Brain Tumor Research

The Brain Tumor Research Program (BTRP) at the University of Pittsburgh is one of the largest and most productive basic and translational brain tumor science programs in the country, encompassing research across the adult and pediatric brain tumor science spectrum and supported heavily in funding from the National Institutes of Health and other generous foundations. 

The BTRP is a world-class effort focused on delivering novel brain tumor therapies from the laboratory to the bedside. Areas of active investigation include immunotherapy, signal transduction pathways that contribute to the growth of tumor cells, metabolomics, oncolytic viruses, rare tumor exome sequencing, impact of hormonal treatments, and the development of preclinical models for the treatment of brain tumors.

At the core of our program is a commitment to high impact patient-centric therapies. This commitment begins in the operating room where—with patient consent—tumor samples are retrieved for laboratory investigation under controlled research tumor banking protocols. These specimens are critical to the understanding of tumor genetics and to the development of translational targets for brain tumor therapy. This initiative has led to the banking and study of thousands of unique tumor samples, facilitating impactful, patient-centered research.

Basic Science Advances

Brain tumors are inherently immunosuppressive. Previous work in our brain tumor program identified new vaccine strategies for the treatment of gliomas. Researchers in our group developed glioma-associated antigen peptide vaccines to boost tumor-specific immune responses. Phase I clinical trials of these vaccines demonstrate robust induction of antigen-specific immune responses and some clinical activity in both adult and pediatric patients with glioma. These trials are ongoing at the University of Pittsburgh Cancer Institute and UPMC Children’s Hospital of Pittsburgh. Recent studies have identified patterns of gene expression in peripheral blood mononuclear cells that are associated with response and resistance to peptide-based vaccination in pediatric low-grade gliomas. Future studies will evaluate whether these features are also seen in other subgroups of childhood brain tumors incorporated on our vaccine trials.

Another strategy in brain tumor research is to inhibit the pathways that promote tumor growth or to stimulate those that promote tumor cell killing. The poor response of malignant gliomas to conventional therapies, such as cytotoxic chemotherapy or radiotherapy, reflects resistance of these tumors to undergoing apoptosis in response to DNA damage or mitogen depletion. Through a large-scale screening study, we have identified several exploitable targets, which when inhibited induce tumor cytotoxicity. We have been examining pharmacological agents to inhibit these targets, alone and in combination with agents that induce apoptotic signaling in these tumors.

Each tumor develops unique mechanisms to escape natural anti-tumor immune responses. We have recently discovered a unique immune escape mechanism that involves silencing of immune recognition genes. Importantly, we have discovered that a new class of tumor drugs, called ‘hypomethylating agents’, can awaken the expression of these genes and allow effective immune responses in IDH mutant gliomas. A Phase I clinical trial is currently being designed based on these findings and is currently being refined by the Alliance for Clinical Trials in Oncology consortium in preparation for a multicenter clinical trial. Recently, the BTRP has made several critical advances regarding depletion of tumor-associated myeloid cells, including development of an immunoPET strategy using a radiolabeled antibody to quantify myeloid cells in CNS cancer (Front Immunol 12:637146, 2021). We recently showed using a new chelator with two separate radionuclide-labeled antibodies that myeloid cells could be imaged and targeted to improve immunotherapy for gliomas. This work is complemented by ongoing studies to develop and evaluate immunoPET strategies to quantify T-cell activation and cytotoxicity to allow for early detection of immunotherapy responsiveness in CNS tumors. Our ongoing work includes using a single-cell RNAseq and single-cell TCR sequencing to develop both personalized and off-the-shelf T-cell receptor engineered T-cells (TCR-T) as adoptive cell therapy strategies for brain tumor patients. 

Our program has additionally made some recent seminal discoveries that may provide translational relevance in both pediatric and adult high-grade gliomas (HGG). In some cases, such as diffuse midline gliomas (DMGs), maximum surgical resection may not be possible (Nat Cancer 2(6):584-586, 2021). Therefore, there is an urgent need to identify non-invasive ways to diagnose and treat these tumors. In a landmark multi-institutional collaboration headed by the University of Pittsburgh Department of Neurological Surgery, clinicians and researchers discovered that DMG tumors are uniquely dependent on methionine, an amino acid that humans must receive from food. Low-methionine dietary intervention, or use of clinical grade therapies targeting a key enzyme involved in converting methionine into other components indispensable for brain tumor cells, increased survival by 50% in pre-clinical models of DMG. Current research is focussed on preclinical testing of methionine metabolism inhibitors and the development of a Phase 1 clinical trial.

In an inter-departmental collaboration with the UPMC Hillman Cancer Center, researchers in the BTRP have identified that platelet-derived growth factor (PDGF) signaling induces N6-methyladenosine (m6A) accumulation, the most abundant RNA modification in human cells. Emerging evidence suggests that this modification, a critical driver of the activation of several GBM pathways and regulators of this pathway, are associated with poor clinical outcomes. We identified that Methyltransferase-Like 3 (METTL3) promotes GBM growth and pharmacologic targeting of METTL3 augmented the anti-tumor efficacy of PDGF receptor (PDGFR)-based therapy, a druggable target of interest in GBM. This work, and others, has opened an exciting and emerging field of epitranscriptomics presenting a new class of druggable targets and combinations previously not appreciated in GBM. 

We have also initiated studies that define the mechanisms underlying resistance in childhood and adult malignant gliomas. We have developed a repertoire of “drug-resistance” tumor model systems, paired with treatment naïve counterparts (Mol Cancer Res 18:1004-1017, 2020). We have leveraged this unique resource to identify the NAD metabolic pathway as a key intermediate through which multiple cell lines achieve treatment resistance. Using RNA sequencing studies and pathway analysis we have identified several common molecular drivers of this process, such as QPRT and NMNAT2. Gene set enrichment analysis demonstrated that these mediators hijack glycolytic signaling. Metabolomic analysis of downstream signaling pathway components have shown an involvement of both glycolytic intermediates and mitochondrial energy metabolites that are amenable to therapeutic intervention. These observations have provided a basis for pharmacological and RNA interference-based strategies for reversing resistance as well as metabolic manipulations that may provide novel approaches for promoting tumor cell killing. We have demonstrated dramatic enhancement in survival with treatment in one orthotopic xenograft model and are planning studies using other models and dietary modulation, which may open up several novel strategies for clinical therapies.

Another exciting area of research in our program involves the development of genetically engineered oncolytic herpes-simplex viruses (oHSV) that can selectively kill proliferating glioma cells but not normal brain cells. Promising preclinical studies in mouse models indicate that this strategy is highly effective for the treatment of glioblastoma. Several patents have been generated and licensed based on this work, and studies are ongoing to evaluate safety testing in preclinical models in anticipation of oHSV clinical trials soon. This is in addition to a strong emphasis on developing personalized brain tumor therapy by studying humanoid brain organoid tumor models, a biologically more accurate model that simulates a patient’s condition. These organoids are subsequently used to evaluate the biological and genetic evolution of individual brain tumors and, subsequently, to generate and test personalized therapies based on these findings. The desire to develop truly personalized medicine strategies is at the heart of these efforts.

The Laboratory of Brain Tumor Evolution & Therapy has recently shown that cancer cell-intrinsic signaling reprograms tumor-associated macrophages (TAMs) to mediate tumor suppression by novel protein binding complexes CHI3L1-Gal3-Gal3BP (J Clin Invest 131(16):e147552, 2021). These studies are focused on understanding how these protein complexes regulate TAM recruitment, polarization, cytokine production, tumor-infiltrating lymphocyte inactivation, and how to target these protein complexes by developing new drugs in brain tumor immunotherapy.

The ability to develop preclinical models for glioma extends to specimens created directly from tumor resections, known as surgically explanted organoids (SXOs). These efforts have led to recent work demonstrating the first known ex vivo models of low-grade gliomas and an ability to rapidly assess tissue treatment change using advanced microscopy. Translational efforts to identify druggable targets in high grade glioma and further leverage these models has also led to the preclinical development of promising therapeutics and a modified nucleoside (6-thio-dG) that exhibits antitumor activity in gliomas (Clin Cancer Res 27(24):6800-6814, 2021). These developments have led to the University of Pittsburgh Department of Neurological playing a key role in the National Cancer Institute’s Glioma Therapeutic Network, joining other leading medical centers in a collaborative effort to bring therapeutics to trial for high grade gliomas. 

Other recent work in the BTRP includes the establishment of the Brain Tumor Metabolism and Functional Cancer Genomics Laboratory which explores the molecular network and metabolic dependencies which are essential for pediatric supratentorial ependymomas survival and proliferation. The Antony Michaelraj, PhD, lab explores single and combined therapeutic approaches to target this tumor by blocking the metabolic activity by selective and blood-brain barrier penetrant small molecules and nutrient limited diet. For the first time, they established a transgenic mouse model for supratentorial ependymoma which will be used as primary tool for investigating disease mechanism and novel therapeutic discoveries/validations. 

Translational Advances 

The clinical research branch of our Brain Tumor Program currently runs “personalized” clinical studies based on patients’ gene markers, such as human leukocyte antigen (HLA)-A2 (for immunotherapy studies), epidermal growth factor receptor (EGFR) variant III and chromosome 1p/19q co-deletion. In addition, the program offers a host of molecularly targeted treatment approaches for children whose brain tumors have genomic alterations that make them ideally suited for specific novel-agent trials. These include studies of MEK inhibitors (e.g. Selumetinib) for children with BRAF-altered low-grade gliomas, which are being conducted by the PBTC and more recently, the Children’s Oncology Group.

Similarly, members of our group are studying rare skull base tumors such as chordoma by performing whole exome sequencing to search for novel genetic alterations in these tumors that could lead to a better understanding of their oncogenesis as well as targets for treatment. These targets are then evaluated to see if current therapies can be applied to these rare tumors. The impact of methylation in skull base tumors is also being studied to understand if these genetic changes, which occur throughout life, play a role in tumor prognosis. In addition, our surgeons and pathologists have identified a molecular panel that can help predict chordoma clinical behavior and prognosis. This panel is now applied on a regular basis to our patients to provide a personalized approach for current and future treatment.

In addition to these efforts, this year the Georgios Zenonos Lab established the most comprehensive full scale integrated molecular assessment of skull base chordomas in its field, leveraging the unique and world-leading clinical volume at UPMC to investigate best management options in this uncommon but important skull base tumor, and the Zinn Lab utilized molecular datasets to link a history of allergy to survival benefits in diffuse low grade glioma. 

Clinical Care Advances

As one of the highest volume tumor centers in the country, care of our neurooncology patients is facilitated by an emphasis on cutting-edge technology and clinical advances. Currently, clinical care of patients with skull base tumors, primary brain tumors and metastatic brain tumors related to systemic cancer represent a major focus for our department’s activities. During the last 41 years, the Center for Image-Guided Neurosurgery has provided care to more than 20,000 patients with such tumors using minimally invasive options to biopsy, resect, or provide adjuvant therapies. One of the most important adjuvant strategies to control brain tumor progression is optimization of radiation delivery techniques. Using technologies such as Gamma Knife® radiosurgery at UPMC Presbyterian (over 17,750 patients have been treated and over 1,400 articles, books, or chapters have been published) and linear accelerator radiation technologies at UPMC Shadyside, methods to enhance the efficacy and safety of radiation delivery have been pioneered.

Our BTRP has made recent significant clinical advances that have contributed to the scientific and clinical community. Jan Drappatz, MD, and colleagues described the UPMC experience with immune checkpoint inhibitors in meningioma (Journal of Neurooncology). Kalil Abdullah, MD, and colleagues described outcomes of bevacizumab vs. laser interstitial thermal therapy in cerebral radiation necrosis (Journal of Neurooncology) and Pascal Zinn, MD, PhD, and team described a first in-human working system to use enabled loupes to fluorescently guide glioma resection (Operative Neurosurgery and Journal of Neurosurgical Science). The BTRP continues to conduct numerous clinical trials as part of national collaborative efforts, led by neurooncologists Frank Lieberman, MD; Megan Mantica, MD; Jan Drappatz, MD; and Jeremy Rich, MD. Our pediatric program is also one of the founding sites of the Pediatric Brain Tumor Consortium (principal investigator, Ian Pollack, MD), an NCI-funded consortium that is designed to bring cutting edge clinical therapeutics to childhood brain tumors, and a founding member of the Children’s Brain Tumor Network (principal investigator, Ian Pollack, MD), which seeks to translate advances in molecular diagnostics to clinical therapeutics.

Working in concert with these advanced radiosurgery and radiation technologies, the UPMC Center for Cranial Base Surgery is the oldest skull base center in North America. They have been a source of innovation for decades, helping develop new and less invasive approaches, such as the endoscopic endonasal and transorbital approaches, to limit the impact of surgery for these challenging tumors. This year, Paul Gardner, MD, and colleagues described key postoperative care protocols in the management of patients with skull base tumors and a multimodality treatment paradigm for patients with esthesioneuroblastoma (Otolaryngology Clinics of North America and Surgical Neurology International).

Since 1975 the department has been noted as a source of innovation in brain tumor diagnosis and management. In 1981 the first dedicated CT scanner was installed in a unique operating room at UPMC Presbyterian to facilitate minimally invasive surgical techniques. Updated in 2009, this facility also serves as a site to explore less invasive strategies for tumor removals such as the endoscopic endonasal approaches, endoport resection using guiding technologies coupled with endoscopic removal, and transorbital approaches. Working hand in hand with our skull base program innovative combined strategies for tumor biopsy or removal followed by adjuvant radiosurgery, chemotherapy, or immunotherapy has offered new advances in patient care resulting in ever longer high-quality outcomes. Our pediatric program has also been enhanced by the opening of an intraoperative MRI suite, which facilitates the goal of achieving safer and more extensive resections in challenging childhood brain tumors. This year, the UPMC Hillman Cancer Center obtained the AIRO/BrainLab system, allowing for intraoperative CT scanning to allow navigated instrumentation during oncologic spinal reconstruction, and high-fidelity intraoperative frameless registration for patients with brain tumors. This substantial investment is a foundational commitment to advancing state-of-the-art brain neurosurgical oncology care.

Innovative imaging techniques are being developed and applied to better understand brain tumors and their structural relationship with surrounding white matter tracts. High-Definition Fiber Tractography (HDFT) provides a superior presurgical evaluation of the fiber tracts for patients with complex brain lesions, allowing us to reconstruct fiber tracts and design a less invasive trajectory into the target lesion. We are currently investigating its potential for not only presurgical planning and intraoperative navigation but also for neurostructural damage assessment, estimation of postsurgical neural pathway damage and recovery, and tracking of postsurgical changes, neuroplasticity, and responses to rehabilitation therapy. The ability to obtain fiber-tracking preoperatively has now been expanded to the UPMC Hillman Cancer Center at UPMC Shadyside, allowing a multimodal approach to tumor resection. The ultimate goal is to facilitate brain function preservation and recovery in patients undergoing complex brain tumor surgery. For brain tumor patients presurgical brain mapping is performed using magnetoencephalography (MEG). MEG is a cutting-edge technology and the most advanced method of functional brain imaging. MEG recordings provide a direct measurement of brain functions. MEG allows brain surgeons to view critical functional areas of brain to determine the best way for removing brain tumors, while preserving brain function and improving recovery.