Abstract 5354: Novel genomic alterations in renal medullary carcinoma tumors
Authors: Fox Jesse , Young Denise , Song Yingjie , Hu Heng Cheng , Soltis Anthony , Wilkerson Matthew D. , Dalgard Clifton L. , Rosner Inger L. , Sesterhenn Isabell A. , Srivastava Shiv , Tan Shyh-Han 
Published: August 2018

Abstract
Introduction: Renal medullary carcinoma (RMC) is an rare but aggressive non-clear cell carcinoma that occurs predominantly in young African American (AA) men who carry the sickle cell trait. Our knowledge of the molecular basis for the initiation and progression of this cancer remains inadequate to establish standard of care treatments. As a result, even with surgery and chemotherapy, outcomes have remained dismal, with a median overall survival of approximately 13 months. Most patients with RMC exhibit deletion of the SMARCB1 gene, which encodes for a subunit of the SWI/SNF chromatin remodeling complex. Subtypes of RMC without SMARCB1 loss but harbor a rare gene fusion between Vinculin and Anaplastic Lymphoma Kinase have also been reported. We hypothesize that whole exome sequencing (WES) of RMC tumors will identify novel genomic alterations responsible for RMC tumor initiation and progression, which may provide actionable targets for treatment.
Methods: Formalin fixed paraffin embedded (FFPE) RMC tumor and adjacent tissue specimens of 21 African American patients were obtained from the Joint Pathology Center. DNA were isolated from tumor and normal tissues with the Qiagen FFPE All Prep kit and measured by using the Qubit fluorometer. Integrity of the DNA samples were evaluated by using the Advanced Analytics Fragment Analyzer. WES DNA libraries were prepared from DNA samples that passed quality control using the Illumina TruSeq WES kit. Paired end sequencing (2x75) was performed on the Illumina HiSeq3000 platform. RMC tissues sections were analyzed for the expression of SMARCB1, VHL, HIF2A, AURKA, and EZH2 proteins by immunohistochemistry (IHC).
Results: Somatic copy number alterations were estimated from the WES of seven RMC cases. These include recurrent large scale DNA alterations involving chromosome 7 and 8 amplification and chromosome 15 deletion. Focal DNA copy number alterations were also identified in the cohort, including deletion of SMARCB1. Analysis of somatic sequence mutations detected a canonical hotspot mutation (R132C) in IDH1 and recurrent non-silent mutations on RBM47 and NF2. Evaluation by IHC showed the loss of SMARCB1 expression in all cases assayed. Upregulation of EZH2 and AURKA, which are negatively regulated by SMARCB1, were detected in 3 of 21 and 11 of 21 cases, respectively. Focal HIF2A staining was detected in 7 of 21 tumor cases.
Conclusions: The recurrent somatic sequence mutations, gene amplifications and deletions identified in this study reveal potential novel oncogenic drivers of RMC. Further validation of these genomic alterations may offer additional insight into the initiation and progression of RMC and provide actionable targets for establishing standard of care treatments.
Source of Funding: The work is supported a grant award (HU0001-14-2-0041) to ST from the Collaborative Health Initiative Research Program (CHIRP), a precision medicine-based collaborative effort between the NIH and the DOD.
Citation Format: Jesse Fox, Denise Young, Yingjie Song, Heng Cheng Hu, Anthony Soltis, Matthew D. Wilkerson, Clifton L. Dalgard, Inger L. Rosner, Isabell A. Sesterhenn, Shiv Srivastava, Shyh-Han Tan. Novel genomic alterations in renal medullary carcinoma tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5354.