Next Generation Sequencing in Renal Cell Carcinoma:
Towards Precision Medicine
Roy Elias1,2 Akanksha
Sharma1
Nirmiah Singla3 James
Departments of Internal Medicine1 Kidney Cancer Program2, and
Department of Urology3, Simmons Comprehensive Cancer Center,
University of Texas Southwestern Medical Center, Dallas TX, 75390
Introduction
Worldwide, there were over 400,000 new cases and 175,000
deaths attributable to renal cell carcinoma (RCC) in 2018.1
In the United States alone, there are predicted to be over
73,000 new cases of RCC, accounting for nearly 15,000 deaths.
2 17% of patients present with metastatic disease with
only 12% of patients surviving 5 years.3 Fortunately, outcomes
are improving. The number of efficacious systemic therapies
for RCC has increased over the past decade and there
are now over a dozen FDA approved agents and combinations
for use in metastatic RCC.4-6 The treatment landscape
has changed from one comprised exclusively of recombinant
cytokines to one which includes angiogenesis inhibitors
(mostly tyrosine kinase inhibitors, TKI), mammalian
target of rapamycin (mTOR) inhibitors, and most recently,
the immune checkpoint inhibitors (ICI).4,7 Despite this progress,
precision medicine has advanced little and there are
no biomarker tests approved by the FDA to guide treatment
selection.
Classically, RCC is subdivided histologically into clear
cell RCC (ccRCC) accounting for 75% of cases, type I and II
papillary RCC (pRCC) accounting for 10% of cases, chromophobe
RCC (chRCC) accounting for 5% of cases, and
other less frequent subtypes.8 RCC is now recognized to be
a diverse group of diseases with updated society guidelines
incorporating molecular and genomic data along with histologic
information when defining RCC subtypes.9,10
Discovery of the von Hippel-Lindau
Tumor Suppressor Gene
The first tumor suppressor discovered in ccRCC was the von
Hippel-Lindau (VHL) gene. VHL syndrome is an autosomal
dominant disease caused by germline mutations in the VHL
gene. This syndrome results in development of numerous
ccRCCs among other manifestations.11 Genetic linkage analysis
of affected kindreds located the responsible gene to the
chromosome region 3p25-26 in the late 1980s.12,13 Latif and
94 Kidney Cancer Journal
colleagues were the first to identify the VHL gene,14 and the
following year VHL was also shown to be mutated in sporadic
ccRCC.15 Nearly two decades later, Nickerson and colleagues
evaluated a cohort of 205 ccRCC samples, the
largest cohort at that time, for aberrations in the VHL gene
through targeted sequencing. They identified non-silent somatic
mutations with a prevalence of 82% and VHL promoter
hypermethylation in an additional 8.3% of tumors, for
a total of 90% of tumors.16 In sporadic ccRCC, the initiating
event is thought to be loss of 3p through a chromothripsis
event.17 This is likely followed by mutation or epigenetic silencing
of the second allele. While VHL loss is nearly universal
in ccRCC, VHL inactivation has also been shown in
preneoplastic cysts, and mice with VHL disruption in the
kidneys do not develop ccRCC.18-20 Thus, while VHL loss is
an important initiating step in the development of ccRCC,
additional driver mutations were suspected.
The VHL protein forms a complex with Elongin B, Elongin
C, CUL2, and RBX1 that serves as an E3 ubiquitin ligase
which, at normal oxygen tension, acts on the alpha unit of
hypoxia inducible factor (HIF) transcription factors, leading
to their degradation.21 Loss of VHL in ccRCC results in constitutive
activation of HIF and expression of its target
genes.21,22 Interestingly, mutations in TCEB1 (encoding
Elongin C) have been reported in up to 5% of ccRCC cases
and are associated with loss of heterozygosity of chromosome
8, which contains TCEB1.23 In addition, mutations in
CUL2 were found in up to 1% of ccRCCs.24 Mutations in
TCEB1 and CUL2 tend to be mutually exclusive with VHL
mutations and likely represent other mechanisms to disrupt
VHL function.25
Identification of the PBRM1 and
BAP1 Tumor Suppressor Genes
The first large scale sequencing reports in ccRCC came out
in 2009, and demonstrated frequent mutations in the chromatin
remodeling genes SETD2, KDM6A (also known as
UTX), KDM5C (also known as JARID1C), and MLL2.26,27
These reports were limited to sequencing a panel of ~3,500
genes, a small subset of the entire human exome, and the
genes identified were mutated in up to 15% of tumors. In
the subsequent two years, whole exome sequencing (WES)
allowed the discovery of two major drivers of ccRCC; polybromo
1 (PBRM1) and the BRCA1 associated protein-1
(BAP1). Varela and colleagues performed WES of seven
Keywords: Kidney cancer, molecularly targeted therapies, immune checkpoint
inhibitor, next generation sequencing, genomics, renal cell carcin
oma, BAP1, PBRM1
Corresponding Author: James Brugarolas, University of Texas Southwestern
Medical Center. 5323 Harry Hines Blvd., Dallas, TX, USA, 75390-
8852. Phone: 214-648-4059; Fax: 214-648-1955.
E-mail: james.brugarolas@utsouthwestern.edu
Brugarolas1,2
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