Immunotherapy in cholangiocarcinoma works for some patients, but not others.

Understanding why most tumours remain invisible, and how dMMR creates tumours that the immune system can clearly see.

Most cholangiocarcinomas are described as cold tumours.

Cold means:
→ the immune system is not recognising the tumour
→ so is not attacking it

They remain largely invisible.
But that leads to the question that matters:

Why are they invisible?

These cells form a protective layer between the duct tissue and the constant flow of bile.

Because of where they sit, they are continuously exposed to:

• Chemical stress
• Pressure
• Inflammation

Injury is common.
It is part of normal function.
But what matters is repetition.

When injury happens again and again:

• The cell does not fully recover
• The immune system is constantly responding

Over time, that response can fall behind.
When that happens:

• Damage can reach inside the cell
• Including the genes within the nucleus

Think of DNA as the cell’s instruction system.
Inside the nucleus, genes carry those instructions that guide how the cell functions and stays stable.

Each gene is like a page of those instructions.
But when injury reaches the DNA:

• Those instructions can be damaged
• They are no longer read correctly

This creates a mutation.

Most mutations are small.
On their own, they do very little and are easy for the body to miss.

This is where repetition becomes the problem.
With repeated injury:

• More cells are affected
• More mutations accumulate
• More daughter cells carry those mutations forward

But here is the critical point. These mutations are:

• Scattered
• Unrelated
• Low in number

They do not combine to create a strong signal.

So, when does it become cancer?
A single mutated cell is not cancer.
Cancer begins when mutated cells:

• Group together
• Organise into a structure that the body can no longer control

This structure is the tumour.

Why does the immune system not respond
Because the cell mutations in the tumour are:

• Small
• Inconsistent
• Uncoordinated

The signal remains weak, so even though something is wrong:

• The tumour is not clearly seen
• And the immune system does not react

Anchor in this understanding
A quiet process that does not trigger an alarm.
The problem is not that nothing is happening.
The problem is: nothing is being clearly seen.

A small, scattered gathering of abnormal, mutated cells is happening inside it.
Each is:

• Quiet
• Different
• Spread out
• Staying out of sight

Each abnormal cell creates only a small disruption.

But no single event is enough to trigger a response.
So:

• No alarm sounds
• No system reacts
• No action is taken

From the outside, everything appears stable.

Most cholangiocarcinomas are cold tumours.

This means they do not produce a strong, shared signal that the immune system can clearly recognise.

They are typically low in mutation burden.
Instead, they carry a diverse mix of mutations that do not combine into a clear signal.

But that does not make them less dangerous.

They develop in an environment where:

• Early growth causes few symptoms
• Immune detection is limited
• Changes are not easily seen

Because they remain:

• Low signal
• poorly recognised
• largely invisible

They are not detected early.

Time becomes their advantage
While the tumour is not being seen:

• It continues to grow
• It continues to adapt
• It continues to spread

Nothing interrupts it.
Nothing slows it down.

By the time it is detected:
It is already advanced

Anchor in this understanding
A cold tumour exists under the radar.

Its cells are not clearly seen by the immune system
because they do not produce a strong, shared signal.

These tumours are not dangerous because they are aggressive early.

They are dangerous because they are not seen.

Immunotherapy does not create a response.
It releases one that is already there.

It works by:
→ releasing the brakes on an existing immune response

PD-L1 often reflects that T cells are, or have been, present in the tumour.

This means:
→ the immune system has already recognised something abnormal

But in a cold tumour:
→ there has been very little or no immune response, nothing to release

So blocking PD-1:
→ changes very little

In the bile ducts, cells exist in a constant state of exposure.
They are affected by:

• Bile composition
• Pressure
• Inflammation

Together, these create repeated irritation to the epithelial lining.
With each injury:

• The cell is damaged
• That damage can reach the DNA inside the nucleus

If the damage is not repaired, mutations form

Over time:

• Mutations accumulate
• Cells divide
• Altered cells group together

This is how a tumour forms.

Not all tumours follow this path.
A small group begin differently.

They are not:

• Quiet
• Low signal
• Difficult to detect

They are visible from the beginning.

This is not a tumour type that becomes visible.
It is a tumour that was built differently from the start.

This is the dMMR pathway.

Cold tumours do not naturally become visible.
They remain difficult for the immune system to recognise.

This is what makes cholangiocarcinoma so difficult to treat.

Attempts to turn cold tumours into “hot” tumours are trying to overcome this biology.

It is not what normally occurs.

A different starting point

A small group of tumours are different from the beginning.

They are not:

• Quiet
• Low signal
• Difficult to detect

They are visible from the start.

This is not a tumour changing state.
It is a tumour that was built differently from the beginning.

This is the dMMR pathway.

Anchor in this understanding
Most patients are not “failing immunotherapy”.
Their tumour was never visible to begin with.

In these tumours, the repair system inside the cell has failed.

This changes the nature of the mutations completely.

They are no longer:

• Small
• Scattered
• Unrelated

They become:

• Large structural errors
• Repeated patterns
• Highly abnormal sequences

And they accumulate quickly.
What this creates

• A strong, consistent signal
• One the immune system can recognise

A small group of cholangiocarcinomas, around 2.5%, behave this way.

They are visible from the beginning.

What this means
These tumours often grow quickly.
But:

• They can also respond to immunotherapy
• Sometimes dramatically
• And enduring

This is why right action becomes critical.

What changes inside the cell

To understand why this happens, we need to look inside the cell.

Think of DNA like a written document that is copied over and over again.

Each time it is copied:

→ small mistakes can occur

Normally, there is a system running in the background.

It:

• Finds mistakes
• Corrects them
• Keeps the sequence stable

But if that system fails:

• Mistakes are no longer corrected
• They begin to accumulate

At first, this may seem small.

But very quickly:

• The structure of the sequence changes
• The meaning begins to break

And eventually:
The information becomes distorted and unreliable

Bring it back to the tumour
This is what is happening inside the cells that form the tumour.

Inside the cell’s nucleus, there is a system that protects DNA as it is copied.

This system is called:
The Mismatch Repair (MMR) system

Its role is simple:

• Find errors
• Fix errors
• Keep the sequence stable

It is built from four key genes:

MLH1
MSH2
MSH6
PMS2

They work together in pairs.

Detection team
MSH2 + MSH6

• They scan the DNA
• They find copying errors

Repair team
MLH1 + PMS2

They remove the error
They repair the sequence

When this system fails
If one of these genes is lost or switched off:
the process breaks

Errors are no longer repaired.
They begin to accumulate.

This is called:
dMMR (deficient mismatch repair)

What this leads to
The DNA sequence becomes unstable.

Errors are no longer controlled.
The structure of the genetic code begins to break down.

Without repair, copying errors build up quickly.

These are not small changes.
They disrupt the structure of the DNA sequence.

This creates:

• Instability in the genetic code
• Repeated errors
• Increasing disruption over time

You may see terms such as:

dMMR
pMMR

dMMR (deficient mismatch repair)

This means:

• The repair system is not working
• Errors are not being corrected
• Mutations accumulate quickly

pMMR (proficient mismatch repair)

This means:

• The repair system is working
• Errors are still being corrected

When the repair system fails, another feature appears.
This is called:
→ MSI (Microsatellite Instability)

Microsatellites are short, repeated sections of DNA.

Think of a sequence like:
“cat cat cat cat cat”

These regions are naturally prone to copying errors.

When the repair system is working:

• Errors are corrected
• The sequence remains stable

When the repair system fails:

• The copying process slips
• The number of repeats changes

You might get:
“cat cat cat cat”
or
“cat cat cat cat cat cat”

The sequence becomes unstable.

What this means
This instability is called:

→ microsatellite instability (MSI)

When this occurs across many regions of DNA:
→ it is called MSI-High (MSI-H)

MSI is the visible footprint of repair failure.
These unstable regions are where many frameshift mutations occur.

How these terms relate

dMMR and MSI are not separate ideas.
They are part of the same process.

• dMMR = the repair system has failed
• MSI-High = the visible result of that failure

So when you see:

• dMMR
• MSI-High

They are telling you the same underlying story:
The repair system is not working, and errors are accumulating.

This rapid accumulation of errors drives:

• Large structural mutations
• Abnormal protein fragments
• Strong signals that the immune system can recognise

This is what makes these tumours visible.

When the repair system fails, the errors that build up are not small.

They change the structure of the DNA sequence itself.

These are called:
→ frameshift mutations

A simple sentence:
“The cat ate the rat”

Now shift the structure slightly:
“The cta aet thr at”

The letters are still there.
But the structure has changed.

The meaning is lost.

DNA is read in a fixed sequence.

When that sequence shifts:
Everything that follows is misread

• This produces:
  Broken instructions
• Abnormal proteins
• Structures that no longer function correctly

These abnormal proteins are processed inside the cell.

Fragments of them are displayed on the cell surface.

If the DNA is normal:

• The fragments look normal
• The immune system ignores them

If the DNA is disrupted

• The fragments look abnormal
• The immune system recognises them

In dMMR tumours:

• Many abnormal fragments are produced
• Strong signals are displayed

This is why:
the tumour becomes visible

The abnormal DNA created by frameshift mutations is still used by the cell.

It is translated into proteins.
Cells use proteins to build and run everything inside them.

When proteins are made, small fragments are displayed on the surface of the cell.
These fragments are called:
→ peptides

Think of these as ID tags
Each peptide shows the immune system:
→ what is happening inside the cell

If the DNA is normal:
→ the peptides look normal
→ the immune system ignores the cell

If the DNA is disrupted:
→ the peptides look abnormal
→ the immune system recognises that something is wrong

Because frameshift mutations are common:

• Many abnormal proteins are produced
• Many abnormal peptides are displayed

This creates:
→ a strong and consistent signal

Why this matters
For the first time:
→ the tumour is clearly visible to the immune system

Seeing is not the same as destroying.

The immune system can now recognise the tumour.
It can see the abnormal peptides.

It can detect that something is wrong.
But it does not automatically attack.

T cells are the immune system’s attack cells.
When they recognise abnormal peptides, they are activated to respond.

But before they act, they check for a signal.
This system is regulated by:

• PD-1 (on the T cell)
• PD-L1 (on other cells, including tumour cells)

PD-1 acts as a control switch.

When it is activated:
→ the T cell slows down
→ or stops completely

It applies a brake.

This system exists for a reason.
It protects normal tissue from damage.
It prevents the immune system from overreacting.

Tumour cells can produce PD-L1.

When PD-L1 binds to PD-1:
→ the T cell is switched off

So even though the T cell can see the tumour:
→ it is being told not to act

Now we bring all the pieces together.

dMMR creates:
→ large numbers of abnormal mutations
→ abnormal proteins
→ abnormal peptides displayed on the cell surface

This makes the tumour:
→ clearly visible to the immune system

As a result:
→ T cells recognise the tumour
→ they move into the tumour
→ they begin to respond

But:
→ PD-L1 is activated
→ PD-1 is engaged
→ the brake is applied

What this creates

The tumour becomes:
visible, but protected

As the immune system responds:
→ the tumour increases PD-L1
→ the brake is reinforced

So the system reaches a balance:
→ recognition is present
→ but action is suppressed

Why this matters

This is why some tumours continue to grow:
→ even when the immune system can see them

Immunotherapy targets the brake.
Drugs such as pembrolizumab and nivolumab:
→ block PD-1

This prevents PD-L1 from activating the brake on the T cell.

What happens next

Now:
→ the T cell can still see the tumour
→ but it is no longer being stopped

The attack continues.

Why this is the turning point
For the first time:
→ visibility is present
→ the immune system is active
→ and the brake cannot stop it

What this allows
→ recognise the tumour
→ continue attacking the tumour

Anchor In This Understanding

Immunotherapy does not create a response.
It releases one that is already there.

Visibility alone is not enough.

The immune system must be able to act.

If the tumour is visible:
→ but the PD-1 brake is engaged
→ the response is stopped

If the tumour is visible:
→ and the PD-1 brake is blocked
→ the response continues

The line to hold

dMMR makes the tumour visible.

PD-1, when engaged, stops the immune response.

Immunotherapy blocks this brake.

This allows the immune system to continue its attack.

Most cholangiocarcinoma tumours do not respond to immunotherapy.

This is not random.
It depends on whether three conditions are present at the same time.

1. The tumour must be visible
The tumour must produce strong abnormal signals.

This comes from:
→ a high number of mutations
→ abnormal proteins
→ abnormal peptides displayed on the cell surface

Without this:
→ the immune system has very little to recognise

2. The immune system must already be present
T cells must be:
→ inside the tumour
→ recognising something abnormal

Without this:
→ there is no response to release

3. The response must be blocked
The immune system must be:
→ active
→ but held back

This occurs when:
→ PD-1 is engaged
→ the brake is applied

Without this:
→ there is nothing for immunotherapy to remove

These conditions are not independent.
They are connected.

Bringing it all together
For immunotherapy to work, all three must align.

When these three align:
→ the system is already active
→ but being held back

What immunotherapy does
It removes the brake.

The existing response continues.

PD-L1 is often measured.

Higher levels can indicate that:
→ T cells are present
→ the immune system has recognised something abnormal
→ the tumour is applying the brake

But this is not enough on its own.

PD-L1 tells you:
→ the brake may be engaged

It does not tell you:
→ how strong the underlying immune response is

What patients need to understand

PD-L1 can appear in different situations.
It may reflect a genuine immune response.

But it can also appear when:
→ inflammation has triggered it without strong tumour recognition
→ only part of the tumour is expressing it
→ T cells are present but weak or exhausted
→ there are not enough abnormal signals

Anchor In This Understanding

PD-L1 shows the brake.
It does not show the strength of the attack.

For immunotherapy to work, the system must already be active.
These conditions must align.

This is the moment that matters.
When these occur together:
→ the immune system can already see the tumour
→ it has already moved in
→ it is already trying to act

But:
→ it is being stopped

The moment that changes the outcome

When immunotherapy is introduced:
→ the brake is blocked
→ the response continues

What defines this biology

This is why the most responsive tumours often show:
→ dMMR or MSI-High
→ high mutation load
→ higher PD-L1 expression

These are not separate findings.
They are signs that the system is aligned.

What this means in practice

When these conditions are present:
→ immunotherapy can unlock a powerful and durable ongoing response

When these conditions are not present:
→ removing the brake changes very little

Most cholangiocarcinoma tumours will not respond to immunotherapy.

This is not random.
It depends on whether the system you have just seen is present.

The key questions

Not:
Do I have PD-L1?

But:
Is my tumour visible, and is my immune system already trying to act?

What testing is trying to answer

Doctors look for signs that the system is aligned:
→ dMMR or MSI-High
→ tumour mutation burden (TMB)
→ PD-L1 expression

These are not independent results.
They are parts of the same system.

How to understand your results

dMMR:
→ suggests high mutation load
→ increased visibility

MSI-High:
→ reflects widespread instability
→ supports the presence of strong abnormal signals

PD-L1:
→ suggests the immune system is present
→ but being held back

Final point to carry
Immunotherapy only works when a response is already present.

Estimated date of publishing: Mid April 2026

“A response is only meaningful if it lasts.”
Part One has shown you how this system works.

You have seen:
→ why most tumours remain invisible
→ how dMMR creates visibility
→ why immunotherapy only works when the system is already engaged

What comes next

Understanding the system is only the first step.

Part Two moves from understanding to application.
We will now answer three critical questions:

How does dMMR arise?
What causes the repair system to fail?
Why pembrolizumab (Keytruda) can deliver durable multi-year responses in dMMR tumours

What makes the outcome different when the system is aligned?

What should you do with this information?
How do you use this understanding when making treatment decisions?

A necessary distinction

This is not a superficial comparison.
Pembrolizumab and nivolumab both target the same pathway.
But they do not behave identically.

What matters is not the pathway alone.

What matters is what each produces over time.

Where this fits
This article is part of a broader survival system developed through Cholangio.org.

Doctrines of Cholangio
Developed by Steve Holmes
The biological and cognitive pathway
The foundational thinking behind the system

↓

Cholangio.org OS
Systemising cholangiocarcinoma
Turning understanding into a structured response

↓

How We Win
The public application of the system
Activating a patient-led survival response

↓

The Survival System
The framework driving the Foundation
Coordinating action across patients, caregivers, and clinicians

↓

The Three Survival Disciplines
The human interface
How a patient engages and responds within the system

Disclaimer
This article is for educational purposes only.
It is designed to help patients and caregivers understand the biology of cholangiocarcinoma and how immunotherapy works.

It is not medical advice and does not replace discussion with your treating team.

Every patient’s situation is different. Treatment decisions should always be made in consultation with qualified medical professionals.

Attribution
This work represents original patient-led frameworks and educational models developed by Steve Holmes through Cholangio.org.

Unauthorised reproduction or adaptation without attribution undermines the integrity of this work and the patients it is designed to support.

Please credit the original source when sharing or referencing.
cholangio.org/immunotherapy-cholangiocarcinoma

Support this work
This is independent, patient-led work.

If it has helped you or someone you care about, you can support its continued development through the Cholangiocarcinoma Foundation Australia.

Donate Here