Download Comprehensive Genomic Profiling Of 295 Cases of Clinically

Comprehensive Genomic Profiling Of 295 Cases of Clinically
Advanced Urothelial Carcinoma of the Urinary Bladder Reveals a
High Frequency of Clinically Relevant Genomic Alterations
JS Ross1,2, K Wang2, D Khaira2, SM Ali2, HAG Fisher1, B Mian1, T Nazeer1,JA Elvin2, J
Chmielecki2, N Palma2, R Yelensky2, D Lipson2, VA Miller2, PJ Stephens2, V Subbiah3, S Pal4
1Albany
Medical College Albany, NY, 2Foundation Medicine, Inc., Cambridge, MA, 3The University of Texas MD Anderson Cancer
Center, Houston, TX, 4City of Hope Cancer Center, Duarte, CA
abstract #141112
Background
•
When cancer of the urinary bladder progresses to incurable metastatic disease, it is a
major cause of morbidity and mortality around the world
•
Although standard of care cytotoxic therapies can provide significant benefit and new
strategies of neo-adjuvant chemotherapy have recently emerged
•
Despite significant success of targeted anti-cancer therapy in other common solid tumors
such as breast and lung cancer, patients with loco-regionally advanced and metastatic
urothelial carcinoma (UC) currently have limited therapy options, especially as
chemoresistance develops to standard anti-cancer therapies
•
Herein, we present a comprehensive genomic profiling (CGP) study of UC designed to
detect clinically relevant genomic alterations (CRGA) that could inform the selection of
established and novel targeted therapies
Presented by:
Methods (1)
•
Hybridization capture of all coding exons of 236 cancer-related genes and selected introns
of 19 genes commonly rearranged in cancer
•
≥50ng of DNA extracted from 295 clinically advanced urothelial carcinoma specimen
•
All FFPE samples were sequenced to high (average >600X) with uniform coverage where
no exon was sequenced at less than 100X
•
All classes of genomic alterations including base substitutions (sub), small indels, copy
number alterations (CNA) and rearrangements/fusions were determined and then reported
for these patient samples
•
Clinically relevant GA were defined as those identifying anti-cancer drugs on the market or
in registered clinical trials (CT).
Presented by:
Methods (2)
Post-Analytic Process
Pre-Analytic Process
(Pre-Sequencing)
(Post-Sequencing))
1) DNA/RNA extraction:
2) LC, Hybrid Capture:
Extensive optimization
Extensive optimization
Presented by:
3) Analysis pipeline:
Advanced computational biology
4) Clinical report:
Resource intensive
Results (1)
• There were 75% male and 25% female patients with a mean age of 66
years
• 295/295 (100%) of UC were high grade 295/295 (100%) of UC were
advanced stage (III and IV)
• 294/295 (99.7%) UC featured at least 1 genomic alteration (GA) on
comprehensive profiling with a mean of 6.4 GA/UC
– 61% SUB + INDEL
– 37% CNA
– 2% fusions.
Presented by:
Results (2)
•
275 (93%) UC had at least 1 CRGA involving 75 individual genes with a mean of
2.6 CRGA/UC
•
The most common clinically relevant GA (CRGA) involved
–
CDKN2A (34%)
–
FGFR3 (21%
–
PIK3CA (20%)
–
ERBB2 (17%).
•
FGFR3 GA were of diverse type and included 10% fusions.
•
ERBB2 GA were equally divided between amplifications (CNA) and SUB.
•
ERBB2 SUB were predominantly in the extracellular domain and were highly
enriched in the micropapillary UC subgroup.
Presented by:
Most Frequent Genomic Alterations
Fusion/
Deletion Rearrangement Total count % of samples
Gene
Subsitution
Truncation
Amplification
TP53
108
54
0
2
0
164
55.6%
CDKN2A
11
9
0
81
0
101
34.2%
CDKN2B
0
0
0
79
0
79
26.8%
ARID1A
3
73
0
0
0
76
25.8%
MLL2
0
68
0
0
1
69
23.4%
KDM6A
0
59
0
5
0
64
21.7%
FGFR3
53
2
1
0
7
63
21.4%
PIK3CA
58
0
1
0
0
59
20.0%
RB1
0
46
0
8
1
55
18.6%
ERBB2
22
1
26
0
0
49
16.6%
Presented by:
% of samples
Distribution of Genomic Alterations in 295 Advanced Urothelial Carcinomas
Presented by:
)& of Micropapillary Urothelial Carcinomas
ERBB2 Mutations in 6 Cases
Figure&2&(Ross
(Case&1)&
ERBB2:"S310F"
TP53:"R282W"
FBXW7:"G423V"
(Case&2)&
ERBB2:"S310F"
TP53:"E294fs*52"
CCND1:"amplifica<on""
MYCL1:"amplifica<on"
EPHA3:"amplifica<on"
PTEN:"Q298*"
MSH2:""S612*"
"
ERBB2
TP53
RB1
MCL1
(case&3)&
ARID1A
CCND1
RICTOR
MYCL1
MLL2
EGFR
RUNX1
RAF1
PTEN
(Case&
7)&
PTCH1
PIK3R1
PIK3CA
NF2
MSH2
MDM2
KRAS
JAK2
(Case&
9)&
IRS2
IDH2
HRAS
FBXW7
EPHA3
CCNE1
CCND3
BAP1
(Case&15)&
AURKA
AKT2
AKT1
ERBB2:"S310Y"
ARID1A:"V661fs*158"
BAP1:8loss8
MCL1:"amplifica<on"
ERBB2:"R157W"
•
The micropapillary variant of urothelial carcinoma, a
known clinically aggressive subtype of urinary bladder
cancer, harbors an unprecedented high frequency of
ERBB2 mutations especially in the extracellular regulatory
domain of the ERBB2 gene
•
IHC and FISH will not identify UC that hoarbors a nonamplification ERBB2 sequence alteration
•
The well-documented aggressive clinical course attributed
to MPUC has also been linked to micropapillary
carcinomas of the endometrium, breast and lung,
however, no association with ERBB2 mutations in these
other aggressive types of micropapillary carcinomas has
been reported to date
•
Preliminary evidence suggests that ERBB2-mutated
MPUC may respond to anti-ERBB2 targeting agent
ERBB2:8S310F"
TP53:8G244S"
RB1:8Q762*"
ARID1A:8E1767*"
NF2:"E463K"
2
9
15
Substitution/Indel
3
1
7
4
Gene amplification
6
ERBB2:8S310F"
RB1:8Q344*"
EGFR:"amplifica<on8
MDM2:"amplifica<on"
MCL1:"
amplifica<on"
5
13
12
8
11
Gene homozygous deletion
10
14
Truncation
Presented by:
65 year old male with high grade stage IV urothelial carcinoma of the bladder
Presented by:
•
Advanced high grade UC invading through the
bladder wall into the perivesicle fat at total
cystectomy
•
The copy number plot from the CGP assay
revealed amplification of ERBB2 (HER2) at 40
copies
•
Base substitutions in TP53 R280T and ARID1A
Q611*, S614* were also identified
•
This tumor would be HER2 positive by either
IHC or FISH
•
Clinical trials of HER2 targeting agents in
ERBB2 (HER2) amplified UC are ongoing
FGFR3-TACC3 Fusion in UC
FGFR3%
FGFR (3%) TACC3
FGFR3)TACC3%fusion'gene'
(3%) Fusion Gene
TACC3%
Ex'2416'
Ex'1418'
!!!!!!!aa1!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!aa794!!!!!!aa1!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!aa838!
Protein'domains'
'Ig'''''''''I4set''''I4set'
TM'
PKinase'
TACC'
Presented by:
•
66 year old female patient with high
grade trans-mural UC progressed to
stage IV disease post-cystectomy
•
On comprehensive genomic profiling
this tumor featured an FGFR3-TACC3
fusion as well as CDKN2A/B loss,
MDM2 amplification and the MLL2
G5467fs*20 mutation
•
21.4% of the UC in this study harbored
alterations of FGFR3 including base
substitutions (83%), amplifications
(2%) and fusions (11%)
NTM-FGFR1 Fusion Driven Metastatic Urothelial
Carcinoma Responds to Pazopanib + Everolimus
FGFR1%
NTM%
FGFR1-NTM
FGFR1)NTM%
Rearrangement
!!!!!!!!!!!!!noncoding!!!!!!aa29!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!aa344!
A 73 year old male patient with relapsed metastatic urothelial carcinoma.
After a 6 year interval post cysto-prostatectomy. Various cytotoxic therapy
regimens were not effective and associated with significant adverse
events. Comprehensive genomic profiling was performed and revealed
an FGFR1-NTM rearrangement as well as amplifications of CCND3
,CDK4, MCL1, MDM2 and MYC genes. Images to the right demonstrate
response of a lung metastasis to treatment with the FGFR inhibitor,
pazopanib and the MTOR inhibitor, everolimus.
Presented by:
ERBB2 insertion mutation A775_G776insYVMA In
Metastatic Urothelial Carcinoma
• Liver biopsy showing high grade metastatic urothelial
carcinoma in a 49 year old man
• Genomic profiling revealed an ERBB2 insertion
mutation A775_G776insYVMA, CDKN2A/B loss and
CREBBP S893L substitution
• In the bladder urothelial carcinoma TCGA dataset,
mutation of ERBB2 has been found in 14.3% (4/28) of
cases
• Preclinical assays have demonstrated that this ERBB2
mutation can transform cells that were sensitive to
lapatinib and trastuzumab
• ERBB2 kinase and extra-cellular domain mutations are
not detected by IHC and FISH
Presented by:
NF2 Deletion in Advanced UC Responds to Everolimus
• A 60 year old female post neo-adjuvant cisplatin and gemcitabine with cystectomy
showing advanced UC
• After tumor progression, CGP revealed alterations in NF2 Y153*1 (minor allele
frequency [MAF]: 7%), ATM V2119fs*8 (MAF: 8%), ATR splice site 7349+2T>C
(MAF: 44%), and TP53 R280K (MAF: 6%)
• Given preclinical work suggesting NF2 loss may be associated with sensitivity to
MTOR inhibitors, the patient was started on everolimus and paclitaxel using a dosing
regimen currently being examined in a phase II study in urothelial carcinoma
(everolimus at 10 mg oral daily and paclitaxel at 80 mg/m2 intravenous weekly)
• Imaging over 11 months of therapy with this regimen has demonstrated continued
regression of the vaginal cuff lesion and disappearance of the previously noted iliac
adenopathy
Presented by:
FGFR3 Amplification and Base Substitution in UC with Response to
Pazopanib
•
67 year old female patient with relapsed /refractory urothelial carcinoma
•
On comprehensive genomic profiling, the tumor harbored amplification of FGFR3
(11 copies), CCND1 (21 copies), and FGF19 (21 copies) and an FGFR3 S249C
mutation with estimated mutant allele frequencies (MAF) of 58% respectively
•
On the basis of these findings, the patient was initiated on pazopanib
•
After 3 months of therapy, the patient mounted a RECIST-defined partial response
(PR) which has been maintained in excess of 6 months of follow-up
Baseline
Presented by:
6 Months
Conclusions
•
Using a CGP assay capable of detecting all classes of GA
simultaneously, an extraordinary high frequency of CRGA were
identified in a large series of patients with clinically advanced UC
•
More than one-third of these relapsed/refractory cases of UC harbored
alterations in NF2, FGFR3 and ERBB2 with selected patients showing
active responses to targeted therapies
•
Continued evaluation of CGP for UC and the development of genomic
driven clinical trials designed to employ targeted agents potentially in
combination with cytotoxic drugs for this challenging disease appears
warranted.
Presented by: