introduction to cancer vaccines
=biology =medicine =cancer
cancer neoantigens
For cells to become cancerous, they must have mutations that cause
uncontrolled replication and mutations that prevent that uncontrolled
replication from causing apoptosis. Because cancer requires several
mutations, it often begins with damage to mutation-preventing mechanisms. As
such, cancers often have many mutations not required for their growth, which
often cause changes to structure of some surface proteins.
The
modified surface proteins of cancer cells are called "neoantigens". An
approach to cancer treatment that's currently being researched is to
identify some specific neoantigens of a patient's cancer, and create a
personalized vaccine to cause their immune system to recognize them. Such
vaccines would use either mRNA or synthetic long peptides. The steps
required are as follows:
1. The cancer must develop neoantigens that are sufficiently distinct from
human surface proteins and consistent across the cancer.
2. Cancer
cells must be isolated and have their surface proteins characterized.
3.
A surface protein must be found that the immune system can recognize well
without (much) cross-reactivity to normal human proteins.
4. A
vaccine that contains that neoantigen or its RNA sequence must be produced.
Most drugs are mass-produced, but with cancer vaccines that target neoantigens, all those steps must be done for every patient, which is expensive.
protein characterization
The current methods for (2) are DNA sequencing and mass spectrometry.
sequencing
DNA
sequencing is now good enough to sequence the full genome of cancer cells.
That sequence can be compared to the DNA of normal cells, and some
algorithms can be used to find differences that correspond to mutant
proteins. However, guessing how DNA will be transcribed, how proteins
will be
modified,
and which proteins will be displayed on the surface is difficult.
Practical nanopore sequencing has been a long time coming, but it's recently
become a good option for sequencing cancer cell DNA.
MHC mass spec
Proteins are often bound to a
MHC for
presentation on the surface, and those complexes can be isolated by mass
spectrometry. You then know that the attached proteins can be on the cell
surface. However...
- It's currently hard to guess which of those MHC-bound proteins could have
a good immune response.
- This requires more cells than sequencing.
-
This doesn't find all the mutant surface proteins.
-
Peptide
sequencing is
necessary, and it's not easy.
comments on AlphaFold
I've seen a lot of comments on
AlphaFold by people who don't
really understand how it works or what it can do, so I thought I'd explain
that.
AlphaFold (and similar systems) input the amino acid sequence
of a protein to a neural network, using a typical Transformer design. That
NN predicts relative positions of atoms, which is possible because:
- Some sequences form common types of
local structures, and relative positions within those structures can be
predicted.
- Some distant pairs of sequences tend to bind to each other.
- AlphaFold training included evolutionary history, and multiple mutations
that happen at the same time tend to be near each other.
The positions predicted by the neural network are not used directly; they're
an initial guess for a protein force field model. What neural networks
provide is a better initialization than previous approaches.
The
above points indicate some limitations that AlphaFold-type approaches have,
such as:
- They're not as good for prions or otherwise "unnatural" proteins.
-
They don't predict protein functions from structure, or vice-versa.
-
They're not as good when evolutionary history isn't available.
While this approach is more limited than some people seem to think, it's still effective enough that, if a surface protein can be sequenced, its structure can probably be determined well enough to design affimers for it.
related methods
cryo-EM
Cryo-EM
is relatively new, it's one of the most powerful techniques for protein
characterization, and it's produced many interesting results such as
the
structure of bacterial
flagellal motors, so I feel practically obligated to mention it at every
opportunity.
Cryo-EM can produce structures from small crystals. If a
protein can be isolated, "single particle cryo-EM"
can even produce structures without crystallizing them at all. Still, it's
currently easier to determine protein sequences with mass spectrometry, and
I think nanopore approaches have more chance of reducing costs for this
application.
nanopore protein analysis
The same basic approach used for current nanopore DNA sequencing
can be
used
to detect protein post-translational modifications.
Because such
nanopore sequencing detects changes in ion flow through the nanopore, it's
obviously better at detecting something like phosphorylation or
glycosylation than the (smaller) differences between amino acids. But it
should be fairly good at detecting charged groups - which does provide some
data about protein sequences that could be combined with mass spec data.
monoclonal antibodies
Rather than inducing production of antibodies that target cancer
neoantigens, it's also possible to produce those antibodies directly and
inject them.
There are already
monoclonal
antibody treatments for cancer, such as
Nivolumab, but
they're not individualized. Surface proteins that are common in cancers
across different people are normal human receptors that are overexpressed by
the cancer cells, not neoantigens that don't occur in normal cells. So,
there are serious side effects to drugs targeting them.
Monoclonal
antibodies treatments are expensive, but individualized treatments targeting
cancer-specific proteins would be much more expensive.
Wikipedia also
has a decent page on
cancer immunotherapy in general.
affimers
Instead of
creating antibodies that bind to a target and directly signal immune cells
with the
crystallizable
region, it's
possible to create smaller proteins that bind to a target and expose a
native antigen that natural antibodies bind to. In other words, the cancer
neoantigens (that don't trigger an immune response) would get covered by
something that does trigger an immune response, producing a similar effect
with a smaller protein. On the other hand, such aptamers could also get
bound to antibodies and captured by immune cells before they bind to cancer
cells.
aptamers
Instead of
using synthetic proteins that bind to neoantigens, it's sometimes possible
to use synthetic DNA sequences instead; those are sometimes called
aptamers. DNA has less versatility
than proteins in terms of the structures it can form and bind to, but DNA
sequences can be easily amplified by PCR, which could make them cheaper to
produce than proteins.
other cancer treatments
To evaluate the merits of research on a cancer treatment approach, we
have to briefly consider how it compares to other promising approaches.
replication disruptors
Cancer treatments involve targeting some difference between cancer cells
and normal cells. The most obvious such difference is that cancer cells
replicate more, and the most common cancer treatments (besides surgery)
target that. Mitosis is a complex process that can be disrupted in many
ways; a notable example is cisplatin.
Obviously, cell
replication is normally important, and even if replicating cells could be
targeted without any effect on other cells, disrupting it results in serious
side effects. This puts some limits on how good this approach could
theoretically be, but currently the bigger problem is that cancers tend to
find a way to replicate anyway.
mitochondria-mediated apoptosis
Normal cells have several safeguards that cause apoptosis before they'd
become cancerous. One of the most important is mitochondria-mediated
apoptosis, so cancer cells often disrupt normal mitochondria function.
Targeting this difference is the basis of most of my own thoughts on
potential cancer treatments.
There are 2 basic approaches to this:
reactivating mitochondria-mediated apoptosis, and disrupting
mitochondria-independent metabolism to prevent cancer ATP generation. I
consider both approaches worth pursuing, but details are beyond the scope of
this post.
vaccine production
DNA can be amplified by PCR, but RNA amplification is somewhat more complex;
mRNA for vaccines is currently produced with "in vitro transcription".
Directly synthesizing polypeptides (using
native chemical ligation) isn't harder than
directly synthesizing mRNA. If direct synthesis is used, synthetic long
peptides seem better to me than mRNA, because the immune response works
somewhat better, but details are beyond the scope of this post.
The
immune system often recognizes non-human proteins; the mRNA vaccines for
COVID don't need adjuvants because the COVID spike protein is recognized as
foreign. However, if cancer neoantigens provoke an immune response, the
immune system kills those cells, so remaining cancer neoantigens wouldn't be
recognized on their own. This also means that cancers are strongly selected
to have fewer and more human-like neoantigens, which makes it harder to
produce vaccines for them, and makes cross-reactivity with normal surface
proteins more likely. Also, cancers can mutate ("tumor antigen loss") such
that they stop producing some surface proteins.
Synthesized cancer
neoantigens can be directly attached to a native antigen, and when the
immune system recognizes the native antigen it will produce antibodies for
the neoantigen part. With mRNA vaccines, either a native antigen would be
added to the sequence (in a way that doesn't interfere with the neoantigen
structure) or adjuvants would be added. Typically, adjuvants kill some
cells, causing release of human double-stranded DNA fragments that indicate to immune cells
that something killed some cells nearby, and triggering production of
antibodies to everything foreign in the area. But that obviously only works
if the neoantigens are recognizable enough that an indication that
"something bad is in this area" is sufficient.
conclusion
Individualized cancer vaccines are not yet practical, but I consider them a
promising possibility for significantly better cancer treatments. I think
research on that should prioritize:
- combining mass spectrometry and nanopore data for protein characterization
- continued development of nanopore sequencing
- continued surveying of
cancer genomes, such as TCGA
- developing lower-cost methods for
isolation of cell surface proteins
- developing equipment and methods for
lower-cost production of long polypeptides
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This post has some comments at LessWrong.