Biology subjects

Rushing, E. J.

Publications and source records attributed to Rushing, E. J..

6 recordsLinked to original sources

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↗

bioRxiv2022

Targeting tumour-intrinsic neural vulnerabilities of glioblastoma

Glioblastoma is the most common yet deadliest primary brain cancer1. The neural behavior of glioblastoma, including the formation of synaptic circuitry and tumour microtubes, is increasingly understood to be pivotal for disease manifestation2-9. Nonetheless, the few approved treatments for glioblastoma target its oncological nature, while its neural vulnerabilities remain incompletely mapped and clinically unexploited. Here, we systematically survey the neural molecular dependencies and cellular heterogeneity across glioblastoma patients and diverse model systems. In 27 surgical patient samples, we identify cancer cell morphologies indicative of poor prognosis, and discover repurposable neuroactive drugs with anti-glioblastoma efficacy by image-based drug screening. Glioblastoma cells exhibit functional dependencies on highly expressed neuroactive drug targets, while interpretable molecular machine learning (COSTAR) reveals their downstream convergence on AP-1-driven tumour suppression. This drug-target connectivity signature is confirmed by accurate in silico drug screening on >1 million compounds, as well as by multi-omic profiling of glioblastoma drug responses. Thus, Ca2+-driven AP-1 pathway induction represents a tumour-intrinsic vulnerability at the intersection of oncogenesis and neural activity-dependent signaling. Opportunities for clinical translation of this neural vulnerability are epitomized by the antidepressant Vortioxetine synergizing with current standard of care treatments in vivo. Together, the results presented here provide a mechanistic foundation and conceptual framework for the treatment of glioblastoma based on its neural origins.

cancer biology↗

bioRxiv2020

The Genomic Landscape of Prostate Cancer Brain Metastases

Lethal prostate cancer commonly metastasizes to bone, lymph nodes, and visceral organs but with more effective therapies, there is an increased frequency of metastases to the brain. Little is known about the genomic drivers of prostate cancer brain metastases (PCBM). To address this, we conducted a comprehensive multi-regional, genomic, and targeted transcriptomic analysis of PCBM from 28 patients. We compared whole-exome and targeted RNA sequencing with matched primary tumors when available (n = 10) and with publicly available genomic data from non-brain prostate cancer metastases (n = 416). In addition to common alterations in TP53, AR, RB1, and PTEN, we identified highly significant enrichment of mutations in NF1 (25% cases (6/28), q = 0.049, 95% CI = 2.38 - 26.52, OR = 8.37) and RICTOR (17.9% cases (5/28), q = 0.01, 95% CI = 6.74 - 480.15, OR = 43.7) in PCBM compared to non-brain prostate cancer metastases, suggesting possible activation of the druggable pathways RAS/RAF/MEK/ERK and PI3K/AKT/mTOR, respectively. Compared to non-brain prostate cancer metastases, PCBM were almost three times as likely to harbor DNA homologous repair (HR) alterations (42.9% cases (12/28), p =0.016, 95% CI = 1.17 - 6.64, OR = 2.8). When considering the combination of somatic mutations, copy number alteration, and Large-scale State Transitions, 64.3% of patients (18/28) were affected. HR alterations may be critical drivers of brain metastasis that potentially provide cancer cells a survival advantage during re-establishment in a special microenvironment. We demonstrate that PCBM have genomic dependencies that may be exploitable through clinical interventions including PARP inhibition.

cancer biology↗

bioRxiv2019

Microglia control small vessel calcification via TREM2

Microglia participate in CNS development and homeostasis and are often implicated in modulating disease processes in the CNS. However, less is known about the role of microglia in the biology of the neurovascular unit (NVU). In particular, data are scant on whether microglia are involved in CNS vascular pathology. In this study, we use a mouse model of primary familial brain calcification (PFBC) - Pdgfbret/ret to investigate the role of microglia in calcification of the NVU. We report that microglia enclosing vessel-calcifications, coined calcification-associated microglia (CAM), display a distinct activation signature. Pharmacological ablation of microglia with the CSF1R inhibitor - PLX5622 leads to aggravated vessel calcification. Additionally, depletion of microglia in wild-type and Pdgfbret/ret mice causes the development of bone protein (osteocalcin, osteopontin) containing axonal spheroids in the white matter. Mechanistically, we show that microglia require functional TREM2 for controlling vessel-associated calcification. In conclusion, our results demonstrate that microglial activity in the setting of pathological vascular calcification is beneficial. In addition, we identify a new, previously unrecognized function of microglia in halting the expansion of ectopic calcification.

neuroscience↗

bioRxiv2019

Transmission of prion infectivity from blood by peptoid-conjugated beads

Prions cause transmissible infectious diseases in humans and animals and have been found to be transmissible by blood transfusion even in the presymptomatic stage. However, the concentration of prions in body fluids such as blood and urine is extremely low, and therefore direct diagnostic tests on such specimens often yield false-negative results. Quantitative preanalytical prion enrichment may significantly improve the sensitivity of prion assays by concentrating trace amounts of prions from large volumes of body fluids. Here we show that beads conjugated to positively charged peptoids not only captured PrP aggregates from plasma of prion-infected hamsters, but also adsorbed prion infectivity in both the symptomatic and preclinical stages of the disease. Bead absorbed prion infectivity efficiently transmitted disease to transgenic indicator mice. We found that the readout of the peptoid-based misfolded protein assay (MPA) correlates closely with prion infectivity in vivo, thereby validating the MPA as a simple, quantitative, and sensitive surrogate indicator of the presence of prions. The reliable and sensitive detection of prions in plasma will enable a wide variety of applications in basic prion research and diagnostics.

neuroscience↗

bioRxiv2018

Active Receptor Tyrosine Kinases, but not Brachyury, are sufficient to trigger chordoma in zebrafish

The aberrant activation of developmental processes triggers diverse cancer types. Chordoma is a rare, aggressive tumor arising from transformed notochord remnants. Several potentially oncogenic factors, including several receptor tyrosine kinase (RTK) genes, have been found deregulated in chordoma, yet causation remains uncertain. In particular, sustained expression of the developmental notochord transcription factor Brachyury is hypothesized as key driver of chordoma; nonetheless, experimental evidence for an oncogenic role of Brachyury in chordoma and its prognostic impact remains missing. Here, we developed and applied a zebrafish chordoma model to identify the notochord-transforming potential of implicated genes in vivo. We find that Brachyury, including a form with augmented transcriptional activity, is insufficient to initiate notochord hyperplasia. In contrast, the chordoma-implicated RTKs EGFR and KDR/VEGFR2 are sufficient to transform notochord cells within two to five days of development. Transcriptome and structural analysis of transformed notochords revealed that the aberrant activation of RTK/Ras signaling attenuates processes required for notochord differentiation, including of the unfolded protein response. Our results provide first in vivo indication against a tumor-initiating potential of Brachyury in the notochord, and imply activated RTK signaling as possibly initiating event in chordoma. These results provide a mechanistic framework for the pursuit of chemotherapeutic compounds to combat this aggressive tumor type.

cancer biology↗