Biology subjects

De Micheli, A. J.

Publications and source records attributed to De Micheli, A. J..

9 recordsLinked to original sources

bioRxiv2026

Single-cell multi-omic analyses resolve the cellular diversity of ALK/ROS1/MET/NTRK-fused gliomas in infants and older children

Pediatric cancers are thought to arise from dysregulation of developmental programs, otherwise tightly regulated in time and space. Infant-type hemispheric gliomas (IHGs) arise in early childhood, driven by characteristic ALK/ROS1/MET/NTRK receptor tyrosine kinase (RTK) gene fusions. We dissected the cellular hierarchies of 24 fusion-positive gliomas, spanning infants through adolescents, using single-cell and single-nucleus RNA/ATAC-seq, and spatial transcriptomics. We identified five cancer cell states, with radial glia-like cells at the apex of a neoplastic hierarchy resembling neuronal- and glial-like trajectories. Neuronal-like cells were enriched in most IHGs but diminished in ROS1-fused IHGs and older patients. Integration of chromatin profiling revealed FOS/JUN-driven oncogenic programs and high inferred plasticity across all cancer cell populations. Myeloid cells, the most abundant non-neoplastic population, comprised distinct subgroups, suggesting context-dependent functions. Despite lacking high-order structure, spatial transcriptomics revealed discrete cellular niches within IHGs. Collectively, our findings elucidate the cellular states and developmental programs underlying IHGs and RTK-fused gliomas in older patients, opening new avenues for research and therapy innovation.

cancer biology↗

bioRxiv2025

Functionally distinct ALK and ROS1 fusions detected in infant-type hemispheric gliomas converge on STAT3 and SHP2 activation

ALK and ROS1 fusions are emerging as key drivers of infant-type hemispheric gliomas (IHG). With diverse gene partners, the impact of ALK and ROS1 oncoprotein heterogeneity on glioma biology remains unknown. We developed an integrative phospho-proteomic and transcriptomic approach to discover biological functions regulated by five IHG-associated fusions: CCDC88A::ALK, PPP1CB::ALK, GOPC::ROS1, CLIP1::ROS1 and KIF21A::ROS1. Here, we report fusion-specific oncogenic functions conferred by the 5 gene partner, including increased cell motility driven by microtubule-interacting fusions CCDC88A::ALK and CLIP1::ROS1. All studied fusions converged on a non-canonical STAT3 activation. Using affinity purification mass spectrometry, we identify SHP2 in direct interaction with all three ROS1 oncoproteins, but with none of the ALK oncoproteins, which in turn interact with SHC1/SHC3. ROS1 fusions phosphorylated SHP2 to a larger extent than ALK fusions, and analyses of downstream pathways suggested MAPK-independent, non-canonical SHP2-driven functions. Our findings reveal both common and fusion-specific dependencies, offering opportunities to optimize therapeutic strategies for pediatric gliomas.

cancer biology↗

bioRxiv2025

Mapping Tumor Microenvironment and Treatment Response of Diffuse Midline Glioma Using Multiplexed Immunofluorescence and AI Models

BackgroundDespite its clinical promise in non-solid tumor, immunotherapy is yet to show significant clinical efficacy for brain tumors including pediatric diffuse midline glioma (DMG). This indicated the need to fully explore DMG immune tumor microenvironment (TME). MethodWhole brains (49 DMGs, 20 non-DMG, 10 non-malignant) from 79 pediatric patients were used to establish a tissue microarray (918 cores) representing primary, metastatic, and adjacent healthy sites. CellDIVE MxIF multiplex assay was used to probe for 33 immune and cell type markers. RNA sequencing (n=62 patients) defined additional immune signatures. Findings were validated using patient plasma and DMG PDX models. Our annotated single-cell atlas was used to train a spatial AI model to predict antigens from H&E staining. FindingsWe found enrichment of M1-activated microglia in primary versus adjacent healthy tissue. PD1 positive cells were significantly (p<0.01) higher in tumor compared to adjacent controls. This was validated by mRNA profiling, further indicating two distinct groups with top 35 significant (p<0.05) genes revealing synaptic signature in the metastatic cohort. We stratified the patient cohort by treatment. Imipridone cohort (n=5) showed decreased progenitor (Nestin+, Vimentin+, and SOX2+) and increased macrophages/microglia infiltration. Increased T and B cells was validated in patient plasma following imipridone therapy. Combination therapy of imipridone and immunotherapy (n=7) resulted in increased myeloid (Iba1, CD68, CD163) and lymphoid (CD3, CD8) cells. Enhanced immune engagement was validated in DMG PDX models. Machine learning resulted in a spatial AI model capable of predicting 22 antigens using H&E slides. InterpretationsDMG tumors maintain a cold immune microenvironment, which is nevertheless dynamic and responsive to therapy, indicating the need to explore combination therapies. AI-assisted antigen detection is suitable for rapid interpretation of clinical biospecimens. FundingThis work was supported by Rising Tide, SNF, LilaBean Foundation, Swifty Foundation, Swiss to Cure DIPG and Yuvaan Tiwari Foundation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=45 SRC="FIGDIR/small/644698v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@198b382org.highwire.dtl.DTLVardef@312e0forg.highwire.dtl.DTLVardef@c71b82org.highwire.dtl.DTLVardef@1df1c35_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG

cancer biology↗

bioRxiv2023

Pre-ciliated tubal epithelial cells are prone to initiation of high-grade serous ovarian carcinoma

The distal region of the uterine (Fallopian) tube is commonly associated with high-grade serous carcinoma (HGSC), the predominant and most aggressive form of ovarian or extra-uterine cancer. Specific cell states and lineage dynamics of the adult tubal epithelium (TE) remain insufficiently understood, hindering efforts to determine the cell of origin for HGSC. Here, we report a comprehensive census of cell types and states of the mouse uterine tube. We show that distal TE cells expressing the stem/progenitor cell marker Slc1a3 can differentiate into both secretory (Ovgp1+) and ciliated (Fam183b+) cells. Inactivation of Trp53 and Rb1, whose pathways are commonly altered in HGSC, leads to elimination of targeted Slc1a3+ cells by apoptosis, thereby preventing their malignant transformation. In contrast, pre-ciliated cells (Krt5+, Prom1+, Trp73+) remain cancer-prone and give rise to serous tubal intraepithelial carcinomas and overt HGSC. These findings identify transitional pre-ciliated cells as a previously unrecognized cancer-prone cell state and point to pre-ciliation mechanisms as novel diagnostic and therapeutic targets.

cancer biology↗

bioRxiv2022

Single-cell mapping of tumor heterogeneity in pediatric rhabdomyosarcoma reveals developmental signatures with therapeutic relevance

Rhabdomyosarcoma (RMS) is an aggressive human pediatric cancer. Despite robust expression of myogenic regulatory factors, RMS cells are blocked in a proliferative state and do not terminally differentiate. The extent to which the skeletal muscle lineage is represented in RMS tumors and the mechanisms leading to developmental arrest remain elusive. Here, we combined single-cell RNA sequencing (scRNAseq), mass cytometry (CyTOF) and high-content imaging to resolve RMS heterogeneity. ScRNAseq and CyTOF analysis of a total of 17 patient-derived primary cultures and three cell lines uncovered plastic myogenic subpopulations that delineate a branched trajectory. The less aggressive embryonal RMS (eRMS) harbor primarily muscle stem cell (MuSC)-like cells and exhibit sparse commitment to differentiation. The more aggressive alveolar RMS (aRMS) comprise primarily actively cycling committed progenitors with a paucity of differentiated cells. The oncogenic fusion protein PAX3:FOXO1 sustains aRMS cells in the cycling trajectory loop, which we show can re-wired towards differentiation upon its downregulation or by dual pharmacological RAF and MEK inhibition. Our findings provide insights into the developmental states and trajectories underlying RMS progression and identify the RAS pathway as a promising target of differentiation therapy for human aRMS. STATEMENT OF SIGNIFICANCEWe present the first comprehensive single-cell transcriptomic and proteomic atlas of pediatric rhabdomyosarcoma (RMS), in which we identify impaired myogenic trajectories with prognostic value. We demonstrate that RAS pathway inhibitors disrupt the oncogenic trajectory and induce terminal differentiation, revealing novel therapeutic targets for the aggressive alveolar RMS subtype.

cancer biology↗

bioRxiv2020

A reference single-cell transcriptomic atlas of human skeletal muscle tissue reveals bifurcated muscle stem cell populations

AbstractSingle-cell RNA-sequencing (scRNA-seq) facilitates the unbiased reconstruction of multicellular tissue systems in health and disease. Here, we present a curated scRNA-seq dataset of human muscle samples from 10 adult donors with diverse anatomical locations. We integrated [~]22,000 single-cell transcriptomes using Scanorama to account for technical and biological variation and resolved 16 distinct populations of muscle-resident cells using unsupervised clustering of the data compendium. These cell populations included muscle stem/progenitor cells (MuSCs), which bifurcated into discrete "quiescent" and "early-activated" MuSC subpopulations. Differential expression analysis identified transcriptional profiles altered in the activated MuSCs including genes associated with ageing, obesity, diabetes, and impaired muscle regeneration, as well as long non-coding RNAs previously undescribed in human myogenic cells. Further, we modeled ligand-receptor cell-communication interactions and observed enrichment of the TWEAK-FN14 pathway in activated MuSCs, a characteristic signature of muscle wasting diseases. In contrast, the quiescent MuSCs have enhanced expression of the EGFR receptor, a recognized human MuSC marker. This work provides a new technical resource to examine human muscle tissue heterogeneity and identify potential targets in MuSC diversity and dysregulation in disease contexts.

cell biology↗

bioRxiv2019

PAX8 expressing epithelial cells are a cancer-prone source of clonal cyclical regeneration of endometrial epithelium

bioRxiv has withdrawn this manuscript after a formal investigation by Cornell University that concluded that it was submitted and made public without listing all contributing authors. The list of authors in this preprint should have been: Dah-Jiun Fu, Andrea J. De Micheli, Blaine A. Harlan, Mallikarjun Bidarimath, Minseok Kim, Lora H. Ellenson, Benjamin D. Cosgrove, Andrea Flesken-Nikitin and Alexander Yu. Nikitin, with DJF, AJDM and BAH indicated as equal contributors. Therefore, this work should not be cited as reference for the project. If you have any questions, please contact the corresponding authors.

cancer biology↗

bioRxiv2019

A single-cell transcriptional atlas identifies extensive heterogeneity in the cellular composition of tendons

Tendon is a connective tissue that transmits forces between muscles and bones. Cellular heterogeneity is increasingly recognized as an important factor in the biological basis of tissue homeostasis and disease, but little is known about the diversity of cells that populate tendon. Our objective was to explore the heterogeneity of cells in mouse Achilles tendons using single-cell RNA sequencing. We assembled a transcriptomic atlas and identified 11 distinct cell types in tendons, including 3 previously undescribed populations of fibroblasts. Using trajectory inference analysis, we provide additional support for the notion that pericytes are progenitor cells for the fibroblasts that compose adult tendons. We also modeled cell-interactions and identified ligand-receptor pairs involved in tendon homeostasis. Our findings highlight notable heterogeneity between and within tendon cell populations, which may contribute to our understanding of tendon extracellular matrix assembly and maintenance, and inform the design of therapies to treat tendinopathies.

cell biology↗

bioRxiv2019

Single-cell analysis of the muscle stem cell hierarchy identifies heterotypic communication signals involved in skeletal muscle regeneration

Muscle stem cells (MuSCs) are an essential adult stem cell population with the capacity to self-renew and regenerate muscle tissue. Functionally heterogeneous subpopulations of MuSCs have been identified based on their expression of myogenic regulatory factors and surface markers. However, a unified organization of muscle stem and progenitor cells and their subpopulations remains unresolved. Here, we performed temporal analysis of skeletal muscle regeneration using single-cell RNA-sequencing (scRNA-seq) of myotoxin-injured adult mouse hindlimb muscles. We generated over 34,000 single-cell transcriptomes spanning four muscle regeneration time-points and identified 15 distinct cell types, including a heterogeneous population of MuSCs and progenitor cells. Our analysis provides a hierarchical map of myogenic cell populations and identifies stage-specific regulatory programs that govern their contributions to muscle regeneration. In this transcriptomic atlas, we observed cell type-specific regenerative dynamics, exemplified by waves of transient amplification and diversification of multiple immune cell types and, subsequently, myogenic cells. Unbiased trajectory inference organized the myogenic cell populations within the atlas into a continuum, consisting of a hierarchy of quiescent MuSCs, cycling progenitors, committed myoblasts, and terminally differentiated myocytes. This myogenic trajectory matched prior understanding and also revealed that MuSC stages are defined by synchronous changes in regulatory factors, cell cycle-associated, and surface receptor gene expression. Lastly, we analyzed the transcriptomic atlas to identify over 100 candidate heterotypic communication signals between myogenic and non-myogenic cell populations, including many involving the fibroblast growth factor (FGF), Notch, and Syndecan receptor families and their associated ligands. Syndecan receptors were implicated in a large fraction of these cell communication interactions and were observed to exhibit transcriptional heterogeneity within the myogenic continuum. Using multiparameter mass cytometry (CyTOF), we confirmed that cycling MuSCs exhibit diversified Syndecan-1/2 expression, which suggests that dynamic alterations in Syndecan signaling interactions may coordinate stage-specific myogenic cell fate regulation. This scRNA-seq reference atlas provides a resolved hierarchical organization of myogenic subpopulations as a resource to investigate cell-cell interactions that regulate myogenic stem and progenitor cell fates in muscle regeneration.

cell biology↗