About

Olena Vaske is an Associate Professor of Molecular, Cell & Developmental Biology and holds the Colligan Presidential Chair in Pediatric Genomics. She earned her B.Sc. (Hons.) from the University of Toronto and her Ph.D. from the University of British Columbia. She completed a Postdoctorate Fellowship at UC Santa Cruz and a Clinical Molecular Genetics Fellowship at UC San Francisco. Her research focuses on genomic medicine for pediatric cancers and constitutional genetic disorders. Her lab is dedicated to improving the diagnosis and treatment of children affected by rare genetic diseases through genomic analysis and the development of novel molecular diagnostic tests. She studies the genetic and epigenetic changes driving pediatric tumors, utilizing advanced sequencing technologies, genome science, and bioinformatics. She is involved in the Treehouse Childhood Cancer Initiative, which aims to increase the benefit of genomic characterization for pediatric cancer patients by studying tumor RNA to understand genetic and epigenetic drivers of cancer. Her work also extends to the study of constitutional genetic diseases, such as structural birth defects, with the goal of understanding disease etiology and identifying new molecular targets for treatment.

Research topics

• Computer Science
• Biology
• Medicine
• Computational biology
• Oncology
• Genetics
• Pathology
• Political Science
• Cell biology
• Bioinformatics
• Emergency medicine
• Internal medicine
• Chemistry
• Medical emergency
• Cancer research
• Medical physics
• Biochemistry

Selected publications

• Glial Maturation and Immune Landscape Dynamics in <i>MN1::PATZ1</i> Fusion-Positive CNS Tumor Recurrence

  medRxiv · 2026-02-24

  articleOpen access

  Abstract Background PATZ1 fusion-positive central nervous system (CNS) tumors frequently harbor MN1::PATZ1 fusions as driver mutations, provisionally classified as a rare DNA methylation class of low-grade neuroepithelial tumors. Radiographically, they resemble pilocytic astrocytomas with tumor and cystic components, but their supratentorial cortex location and higher recurrence rates are distinguishing features. An intermediate clinical course, despite focal high-grade histopathology, underscores the need for longitudinal molecular and immune analyses to refine classification and standard therapy. Case Summary A female pediatric patient presented with neurological symptoms, including headache and right upper extremity weakness. MRI revealed a large cystic lesion in the left frontal lobe, leading to a differential diagnosis of low-grade glioma and ependymoma. Genomic analysis identified an MN1::PATZ1 fusion. The tumor recurred after gross total resection prompting a second resection. Transcriptomic and histopathologic assessments identified multiglial lineage, and high-grade features closely related to adult glioblastoma alongside pro-inflammatory activity in the primary tumor. The recurrent tumor showed reduced malignancy, and oligodendroglioma-like features. Increased MHC gene expression, immune checkpoint receptors ( PDCD1, CTLA4, TIGIT,TIM3 ), T cell regulators ( CXCR6 ), and elevated macrophage frequency, coupled with reduced PD-L1 in the recurrent tumor, suggest a complex anti-tumor immune response constrained by T cell dysregulation. This case, along with two other MN1::PATZ1 fusion-positive tumors, identifies a distinct transcriptomic subtype separate from circumscribed astrocytic glioma, highlighting upregulation of growth factor receptor pathways, like PI3K/AKT, and immune dysfunction linked to recurrence. Conclusion Longitudinal multi-omics analyses of recurrent MN1::PATZ1 fusion-positive CNS tumors revealed tumor maturation, immune dysfunction, and potential therapeutic targets. Introductory Paragraph PATZ1 fusion-positive central nervous system (CNS) tumors are rare, predominantly pediatric and frequently recurrent neoplasms provisionally classified as neuroepithelial tumors. Their pronounced histopathological and clinical heterogeneity, along with limited immunological characterization complicates their treatment standardization. We report a new case of an MN1::PATZ1 fusion-positive CNS tumor with recurrence, highlighting its radiographic similarities to low-to-intermediate grade pediatric glioma. Longitudinal multi-omics analyses of this case, along with additional MN1::PATZ1 fusion-positive CNS tumors, however, delineates a transcriptome subtype resembling adult high-grade glioma, with activated oncogenic and pro-inflammatory programs. The recurrent tumor exhibits features of decreased malignancy and enhanced glial differentiation, phenotypically shifting towards oligodendroglioma, suggesting tumor maturation. This was accompanied by increased antigen presentation programs, indicating immune engagement, while increased immune checkpoint expression and microglia/macrophage frequency indicate T cell exhaustion and immunomodulation, respectively. This longitudinal study highlights potential therapeutic strategies targeting both the tumor and its immune environment in MN1::PATZ1 fusion-positive CNS tumors.

  PublisherDOI

• CNSC-74. COMPARATIVE PATHOLOGY OF A RARE <i>MN1::PATZ1</i> -FUSION NEUROEPITHELIAL PRIMARY TUMOR AND RECURRENCE DEMONSTRATING MARKED HETEROGENEITY, POTENTIAL CHANGES IN TUMOR IMMUNE COMPOSITION, AND CELL-STATE TRANSITIONS

  Neuro-Oncology · 2025-11-01

  articleOpen access

  Abstract PATZ1-rearranged central nervous system (CNS) tumors are a recently identified subset of primitive neuroepithelial tumors (CNS-PNETs) characterized by significant heterogeneity in histopathologic features, age at presentation, and tumor grade. MN1::PATZ1 fusions are rare alterations with only fourteen cases captured in the literature thus far. Histologically, these tumors may present with characteristics of low-grade, high-grade, and mixed tumors. These tumors can vary significantly immunohistochemically. Clinically, these tumors can be associated with an indolent or even aggressive course. It is unknown whether complete surgical excision is curative for MN1::PATZ1 tumors, but incomplete resection, recurrence, malignant transformation, or metastases may necessitate adjuvant chemotherapy, posing risks. We will present comparative analyses of disease with indolent and aggressive course to better understand the progression of disease and clinical course. We conducted our analysis utilizing bulk transcriptomics, comparative transcriptomics, CIBERSORT, immunohistology, next generation sequencing, DNA methylation, and bioinformatics. We report the first molecular characterization of a paired primary and recurrent MN1::PATZ1 fusion, initially presenting on MRI imaging in a 6-year old female. Neuroimaging revealed a large cystic tumor with ring enhancement. Gross-total resection was completed revealing a neuroepithelial tumor harboring an MN1::PATZ1 fusion mutation via next generation sequencing. Resection was repeated on recurrence. The primary specimen revealed a triphasic tumor with an astrocytic morphology, and oligodendroglial-like morphology, but arranged in ependymoma-like perivascular pseudorosettes and sheets. Individual cell cytology appeared low-grade, but with high-grade architectural features such as necrosis and robust microvascular proliferation. The recurrence retained the appearance of the oligodendroglial-like component, showing monomorphic, round glial cells arranged in sheets with a delicate capillary network and perivascular pseudorosettes. However, the pseudorosettes appeared more astroblastoma-like, evidenced by thicker glial foot processes. Also, portrayed was less microvascular proliferation, no palisading necrosis, and no astrocytic component. Indolent disease course may correlate with loss of astrocytic component, and an increase in CD8+ cytotoxic T cells in these fusions. Considering there is no defined standard of care, targeted immunotherapy should be explored.

  PublisherOA PDFDOI

• STEM-08. Bioprocessing of viable surgical pediatric brain tumor specimens for genome-guided personalized drug testing in conjunction with the Human Cancer Model Initiative

  Neuro-Oncology Pediatrics · 2025-08-01

  articleOpen access

  Abstract Novel treatment approaches are urgently needed for pediatric central nervous system (CNS) tumors as they are the leading cause of cancer-related deaths in children. A lack of research materials impedes progress towards developing such therapies. Although various brain cancer biobanks exist, these rarely store viable patient-derived tissue and cells for live cell analyses, including cell fate assays and testing for drug sensitivities. A biorepository of viable cell dissociates and tissue representing CNS tumor entities could mitigate these limitations. From over 130 samples collected, we generated a biorepository of 39 distinct entities of pediatric CNS tumors in our Stanford neuro-bioprocessing cohort. Based on the Central Brain Tumor Registry of the United States, the proportion of subtypes represented in our cohort match that of the general population with exceptions. We established a standardized bioprocessing pipeline that can be used as a template for tissue collection and model development in the broader disease context and for multiple downstream applications. Pediatric brain tumor model development in vitro poses challenges related to genetic drift impairing fidelity to the parent tumor. We will present optimized growing conditions for several pediatric low grade glioma models alongside their validation by immunophenotyping and molecular analysis. Comparing RNA expression profile of an individual patient’s pilocytic astrocytoma with a compendium of 12,747 brain and non-brain tumor cases revealed outliers. These were orthogonally tested in patient-matched cancer models using pharmacological inhibitors, validating them as potential novel drug targets. These studies illustrate that biobanking of viable patient-­derived material enables developing personalized therapies with the goal of improving patient outcomes. Conclusively, patient-derived cancer models facilitate identifying and validating drug vulnerability, creating an opportunity for rapid translation of personalized treatment for patients with CNS tumors.

  PublisherDOI

• Comparative analysis of RNA expression identifies effective targeted drug in myoepithelial carcinoma

  Research Square · 2025-04-16

  preprintOpen access
  PublisherOA PDFDOI

• The children's brain tumor network (CBTN) - Accelerating research in pediatric central nervous system tumors through collaboration and open science

  UNC Libraries · 2025-07-26

  articleOpen access
  PublisherDOI

• Comparative analysis of RNA expression identifies effective targeted drug in myoepithelial carcinoma

  npj Precision Oncology · 2025-05-16 · 1 citations

  articleOpen access

  Myoepithelial carcinoma is an ultra-rare pediatric solid tumor with no targeted treatments. Clinical implementation of tumor RNA sequencing (RNA-Seq) for identifying therapeutic targets is underexplored in pediatric cancer. We previously published the Comparative Analysis of RNA Expression (CARE), a framework for incorporating RNA-Seq-derived gene expression into the clinic for difficult-to-treat pediatric cancers. Here, we discuss a 4-year-old male diagnosed with myoepithelial carcinoma who was treated at Stanford Medicine Children's Health. A metastatic lung nodule from the patient underwent standard-of-care tumor DNA profiling and CARE analysis, wherein the patient's tumor RNA-Seq profile was compared to over 11,000 uniformly analyzed tumor profiles from public data repositories. DNA profiling yielded no actionable mutations. CARE identified overexpression biomarkers and nominated a treatment that produced a durable clinical response. These findings underscore the utility of data sharing and concurrent analysis of large genomic datasets for clinical benefit, particularly for rare cancers with unknown biological drivers.

  PublisherOA PDFDOI

• Consistently processed RNA sequencing data from 50 sources enriched for pediatric data

  Scientific Data · 2025-07-02 · 2 citations

  articleOpen accessSenior author

  Larger cohorts improve the power of tumor gene expression analysis, but the signal is muddied if datasets are processed using different methods or have inaccurate metadata. Here we present five compendia containing consistently processed gene expression data derived from 16,446 diverse RNA sequencing datasets. To create the compendia, we obtained access to RNA sequence data from repositories containing public data as well as clinical partners with access to non-published data. We then assessed the quality, quantified gene expression, harmonized clinical metadata, and released the expression values and metadata without access restrictions. These datasets have been used for diverse projects ranging from identifying similarities between tumor types to assessing how well cell lines recapitulate tumors. They have also been used for n-of-1 analysis to identify genes with unusual expression patterns in a single sample and to infer molecular diagnosis. The comparison to new data is enabled by our dockerized, freely available pipeline. The compendia have been cited in at least 20 publications.

  PublisherOA PDFDOI

• Abstract A004-PR012: Investigating the potential of extracellular vesicle biomarkers for synovial sarcoma detection

  Cancer Research · 2025-09-25

  articleSenior author

  Abstract Synovial sarcoma (SS) is a rare and aggressive soft tissue cancer with high heterogeneity, low 5- and 10-year survival rates, and a high risk for recurrence and metastasis. SS tumors are characterized by the t(X;18)(p11.2;q11.2) chromosomal translocation that results in a unique SS18:SSX gene fusion. Current diagnostic approaches include histology, PCR, and fluorescent in situ hybridization (FISH), however these methods require surgically resected tumor samples. There are currently no viable options for non-invasive detection of SS, which contributes to delays in detecting advanced disease. Recent studies suggest that extracellular vesicles play important roles in various aspects of cancer biology and can be used as non-invasive biomarkers for diagnosis. We have performed bulk RNA sequencing (RNA-seq) of extracellular vesicular RNA (evRNA) and have confirmed that SS18:SSX fusion transcripts are packaged into extracellular vesicles (EVs) secreted by patient-derived SS cell lines. This project aims to develop a non-invasive liquid biopsy detection technique by applying emerging breakthrough technologies in nanopore-integrated optofluidic platforms. This system has been shown to provide a label-free and amplification-free single-molecule detection in the attomolar concentration range, which is commensurate with clinically-relevant biomarker concentrations (Sampad et al, 2024. PNAS). We anticipate that capturing the secreted SS18-SSX biomarker from SS-derived EVs via this system will provide a low complexity, highly sensitive, and clinically feasible method for SS diagnosis and disease monitoring, as well as provide a proof-of-concept method that we aim to expand in SS patient blood samples. Citation Format: Maryke Grobler, S M Saiduzzaman, Ruiting Xu, Yvonne Vasquez, Anouk van den Bout, Holly C. Beale, Ranxin Zhang, David Geller, Rui Yang, Bang Hoang, Holger Schmidt, Olena Vaske. Investigating the potential of extracellular vesicle biomarkers for synovial sarcoma detection [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Discovery and Innovation in Pediatric Cancer— From Biology to Breakthrough Therapies; 2025 Sep 25-28; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2025;85(18_Suppl_2):Abstract nr A004-PR012.

  PublisherDOI

• STEM-12. Coculturing pediatric glioma cells with dorsal forebrain organoids alters their gene expression to better match the parental tumor

  Neuro-Oncology Pediatrics · 2025-08-01

  articleOpen access

  Abstract There is an urgent need for new therapeutics for pediatric gliomas, but current in vitro and patient derived xenograft (PDX) models lose heterogeneity and fidelity to the patient’s original tumor as they are expanded to generate material for screening assays. Further, since pediatric gliomas are driven, at least in part, by transcriptional dysregulation as opposed to the high number of somatic mutations commonly driving adult cancers, prolonged culture in non-native growth environments is particularly problematic. 3-D stem cell derived tissue cultures such as organoids more accurately mimic in vivo tissue architecture providing a tumor microenvironment with the potential to preserve the transcriptomic state of pediatric glioma cells grown in vitro. To test this, we established conditions that enable low passage pediatric glioma cell lines to invade into cerebral organoids and measured how their gene expression changes via RNA sequencing. These results were compared to RNA sequencing done on the parental tumor. Preliminary results show substantial rescue of tumor transcriptomic state by coculturing the cell lines with organoids. This showcases how stem cell based organoids can be used to expand patient derived tissues in an environment more faithful to the primary tumor. Additionally, this system is more amenable to high throughput assays than PDX models. By establishing the relevance of this preclinical culturing platform it can one day be used to expand patient derived tissues in a more biologically accurate way and allow for more rapid, accurate cancer therapeutic screening.

  PublisherDOI

• Parental and Young Adult Perspectives on Investigative Genomic Tumor Profiling in High‐Risk, Recurrent, or Rare Pediatric Cancers: A Qualitative Study

  Pediatric Blood & Cancer · 2025-03-25 · 1 citations

  articleOpen access

  BACKGROUND: Although research has improved the prognosis of childhood cancer, many challenges remain, especially for high-risk, recurrent, and rare cancers. The recognition that diverse cancer types may share molecular alterations that can be therapeutically targeted has stimulated "precision medicine" approaches in research. Understanding parent and patient interest in genomic-derived therapeutic options in the clinical setting is limited and offers a potential for improved care. METHODS: A qualitative study was conducted to explore how young adult (YA) patients and parents of children and adolescent patients regard targeted therapy options. These patients had high-risk, recurrent, or rare cancer for which there was no known curative therapy and were enrolled in a study evaluating investigational genomic tumor profiling. Clinical data were retrieved from medical records, and interviews were conducted. RESULTS: Seventeen participants were interviewed (11 parents and six YA patients). Six themes emerged: (i) Genomic Understanding, (ii) Partnerships in Decision-Making, (iii) Connection with and Trust in Providers, (iv) Quality-of-Life (QOL) Considerations, (v) Understanding of Prognosis, and (vi) Nurturing Hope. Treatment decision-making is complex and depends on the connection (with providers and others), understanding (of prognosis, genomic literacy), care goals (QOL considerations), and planning for the future (hope). CONCLUSIONS: Participants favored partnership in decision-making, expressed trust in their providers, and recognized the value of research. Engaging parents and YA patients in the planning of precision medicine translational research may be a path to designing an integrated research and care model that maximizes translational research implemented in real time, leading to improved outcomes.

  PublisherOA PDFDOI

Frequent coauthors

• David Haussler

  University of California, Santa Cruz

  42 shared

• Katrina Learned

  University of California, Santa Cruz

  34 shared

• Holly C. Beale

  33 shared

• Sofie R. Salama

  University of California, Santa Cruz

  30 shared

• Ellen Kephart

  29 shared

• Lauren Sanders

  Ames Research Center

  28 shared

• Isabel Bjork

  23 shared

• Jacob Pfeil

  22 shared

Labs

• Olena Morozova Vaske LabPI

Education

• Doctor of Philosophy

  University of British Columbia

  2012

• Honours Bachelor of Science

  University of Toronto

  2006

Awards & honors

• Colligan Presidential Chair in Pediatric Genomics
• Postdoctorate Fellowship, UC Santa Cruz
• Clinical Molecular Genetics Fellowship, UC San Francisco