of networks found in both dormant and activated adult NSCs, resulting in constitutive expression of key Q egress transcription factors and their targets (e.g., AP-1 and CCND1/2). As a result, even the longest Q-residing cells ([~]12 days) in xenograft tumors continuously cycle and fail to enter dormant Q states. We provide evidence and hypothesize that transient Q states in primary tumors arise as part of distinct proliferative compartments rather than deterministic developmental hierarchies driven by CSC activity. We further speculate that increases in basal translation rates drive Q instability in GBM tumors.

cancer biology↗

bioRxiv2024

Breaking out of the cell cycle: Including quiescence in cell cycle classification

Single-cell transcriptomics has unveiled a vast landscape of cellular heterogeneity in which the cell cycle is a significant component. We trained a high-resolution cell cycle classifier (ccAFv2) using single cell RNA-seq (scRNA-seq) characterized human neural stem cells. The ccAFv2 classifies six cell cycle states (G1, Late G1, S, S/G2, G2/M, and M/Early G1) and a quiescent-like G0 state (Neural G0), and it incorporates a tunable parameter to filter out less certain classifications. The ccAFv2 classifier performed better than or equivalent to other state-of-the-art methods even while classifying more cell cycle states, including G0. We demonstrate that the ccAFv2 classifier effectively generalizes the S, S/G2, G2/M, and M/Early G1 states across cell types derived from all three germ layers. While the G0, G1, and Late G1 states perform well in neuroepithelial cell types, their accuracy is lower in other cell types. However, misclassifications are confined to the G0, G1, and Late G1 states. We showcased the versatility of ccAFv2 by successfully applying it to classify cells, nuclei, and spatial transcriptomics data in humans and mice, using various normalization methods and gene identifiers. We provide methods to regress the cell cycle expression patterns out of single cell or nuclei data to uncover underlying biological signals. The classifier can be used either as an R package integrated with Seurat or a PyPI package integrated with SCANPY. We proved that ccAFv2 has enhanced accuracy, flexibility, and adaptability across various experimental conditions, establishing ccAFv2 as a powerful tool for dissecting complex biological systems, unraveling cellular heterogeneity, and deciphering the molecular mechanisms by which proliferation and quiescence affect cellular processes.

cell biology↗

bioRxiv2022

Systematic integration of protein affecting mutations, gene fusions, and copy number alterations into a comprehensive somatic mutational profile

Somatic mutations occur as random genetic changes in genes through protein-affecting mutations (PAMs), gene fusions, or copy number alterations (CNAs). Mutations of different types can have a similar phenotypic effect (i.e., allelic heterogeneity) and should be integrated into a unified gene mutation profile. We developed OncoMerge to fill this niche of integrating somatic mutations to capture allelic heterogeneity, assign a function to mutations, and overcome known obstacles in cancer genetics. Application of OncoMerge to the TCGA Pan-Cancer Atlas increased the number and frequency of somatically mutated genes and improved the prediction of the somatic mutation role as either activating or loss of function. Using integrated somatic mutation matrices increased the power to infer gene regulatory networks and uncovered the enrichment of switch-like feedback motifs and delay-inducing feed-forward loops. These studies demonstrate that OncoMerge efficiently integrates PAMs, fusions, and CNAs and strengthens downstream analyses linking somatic mutations to cancer phenotypes. MotivationGenes are mutated in tumors through either PAMs, CNAs, or gene fusions, thereby splitting the signal of the somatic mutation effect across these three mutation types. We developed OncoMerge to systematically integrate the three mutation types into a single mutation profile that better captures the impact of somatic mutations on cancer phenotypes. As a tool OncoMerge fills the gap between the sophisticated variant calling pipelines and downstream analyses.

systems biology↗