Good morning.
Today I'll talk about mutual exclusivity between genomic alteration according -- across multiple
cancer types.
We know -- okay.
We know that in spite of large heterogeneity, recurrent alteration frequently target few
specific epigenic pathways.
And we also observed and recently showed that functional alteration targeting the same pathway
frequently occurred in a mutually exclusive manner.
And we have here a nice example coming from the latest TCGA paper in which we show that
inactivation of BRCA1 and BRCA2 almost never co-occur.
So to systematically identify genes, for they are frequently altered in a mutually exclusive
way, we developed a method called MEMo.
That stands for Mutual Exclusivity Modules.
MEMo integrates mutation, copy number alteration and allows for user to specify a subtle alteration
for one or more genes -- for example, to include BRCA1 hypermethylation.
After a frequently altered gene has been detected, we connect them using a background network.
All the fully connected genes extracted, and alteration affecting each gene set or module
are tested for mutual exclusivity.
Only modules whose set of alteration show a statistically significant trend towards
mutual exclusivity are then pulled out from the matter as a result.
MEMo is being successfully applied through several TCGA cancer project, and I'm focusing
today on five of them, including updated data set for the serous ovarian cancer and the
glioblastoma multiforme as well as more recent project like with colorectal adenocarcinoma,
focusing on the non hyper mutator subtype; the uterine corpus endometriod carcinoma,
focusing again on hyper mutators and non serous subtypes.
And I will talk a bit more on invasive breast cancer, but among these five is the one for
which we have a larger -- the largest data set with a full, complete genomic profiling.
In each of these cancers, MEMo identified mutually exclusive pattern of alteration affecting
several oncogenic pathways, including Rb signaling, p53 signaling, DNA repair and PI(3)K/Akt signaling
cascade.
But today I will focus specifically on this -- on this PI(3)K/Akt pathway, including RTKs
and RAS.
These pathways frequently altered across all these cancer types and more interestingly
by different mechanisms.
I want to give you a first overview of a set of targets that have been identified by the
method, and you can see how high percentages of tumors are altered in each cancer type,
and it's quite interesting seeing the pattern of mutual exclusivity that characterizes alteration
affecting these genes.
Sometimes we spot it an, like for endometriod or colorectal where we have few targets highly
-- altered with high frequency.
Some other times in -- like in GBM or breast where we observe a larger heterogeneity, we
also observe some overlapping cases.
But what probably you may have -- you may have already noticed is that one of the cancer
types that we introduced before is missing here, meaning ovarian cancer.
Indeed, we did not find a strong signal coming from frequently altered genes in serous ovarian
cancer.
So we ask ourselves are there low frequency but functional events affecting the PI(3)K/Akt
signaling cascade in ovarian cancer?
And when we look at the core components of this pathway, we actually see that there are
multiple low frequency event that target the PI(3)K/Akt signaling, including RTK amplification
, a rare but functional mutation in RAS and RAF , P10 down-regulation and MAP2K4 down-regulation.
When we aggregate all this alteration, we can now sum up, up to 24 percent of ovarian
cancer tumors that have alteration in this pathway.
And all these alterations show also a nice pattern of mutual exclusivity; therefore,
we are looking here at the right event.
And in conclusion, we can say that this pathway is actually altered in all but five cancer
types that we analyzed.
Sorry.
Can I go back?
[laughs] Yeah.
I would like to talk a bit more on invasive breast cancer, as I said it before, we observe
here the largest heterogeneity of alteration.
We saw somehow expected, we know that breast cancer is a very heterogeneous disease but
can actually be thought at least as two distinct diseases, and I'm referring here to a distinction
between basal tumors and non basal tumors.
Indeed, this distinction originally identified from mRNA expression signature.
Apparent -- it's clear by looking at whatever kind of genomic or epigenetic alteration in
breast cancer.
So we ask, if this pathway is altered preferentially one of the two subtypes or by different mechanisms
in the two subtype, when we first broke down the set of alteration, what we found -- we
see that up to 74 percent of non basal tumors have alteration of at least one of the gene
from the pathway shown here on the left while only 24 percent of basal tumors have.
So we ask is the Pl(3)K pathway altered by other means in basal tumors?
And to answer this question, we went looking at a part of mRNA expression, meaning up-regulated
genes or down-regulated genes independently of copy number and mutation status.
And the first result that we have was that P10 is frequently down-regulated in basal
tumors independently of copy number and mutation status.
You can see in this plot, P10 expression vs. copy number status and all the yellow dots
are basal tumors.
You can see that most of the down-regulated samples are indeed basal tumors.
When we weren't looking the AKT level, at the AKT phosphorylation level for this tumor,
we actually see that all the P10 down-regulated samples show on average higher AKT phosphorylation.
We suggest that dysfunctional and P10 down-regulated samples actually contribute to activate the
AKT signals.
P10 was not the only gene that we found with having an mRNA expression pattern.
And indeed, we found a very interesting pattern for AKT3 expression in basal tumors.
AKT3 expression in basal -- as a strong bimodal distribution -- and we can see that up of
two -- 30 percent of basal tumors have AKT3 expression.
When we put together this observation, we actually see that we now have 50 percent of
basal tumors that have alteration in the PI(3)K/Akt signaling cascade.
And alteration in AKT -- overexpression of AKT3 is a mutual exclusive with down-regulation
of P10 in these tumors.
So I'd like to give you a summary of overall extent of alteration in the host set of genes
that we identified from our mutual exclusivity analysis.
And you can see from this heat map, each column is one of the cancer type that we analyzed.
You can appreciate some similar pattern like P10, PIK3CA or two or PIK3R1 that are commonly
altered across all cancer types as well as some specific -- cancer specific alteration
like IGF2 over expression in colorectal or amplification in glioblastoma.
In conclusion, I'd like to stress once again that MEMo systematically identified mutually
exclusive alteration, targeting oncogenic pathway across multiple cancer types.
In particular today, I focused on the PI(3)K/Akt signaling, which is consistently altered in
cancer and more -- even more interestingly by a larger heterogeneity of mechanisms.
Finally, I think it's important to stress with all this kind of analysis across these
cancer types have now the ability to unveil the underlying heterogeneity of a disease.
We're suggesting candidate therapeutic targets in each single subtype.
And with this, I'd like to thank all the people that collaborated with me, in particular -- sorry.
Particularly Chris, Niki and Ethan who collaborated with me in developing MEMo as well as analyzing
all the TCGA data sets.
Thank you.
[applause]
Male Speaker: Thank you, Giovanni.
Questions?
Male Speaker: Great talk.
One question is that, with regards to determining significant mutual exclusivity, just from
our observations of relatively, let's say, where the somatic mutation -- mutations or
somatically mutated genes and tumors that it's pretty easy to find, let's say, a set
of five or six genes that show that nice staircase pattern that implies mutual exclusivity -- so
what are the steps that you've taken, whether it's permutation analysis or some analytical
statistical tests that just sort of determines [inaudible]?
Giovanni Ciriello: You're correct.
For -- if you're looking at the rare events, it's easy to find this mutually exclusive
part.
In our case, we test -- we use a permutation test, but it's basically a multi markup chain
permutation strategy but preserve the number of alteration per genes and the number of
alteration per samples.
So in this way, we believe we have an accurate -- we're able to preserve a cancer specificity
in altering oncogenes and tumor suppressor as well as the heterogeneity show by different
samples.
Male Speaker: Giovanni, that was a beautiful talk.
I have a quick question.
Could you speculate a little bit of what you think is -- might turn out to be the basis
for the different mechanisms of pathway alteration in the different types of cancer?
Very broad, very -- I'm asking you to speculate here.
Giovanni Ciriello: Honestly, I figure it's large heterogeneity.
And all of the cancers show different -- alternative mechanism, but we know these alterations most
of the time emerge randomly during --
Male Speaker: But it's -- it's linked to --
Giovanni Ciriello: -- the processes then, they're selected and
if -- for the advantage that may give to the cancer cell to proliferate and altering the
key pathways.
Male Speaker: I guess we're -- we still have to figure out
what causes the different mechanisms to be pursued for the same pathway in different
types of cancer.
Giovanni Ciriello: Yeah.
Male Speaker: It will be an interesting question to sort
out.
Okay.
Thank you very much.
Great talk.