Renal medullary carcinomas depend upon SMARCB1 loss and are sensitive to proteasome inhibition
Abstract
Renal medullary carcinoma (RMC) is a rare and deadly kidney cancer in patients of African descent with sickle cell trait. We have developed faithful patient-derived RMC models and using whole-genome sequencing, we identified loss-of-function intronic fusion events in one SMARCB1 allele with concurrent loss of the other allele. Biochemical and functional characterization of these models revealed that RMC requires the loss of SMARCB1 for survival. Through integration of RNAi and CRISPR-Cas9 loss-of-function genetic screens and a small-molecule screen, we found that the ubiquitin-proteasome system (UPS) was essential in RMC. Inhibition of the UPS caused a G2/M arrest due to constitutive accumulation of cyclin B1. These observations extend across cancers that harbor SMARCB1 loss, which also require expression of the E2 ubiquitin-conjugating enzyme, UBE2C. Our studies identify a synthetic lethal relationship between SMARCB1-deficient cancers and reliance on the UPS which provides the foundation for a mechanism-informed clinical trial with proteasome inhibitors.
Data availability
Data and materials availability: Noted plasmids in the text are available through Addgene or the Genomics Perturbations Platform at the Broad Institute of Harvard and MIT. CLF_PEDS0005_T1, CLF_PEDS0005_T2B, CLF_PEDS0005_T2A and CLF_PEDS9001_T1 cell lines are available through the Cancer Cell Line Factory at the Broad Institute of Harvard and MIT. Sequencing data reported in this paper (whole-genome sequencing and whole-exome sequencing) has been deposited in the database of Genotypes and Phenotypes (dbGaP) and GEO GSE111787.
-
Renal medullary carcinomas depend upon SMARCB1 loss and are sensitive to proteasome inhibitionNCBI Gene Expression Omnibus, GSE111787.
-
Mouse Smarcb1-deficient models recapitulate subtypes of human rhabdoid tumors.NCBI Gene Expression Omnibus, GSE64019.
-
SMARCB1-deficient rhaboid tumors of the kidney and renal medullary carcinomas.NCBI Gene Expression Omnibus, GSE70421.
-
Gene expression data from ATRT tumor samplesNCBI Gene Expression Omnibus, GSE70678.
-
Expression data from the Cancer Cell Line Encyclopedia (CCLE)NCBI Gene Expression Omnibus, GSE36133.
Article and author information
Author details
Funding
National Cancer Institute (U01 CA176058)
- William C Hahn
Wong Family Award
- Andrew L Hong
American Cancer Society (132943-MRSG-18-202-01-TBG)
- Andrew L Hong
National Cancer Institute (U01 CA217848)
- Stuart L Schreiber
National Institute of General Medical Sciences (T32 GM007753)
- Thomas P Howard
National Institute of General Medical Sciences (T32 GM007226)
- Thomas P Howard
Boston Children's Hospital (OFD BTREC CDA)
- Andrew L Hong
U.S. Department of Defense (W81XWH-15-1-0659)
- Gabriel J Sandoval
National Cancer Institute (P50 CA101942)
- Andrew L Hong
Katie Moore Foundation
- Jesse S Boehm
Merkin Family Foundation
- Jesse S Boehm
American Association for Cancer Research (14-40-31-HONG)
- Andrew L Hong
CureSearch for Children's Cancer (328545)
- Andrew L Hong
Eunice Kennedy Shriver National Institute of Child Health and Human Development (K12 HD052896)
- Andrew L Hong
Alex's Lemonade Stand Foundation for Childhood Cancer (Young Investigator Award)
- Andrew L Hong
Cure AT/RT
- Andrew L Hong
- Susan N Chi
Team Path to Cure
- Andrew L Hong
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Animal experimentation: This research protocol (04-111) has been reviewed and approved by the Dana-Farber Cancer Institute's Animal Care and Use Committee (IACUC), in compliance with the Animal Welfare Act and the Office of Laboratory Welfare (OLAW) of the National Institutes of Health (NIH).
Human subjects: Patients assented and / or families consented to Dana-Farber Cancer Institute IRB approved protocols: 11-104, 16-031.
Copyright
© 2019, Hong et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 4,484
- views
-
- 640
- downloads
-
- 37
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Further reading
-
- Cancer Biology
- Immunology and Inflammation
In this study, we present a proof-of-concept classical vaccination experiment that validates the in silico identification of tumor neoantigens (TNAs) using a machine learning-based platform called NAP-CNB. Unlike other TNA predictors, NAP-CNB leverages RNA-seq data to consider the relative expression of neoantigens in tumors. Our experiments show the efficacy of NAP-CNB. Predicted TNAs elicited potent antitumor responses in mice following classical vaccination protocols. Notably, optimal antitumor activity was observed when targeting the antigen with higher expression in the tumor, which was not the most immunogenic. Additionally, the vaccination combining different neoantigens resulted in vastly improved responses compared to each one individually, showing the worth of multiantigen-based approaches. These findings validate NAP-CNB as an innovative TNA identification platform and make a substantial contribution to advancing the next generation of personalized immunotherapies.
-
- Cancer Biology
Most human pancreatic ductal adenocarcinoma (PDAC) are not infiltrated with cytotoxic T cells and are highly resistant to immunotherapy. Over 90% of PDAC have oncogenic KRAS mutations, and phosphoinositide 3-kinases (PI3Ks) are direct effectors of KRAS. Our previous study demonstrated that ablation of Pik3ca in KPC (KrasG12D; Trp53R172H; Pdx1-Cre) pancreatic cancer cells induced host T cells to infiltrate and completely eliminate the tumors in a syngeneic orthotopic implantation mouse model. Now, we show that implantation of Pik3ca−/− KPC (named αKO) cancer cells induces clonal enrichment of cytotoxic T cells infiltrating the pancreatic tumors. To identify potential molecules that can regulate the activity of these anti-tumor T cells, we conducted an in vivo genome-wide gene-deletion screen using αKO cells implanted in the mouse pancreas. The result shows that deletion of propionyl-CoA carboxylase subunit B gene (Pccb) in αKO cells (named p-αKO) leads to immune evasion, tumor progression, and death of host mice. Surprisingly, p-αKO tumors are still infiltrated with clonally enriched CD8+ T cells but they are inactive against tumor cells. However, blockade of PD-L1/PD1 interaction reactivated these clonally enriched T cells infiltrating p-αKO tumors, leading to slower tumor progression and improve survival of host mice. These results indicate that Pccb can modulate the activity of cytotoxic T cells infiltrating some pancreatic cancers and this understanding may lead to improvement in immunotherapy for this difficult-to-treat cancer.