(slow piano music)
- [Voiceover] A piano and piano keys are a bit analogous to
single cells and when those keys harmonize and play
chords together, they can lead to a beautiful piece of music
which is analogous to an organism or a life.
And in that organism, a single cell or a single key
can lead to the destruction of the entire organism
as we see in diseases such as cancer.
I've had several family members very close to me
that have battled cancer and some have lost
and some have won.
I know how important it is to really develop
new drugs, new diagnostics, new ways to make
a big impact on reducing morbidity
in this devastating disease.
(faster piano music)
- [Voiceover] Well thank you very much for
inviting us to Houston and to the lab,
we are really looking forward to seeing it.
- Yeah, we are very excited, we're looking forward to it.
- Oh yes, totally excited.
- [Jacques] I understand that this was a background
project, how did this all start?
- The story really started, for me, as a graduate student
at the Cold Spring Harbor Laboratory and I was very
interested on copy number variation in the human population.
From there I became interested in whether these copy
number differences were also seen within tumors.
And I spent a lot of my thesis cutting up tumors
into smaller and smaller segments, but we never had
information on individual cells.
And so in the background I had a project,
a very high-risk project, trying to amplify DNA
from single cells and many people thought
it was just not possible, but we were able to
figure out amplification methods eventually
that worked for single cells.
- What was the moment when you really started thinking
that this thing is really going to work?
- Some of the first data sets that we got back,
the copy number profiles we got from the single cell
matched very well to a population of cells,
millions of cells, in a cell culture system.
That was very exciting.
And immediately we knew then, okay, we can get
single cell information.
- [Swati] But there's very little material, how complete
could you get those sequences?
- 90% or higher so we could look at mutations
in single cells across the entire genome
at base-pair resolution.
- [Swati] So what additional information
do you get from single cells?
- [Nick] Although a tumor cell might look very similar
from a pathologist or under a tissue section,
the genetic differences can be quite dramatic.
Let's take some time to explain the differences
between a single normal cell and a single tumor cell.
Our traditional model of cancer has been one in which
a tumor is composed of a dominant clone
which out competes all the other populations and is
actually very homogenous within the tumor mass.
Our more modern view is one in which a single cell
within a tumor, it can be genetically very different,
throughout the tumor mass.
There can be multiple forming populations
present that might be interacting and cooperating
during tumor growth.
And we really need tools like single cell sequencing
to be able to isolate out single cells
from the tumor and study their genetic differences.
- [Jacques] This must be challenging,
what is the process you developed?
- So we really developed three steps to do single cell sequencing.
The first step is to isolate that cell,
the second step is to amplify the DNA or RNA,
and the third step is to go on and do the sequencing
reaction, and sequence that DNA that you've amplified.
- [Jacques] It sounds easy when you say it like that.
(laughter)
- [Nick] Let's go into the lab and I'll show you guys.
(calm music)
- [Nick] So this is our cryomicrotome system which allows
to keep the tissue frozen while Anna goes through
and cuts it with a very, very fine blade that will cut
sections that are only one cell thick throughout the tissue.
We're gonna be looking at an early stage breast cancer
called ductal carcinoma in situ and we'll see ducts
at the earliest stages of tumor development
where the tumor cells have started
to proliferate within the ducts.
Anna is going to use this one micron UV laser
to cut around a cell and then use another laser
to burst that cell out of the tissue
and into a collection vessel.
So, now we're gonna go through the whole genome
amplification process to amplify the DNA from six picograms
up to nanogram amounts so that we can generate
sequencing libraries and do our quality control steps.
So all of that work has to be done here
under a clean hood which is sterile.
And it's very critical before the DNA has been amplified
not to contaminate it with any bacteria or even viral DNA.
Okay, so this is the third step of single cell sequencing,
it's the next generation sequencing part.
So this is one of the runs that's going on right now
on the aluminum machine.
We sequence the old genome of the single cell, we'll be
getting back about a terabyte of data from each cell.
(piano music)
- [Swati] That's a lot of data from a single cell.
How do you make sense of all that data analysis,
what's the significance of all that?
- We use this data to detect mutations that are both
biologically important, but also mutations
that are clinically important and might be actionable
by targeted therapies or even chemo therapies
or other therapeutic strategies in the clinic.
So here's an example where we sequenced four different
single cells and in these four cells we've identified
a mutation in PIK3CA and we found that that mutation,
when we sequence it across many, many single cells,
every single tumor cell had that mutation.
And there's actually good PIK3CA inhibitors
so they would have benefited this patient quite a bit.
What's really important for informing precision medicine,
or personalized medicine, and guiding targeted therapy.
Try and get these tools into the clinic where they can
make a big impact on reducing morbidity.
And that's why getting that single cell genomic information
is so important for understanding cancer.
- [Jacques] It was amazing to see that laser
just cut up that single cell.
- [Swati] I know, it just like blew it away.
But to see how far we've progressed in the
field of cancer research from studying masses of tumors
down to the very single cells that make them.
- Just imagine what it will do for
cancer diagnosis and treatment.
(energetic music)