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Aghi Lab Newsletter
Volume 4 - January 2020
“Cancer is a noun but in the body it acts like a verb...”
Manish Aghi, MD PhD, directs a research lab and operates on brain tumor patients at UCSF. His surgical practice and lab emphasize (1) glioblastoma (GBM), an aggressive brain tumor resistant to current treatments; (2) metastases of cancers that spread to the brain from other organs; (3) pituitary adenomas, benign tumors that dramatically impact a patient’s quality of life upon reaching critical size; and (4) medulloblastoma, a devastating pediatric brain tumor. The primary focus of the lab is the microenvironment of these tumors, recognizing that many cancer treatments fail because they do not recognize cancer for what it is, a dynamic organ with complex interplay between tumor cells and their microenvironment. Integrating Dr. Aghi's lab and clinical practice maximizes the impact of both by studying human tissues in the lab and implementing concepts from the lab into clinical trials to help patients. The 8 to 12-person research team consists of postdoctoral fellows, students, and volunteers, whose research is highlighted below.
Current Research
Using CRISPR libraries and 3D bioengineered models of glioblastoma to define novel druggable mediators of invasion
The poor prognosis of glioblastoma is largely due to glioblastoma cell invasion, which enables escape from surgical resection and drives inevitable recurrence, typically 2 cm from the location at diagnosis.  This invasion ultimately proves fatal as tumor cells invade the brain’s essential real estate and sever its intricate synapses, with reoperation exerting equally devastating effects on quality of life. In a sense, GBM is a grenade that has exploded, piercing the brain with its shrapnel of tumor cells. Through a five year NIH R01 grant awarded to the Aghi lab, we are collaborating with the Kumar lab in the UC Berkeley bioengineering department to use 3D engineered culture models of invasion and CRISPR libraries targeting the druggable human genome to identify novel druggable mediators of invasion in GBM.
Shown is a 3D bioengineered model of parenchymal invasion in which tumor cells are loaded into a cell reservoir and are then watched under a microscope for their migration out of the reservoir and into a hydrogel that models the brain parenchyma. By isolating the most invasive cells, we can determine factors mediating invasion, findings that can be validated using the CRISPR library targeting the druggable human genome.
Role of c-Met/β1 integrin complex in the metastatic cascade
Metastasis causes 90% of human cancer deaths with a median survival of less than six months following diagnosis. The five steps of metastasis include local invasion, intravasation, extravasation, colonization at a distal site, and proliferation. Previous research done by graduate student Arman Jahangiri in the Aghi lab demonstrated an increased formation of a structural complex between receptor tyrosine kinase c-Met and β1 integrin in metastases compared to primary tumors. Previous Aghi lab manager Harsh Wadhwa then showed that this complex formation promotes breast cancer cell adhesion to the vessel wall and intravasation into circulation, as well as stem cell formation and activation of the hedgehog/wnt pathways. Current Aghi lab manager Sweta Sudhir is working to elucidate the downstream cascade by using CRISPR to knockout proteins in the hedgehog/wnt pathway to find targetable drivers of brain metastases.

Brain metastases in patients reveal increased c-Met/β1 complex formation (left). A 770 gene multiplex panel demonstrate that this complex formation upregulates expression of mesenchymal genes and the Wnt/hedgehog pathways (right).
Bevacizumab-resistance in glioblastoma: regulators and targetable mediators
Work in the Aghi lab performed by previous HHMI fellow Ankush Chandra identified the transcription factor Zeb1 as a mediator of mesenchymal change seen in bevacizumab-resistant GBM. This study was recently accepted for publication in Cancer Research. Matheus Pereira, a UCSF medical student, is currently evaluating upstream regulators of Zeb1-induced mesenchymal change in bevacizumab-resistant GBM. Matheus is also concurrently developing a new bevacizumab-resistant model utilizing patient-derived GBM cell lines to better study and characterize acquired resistance to anti-angiogenic therapy.
Anti-angiogenic therapy is initially associated with a "response window" during which the tumor vessels normalize. Eventually, prolonged anti-angiogenic therapy starts to prune out normal vessels. This causes severe tumor hypoxia, which upregulates Zeb1, a transcription factor that drives stem cell enrichment, metabolic reprogramming, and perivascular invasion. Through these mechanisms, Zeb1 promotes GBM resistance to anti-angiogenic therapy.
Using immunomodulatory gene circuits to reverse the immunodepleted glioblastoma microenvironment
The GBM microenvironment is incredibly immunosuppressed, contributing to the lack of efficacy seen in clinical trials investigating single-agent immunotherapies. Our lab has developed immunomodulatory gene constructs that fit together in a gene circuit with the potential to overcome the immunodepleted GBM environment. Alex Haddad, a current UCSF medical student in the Aghi Lab, is continuing this work which was started by Jordan Spatz, PhD, a  previous postdoctoral fellow. Current work involves investigating viruses and neural stem cells to directly deliver the constructs to GBM tumors in vivo in a targeted manner.
Viruses and neural stem cells deliver immunomodulators directly to the tumor micoenvironment, targeting T cells against glioblastoma cancer cells. 
Defining pro-tumoral effects of tumor-associated neutrophils in glioblastoma
GBM recurrence following radiotherapy and surgical resection remains a major clinical challenge, and various studies have implicated de-differentiated cancer cells as driving tumor re-population. Prior Aghi lab work from postdoctoral fellow Garima Yagnik and HHMI fellow Sumedh Shah has identified tumor-associated neutrophils (TANs), which comprise approximately 2% of the GBM microevironment, as contributors to glial de-differentiation via osteopontin secretion. Currently, Angad Beniwal, a recent UCLA graduate, is working to gather transcriptomic data from patient GBM and blood samples to further characterize mediators of this pro-tumoral interaction.
Tumor-associated neutrophils (green) are noted to localize near blood vessels (red) in the perivascular space that also houses GBM stem cells.
Identifying cancer-associated fibroblasts in glioblastoma and characterizing their effects on tumor stem cells
Our lab has identified, through a multi-modality approach, the presence of cancer-associated fibroblasts (CAFs) in the GBM tumor microenvironment, which is surprising as fibroblasts have not previously been seen in the brain. Rushikesh Joshi, a UCSD medical student, is following up on research conducted by prior Aghi Lab HHMI fellow Jonathan Rick, to define the pro-tumoral effect exerted by these unique cells. Our research has shown that CAFs are recruited to the tumor microenvironment via platelet-derived growth factor (PDGF), and enrich the GBM stem cell population. We have also shown that CAFs promote polarization of macrophages into the pro-tumoral M2 state. Defining the pathways that mediate these effects may help identify novel therapeutic targets for treatment of GBM.
The cellular makeup of the stem cell niche of glioblastoma. Cancer cells secrete chemoattractants like PDGF, which draw perivascular progenitor cells towards the tumor and transforms them into CAFs.
Single cell sequencing reveals driver genetic changes in the formation of pituitary adenomas
Pituitary adenomas are among the most common primary brain tumors and comprise 15% of all brain neoplasms. Postdoctoral fellow, Saket Jain, in the Aghi lab is using single-cell RNA sequencing to investigate cellular heterogeneity in pituitary adenomas. Copy number variation analysis highlighted loss of chromosomes 2 or 15 appearing across all clones (“early” changes) and other changes such as loss of chromosome 19 appearing in some clones (“late” changes). Saket also identified 3-4 clusters of tumor cells per case: (1) a secretory hormone/neuropeptide secretion cluster; (2) a proliferative cluster; (3) a metabolic cluster; and (4) a pro-angiogenic cluster. Non-tumor cell clusters identified included (1) antigen presenting and processing cells; (2) fibroblast cells; and (3) neuronal cells. Ongoing work by Saket will help us define the molecular fingerprint of pituitary adenomas and provide insights that could be utilized in the clinic for better management of these tumors.
Single cell sequencing of a pituitary adenoma reveals three clusters of tumor cells (secretory, proliferative, and angiogenic), along with several cells in the tumor microenvironment.
Using Fc fusion proteins to target glioblastoma cells' ability to escape the complement cascade

One way GBM cells escape immune surveillance is through inhibition of the complement cascade targeting tumor cells. After UCSF neurosurgery resident Michael Safaee developed intriguing data revealing the previously underappreciated importance of complement inhibitor CD97 in driving GBM invasion, the Aghi lab established a collaboration with Planet Biotechnology, a company that developed DAF-Fc, a small molecule targeting CD97 in GBM. Through an NIH Small Business Innovation Research (SBIR) grant awarded to the Aghi lab and Planet Biotechnology and an F32 postdoctoral fellowship awarded to Dr. Safaee, preclinical evaluation of this treatment was performed.  These studies revealed that Factor H, another molecule that inhibits the complement cascade, could be a potentially more potent target in GBM than CD97.  Thus, research associate Sabraj Gill has continued our Planet Biotechnology Inc collaboration with evaluation of a new Factor H-Fc fusion molecule that shows high affinity for GBM.

Demystifying the Immune Desert of Medulloblastoma
Standard-of-care treatment for medulloblastoma, the most common malignant pediatric brain tumor, can improve patient survival but comes at a cost to neurocognitive function and quality of life. Attempts to treat medulloblastoma via less toxic immunotherapies have been limited by the paucity of immune cells in this tumor, which is unique amongst malignant brain tumors. A new project led by UCSF neurosurgery resident Taemin Oh seeks to discover the mechanisms underlying the paucity of immune cells in medulloblastoma. The goal is to develop targeted translational applications via cytokine modulation that could improve the prognosis of these patients without associated toxicities.
Clinical Studies 2019
Aside from the basic science work described above, physician-scientist members of our team published several clinical studies in 2019. For example,  HHMI fellow Ankush Chandra published a study in  the June 2019 issue of Journal of Neurosurgery in which he found that patients with glioblastoma and medicaid have higher surgical costs, longer lengths of stay, poorer survival, and lower Quality-Adjusted Life Year (QALY) scores due to lack of access to primary care leading them to present later in their disease course, underscoring the importance of access to care for neuro-oncology outcomes.
For More Information
For more information about research in the Aghi Lab or how to support our efforts, visit our website at To schedule a tour, please contact Anders Yang in the UCSF Development Office at 415-502-8309. If you do not wish to receive further fundraising communications from UCSF, please contact: Record Manager, UCSF Box 0248, San Francisco, CA 94143-0248 or email or call 1-888-804-4722.
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