microrna signatures in - comtecgroup · infections, cardiovascular disesase, neurological and...
Post on 08-Aug-2020
8 Views
Preview:
TRANSCRIPT
1
microRNA Signatures in Cancer
1st International Congress on Controversies in Personalized Oncology (CONPO)
BARCELONA, SPAIN
MARCH 9, 2013
E. ROBERT WASSMAN, MD, FAAP, FACMG
CHIEF MEDICAL OFFICER, ROSETTA GENOMICS
2
Safe Harbor Statement
Except
for
historical
information,
the
statements
made
in
the
following
presentation,
including
without
limitation,
statements
relating
to
projected
cash
burn
rate
and
the
expected
timing
of
development
of
our
pipeline
products,
and
the
future
potential
of
microRNA
products
in
diagnostic
and
therapeutic
markets
are
forward‐looking statements.
Such forward‐looking statements
involve
significant
risks
and
uncertainties
that
may
cause
actual
results
and
events
to
differ
materially
and
adversely
from
those
implied
by
the
forward‐
looking statements.
Risks and uncertainties include: that the timing
and successful development of diagnostic
and
therapeutic
products
is
highly
uncertain;
as
well
as
the
risks
and
uncertainties
set
forth
under
“Risk
Factors”
in
Rosetta’s
Annual
Report
on
Form
20‐F
for
the
year
ended
December
31,
2011,
filed
with
the
Securities and Exchange Commission.
Rosetta is presenting this information as of the date of the presentation
and
expressly
disclaims
any
duty
to
update
the
information
contained
in
this
presentation.
This
presentation
contains
information
from
third‐party
sources,
including
data
from
studies
conducted
by
others
and
market
data
and
industry
forecasts
obtained
from
industry
publications.
Although
Rosetta
Genomics
believes
that
such
information
is
reliable,
we
have
not
independently
verified
any
of
this
information
and
we
do
not
guarantee the accuracy or completeness of this information.
3
microRNAs: The Basics
3
4
Discovered in 1993: central to cell
differentiation & development in
C.elegans
microRNAs are ~22nt long single
stranded RNAs
Post‐transcriptional regulation
“Master control”
at translation of
protein coding genes
Identified in humans in 2001 with
~2000 found since
Linked to diseases, notably cancer,
immune mediated disorders, viral
infections, cardiovascular disesase,
neurological and metabolic disorders Winter et al., Nature Cell Biology 2009
4
Biologic role makes microRNAs ideal cancer biomarkers & potential therapeutic candidates
• MicroRNAs are aberrantly expressed in all cancers studied
• MicroRNAs are oncogenes and tumor suppressors
• microRNAs target self sufficiency in growth signals, apoptosis evasion, limitless proliferation, sustained angiogenesis and tissue invasion and metastasis
• MicroRNA genomic deletions correlate with specific cancers (B- cell lymphoma)
Iorio and Croce, EMBO Molecular Medicine 2011
5
5
MicroRNAs are ideal biomarkers for
cancer diagnostics
Short RNAs embedded in protein complex: robust to degradationStable markers in a variety of tissue samples and body fluidsStable at room temperature for years under FFPE conditions MicroRNAs identify tissues by source regardless of sample preparationExpression profiles classify most tumors with high accuracy and may predict clinical outcomes
00.10.20.30.40.50.60.70.80.9
1
2 3 3 5 7 7 8 8 8 9 9 10 11
age (years)
corr
elat
ion
2 years 11 years Equal quality
6
6
MicroRNAs identify tissues by source regardless
of sample preparation
microRNA expression profiles cluster according to the patient/source whether
sourced as fresh‐frozen or formalin‐fixed paraffin‐embedded (FFPE) tissues;
However, mRNA expression profiles most closely reflect the sample type1
6
1. Liu A, et al. (2009) Int J Clin Exp Pathol. 2:519-527.
7
MicroRNAs demonstrate high tissue specificity
Epithelial origin separateted
from non‐epithelial origin using
only 2 microRNAs
–
miR‐200c and miR‐205
Published by Rosetta in March
20081
Subsequent independent
papers suggested same
microRNAs control epithelial
mesenchymal transition (EMT)1 Rosenfeld, N., R. Aharonov, et al. (2008). "MicroRNAs accurately
identify cancer tissue origin." Nat Biotechnol 26(4): 462-9.
8
Historically, in ~20%‐30% of cases,
specimen quantity & quality, and
available methodology limits
correct classification of lung
tumors
qRT‐PCR microRNA analysis of 8
miRs clearly distinguishes between
the 4 main subtypes of lung
tumors
Highly suitable for sub‐optimal
Fine Needle Aspirates (FNA),
brushings, and other small
specimens
High tissue specificity translates into an accurate
lung cancer assay using only small tumor samples
9
Lung cancer discrimination validated
performance higher than histopathology
Results of assay on 45 validation set samples
•
Overall Sensitivity: = 93.7%•
Overall Specificity: = 97.9%•
Sensitivity for pathology specimen: = 92.1%•
Sensitivity for cytology specimen: = 95%•
Overall success rate (samples with answer): = 91%•
Overall correct samples: 384/410Reference: Classification of the four main types of Lung cancer using a microRNA‐based
diagnostic assay. Gilad.S, Lithwick‐Yanai G, Barshack I. et all. J Mol Diagn. 2012 Sep;14(5):510‐7.
Results of assay on 451 validation set samplesTotalFailedSmall CellCarcinoidNon‐SquamousSquamous
384N/A6533153133Correctly
classified
26N/A52136In‐correctly
classified
451417035166139Total
101010
Similarly, high tissue specificity translates into
an accurate renal cancer subtyping assay
10Fridman, E, et al: Accurate Molecular Classification of Renal Tumors Using MicroRNA Expression. J Mol
Diag, 12(5):687‐96, 2010.
11
Renal tumors assessed by KNN (5)
algorithm using 24 microRNAs
Onco‐cytoma
Chromo‐phobe
PapillaryClear Cell
153Clear Cell
150Papillary
339Chromo‐phobe
3241Onco‐cytoma
Overall 174/184 classified correctly 95% accuracy1 sample failed sample QA due to insufficient RNA; 16 samples: no results were generated (8%)
12
12
Non Ep
ithelia
l origin
Epith
elial
GI orig
in
SQ or
iginAden
o orig
inNeuroen
docrin
e
Sarcom
a
microRNA based decision tree also
sorts multiple cancer types effectively
Germ Cell
RCC
13
13
Microarray analysis of 64 miRNAs can
identify 42 distinct tumor origins
Trained with ~1300 FFPE tumor samples Independent validation test set of 509 samples
–
146 (30%) were metastatic tumors–
Result of 1 or 2 tumor types generated from two algorithms –
Only 20 samples (4%) failed to produce result Overall, the correct tissue of origin was predicted by at least one of
the reported answers in 418 (85%) (“sensitivity of prediction”)–
403 samples (82%) received a single answer, of which 361 (90%)
were classified correctly–
Overall specificity up to 99% –
54 samples (11%) resulted in a “unified categorical”
answer, e.g.
Sarcoma, RCC, Thyroid type not specified, etc. (7‐categories)Meiri E, Mueller WC, Rosenwald S, et al. A Second-Generation MicroRNA-Based Assay for Diagnosing Tumor Tissue Origin.
Oncologist 2012 May 22
14
14
Most robust discrimination achieved via
two discrete complementary classifiers
Array resultsSignal
Processing
Signal
Processing
KNN
DecisionMaker
DecisionMaker
Decision
Tree
Two classifiers are employed to
interpret the expression of 64
microRNAs as a combined
classifier
-15 -10 -5 0
-15
-10
-5
0
15
Studies in actual CUP patients at leading
international centers show 80‐92% concordance
• Prospective study on 75 CUP patients at M.D. Anderson done on first generation assay (narrower range of miRNAs & tumor types) and results corroborated with second generation assay
• 84% concordance with final diagnosis1
• Two studies (first* & second** generation) on 52 real CUP patients as well as on metastases of known origin at Heidelberg University
• 80%* & 88%** concordance with final diagnosis2,3
• Study on 84 real CUP patients at University of Ioannina & Hellenic Cooperative Oncology Group
• 92% concordance with final diagnosis4
1. Prospective Gene Signature Study Using microRNA to Identify the Tissue of Origin in Patients with Carcinoma of Unknown Primary (CUP). Varadhachary, Spector et al. Clinical Cancer Research 17 2011
2. Meiri, E, Mueller, WC, Rosenwald, S, et al. A Second-Generation MicroRNA-Based Assay for Diagnosing Tumor Tissue Origin. The Oncologist, 2012; 17(6): 801-812.
3. Accurate classification of metastatic brain tumors using a novel microRNA-based test. Muller, Spector et al. The Oncologist 16:165-74, 20114. G Pentheroudakis, N Pavlidis et al. A Novel microRNA-based Assay demonstrates 92% accuracy in classification of metastatic tumors from
patients diagnosed with carcinoma of unknown primary. Poster presentation at ASCO meeting in Chicago, June 2012
16
Ioannina University Hospital, Greece
study of use in real CUP cases1
Tested Patients84 (100%)
Tested Patients84 (100%)
Clinical DxClinical Dx
Assay ResultsAssay ResultsPresentation Clinical Dx
Presentation Clinical Dx
Final Clinical DxFinal Clinical Dx
Initial Dxprocess
Additional Dxand follow up
Additional IHC for 4 patients
miRview®mets2
59 (70%)
Agreement
Agreement
Agreement
75 (89%)
77 (92%)
1. G Pentheroudakis, N Pavlidis et al. A Novel microRNA-based Assay demonstrates 92% accuracy in classification of metastatic tumors from patients diagnosed with carcinoma of unknown primary. Poster presentation at ASCO meeting in Chicago, June 2012
Retrospective cohort of resected metastatic lesions from 84 CUP patient1
Each prediction was assessed for agreement with:
Pathological information
Clinical information
Follow‐up and outcome data
92% concordance overall
1717
In 77 patients (92%) test results were fully concordant with final
diagnosisFor 18 patients (21%), following test results would have resulted
in administration of different chemotherapeutic regimens–
In 9 patients, different combination chemotherapies likely to be
more active
possibly with superior survival
–
In 16 patients, the change in diagnosis could have been coupled to a change
in targeted therapy employed
In the remaining patients, results in agreement with the
presenting diagnosis were still deemed useful objective
information to narrow the differential diagnosis and increase the
confidence level for treatment strategy
Potential impact of microRNA test results in
Ioannina University Hospital CUP cases1
1. G Pentheroudakis, N Pavlidis et al. A Novel microRNA-based Assay demonstrates 92% accuracy in classification of metastatic tumors from patients diagnosed with carcinoma of unknown primary. Poster presentation at ASCO meeting in Chicago, June 2012
18
18
Case report–brain metastases in a woman
with triple negative breast cancer (TNBC)
H&E
HMB45
S100
x100 x200
A B
Clinical presentation:Female presented with breast mass
several months earlier Pathology: Dx TNBC•Poorly‐differentiated adenocarcinoma
with tumor giant cells, adenoid formations •IHC: negative for Estrogen‐Receptor,
Progesterone‐Receptor and Her2/neu
19
19
microRNA microarray test result: MelanomaIHC after molecular profiling consistent with microRNA:
–
HMB45 ‐
positive–
S‐100 ‐
focally positive–
MELAN A – negative
Breast lesion was then molecularly profiled on microRNA
array and resulted in the same diagnosis of melanomaIHC for breast lesion same as metastasis
Published in: The Oncologist 16:165‐74, 2011‐”Accurate classification of metastatic brain tumors using a novel
microRNA‐based test”
Muller, Spector et al.
Case report–triple negative breast cancer in actuality CUP from “lost” melanoma
20
The challenge of triple negative breast cancer
(TNBC): can microRNA open new paths?
In TNBC cells, 13 microRNAs recently
reported as dysregulated versus normal1
Metastatic signature of TNBC: 6
microRNAs differentially expressed in
tumor vs. metastasis and in normal vs.
metastasis, but not in normal vs. tumormiR‐424 is down regulated in mets vs.
primary
Aberrant miR‐424 has been observed
in progression of other cancer types,
and may indicate a role in the
development of metastases2
1. Cascione L, Gasparini P, Lovat F et al. Integrated MicroRNA and mRNA Signatures Associated with Survival in Triple Negative Breast Cancer. PLoS One. 2013;8(2):e55910
2. Xu J, Li Y, Wang F, Wang X et al. Suppressed miR-424 expression via upregulation of target gene Chk1 contributes to the progression of cervical cancer. Oncogene. 2013 Feb 21;32(8):976-87
21
microRNA expression signatures may be able
to stratify survival in TNBC
4 microRNAs significantly
associated with overall
survival of TNBC patientsCombined 4‐miR signature
stratified median overall
survival of 69 vs. 83 month
between the high and low
microRNA‐based risk groups
Cascione L, Gasparini P, Lovat F et al. Integrated MicroRNA and mRNA Signatures Associated with Survival in Triple Negative Breast Cancer. PLoS One. 2013;8(2):e55910
22
Ovarian Cancer Response To
First Line Platinum Based Treatment
microRNAs from FFPE tumor samples of 57 ovarian cancer patients receiving
platinum‐based therapy as first line hybridized to Rosetta’s microarrays
7 microRNAs were found to be significantly differentially expressed in tumors
from platinum sensitive vs. platinum resistant patients
5 microRNAs were associated with significant difference in survival or
recurrence‐free survival
High expression of hsa‐mir‐27a identified a sub‐group with very poor prognosis
hsa‐mir‐27 expression correlates with survival
surv
ival
Eitan R, Kushnir M, Lithwick-Yanai G, et al., Tumor microRNA expression patterns associated with resistance to platinum based chemotherapy and survival in ovarian cancer patients. Gynecol Oncol. 2009 Aug;114(2):253-9
2323
Mesothelioma diagnosis: orphan clinical unmet
need of increasing importance
G Pentheroudakis, N Pavlidis et al. A Novel microRNA-based Assay demonstrates 92% accuracy in classification of metastatic tumors from patients diagnosed with carcinoma of unknown primary. Poster presentation at ASCO meeting in Chicago, June 2012
Results of further IHC performed
following microRNA test results:A
H&E
B
CK5/6 C
Calretinin
D
Mesothelin
61‐year‐old female presented with
peritoneal carcinomatosis and ascitesPresumptive diagnosis: primary
peritoneal/ovarian carcinoma. Failed response to taxane‐platinum
therapy, but had indolent course, with
overall survival of 30 monthsLater microRNA profile gave a single
answer: mesotheliomaAdditional IHC tests confirmed
diagnosisThis guided diagnosis might suggest
alternative therapy of
pemetrexed/platinum
2424
Despite indolent course in previous patient, mesothelioma remains
highly lethal with Median TTP and survival after surgery 8‐12m and 12‐
20mCurrently, inability to forecast outcomes limits clinicians from
directing
aggressive therapy to the individuals who may actually benefit from such
an approachElevated miR‐29c* Associated With Better Prognosis
Mesothelioma prognosis: orphan clinical
unmet need of increasing importance
2525
Functional Consequences of miR‐29c*
Overexpression in Mesothelioma Cell Lines
Mir29c* is higher in
normal mesothelial
cell lines compared
with MPM Associated with a
more differentiated
phenotypeFunctional analyses
data is compatible
with the clinical
findings
Pass HI, Goparaju C, Ivanov S et al. hsa-miR-29c* is linked to the prognosis of malignant pleural mesothelioma. Cancer Res. 2010 Mar 1;70(5):1916-24
2626
Elevated miR‐29c* Associated With Better
Mesothelioma Prognosis
miR‐29c* had significantly different
expression (p = 0.00036, FC 1.8)
between long and short TTPElevated miR‐29c* was associated
with longer survival time in both
training and test sets
B ad p rog no sis Goo d prog no sis6
7
8
9
10
11
h sa-m iR -29c*p -value 0 .000355fo ld ch ang e 1 .8
Pass HI, Goparaju C, Ivanov S et al. hsa-miR-29c* is linked to the prognosis of malignant pleural mesothelioma. Cancer Res. 2010 Mar 1;70(5):1916-24
27
miRNA biomarkers for stratification of response to novel immunotherapy
• Experimental immunotherapy trial in metastatic solid tumor• 12 miRNAs identified differentiating 10 responders from 10 non-
responders at Day30 (all passed FDR P<0.05) • A classifier using two miRNA’s from day 30 markers also shows
good signal at outset of therapy
22 22.5 23 23.5 24 24.521
21.5
22
22.5
23
23.5
24
hsa‐miR‐A hsa‐miR‐A
hsa‐miR‐B
hsa‐miR‐B
PCR
28
Looking Forward with microRNAs
Blood‐based diagnosticsAdditional Response/Predictive Biomarkers for New Drugs
–
Identify patient sub‐cohorts that respond well to drugs stalled in
development
–
Response prediction suggested in several cancer types to date
Therapeutics–
Up or down regulating a microRNAs can regulate entire pathway
–
Liver cancer (HCC): animal POC successfully completed & published
–
Ovarian cancer: initial, pre‐clinical phase
–
Recent studies in triple negative breast cancers suggest opportunity
Non‐oncology applications
top related