Siyuan Zheng: First of all, I would like to thank the organizers
who give me this opportunity to present this analysis on behalf of the working group. A
few -- background on adrenal cancer. So, adrenocortical carcinoma is a rare cancer type with annual
incidence of about .5 to two per million and the overall five year survival with a metastasis
disease is less than 20 percent, which means this malignancy is pretty bad. There is no
standard system for this disease and Mitotane had been the only drug that was approved by
FDA and the targeted therapy against this disease is quite a disappointing. Many against
IGF-II gene, however this tightening [spelled phonetically] of IGF-II is only effective
in 5 percent of [unintelligible] cases.
Now, it's very important to mention that the adrenal cancer is the endocrine tumor, which
means that adrenal cancer a patient -- about half of the cohort actually have this hormone
access which [unintelligible] this disease with other cancer types. Now, TCGA initiated
the adrenocortical carcinoma project last year. The goal is to collect 92 cases with
exome sequencing, mRNA and microRNA sequencing, DNA copy number, methylation. We -- all of
this data types, the data are almost complete, but we're expecting our protein arrays for
68 cases and we're expecting a complete set of clinical data at this point. The TCGA working
group for adrenal cancer formed last year; we have -- so far we have finished the first
pass analysis, including [unintelligible] different levels of data, and then we have
finished the exome sequencing analysis and we have run first pass of the structure variations
and we have some [unintelligible] analysis that has been done.
Adrenocortical carcinoma compared to other cancer types is a quite pure cancer type.
You can easily appreciate here that each dot in this figure represents one sample and even
though there are few cases that have relatively lower purity, but over all, the medium purity
of adrenocortical carcinoma is very high. So, this tumor type is actually a very good
prototype to study tumor biology. And we have a method called ESTIMATE by which we can look
at the gene expression [unintelligible] activity, so we look at the immune [unintelligible]
activity using this method, and you can see here that adrenal cancer has the lowest immune
score, which is probably related to the hormone cortisol, because cortisol, in adrenal cancer,
actually created a very hostile environment for the T-cell.
So, looking at the genomic level, the adrenal cancer have a relatively lower mutation frequency
compared to other cancer types; it is lower than ovarian cancer, lower than glaucoma,
but it is higher than another endocrine tumor, [unintelligible] here. We used 91 exome sequencing,
we identified six significant mutated genes, including TP53, beta-catenin, MEN1, PRKAR1A,
and a ribosomal protein. If you look at this mutation spectrum, mutation [unintelligible]
pattern of those five significantly tested genes, you can easily see that all of the
mutation, beta-catenin, they are occurring a relatively short region of this gene and,
which the pattern, itself, suggests that all of this mutation could be activating mutations.
And in the other genes, the mutations basically distribute across the gene body, which may
suggest that there're deactivating mutations.
Now, I want to emphasize one gene called PRKAR1A, because the story is that this protein is
a regular subunit of the protein canasA [spelled phonetically]. This protein [unintelligible]
with the catalytic domain, encoded by the gene PRKACA, this gene actually, in the last
two months, there are several papers that report the [unintelligible] mutation catalytic
domain of this protein. So, if you think about this, this could be very interesting because
all of the protein canasA catalytic domain mutation that occurred, they were found in
their adrenal adenoma; however, we found the PRKAR1A [unintelligible] mutation in the carcinoma.
[unintelligible] mention, this is result of not only highlights the importance of this
protein canasA pathway [unintelligible] adrenal tumor, but also it will be interesting to
speculate how the mutations in the regulatory subunit and the catalytic subunit that can
lead to different outcomes in the adrenal gland.
[unintelligible] amplifications and dilutions and we found genes including TERT, CDK4, TERF2,
CCNE1 we found a link on chromosome 4, we found p16 dilutions, RB1, and then our F3
gene. Now, this the TERF2 and ZNRF3 have not been [unintelligible] adrenal cancer. So,
from IGV, you can easily appreciate this focal amplification of TERF2 and focal deletions
of ZNRF3. ZNRF3, this gene is a [unintelligible] gene, so I'll come back to this. With these
genes and we have -- we come up with a landscape -- genomic landscape of adrenocortical carcinoma,
and on the first panel, I show the mutation frequency and on the left side of the [unintelligible]
map, you see the fraction of mutations of those genes [unintelligible], and on the right
side, you see the amplifications and dilutions of those genes. They can see that, the majority
of the [unintelligible] through attrition [unintelligible] due to dilution, now for
[unintelligible] is the mutation. TERF is amplification and beta-catenin is mutation.
So, however, I think, very interesting observation is that -- so, this genomic landscape clearly
separates the adrenal dataset in to two cohorts. One cohort with at least the one putative
driver genes, with another cohort -- about 30 percent of the cohort that does not have
single wise putative driver gene alteration. Now, this results, actually, confirmed the
finding by our European collaborators, they published a new paper in [unintelligible]
Genetics, and in their cohort, they also observed a subset of adrenocortical carcinoma cases
without a putative driver mutations. With unsupervised methylation clustering, we found
three groups with a lower level, low level, intermediate level, and high level methylations;
we call them normal-like, CIMP, and hyper group. miRNA clustering found six robust subgroups
and gene expression identified two groups. Now, our two groups actually recapitulated
the findings by the European group, which they call C1A and C1B.
Now, the C1A group has a bad outcome and the C1B has a [unintelligible] better outcome.
So, by overlaying this subtypes with the genomic landscape, we found a remarkable enrichment
of this different subtypes with this group, for example, the group without putative driver
mutations, they are mostly a C1B group and they have a normal-like methylation pattern.
We also looked at structural variations, gene fusions [unintelligible] and we did not find
a recurrent fusions [unintelligible]; however we found recurrent [unintelligible] genes
and we found sporadic and cancer genes involved in this fusion. For example, we found an MTOR
gene fusion. So, each box here represents one axon, now you can see that -- you can
see a clear activation of this axon expression beyond this fusion size. Now, very interestingly,
this MTOR fusion actually [unintelligible] the catalytic domain MTOR protein. This could
be very important because we know we have an MTOR inhibitor, and there's another case
of the fusion that involves a gene called BRE.
The BRE gene has been reported in tumor -- in adrenal tumor genesis and it was implicated
as a driver gene, so this finding suggests this fusion might be a relevant function,
relevant fusion advance in adrenocortical carcinoma. At a pathway level, we found one
pathway to be the most frequently altered pathway with more than 45 percent of the patients
in our cohort have at least one gene altered in the WNT pathway, but most [unintelligible]
alterations contribute by ZNRF3 [unintelligible] dilution and the beta-catenin activating mutation.
So with this, I would like to summarize what we have for the adrenocortical carcinoma.
We found potential new driver genes including ZNRF3, TERT, and TERF, PRKAR1A, we have subtype
[unintliigible] from mRNA, methylation, copy number, miRNA, integrative analysis highlighted
30 percent of the ACC without any apparent driver alteration. So we're expecting the
RPPA and a complete clinical data where this data might give us some insights in to this
subset. We have infrequent alterations such as sporadic gene fusions and that may contribute
to the adrenal tumorigenesis, and WNT pathway [unintelligible] alter the pathway which we
hope can bring some insights in to the therapeutic development. So, I would like to thank --
return to my slides, please. Okay, so, anyway, so I would like to thank my co -- okay, so
I would like to -- this is a team effort, of course. I would like to thank many people,
but especially my chair, Dr. Giordnao -- Tom Giordano and Dr. Roel Verhaak. Due to the
[unintelligible] limit, I cannot list all the names, but [unintelligible] many people
contributed to this project. Thank you.
[applause]
Han Liang: Any questions? Okay, no more questions. So,
let [unintelligible].
Male Speaker: Before you go, I'm really curious about this
driver negative subset and, as I understand it, these are also tumors with very high purity
as understood by copy number analysis, and I just want to ask how are you -- what are
your thoughts as to, you know, how to pursue the driver negative subset and specifically,
in terms of things like fusion analysis or whole genome sequencing analysis?
Siyuan Zheng: So, right now we are not going to have whole
genome and now we have two things we're thinking to approach at this subset: one is we're going
to look at this driver genes and the known driver genes, we think they're probably just
infrequent and due to our sample size, we cannot find recurrent alterations in those
genes, so we're going to look at that, and potential that can have some percentage of
cases with a driver. Now, another thing is, we should -- we will look at the [unintelligible]
data, and I will want to see if we can find a like 10 to 15 percent of cases with a [unintelligible]
mutation.
Male Speaker: Can I just follow up on that, Matthew? So,
what doesn't come through in this is that those tumors are what we call low-grade adrenal
cancers. Most of them do have IGF alterations, though, so they have sky-high IGF-II expression,
but that is the fascinating part of this project and, so, we really want to focus in on those
tumors, but -- so, I just wanted to make that comment that it's really recapitulating, the
classification that we do, you know, pathologically.
Male Speaker: [unintelligible]
Male Speaker: So, actually, the easiest way to talk about
this, this no mutation -- no driver mutation, you should say there's some driver pathway
involved. That may be easier to understand, because if there's no mutation, but there
is something driving it --
Siyuan Zheng: Yeah, yeah, absolutely.
Male Speaker: [unintelligible]
Siyuan Zheng: Yeah, we hope we will have this data. Thank
you.
Han Liang: No questions? [unintelligible]
[applause]
We are going to resume the afternoon session at 1:00.
Male Speaker: [unintelligible] poster session.
Han Liang: Poster session at 1:00. Yeah, okay.
[end of transcript]