Download Evaluation Of High Stage Skin Squamous Cell Carcinoma (SSCC

Evaluation Of High Stage Skin Squamous Cell Carcinoma (SSCC) By Next Generation
Sequencing (NGS) Opens The Door For New Routes To Targeted Therapies
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RN Al-Rohil , A Tarasen , K Wang , CE Sheehan , JA Carlson ,GA Otto , G Palmer , R Yelensky , D Lipson , SM Ali , D Morosini , VA Miller , PJ Stephens , JS Ross
1Department
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of Pathology and Laboratory Medicine, Albany Medical College, Albany, NY, 2Foundation Medicine, Inc., Cambridge, MA
Abstract
Background: Although skin squamous cell carcinomas (SSCC) are rarely high stage,
on occasion they can be life threatening both due to local extension or metastasis.
We hypothesized that comprehensive genomic profiling of high stage SSCC could
identify genomic-derived drug targets of therapy for patients with conventional
therapy-resistant disease.
Methods: Hybridization capture of3,769 exons from 236 cancer-related genes and
47 introns of 19 genes commonly rearranged in cancer was applied to ≥ 50ng of
DNA extracted from 25 SSCC FFPE specimens and sequenced to high, uniform
coverage. Genomic alterations (base substitutions, small indels, rearrangements,
copy number alterations) were determined and then reported for these patient
samples. Actionable GA was defined as those identifying anti-cancer drugs on the
market or in registered clinical trials (CT).
Results: There were 23 male and 2 female SSCC patients with a median age of 70
years (range 48-91 years). Fourteen (56%) SSCC were grade 2 and 11 (44%) grade 3.
Fourteen (56%) SSCC were stage III and 11 (44%) were stage IV at time of
sequencing. A total of 161 alterations were identified for an average of 6.44
alterations per tumor with 25/25 (100%) of patients harboring at least one
alteration. The dominant mutational signature reflects DNA damage due to
ultraviolet light exposure, a known risk factor for SSCC. The most common nonactionable GA were alterations in TP53 (88%), NOTCH2 (20%) and MLL2 (20%).
Twenty-one (84%) of SSCC had at least 1 actionable GA with an average of 2.08
actionable GA per patient including mutation, amplification or homozygous deletion
of CDKN2A (60%), NOTCH1 (40%), ERBB2 (12%), FGFR3 (12%), NF1 (8%), NF2 (8%),
PIK3CA (8%), SMARCACB1 (8%), BRAF (4%), BRCA1 (4%), BRCA2 (4%), CCND1 (4%),
EGFR (4%), HRAS (4%), PIK3R1 (4%), PIK3R2 (4%) and PTCH1 (4%).
Conclusions: More than three-quarters of SSCC patients harbored actionable GA
which has the potential to treat high stage tumors with targeted therapeutic agents
in addition or in replacement of the currently available treatment options.
Design and Methods
• Hybridization capture of 3,769 exons from 236 cancer-related genes and 47 introns of 19
genes commonly rearranged in cancer
• ≥ 50ng of DNA extracted from 25 SSCC FFPE specimens
• Samples were sequenced to high (average 774X), uniform coverage
• Genomic alterations (base substitutions, small indels, rearrangements and copy number
alterations) were determined and then reported for these patient samples
• Actionable GA were defined as those identifying anti-cancer drugs on the market or in
registered clinical trials (CT).
Case Examples
Results
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23 male and 2 female SSCC patients with a median age of 70 years (range 48-91 years)
14 (56%) SSCC were grade 2 and 11 (44%) grade 3.
14 (56%) SSCC were stage III and 11 (44%) were stage IV at time of sequencing.
161 total GA were identified for an average of 6.44 GA per tumor
25/25 (100%) of patients harboring at least one alteration
The dominant mutational signature reflects DNA damage due to ultraviolet light
exposure, a known risk factor for SSCC.
• The most common non-actionable GA were alterations in TP53 (88%), NOTCH2 (20%)
and MLL2 (20%).
• 21 (84%) of SSCC had at least 1 actionable GA with an average of 2.08 actionable GA
per patient including mutation, amplification or homozygous deletion of CDKN2A
(60%), NOTCH1 (40%), ERBB2 (12%), FGFR3 (12%), NF1 (8%), NF2 (8%), PIK3CA (8%),
SMARCACB1 (8%), BRAF (4%), BRCA1 (4%), BRCA2 (4%), CCND1 (4%), EGFR (4%), HRAS
(4%), PIK3R1 (4%), PIK3R2 (4%) and PTCH1 (4%).
Clinical Features and Genomic Alterations in 25 Cases of High Stage Cutaneous
Squamous Cell Carcinoma
Case Sex Age Specimen Tumor Tumor Total Therapies Therapies Clinical Altered Genes
#
used for Grade Stage at GA w/
w/ lack of trials
NGS
time of
potential response
NGS
benefit
1
2
3
4
5
6
M
M
M
M
M
M
51
53
84
87
88
76
7
M
69
8
9
10
11
12
13
14
15
16
17
F
M
M
M
M
M
F
M
M
M
62
58
70
79
70
64
91
73
48
61
18
M
19
20
21
22
23
24
25
SKIN
SKIN
SKIN
SKIN
SKIN
SKIN
PAROTID
GLAND
SKIN
SKIN
SKIN
BONE
SKIN
SKIN
SKIN
SKIN
SKIN
SKIN
II
II
II
II
II
III
III
III
IV
III
III
III
7
7
4
9
6
3
1
2
0
9
5
0
0
0
0
0
0
0
7
13
3
12
6
0
CDKN2A; FGFR3; NOTCH1; SMAD4; TP53
ATR; BRCA1; CDKN2A; PIK3CA; SMARCB1;TP53; USP3X
CDKN2A; GARA1; NOTCH1; TP53
APC; CDKN2A; KIT; NF2; TP53
CDKN2A; CTNNB1; EGFR; EZH2;TP53
NOTCH1; TP53
II
IV
2
0
0
0
NOTCH1; TP53
II
II
III
III
II
II
II
III
III
III
III
III
III
IV
III
III
IV
III
IV
IV
7
7
2
6
9
5
7
10
6
8
0
2
0
0
0
0
0
0
2
3
0
0
0
0
0
0
0
0
0
0
6
8
2
5
1
3
5
5
5
5
ATM; BRAF; CDKN2A; TP53
ALK; ASKL1; MYCN; PIK3CA; SMARCB1; TP53
CDKN2A; MLL2;
CDKN2A; DNMT3A; GNA11; HGF; TP53
ASXL1; LRP1B; NOTCH1; NOTCH2; TP53
CDKN2A; NOTCH2; SMAD2; TP53
ASXL1; BRCA2; CDKN2A; KDMA6; LRP1B; NOTCH2; TP53
CDKN2A; NOTCH1; PALB2; RUNX1; TP53
CCND1; FGFR3; FGF13; PIK3R2; TP53
ARID2; CDKN2A; ERBB4; MLL2; NOTCH1; NOTCH2; TP53
77 SKIN
III
IV
1
0
0
2
M
M
M
M
48
83
75
84
SKIN
SKIN
SKIN
SKIN
II
III
II
III
III
III
IV
IV
17
2
8
6
3
0
2
12
0
0
0
0
7
1
5
9
M
M
M
69 SKIN
54 SKIN
71 SKIN
III
II
III
IV
IV
III
8
9
5
3
7
7
0
0
0
5
9
6
NRAS;
ARID2; ASXL1; BARD1; BRCA2; CDKN2A; CREBB2;
GRIN2A; MLL2; MPL; NF1; PIK3R1; SMARCB1; TP53
RB1; TP53
CREBB2; FGFR3; KDM6A; MCL1; RB1; SETD2; TP53
CDKN2A/B; KDR; KIT; MLL2; NOTCH1; TP53
APC; ARID2; CDKN2A; NF1; NOTCH1; NOTCH2; TET2;
TP53
ERBB4; MLL2; NF2; NOTCH1; TET2; TP53
ARID1A; ERBB4; PIK3CA; PTCH1;
Case 5. Stage III cutaneous SCC in an 87 year old man with EGFR
amplification and mutation. EGFR R831H is a missense mutation that
is located in the protein kinase domain of the protein. This mutation
has been reported to be activating (Foster J et al 2010). EGFR has
reported to be mutated in 1% of the skin squamous cell carcinoma
samples examined (COSMIC). Amplification of EGFR has ranged from
1% of the skin cancers analyzed (The cBio Cancer Genomics Portal) to
20% of (Toll A et al 2010). Activating mutations, amplification, or
overexpression of EGFR may predict sensitivity to Egfr inhibitors
Cetuximab is approved in head-and-neck squamous cell cancer and
other Egfr-targeted therapies, such as erlotinib and gefitinib, are
being studied in clinical trials of metastatic cutaneous SCC.
EGFR kinase domain missense mutation (Integrated
Genomics Viewer, Broad Institute)
Copy number plot showing EGFR amplification.
Case 25. A stage III cutaneous SCC with basaloid features in a 71 year old man with alterations in
ARID1A, ERBB4, PIK3CA and PTCH1. PTCH1 encodes the protein Ptc1, a receptor for sonic
hedgehog (Shh), indian hedgehog (Ihh), and desert hedgehog (Dhh) (Kogerman et al 2002). The
two alterations in PTCH1 in this case are both inactivating. PTCH1 mutations have been reported
in 8% (6/73) of skin squamous cell carcinoma (SCC) samples (COSMIC). PTCH1 mutation in
cutaneous SCC has not been significantly studied in the scientific literature. Alterations in PTCH1
have been observed in lung and head and neck SCC and correlated with an increased rate of
recurrence and poor prognosis (Ghosh et al 2013). Loss of PTCH1, by mutation, deletion, or
silencing, has been shown to result in constitutive activation of the hedgehog signaling pathway
and may predict sensitivity to Smo inhibitors such as vismodegib. Trials of vismodegib and other
Smo inhibitors continue in multiple tumor types including metastatic cutaneous SCC..
PTCH1 Q576* and splice site
1347+1G>A mutatations
(Integrated Genomics Viewer,
Broad Institute)
Conclusions
More than three-quarters of SSCC patients harbored
actionable GA which has the potential to treat high stage
tumors with targeted therapeutic agents in addition or in
replacement of the currently available treatment options.
References
Frampton GM, Fichtenholtz A, Otto GA et al. Development and validation of a clinical cancer genomic profiling test
based on massively parallel DNA sequencing. Nat Biotechnol. 2013;31(11):1023-31.