Evaluation Of Uterine Leiomyosarcoma By Next

Evaluation Of Uterine Leiomyosarcoma By Next Generation Sequencing Reveals Actionable
Genomic Abnormalities And New Routes To Targeted Therapies.
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A Huho , CE Sheehan , G Otto , K Wang G Palmer , R Yelensky , D Lipson , J Chiemlicki , SM Ali , D Morosini , VA Miller , PJ Stephens , JS Ross
1Department
Abstract
BACKGROUND: Uterine leiomyosarcoma (LMS) is a rare uterine malignancy that arises
from the smooth muscle of the uterine wall. Compared to other types of uterine
cancers, LMS is an aggressive tumor associated with a high risk of recurrence and
death, regardless of stage at presentation. We hypothesized that comprehensive
genomic profiling of clinical LMS samples could identify genomic-derived drug targets
of therapy for patients with this lethal cancer.
Methods: Hybridization capture of 3,769 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 LMS FFPE tumor 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 were defined as those identifying anti-cancer drugs on the market or in
registered clinical trials.
Results: There were 25 female LMS patients with a median age 57 years (range 42-70
years). There were 1(4%) Grade 1, 3(12%) grade II and 21 (84%) grade III tumors. Three
(12%) LMS were Stage I, 5 (20%) were stage II, 3 (12%) were Stage III and 14(56%)
were Stage IV. All patients had sequencing performed on their primary tumors. 23
(92%) of LMS had GA on NGS with A total of 85 GA were identified, with 23/25 cases
(92%) harboring at least one genomic alteration with an average of 3.4 GA per tumor.
The most common non-actionable GA were alterations in RB1 (64%), TP53 (60%), ATRX
(32%)and MYC (16%). Nine (36%) LMS had at least 1 actionable GA with an average of
0.9 actionable GA per patient including: mutation, amplification or homozygous
deletion of: PTEN (16%), RICTOR (12%), TSC1 (8%), ATK2 (8%) and CCNE1 (4%) and
CDKN2A (4%) In a single case, a STK32B-ALK fusion that fused the intact kinase
domains of ALK to STK32B was identified.
Conclusions: More than one third of the LMS patients in this study harbored at least
one actionable GA with the potential to influence and personalize therapy selection.
Given the limited treatment options and poor prognosis of patients with
leiomyosarcoma in general, comprehensive NGS-based genomic profiling has the
potential to identify new treatment paradigms and meet an unmet clinical need for
this disease.
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 uterine leiomyosarcoma FFPE
specimens
• Samples were sequenced to high (average 746X), 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).
of Pathology and Laboratory Medicine, Albany Medical College, Albany, NY, 2Foundation Medicine, Inc., Cambridge, MA
Results
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•
•
•
•
•
•
•
•
Case Examples
25 female LMS patients with a median age 57 years (range 42-70 years)
1(4%) Grade 1, 3(12%) grade II and 21 (84%) grade III tumors
3 (12%) LMS were Stage I, 5 (20%) were stage II, 3 (12%) were Stage III and 14(56%) were Stage IV
100% patients had sequencing performed on their primary tumors
23 (92%) of LMS had GA on NGS
85 total GA were identified
23/25 cases (92%) harboring at least one genomic alteration
3.4 GA average GA per tumor
Most common non-actionable GA were alterations in RB1 (64%), TP53 (60%), ATRX (32%)and MYC
(16%)
9 (36%) LMS had at least 1 actionable GA with an average of 0.9 actionable GA per patient
including: mutation, amplification or homozygous deletion of: PTEN (16%), RICTOR (12%), TSC1
(8%), ATK2 (8%) and CCNE1 (4%) and CDKN2A (4%)
In a single case, a STK32B-ALK fusion that fused the intact kinase domains of ALK to STK32B was
identified.
Genomic Alterations in 25 Cases of Uterine Leiomyosarcoma
•
•
Tumor
Stage Genomic
at time Alteratio Actionable Actionable
Case Age Grade of NGS
ns
alterations Alterations
1
64
3
II
3
0
1
2
70
3
IV
1
0
0
3
NA
3
IV
2
0
1
4
67
3
IV
10
0
ALK ATK2 AR ARID1A ATRX
55
3
IV
2
0
0
6
58
3
IV
1
0
0
7
60
1
III
0
0
0
8
43
3
II
2
0
0
9
61
3
IV
4
0
1
10
57
2
III
3
0
0
11
69
3
IV
0
0
0
12
49
3
IV
1
0
0
RET RICTOR STK11
LOSS
TP53
TSC1
LOSS
LOSS
LOSS
LOSS
SPLICE
5332+1G
SPLICE
>A
2
5
BRAF CCND3 CCNE1 CDKN2A/B CDKN2C ERBB4 FGF10 FGF14 IGF1R JUN KDM6A KIT MCL1 MDM4 MED12 MLL2 MSH2 MSH6 MYC PIK3R1 PTEN PTPRD RB1
LOSS
R680
SPLICE2
6351G>A W414*
AMP
K15*
C283*
AMP
R209FS*6
LOSS
TRUNC
EXON 16
AMP
SPLICE
SITE110
8+1G>A
SPLICE
SITE782+
1G>T
LOSS
AMP
Case 13. High grade stage III LMS in a 54 year old
woman with known Li-Fraumeni syndrome. The
tumor harbored a V216G TP53 mutation. In addition
this tumor featured a fusion of the ALK gene with
intron STK32B. Given the sensitivity of ALK fusions in
NSCLC to targeted therapy, this patient has been
[placed on the ALK inhibitor crizotinib.
LOSS
LOSS
EXON(1
8-27)
SPLICE
Case 4. High grade Stage IV LMS in a 67 year old
woman. The copy number plot demonstrates wide
spread chromosomal gains and losses. This process is
common in sarcomas
and is
known as
chromothrypsis. Noteworthy is the amplification of
RICTOR which h is considered an emerging target for
MTOR inhibitors with early evidence of tumor
responses.
E180*
AMP
LOSS
Conclusions
13
54
3
III
3
0
0
14
53
2
I
2
0
0
15
NA
2
II
1
0
0
16
17
57
55
3
3
IV
IV
4
2
0
0
1
59
3
II
3
0
0
19
NA
3
II
4
0
0
20
42
3
IV
5
0
0
21
52
3
I
7
0
2
59
3
IV
4
0
3
IV
9
0
2
59
3
IV
2
0
0
3
I
6
0
AMP
N477fs*
10
2
V216G
V173G,
V197L
TRUNCA
TION
EXON 13
P153fs*2
8
LOSS
SPLICE
SITE
782+1G>T
LOSS
AMP
E637fs*1
5
AMP AMP
LOSS
L660fs*
8
G44D T1246M
T1582fs*
23
K430fs*
3
57
55
AMP
E492*
24
L491fs*
5
• More than one third of the LMS patients in this study harbored at least
one actionable GA with the potential to influence and personalize
therapy selection
• Given the limited treatment options and poor prognosis of patients
with leiomyosarcoma in general, comprehensive NGS-based genomic
profiling has the potential to identify new treatment paradigms and
meet an unmet clinical need for this disease
AMP
0
23
25
S1845fs
*2
0
18
22
STK32BALK
FUSION
AMP
T319fs*
24
Q679fs*
12
R50H
AMP
AMPLIFI
CATION
AMP
AMP
AMP
Q165*
H193L
LOSS
P177S
LOSS
C135Y
LOSS
References
AMP
LOSS
L359fs*3
R600Q
N2471
L682
fs*3
LOSS
P190del
R692*
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.

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