Stephanie L Skala1, Xiaoming Wang2, Yuping Zhang2, Rahul Mannan2, Lisha Wang2, Sathiya P Narayanan2, Pankaj Vats2, Fengyun Su2, Jin Chen2, Xuhong Cao2, Javed Siddiqui2, Pedram Argani3, Marcin P Cieślik2, Thomas J Giordano1, Arul M Chinnaiyan4, Saravana M Dhanasekaran2, Rohit Mehra5. 1. Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA. 2. Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, Ann Arbor, MI, USA. 3. Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA. 4. Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, Ann Arbor, MI, USA; Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA; Howard Hughes Medical Institute, Ann Arbor, MI, USA. 5. Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, Ann Arbor, MI, USA; Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA. Electronic address: mrohit@med.umich.edu.
Abstract
BACKGROUND: Renal cell carcinomas (RCCs) are a heterogeneous group of neoplasms. Recent sequencing studies revealed various molecular features associated with histologic RCC subtypes, including chromophobe renal cell carcinoma (ChRCC). OBJECTIVE: To characterize the gene expression and biomarker signatures associated with ChRCC. DESIGN, SETTING, AND PARTICIPANTS: We performed integrative analysis on RNA sequencing data available from 1049 RCC specimens from The Cancer Genome Atlas and in-house studies. Our workflow identified genes relatively enriched in ChRCC, including Forkhead box I1 (FOXI1), Rh family C glycoprotein (RHCG), and LINC01187. We assessed the expression pattern of FOXI1 and RHCG protein by immunohistochemistry (IHC) and LINC01187 mRNA by RNA in situ hybridization (RNA-ISH) in whole tissue sections representing a cohort of 197 RCC cases, including both primary and metastatic tumors. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: The FOXI1 and RHCG IHC staining, as well as the LINC01187 RNA-ISH staining, was evaluated in each case for intensity, pattern, and localization of expression. RESULTS AND LIMITATIONS: All primary and metastatic classic ChRCCs demonstrated homogeneous positive labeling for FOXI1, RHCG proteins, and LINC01187 transcript. Unclassified RCC with oncocytic features, oncocytoma, and hybrid oncocytic tumor, as well as all but two cases of eosinophilic ChRCC also stained positive. Importantly, metastatic and primary RCC of all other subtypes did not demonstrate any unequivocal staining for FOXI1, RHCG, or LINC01187. In normal kidney, FOXI1, RHCG, and LINC01187 were detected in the distal nephron segment, specifically in intercalated cells. Two cases of eosinophilic ChRCC with focal expression of FOXI1 and LINC01187, and Golgi-like RHCG staining were found to contain MTOR gene mutations upon DNA sequencing. CONCLUSIONS: We demonstrate a pipeline for the identification and validation of RCC subtype-specific biomarkers that can aid in the confirmation of cell of origin and may facilitate accurate classification and diagnosis of renal tumors. PATIENT SUMMARY: FOXI1, RHCG, and LINC01187 are lineage-specific signature genes for chromophobe renal cell carcinoma.
BACKGROUND: Renal cell carcinomas (RCCs) are a heterogeneous group of neoplasms. Recent sequencing studies revealed various molecular features associated with histologic RCC subtypes, including chromophobe renal cell carcinoma (ChRCC). OBJECTIVE: To characterize the gene expression and biomarker signatures associated with ChRCC. DESIGN, SETTING, AND PARTICIPANTS: We performed integrative analysis on RNA sequencing data available from 1049 RCC specimens from The Cancer Genome Atlas and in-house studies. Our workflow identified genes relatively enriched in ChRCC, including Forkhead box I1 (FOXI1), Rh family C glycoprotein (RHCG), and LINC01187. We assessed the expression pattern of FOXI1 and RHCG protein by immunohistochemistry (IHC) and LINC01187 mRNA by RNA in situ hybridization (RNA-ISH) in whole tissue sections representing a cohort of 197 RCC cases, including both primary and metastatic tumors. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: The FOXI1 and RHCG IHC staining, as well as the LINC01187 RNA-ISH staining, was evaluated in each case for intensity, pattern, and localization of expression. RESULTS AND LIMITATIONS: All primary and metastatic classic ChRCCs demonstrated homogeneous positive labeling for FOXI1, RHCG proteins, and LINC01187 transcript. Unclassified RCC with oncocytic features, oncocytoma, and hybrid oncocytic tumor, as well as all but two cases of eosinophilic ChRCC also stained positive. Importantly, metastatic and primary RCC of all other subtypes did not demonstrate any unequivocal staining for FOXI1, RHCG, or LINC01187. In normal kidney, FOXI1, RHCG, and LINC01187 were detected in the distal nephron segment, specifically in intercalated cells. Two cases of eosinophilic ChRCC with focal expression of FOXI1 and LINC01187, and Golgi-like RHCG staining were found to contain MTOR gene mutations upon DNA sequencing. CONCLUSIONS: We demonstrate a pipeline for the identification and validation of RCC subtype-specific biomarkers that can aid in the confirmation of cell of origin and may facilitate accurate classification and diagnosis of renal tumors. PATIENT SUMMARY: FOXI1, RHCG, and LINC01187 are lineage-specific signature genes for chromophobe renal cell carcinoma.
Authors: Caleb F Davis; Christopher J Ricketts; Min Wang; Lixing Yang; Andrew D Cherniack; Hui Shen; Christian Buhay; Hyojin Kang; Sang Cheol Kim; Catherine C Fahey; Kathryn E Hacker; Gyan Bhanot; Dmitry A Gordenin; Andy Chu; Preethi H Gunaratne; Michael Biehl; Sahil Seth; Benny A Kaipparettu; Christopher A Bristow; Lawrence A Donehower; Eric M Wallen; Angela B Smith; Satish K Tickoo; Pheroze Tamboli; Victor Reuter; Laura S Schmidt; James J Hsieh; Toni K Choueiri; A Ari Hakimi; Lynda Chin; Matthew Meyerson; Raju Kucherlapati; Woong-Yang Park; A Gordon Robertson; Peter W Laird; Elizabeth P Henske; David J Kwiatkowski; Peter J Park; Margaret Morgan; Brian Shuch; Donna Muzny; David A Wheeler; W Marston Linehan; Richard A Gibbs; W Kimryn Rathmell; Chad J Creighton Journal: Cancer Cell Date: 2014-08-21 Impact factor: 31.743
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Authors: Xiao-Ming Wang; Yuping Zhang; Rahul Mannan; Stephanie L Skala; Roshni Rangaswamy; Anya Chinnaiyan; Fengyun Su; Xuhong Cao; Sylvia Zelenka-Wang; Lisa McMurry; Hong Xiao; Daniel E Spratt; Ankur R Sangoi; Lina Shao; Bryan L Betz; Noah Brown; Satish K Tickoo; Jesse K McKenney; Pedram Argani; Sounak Gupta; Victor E Reuter; Arul M Chinnaiyan; Saravana M Dhanasekaran; Rohit Mehra Journal: Mod Pathol Date: 2021-04-14 Impact factor: 7.842
Authors: Kiril Trpkov; Sean R Williamson; Anthony J Gill; Ondrej Hes; Adebowale J Adeniran; Abbas Agaimy; Reza Alaghehbandan; Mahul B Amin; Pedram Argani; Ying-Bei Chen; Liang Cheng; Jonathan I Epstein; John C Cheville; Eva Comperat; Isabela Werneck da Cunha; Jennifer B Gordetsky; Sounak Gupta; Huiying He; Michelle S Hirsch; Peter A Humphrey; Payal Kapur; Fumiyoshi Kojima; Jose I Lopez; Fiona Maclean; Cristina Magi-Galluzzi; Jesse K McKenney; Rohit Mehra; Santosh Menon; George J Netto; Christopher G Przybycin; Priya Rao; Qiu Rao; Victor E Reuter; Rola M Saleeb; Rajal B Shah; Steven C Smith; Satish Tickoo; Maria S Tretiakova; Lawrence True; Virginie Verkarre; Sara E Wobker; Ming Zhou Journal: Mod Pathol Date: 2021-02-01 Impact factor: 7.842
Authors: Kiril Trpkov; Ondrej Hes; Sean R Williamson; Anthony J Gill; Adebowale J Adeniran; Abbas Agaimy; Reza Alaghehbandan; Mahul B Amin; Pedram Argani; Ying-Bei Chen; Liang Cheng; Jonathan I Epstein; John C Cheville; Eva Comperat; Isabela Werneck da Cunha; Jennifer B Gordetsky; Sounak Gupta; Huiying He; Michelle S Hirsch; Peter A Humphrey; Payal Kapur; Fumiyoshi Kojima; Jose I Lopez; Fiona Maclean; Cristina Magi-Galluzzi; Jesse K McKenney; Rohit Mehra; Santosh Menon; George J Netto; Christopher G Przybycin; Priya Rao; Qiu Rao; Victor E Reuter; Rola M Saleeb; Rajal B Shah; Steven C Smith; Satish Tickoo; Maria S Tretiakova; Lawrence True; Virginie Verkarre; Sara E Wobker; Ming Zhou Journal: Mod Pathol Date: 2021-03-04 Impact factor: 8.209