title: An integrated genomic analysis of papillary renal cell carcinoma type 1 uncovers the role of focal adhesion and extracellular matrix pathways.
abstract: Papillary renal cell carcinoma (pRCC) is the second most common RCC subtype and can be further classified as type 1 (pRCC1) or 2 (pRCC2). There is currently minimal understanding of pRCC1 pathogenesis, and treatment decisions are mostly empirical. The aim of this study was to identify biological pathways that are involved in pRCC1 pathogenesis using an integrated genomic approach. By microarray analysis, we identified a number of significantly dysregulated genes and microRNAs (miRNAs) that were unique to pRCC1. Integrated bioinformatics analyses showed enrichment of the focal adhesion and extracellular matrix (ECM) pathways. We experimentally validated that many members of these pathways are dysregulated in pRCC1. We identified and experimentally validated the downregulation of miR-199a-3p in pRCC1. Using cell line models, we showed that miR-199a-3p plays an important role in pRCC1 pathogenesis. Gain of function experiments showed that miR-199a-3p overexpression significantly decreased cell proliferation (p = 0.013). We also provide evidence that miR-199a-3p regulates the expression of genes linked to the focal adhesion and ECM pathways, such as caveolin 2 (CAV2), integrin beta 8 (ITGB8), MET proto-oncogene and mammalian target of rapamycin (MTOR). Using a luciferase reporter assay, we further provide evidence that miR-199a-3p overexpression decreases the expression of MET and MTOR. Using an integrated gene/miRNA approach, we provide evidence linking miRNAs to the focal adhesion and ECM pathways in pRCC1 pathogenesis. This novel information can contribute to the development of effective targeted therapies for pRCC1, for which there is none currently available in the clinic.
authors.affiliation: The Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, Ontario M5B 1W8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada. Electronic address: Samantha.wala@gmail.com.
authors.forename: Samantha Jane
authors.initials: SJ
authors.lastname: Wala
authors.affiliation: Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada. Electronic address: jkaramch@gmail.com.
authors.forename: Jason Raj
authors.initials: JR
authors.lastname: Karamchandani
authors.affiliation: Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada. Electronic address: rola.saleeb@mail.utoronto.ca.
authors.forename: Rola
authors.initials: R
authors.lastname: Saleeb
authors.affiliation: Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada; Department of Pathology, Toronto General Hospital, Toronto, Ontario, Canada. Electronic address: andrew.evans@uhn.on.ca.
authors.forename: Andrew
authors.initials: A
authors.lastname: Evans
authors.affiliation: The Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, Ontario M5B 1W8, Canada. Electronic address: DingQ@smh.ca.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Ding
authors.affiliation: The Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, Ontario M5B 1W8, Canada. Electronic address: IbrahimR@smh.ca.
authors.forename: Rania
authors.initials: R
authors.lastname: Ibrahim
authors.affiliation: Department of Surgery, Princess Margaret Hospital, 610 University Avenue, Toronto, Ontario M5G 2M9, Canada. Electronic address: m.jewett@utoronto.ca.
authors.forename: Michael
authors.initials: M
authors.lastname: Jewett
authors.affiliation: Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada; Department of Laboratory Medicine, St. Joseph's Health Centre, 30 Queensway, Ontario M6R 1B5, Canada. Electronic address: pasicm@stjoe.on.ca.
authors.forename: Maria
authors.initials: M
authors.lastname: Pasic
authors.affiliation: Department of Surgery, Princess Margaret Hospital, 610 University Avenue, Toronto, Ontario M5G 2M9, Canada. Electronic address: antonio.finelli@uhn.ca.
authors.forename: Antonio
authors.initials: A
authors.lastname: Finelli
authors.affiliation: Department of Surgery, St. Michael's Hospital, 30 Bond Street, Toronto, Ontario M5B 1W8, Canada. Electronic address: pacek@smh.ca.
authors.forename: Kenneth
authors.initials: K
authors.lastname: Pace
authors.affiliation: Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, 15771 Athens, Greece. Electronic address: lianidou@chem.uoa.gr.
authors.forename: Evi
authors.initials: E
authors.lastname: Lianidou
authors.affiliation: The Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, Ontario M5B 1W8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada. Electronic address: yousefg@smh.ca.
authors.forename: George Makram
authors.initials: GM
authors.lastname: Yousef
mesh_terms: D002292:Carcinoma, Renal Cell / Q000145:classification / Q000235:genetics* / Q000473:pathology; D049109:Cell Proliferation / Q000235:genetics; D005109:Extracellular Matrix / Q000502:physiology*; D022001:Focal Adhesions / Q000502:physiology*; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D023281:Genomics / Q000379:methods*; D006801:Humans; D007668:Kidney / Q000378:metabolism / Q000473:pathology; D007680:Kidney Neoplasms / Q000145:classification / Q000235:genetics* / Q000473:pathology; D035683:MicroRNAs / Q000235:genetics; D000090063:Proto-Oncogene Mas; D015398:Signal Transduction / Q000502:physiology; D018511:Systems Integration; D014407:Tumor Cells, Cultured
chemical_list: C000715470:MAS1 protein, human; D035683:MicroRNAs; D000090063:Proto-Oncogene Mas
keywords: Extracellular matrix; Focal adhesion; Genetics; MET; Papillary renal cell carcinoma; miR-199a-3p