Over the past 25 years, our group has identified and validated diagnostic and prognostic biomarkers in cancers, several of which are now used in clinical practice. For example, through transcriptome profiling, we identified GATA3 upregulation in bladder cancer, which is now an immunohistochemical marker that is widely used in clinical pathology. In localized prostate cancer, we identified AZGP1, TPX2, NUSAP1, and several others that have been incorporated into transcriptome panels now commercialized for use for treatment selection in localized prostate cancer. More recently, we have used unique Patient Derived Xenograft (PDX) models for kidney and prostate cancer to identify secreted proteins and glycoproteins in the blood.

Renal obstruction has multiple causes, such as congenital ureteropelvic junction obstruction or kidney stones, and is a very common cause of renal damage and kidney failure. We have used transcriptomics to identify candidate urine biomarkers (protein and RNA) that could be used to monitor patients with kidney obstruction of uncertain clinical significance and direct timing of surgery. We also seek to understand the pathways activated by obstruction and are exploring how those pathways relate to renal damage. We have found that one gene, Sprr2f, is not only expressed in high levels in the kidney quite rapidly after obstruction, but it has potential roles in kidney and urothelial development. To test its role in obstruction, we developed a mouse knockout model and found Sprr2f acts as a sponge for reactive oxygen species, protecting normal renal tubular cells from death by preventing ferroptosis. We are currently exploring additional pathways that affect ferroptosis in kidney cells as this appears to be a critical pathway in renal damage.

In close collaboration with Sharon Pitteri’s laboratory, we have identified protein glycosylation changes in human, PDX and cell models of prostate and kidney cancer. In addition to testing these as possible cancer biomarkers, we are exploring the implications of these changes. For example, prostate cancer is characterized by widespread increases in sialylation (a modification of protein and lipid bound glycans by the addition of terminal sialic acids). Sialylated glycoproteins have been shown to bind to specific “Siglec” receptors (Sialic-acid-binding immunoglobulin-like lectins) that are found on diverse immune cells and repress immune cell function. We are exploring whether the sialic acids glycans present on prostate and kidney cancers are Siglec ligands and thereby act as immune checkpoints. We also seek to identify specific sialylated glycoproteins in prostate and kidney cancer that are ligands for Siglec receptor family members. Working with Carolyn Bertozzi’s group, we are exploring mechanisms and candidate Siglec-based checkpoint inhibitors as novel immune checkpoint inhibitors.

We are currently exploring the mechanisms of action of several candidate biomarkers we have identified in urological diseases. In prostate cancer, we have found that NUSAP1 over-expression is associated with aggressive localized disease, metastasis, and death from prostate cancer. We have identified key regulatory pathways driving NUSAP1 over-expression, demonstrated that NUSAP1 drives metastasis in prostate cancer, and recently have shown that NUSAP1 interacts with ILF2 and DHX9 to regulate R-loop formation (DNA/RNA hybrid structures in the genome). NUSAP1 over-expression increases R-loop abundance and increases mutations in prostate cancer, thereby driving clinical progression. Additional biomarkers we are investigating include FTO in kidney cancer, and AZGP1 in prostate cancer. We are also developing and testing therapies that target these and other pathways using our patient derived xenograft mouse models.

BPH affects more than half of men over the age of 60, causing significant erosion of quality of life due to urinary symptoms, and costs the health care system billions of dollars. Why discrete regions of the prostate grow and expand late in life remains a mystery. Dr. Brooks leads the U54 Stanford O’Brien Urology Research Center that focuses understanding the molecular and cellular architecture of BPH. The team of investigators from the Departments of Urology and Pathology are using single cell profiling, laser capture microdissection and multiplex immunohistochemistry using MIBI-TOF to identify changes in the cell types and signaling pathways that underlie BPH growth and urinary symptoms. Our research focuses on the human disease using surgical specimens, since BPH appears to be unique to humans, and there are no animal or cell models of BPH. In addition, the Brooks laboratory is leveraging their expertise to develop a novel PDX model of human BPH by implanting fresh human prostate samples under the renal capsule of mice. This model will contribute to understanding how BPH grows and is maintained and will be important for testing new therapies for BPH as we deepen our understanding of the disease and identify new therapeutic targets.