Biology subjects

Sarver, A. L.

Publications and source records attributed to Sarver, A. L..

11 recordsLinked to original sources

bioRxiv2026

Longitudinal single-cell and spatial transcriptomics reveals intratumor heterogeneity, therapeutic response, and comparative value of canine marginal zone lymphoma

Diffuse B-cell lymphomas are the most prevalent canine hematologic malignancies, and their clinical presentation resembles that of human B-cell non-Hodgkin lymphomas (NHLs). However, a lack of a clear subtyping framework perpetuates imprecise treatment approaches that fail to address mechanisms of therapy resistance. Here, we employed deep phenotyping via serial sampling and longitudinal transcriptomics to evaluate intratumoral composition and therapy response in a 6-year-old neutered male goldendoodle with stage 5A marginal zone lymphoma (MZL). Following sequential treatment consisting of a single IV dose of oncolytic vesicular stomatitis virotherapy (VSV) and standard CHOP chemotherapy 30 days later, we performed scRNAseq on seven serial lymph node biopsies and spatial sequencing on a resection taken 10 days post-VSV treatment. B cells (>90%) comprised three transcriptionally distinct and temporally stable subpopulations, with specific copy number profiles and robust spatial organization despite disrupted lymph node architecture. Analysis across subpopulations revealed downregulation of the quiescence program including KLF2, suggesting similarity to KLF2-deficient human MZL. While VSV successfully reached target B cells, downstream transcriptional responses were predominantly localized to the T-cell compartment. T cells ([≤]6%) showed increased proliferation and upregulation of cytotoxicity markers post-VSV administration, enriching for leukocyte-mediated cytotoxicity pathways consistent with an anti-viral immune response. Ultimately, these results provide an in vivo proof-of-concept for the treatment paradigm in canine lymphoma, while emphasizing the need for improved subtyping frameworks and multidimensional treatment strategies targeting intratumoral heterogeneity.

cancer biology↗

bioRxiv2026

Multiomic profiling of human and canine soft-tissue sarcomas reveals extensive molecular homology across species and identifies clinically relevant subgroups

Soft-tissue sarcoma (STS) are rare and heterogeneous mesenchymal tumours with over 100 recognized human subtypes. Despite advances in cytogenetic and molecular characterization, diagnostic precision and therapeutic options remain limited for most subtypes. Spontaneously occurring canine STS could represent valuable translational models, due to their higher incidence and clinical similarity to human counterparts. However, molecular cross-species comparisons of specific subtypes are largely missing. Here, we performed a tissue-resolved, cross-species analysis of tumour and matched adjacent normal tissue (NT) in human and canine fibrosarcoma (FSA) and myxofibrosarcoma (MFS) by laser-capture microdissection of FFPE specimens combined with RNAseq and LC-MS/MS. Multimodal profiling revealed FSA and MFS to represent a molecular continuum rather than distinct entities in both species, resulted in identification of clinically relevant subgroups based on immune activation, proliferative activity and copy number alterations, and identified a novel canine STS subtype associated with a gene fusion. Moreover, our analyses revealed cross-species conserved transcriptomic and proteomic alterations distinguishing tumour from NT, including pathways linked to extracellular matrix remodelling, immune modulation, and cell proliferation. These data establish the first comprehensive molecular comparison of canine and human FSA and MFS, highlight the translational relevance of canine models, and identify candidate biomarkers for diagnostic refinement and development of targeted therapeutic modalities.

cancer biology↗

bioRxiv2026

Integrative Single-cell and Spatial Transcriptomic Analysis of Osteosarcoma Reveals Conserved and Distinct Ecosystems Across Sites and Species

Osteosarcoma is a heterogeneous malignancy, exhibiting significant variability among patients, individual cancer cells within a tumor, and the stromal cells that compose primary and metastatic lesions. To facilitate the study of this complex disease, we compiled a unique cross-species single-cell transcriptomic dataset totaling over a million cells/nuclei from human specimens, canine specimens, patient-derived xenografts/PDX, and syngeneic mouse models at both primary (bone) and metastatic (lung) sites. Using a rigorous process for multi-species alignment and annotation, we identified six conserved tumor cell transcriptional states organized along hierarchical differentiation trajectories from progenitor to differentiated phenotypes. Parallel analysis of tumor-associated cells identified conserved macrophage, fibroblast, and endothelial populations that exhibit species- and site-specific reprogramming. Validation by mapping cell types using spatial transcriptomics revealed structured neighborhood architectures that were reproduced across multiple samples. Cell-cell interaction analysis revealed similarities and differences in tumor-host networks across primary and metastatic sites and across species. This analysis enabled pathway-specific assessment of tumor-host communication fidelity across osteosarcoma model systems relative to humans, revealing canine osteosarcoma as a more faithful model. Metastatic lung lesions, counterintuitively, exhibited more intense and complex extracellular matrix (ECM) signaling than primary bone tumors. A key example was tumor-derived fibronectin (FN1), which engages integrin and syndecan receptors on lung epithelial cells, driving a pathological mesenchymal and profibrotic state that promotes fibrotic niche formation and metastatic lung colonization. Together, this cross-species resource delineates both conserved and divergent tumor microenvironment programs, demonstrates how model-aware analyses uncover previously unrecognized tumor-host interactions, and underscores the need for therapies that co-target tumor heterogeneity and its supportive metastatic niche. Statement of SignificanceWe show that the tumor microenvironment in human osteosarcoma patients has biological phenotypes that are conserved across both patients and species. This points towards underlying molecular mechanisms that could be therapeutically targeted.

cancer biology↗

bioRxiv2023

Oncolytic vesicular stomatitis virus is safe and provides a survival benefit for dogs with naturally occurring osteosarcoma

Osteosarcoma is a devastating bone cancer that disproportionally afflicts children, adolescents, and young adults. Standard therapy includes surgical tumor resection combined with multiagent chemotherapy, but many patients still suffer from metastatic disease progression. Neoadjuvant systemic oncolytic virus (OV) therapy has the potential to improve clinical outcomes by targeting primary and metastatic tumor sites and inducing durable antitumor immune responses. Here we described the first evaluation of neoadjuvant systemic therapy with a clinical-stage recombinant oncolytic Vesicular stomatitis virus (VSV), VSV-IFN{beta}-NIS, in naturally occurring cancer, specifically appendicular osteosarcoma in companion dogs. Canine osteosarcoma has a similar natural disease history as its human counterpart. VSV-IFN{beta}-NIS was administered prior to standard of care surgical resection, permitting microscopic and genomic analysis of tumors. Treatment was well-tolerated and a "tail" of long-term survivors ([~]35%) was apparent in the VSV-treated group, a greater proportion than observed in two contemporary control cohorts. An increase in tumor inflammation was observed in VSV-treated tumors and RNAseq analysis showed that all the long-term responders had increased expression of a T-cell anchored immune gene cluster. We conclude that neoadjuvant VSV-IFN{beta}-NIS is safe and may increase long-term survivorship in dogs with naturally occurring osteosarcoma, particularly those that exhibit pre-existing antitumor immunity.

cancer biology↗

bioRxiv2022

Differential migration mechanics and immune responses of glioblastoma subtypes

Glioblastoma remains a deadly cancer driven in part by invasion of tumor cells into the brain. Transcriptomic analyses have identified distinct molecular subtypes, but mechanistic differences that account for clinical differences are not clear. Here, we show that, as predicted by the motor-clutch model of cell migration, mesenchymal glioma cells are more spread, generate larger traction forces, and migrate faster in brain tissue compared to proneural cells. Despite their rapid migration and comparable proliferation rates in vitro, mice with mesenchymal tumors survive longer than those with proneural tumors. This improved survival correlated with an immune response in the mesenchymal tumors, including T cell-mediated. Consistently, inducing mesenchymal tumors in immunodeficient mice resulted in shorter survival supporting a protective immune role in mesenchymal tumors. Thus, mesenchymal tumors have aggressive migration, but are immunologically hot which suppresses net proliferation. These two features counteract each other and may explain the lack of a strong survival difference between subtypes clinically, while also opening up new opportunities for subtype-specific therapies. Significant StatementThis study highlights new mechanical and immunological insights into glioblastoma molecular subtypes using an integrated modeling-genome engineering strategy, which can potentially facilitate glioblastoma subtype-specific therapeutic strategies.

cancer biology↗

bioRxiv2021

Transcriptional and Functional Activity of Canine Hemangiosarcoma to Support Hematopoiesis Demonstrate Bone Marrow Nurse Cell Ontogeny

Hemangiosarcoma and angiosarcoma are soft-tissue sarcomas of blood vessel-forming cells in dogs and humans, respectively. These vasoformative sarcomas are aggressive and highly metastatic, with disorganized, irregular blood-filled vascular spaces. Our objective was to define molecular programs which support the niche that enables progression of canine hemangiosarcoma and human angiosarcoma. Dog-in-mouse hemangiosarcoma xenografts recapitulated the vasoformative and highly angiogenic morphology and molecular characteristics of primary tumors. Blood vessels in the tumors were complex and disorganized, and they were lined by both donor and host cells, a trait that was not observed in xenografts from canine osteosarcoma and lymphoma. In some cases, the xenografted hemangiosarcoma cells created exuberant myeloid hyperplasia and gave rise to lymphoproliferative tumors of mouse origin. We did not uncover a definitive transmissible etiology, but our functional analyses indicate that hemangiosarcoma cells generate a microenvironment that supports expansion and differentiation of hematopoietic progenitor populations. We conclude that canine hemangiosarcomas, and possibly human angiosarcomas, originate from stromal cells that are part of the bone marrow niche and that these cells may also support the growth of hematopoietic tumors. SignificanceWe demonstrate that molecular programs supporting expansion of immune and inflammatory cells in hemangiosarcoma resemble those of bone marrow niche cells, providing insights into the potential roles of these cells - whether physiological or pathological - in creating a permissive environment for the progression of hematopoietic malignancies.

cancer biology↗

bioRxiv2020

Identification of mutations that cooperate with defects in B cell transcription factors to initiate leukemia

The transcription factors EBF1 and PAX5 are frequently mutated in B cell acute lymphoblastic leukemia (B-ALL). We demonstrate that Pax5+/- x Ebf1+/- compound heterozygous mice develop highly penetrant leukemia. Similar results were seen in Pax5+/- x Ikzf1+/- and Ebf1+/- x Ikzf1+/- mice for B-ALL, or in Tcf7+/- x Ikzf1+/- mice for T cell leukemia. To identify genetic defects that cooperate with Pax5 and Ebf1 compound heterozygosity to initiate leukemia, we performed a Sleeping Beauty (SB) transposon screen that identified cooperating partners including gain-of-function mutations in Stat5 ([~]65%) and Jak1([~]68%), or loss-of-function mutations in Cblb (61%) and Myb (32%). These findings underscore the role of JAK/STAT5 signaling in B cell transformation and demonstrate unexpected roles for loss-of-function mutations in Cblb and Myb in leukemic transformation. RNA-Seq studies demonstrated upregulation of a PDK1>SGK3>MYC pathway; treatment of Pax5+/- x Ebf1+/- leukemia cells with PDK1 inhibitors blocked proliferation in vitro. Finally, we identified conserved transcriptional variation in a subset of genes between human leukemias and our mouse B-ALL models. Thus, compound haploinsufficiency for B cell transcription factors likely plays a critical role in transformation of human B cells and suggest that PDK1 inhibitors may be effective for treating patients with such defects.

cancer biology↗

bioRxiv2020

Genomically Complex Human Angiosarcoma and Canine Hemangiosarcoma Establish Convergent Angiogenic Transcriptional Programs

Sporadic angiosarcomas (ASs) are aggressive vascular sarcomas whose rarity and genomic complexity present significant obstacles in deciphering the pathogenic significance of individual genetic alterations. Numerous fusion genes have been identified across multiple types of cancers, but their existence and significance remain unclear in sporadic ASs. In this study, we leveraged RNA sequencing data from thirteen human ASs and 76 spontaneous canine hemangiosarcomas (HSAs) to identify fusion genes associated with spontaneous vascular malignancies. Ten novel protein-coding fusion genes, including TEX2-PECAM1 and ATP8A2-FLT1, were identified in seven of the thirteen human tumors, with two tumors showing mutations of TP53. HRAS and NRAS mutations were found in ASs without fusions or TP53 mutations. We found fifteen novel protein-coding fusion genes including MYO16-PTK2, GABRA3-FLT1, and AKT3-XPNPEP1 in eleven of the 76 canine HSAs; these fusion genes were seen exclusively in tumors of the angiogenic molecular subtype that contained recurrent mutations in TP53, PIK3CA, PIK3R1, and NRAS. In particular, fusion genes and mutations of TP53 co-occurred in tumors with higher frequency than expected by random chance, and they enriched gene signatures predicting activation of angiogenic pathways. Comparative transcriptomic analysis of human ASs and canine HSAs identified shared molecular signatures associated with activation of PI3K/AKT/mTOR pathways. Our data show that, while driver events of malignant vasoformative tumors of humans and dogs include diverse mutations and stochastic rearrangements that create novel fusion genes, convergent transcriptional programs govern the highly conserved morphological organization and biological behavior of these tumors in both species.

cancer biology↗

bioRxiv2020

PI3Kγ inhibition suppresses microglia/TAM accumulation in glioblastoma microenvironment to promote exceptional temozolomide response

Precision medicine in oncology leverages clinical observations of exceptional response. Towards an understanding of the molecular features that define this response, we applied an integrated, multi-platform analysis of RNA profiles derived from clinically annotated glioblastoma samples. This analysis suggested that specimens from exceptional responders are characterized by decreased accumulation of microglia/macrophages in the glioblastoma microenvironment. Glioblastoma-associated microglia/macrophages secreted interleukin 11 (IL11) to activate STAT3-MYC signaling in glioblastoma cells. This signaling induced stem cell states that confer enhanced tumorigenicity and resistance to the standard-of-care chemotherapy, temozolomide (TMZ). Targeting a myeloid cell restricted isoform of PI3K, PI3K{gamma}, by pharmacologic inhibition or genetic inactivation, disrupted this signaling axis by suppressing microglia/macrophage accumulation and associated IL11 secretion in the tumor microenvironment. Mirroring the clinical outcomes of exceptional responders, PI3K{gamma} inhibition synergistically enhanced the anti-neoplastic effects of TMZ in orthotopic murine glioblastoma models. Moreover, inhibition or genetic inactivation of PI3K{gamma} in murine glioblastoma models recapitulated expression profiles observed in clinical specimens isolated from exceptional responders. Our results suggest key contributions from tumor-associated microglia/macrophages in exceptional responses and highlight the translational potential for PI3K{gamma} inhibition as a glioblastoma therapy. Significance StatementUnderstanding the basis for exceptional responders represents a key pillar in the framework of precision medicine. In this study, we utilized distinct informatics platforms to analyze the expression profiles of clinically annotated tumor specimens derived from patients afflicted with glioblastoma, the most common form of primary brain cancer. These analyses converged on prognostic contributions from glioblastoma-associated microglia/macrophages. Glioblastoma-associated microglia secreted interleukin 11 (IL11) to activate a STAT3-MYC signaling axis in glioblastoma cells, facilitating resistance to the standard-of-care chemotherapy, temozolomide. Microglia recruitment and IL11 secretion were dependent on the myeloid specific phosphoinositide-3-kinase gamma isoform (PI3K{gamma}). Inhibition or genetic inactivation of PI3K{gamma} in murine glioblastoma models recapitulated expression profiles observed in specimens derived from exceptional responders, suggesting potential for clinical translation.

cancer biology↗

bioRxiv2020

Comparative analysis of genome-wide DNA methylation identifies patterns that associate with conserved transcriptional programs in osteosarcoma.

Osteosarcoma is an aggressive tumor of the bone that primarily affects young adults and adolescents. Osteosarcoma is characterized by genomic chaos and heterogeneity. While inactivation of tumor suppressor p53 TP53 is nearly universal other high frequency mutations or structural variations have not been identified. Despite this genomic heterogeneity, key conserved transcriptional programs associated with survival have been identified across human, canine and induced murine osteosarcoma. The epigenomic landscape, including DNA methylation, plays a key role in establishing transcriptional programs in all cell types. The role of epigenetic dysregulation has been studied in a variety of cancers but has yet to be explored at scale in osteosarcoma. Here we examined genome-wide DNA methylation patterns in 24 human and 44 canine osteosarcoma samples identifying groups of highly correlated DNA methylation marks in human and canine osteosarcoma samples. We also link specific DNA methylation patterns to key transcriptional programs in both human and canine osteosarcoma. Building on previous work, we built a DNA methylation-based measure for the presence and abundance of various immune cell types in osteosarcoma. Finally, we determined that the underlying state of the tumor, and not changes in cell composition, were the main driver of differences in DNA methylation across the human and canine samples. SignificanceThis is the first large scale study of DNA methylation in osteosarcoma and lays the ground work for the exploration of DNA methylation programs that help establish conserved transcriptional programs in the context of different genomic landscapes.

cancer biology↗

bioRxiv2019

Genomic analysis reveals shared genes and pathways in human and canine angiosarcoma

Angiosarcoma is a highly aggressive cancer of blood vessel-forming cells with high fatality and few effective treatment options. It is both rare and heterogenous, making large, well powered genomic studies nearly impossible. In dogs, angiosarcoma is common, with breeds like the golden retriever carrying heritable genetic factors that put them at very high risk. If the clinical similarity of canine and human angiosarcoma reflects shared genomic etiology, dogs could be a critically needed model for advancing angiosarcoma research. We assessed the genomic landscape of canine angiosarcoma via whole exome sequencing (47 golden retriever angiosarcomas) and RNA sequencing (74 angiosarcomas from multiple breeds). The predominant mutational signature was the age-associated deamination of cytosine to thymine, and somatic coding mutations occurred most frequently in the tumor suppressor TP53 (59.6% of cases) as well as two genes in the PI3K pathway: the oncogene PIK3CA (29.8%) and its regulatory subunit PIK3R1 (8.5%). We compared the canine data to human data recently released by The Angiosarcoma Project, and found the same genes and many of the same pathways significantly enriched for somatic mutations, most notably protein kinases, glycoproteins, fibronectin Type III domains, EGF-like domains, and cell adhesion proteins such as cadherins. As in human angiosarcoma, CDKN2A/B was recurrently deleted and VEGFA, KDR, and KIT recurrently gained. Canine angiosarcoma closely models human angiosarcoma on a genomic level, and is a powerful tool for investigating the pathogenesis of this devastating disease.

genomics↗