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- Hey, Jacques.
Thanks for inviting me to your home.
- Thanks for coming it will be great
to go over some of the discussions
that did not make it to the main episode.
- It is amazing how far cancer genomics
has come in such a short period of time.
- Yes, the first cancer genome was sequenced in 2008
and it required a milligram of DNA
to make just one library.
And now, seven years later, they can sequence single cells.
It's almost unbelievable.
- It's just fascinating.
This is a supplement to the main episode
'Adventures in Genomics' so if you haven't
seen that, it would be better if you checked that out first.
The link will be in the description below.
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- So, I'd like to take a few minutes to talk about
the differences between a normal single cell
and a tumor cell.
So, what we know about a normal cell is that
they often are somewhat square or rectangular,
depending on the cell type.
They have a nucleus and that one cell
it has about 10 picograms of RNA
and about 6 picograms of DNA.
Now, in that nucleus, there's also 23 chromosomes.
Pairs of chromosomes.
Pairs.
And there's also 6.4 billion nucleotides of DNA.
I'll say base pairs.
So, that's a whole lot of information.
A cell is about 10 microns across.
So, 10 microns, or micrometers.
And to think about it and conceptualize it
the size of the cell relative to the body
is about the size of a typical suburban home
relative to planet Earth.
So, it's about the size differential is about 1:100,000.
So it's quite remarkable how small these cells are.
Now, a cancer cell, which I'll draw over here.
Cancer cells can be a lot larger.
They can be, they can range from 10 microns
anywhere to, let's say 50 or even 100 microns.
Instead of just 23 pairs of chromosomes,
they can have genome duplication events
and they can have hundreds of chromosomes.
They can range from 23 to hundreds.
And the DNA content, therefore, can be increased
depending on whether that cell is aneuploidy or not.
A big difference is that these cells tend
to be very migratory tumor cells.
As we know, they can exit the primary tumor site,
they can invade the tissues, they can go into the blood,
and they can see metastatic tumors.
So, that's one big difference between
a typical tumor cell and a normal cell.
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- Nick's description of the single cell evolution
was very helpful to understand the disease progression.
- Absolutely.
You know, you have to remember all those changes
are all genomic.
I mean, all the cells look the same.
- And here is a longer explanation
that gives more details.
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- For the most part, normal cells
are relatively homogeneous.
So, even though after each cell division
you have a one nucleotide error typically,
over all, normal tissues are pretty much homogeneous.
Most cells are very identical in their genetic make up.
In a tumor, however, as the tumor cell
starts to acquire mutations and begins to transform
and divide to become malignant tissue,
the cells that kind of form these lineages
and as the cells continue to evolve,
they acquire new mutations
and this can lead to a lot of genetic diversity.
And so in this tree, I'm just going to draw
a few different populations.
And you can think of this as a cell lineage,
or an evolutionary lineage that occurs
as these cells continue to divide and proliferate.
So when you look at the final tumor mass,
instead of having a nice, homogeneous group of cells
like over here, you actually see cells with
all these different colors
that exhibit a lot of genetic diversity.
And this is what we call intratumor heterogeneity.
Now, this intratumor heterogeneity, can be a big problem
for clinical diagnostics, especially when the different
clones are spatially segregated to different regions.
So, in this tumor that I have drawn right here,
you can see that we have several different clones.
And let's imagine that you sampled this tumor
from up here, you might detect some mutations.
Let's just imagine that you're trying to genotype for
a mutation like PTEN.
Well, if you had sampled down in this region over here,
where these black clones are,
you might not detect that mutation.
So, it's a big problem in the clinic for sampling tumors,
but also in the research setting when you're
trying to do analysis.
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- [Dr. Kadam] Single cell sequencing is still
obviously just research.
and it will take a while before it is robust,
validated and approved by the FDA.
- Just as importantly, it has to be accepted by
the medical community and then become standard of care.
And that can take a really long time.
- It was interesting to meet Mary Edgerton
and Bora Lim to get a pathologist's and
and oncologist's perspective on this work.
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- Okay, so we are here with Mary Edgerton, she is a
pathologist at MD Anderson and she's
going to give us a nice clinical perspective
of some of the applications of single cell sequencing.
- So, sequencing is a diagnostic test, a prognostic test.
Diagnosis is essentially in pathology and then we
aggregate this information and pass it on to the oncologist
who then decides how to treat the patient.
And indeed, in pathology, we set those guidelines,
you know, here's the line, okay.
Above the line is when you give Trastuzumab,
below the line, don't.
And so, we'll be needing to bring these tests in
and understand how they function in terms of
identifying those patients who should receive that target.
- When you do pathology, you classify cells based
mostly on qualitative characteristics of how they look,
but then you can go in and classify them both
on the genetics, but also on the histopathological features.
So, I think it's going to be very powerful in the future.
- What are some of the challenges
that a pathologist has to overcome?
- On a very mundane level, we need our aggregated
information from multiple sources.
And so, breast cancer has been neatly categorized into
four sub-types: ER/PR positive, HER2 new positive,
triple negative, where as I used to grade based
on the nuclear morphology and the architecture
and the mitotic activity, how's that going to combine
with the molecular information and I don't think
the grade will be just one, two, three,
it will be one to a hundred, but then we relate
to how the patient is being treated.
So, I think we are going to have to really
redo our algorithms of prognosis in understanding these.
- In thinking about targeting pathways, instead of
targeting individual genes or mutations.
- Right. It's a cleaner, cleaner piece of information.
Did I say cleaner twice?
That's because it is a lot cleaner.
(laughter)
- [Jacques] That is the way to go.
- [Nick] I think one of the really beautiful things
right now is a lot of clinicians and pathologists
are learning on genetics, and pathways,
and sequencing technologies and a lot of the
researchers are learning more about clinical parameters
and histopathological classifications of cancers
and so it is a really exciting time right now.
- Definitely, early detection should be revolutionized by
single cell sequencing.
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- So I would like to talk now to our clinical
collaborator, this is Bora Lim, she is in breast medical
oncology and I want to ask you about
some of the potential applications of single cell sequencing
in the clinic for future translational utility.
- So, I mean, Nick and I have been starting off this
collaboration project and one of the areas we have been
focusing, for example, triple negative breast cancer
where there is a lot of challenges in terms of
there is a lot of heterogeneity within the tumor which
is a lot of the diversity index that you, Nick, is trying
to develop within the clinic or
without the clinical application.
As well as the lack of therapeutic applications
that the main standard of treatment for triple negative
at this point is only chemotherapy and the question is
always, can we develop a better targeted drug to reduce the
mortality and morbidity of these patients.
So, this sort of non-invasive monitoring
or the diagnostic technique including the circulating
tumor cells , single nucleus sequencing, would actually
open a very wide field of new way we can detect
and guide the targeted therapy within our
breast cancer population.
- For non-invasive monitoring, we would typically
collect the blood sample, 7.5 ml, and then
we would isolate out the circulating tumor cells
and then potentially we can sequence those,
look at the genome wide of exome wide mutations
or maybe the transcriptional profiles.
And those mutations might be representative
of the primary or the metastatic tumors
and the next thing is that it is a very non-invasive
approach to be able to measure those mutations.
And then we can do that over the course of therapy, right?
- Sure. As you can see, if you are giving one therapeutics
it's really hard to biopsy every single time and then
so far, that has been the gold standard of some sort of
therapeutic response or the monitoring.
But you cannot put your patients on
these needles or the biopsy every single time, so this
is very novel technique that the field
is really in need overall.
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