CLL Prognosis Markers Defined

One of the "legnedary" papers in CLL literature is the Dohner paper in New England Journal of Medicine from 2000.  It is the landmark paper that taught us about 13q, 11q, 17p, trisomy 12, and normal cytogenetic CLL.  The FISH technology it employed was developed in the early 1980's.  For the last 13 years knowing the "FISH" status helped with prognosis and treatment selection.  We are now on the eve of a major change of how we think about molecular markers in CLL.  These markers will help us pick treatments that are best for a patient, monitor dangerous subclones, and give a much more clear picture of prognosis when the disease is diagnosed and at each relapse. 

The human genome project took 13 years and 6 billion dollars to “sequence” the genomes of four individuals.  DNA is the “building plans” for just about every important task a cell has to do.  Even though it is given this amazing task it does so with only four different building blocks called “bases.”  There are two purines: guanine (G), adenine (A) and two pyrimidines: thymidine (T) and cytosine (C).  The complexity comes by putting these together in very long sequences that make them unique.  Add some extra bells and whistles and you have a “gene.”  Actually determining the sequence (ie. g-a-a-t-c-c-a-a-c-a-t-g-c and so forth) or order of a particular segment of DNA is called sequencing.

What is remarkable is that the same amount of work that went into the human genome project can now be done in a matter of days to weeks with considerably higher resolution for several thousand dollars.  The cost and efficiency of sequencing is dropping faster than microchips are getting faster.  We are getting very close to being about to sequence an entire genome in only a day for a thousand dollars.

With that diagnostic power comes an incredible ability to probe the very fundamental causes of a particular cancer.  CLL has been a beneficiary of this effort and we now have a very nice short list of the most common mutations found in CLL and several groups have done a great job figuring out the clinical significance of each of them.  Since most of these are likely to be new terms, I thought a brief write up on what these mutations do and what they mean would be great.  I think we are very close to incorporating these markers into our routine work up of a new CLL patient.

Quick note about biology: genes are found in DNA and DNA pretty much hangs out in the nucleus of a cell.  They serve as a template for making RNA.  Once a gene gets “transcribed” from a region of DNA into a much shorter strand of RNA (often times one RNA molecule per gene), it goes out into the main part of the cell called the “cytoplasm” where the RNA gets “translated” into a protein.  Proteins are the tools that do most of the tasks in the cell.   When there is a mutation in DNA, it gets copied into the RNA (which is a lot like DNA but gets out of the nucleus), and leads to the synthesis of an altered / mutated protein.  Sometimes we speak of mutations as though they occur in a protein but really it is in the DNA.  Just in case I am sloppy in my descriptions, I wanted to clarify the biology.

NOTCH1

NOTCH1 is the most interesting of the new markers to me.  It is highly associated with CLL cases that have trisomy 12 as the chromosome change and especially those cases that have an “unmutated” B cell receptor.  NOTCH1 has been a well-known protein because it is extremely important in childhood acute lymphoblastic leukemia where it is present in almost half of all cases.  Over the past few years, there have been a number of efforts to find drugs for mutated NOTCH.  So far I wouldn’t consider those efforts successful, but I am really hopeful about a new class of drugs just entering the clinic now.

NOTCH hangs out in the plasma membrane which keeps the inside of cells in and the outside of the cells out.   NOTCH is like a light switch stuck in the off position waiting to be turned on by another cell.   When that other cell comes by and “flips the switch” a piece of NOTCH gets cut free from its membrane anchor so that it can float away from the membrane.  NOTCH then travels to the nucleus where it interacts with the DNA and makes a bunch of other genes get turned on.  Those genes get copied (transcribed) into RNA and then proteins are synthesized (translated) to do their tasks.  For this reason NOTCH is called a “transcription factor.”  Once it has the right cue, it turns on the transcription of a bunch of genes and therefore determines a whole bunch of important functions.

The genes turned on by NOTCH are really important.  One critically important NOTCH regulated gene that helps cause Richter’s syndrome is MYC.  That is a protein that is a really bad actor in a bunch of different types of lymphoma and leukemia. 

Once NOTCH has done its job and turned on / off a bunch of other genes it gets marked for its own destruction.  The cell wouldn’t want to leave that signal on forever so it needs to turn it off.  Sure enough there is an entire system in place to make sure NOTCH gets shut down after it has done its task.  The particular mutation in this case makes it harder for the cell to turn off NOTCH so it ends up being a signal that won’t stop – sort of like a car where the brake pedal isn’t actually attached to the brakes.  Press all you want and the car won’t stop.

Clinically, the most important thing about NOTCH mutations is that they pretty much split the trisomy 12 patients into two groups, the good ones and the bad ones.  The good ones who lack a NOTCH mutation end up behaving as though they have normal cytogenetics (chromosomes).  The bad ones with a NOTCH mutation are now considered high risk.  They undergo transformation to Richter’s syndrome a lot more frequently and survival is shortened.  See my other post on “new risk groups.”

FBXW7

If NOTCH is important you were probably all expecting that this protein should be on the list too (well ok, maybe just some of you).  Remember all that business about turning off NOTCH?  FBXW7 is the protein that does it.  Take the same car analogy – now just throw out the brake pedal altogether. 

FBXW7 has not been evaluated as closely in terms of clinical significance so I can’t really tell you what it means to have a mutation here – but safe money would bet that will be a lot like a NOTCH mutation.

P53

I have written about P53 before.  It is the protein encoded by the TP53 gene which lives on the short arm of chromosome 17 (yes – that would be 17p).  I would encourage the interested reader to read my post about 17p deletion as well as my post about new risk groups in CLL because it really goes into deep detail about this protein.

Turns out that P53 can be mutated even when 17p is normal and they are just as bad.  The problem is that right now we don’t test for P53 mutations.  Fortunately most of the time you have a mutation in P53 you also have a deletion of 17p on the other chromosome (remember – we have a pair of each chromosomes) but that relationship isn’t air tight.  You can have mutation without deletion, deletion without mutation, deletion with mutation, or normal/normal.  The more 17p dysfunction the worse off you are.  In other words, having one good copy is better than none.  It has been a while since I have seen the number so I might be off a little bit, but something like 20% of cases with P53 mutation do not have 17P deletion so you might have a high risk marker and have no idea based on current testing.

The quick explanation of why this marker is SO IMPORTANT is that it is the protein that pretty much tells the cancer cell to die in response to damaged DNA.  Since drugs like fludarabine, bendamustine, chlorambucil, cyclophosphamide and so forth attack DNA – you need a functional P53 for the chemotherapy to work.

Patients with P53 mutations are considered “ultra-high risk” – it would be nice if we routinely tested for this – but we don’t!

ATM

ATM is to 11q as P53 is to 17p (are you following me?)  ATM lives on the long arm of chromosome 11 (long arms are designated “Q”).  When patients have deletion of chromosome 11q it is a pretty big chunk of DNA that goes missing and includes a handful of genes but ATM is one of the ones that almost always goes missing.

Like P53/17P above, you can have mutation of ATM with or without deletion of the other chromosome.  While a high frequency of 17P deleted cases (70-80%) ALSO have P53 mutation, only about 30% of 11q deleted cases of ATM mutation.  On the other hand, mutations of ATM without deletion of 11q can happen too and once again although it isn’t too common.

Like P53, ATM is important for sensing DNA damage.  If you recall DNA is what we call “double stranded.”  It is like a set of train tracks that gently twist around each other.  When DNA gets damaged it can result in a single or a double stranded break.  ATM is one of the sensors of this broken DNA and it sounds the alarm to stop cell division and also activates our friend P53.

In some studies we’ve seen that having both 11q deletion and ATM mutation is worse than just having one or the other.  Once again, current testing does not look for this.  ATM is an ENORMOUS protein.  It is hard to measure all the possible alterations but new technology is making it a lot easier.

I’ve written previously about clonal evolution both here and here.  It might not be immediately obvious if you haven’t thought about it before but I think it is fairly intuitive that when you use DNA damaging chemotherapy, the cells that survive are the ones that have higher frequency of alterations in 11q/ATM or 17p/P53.  It is sort of like taking a short course of antibiotics for a sore throat and finding that those same antibiotics don’t work well the next time around.  We therefore see a lot more alterations in 11q/17p in patients with relapsed disease than we do in newly diagnosed patients.  This is why it is so imperative to repeat molecular testing before each new line of therapy.

Clinically we think it isn’t enough to give fludarabine / rituxan for patients with 11q.  There is some data to suggest that they do better with cyclophosphamide and fludarabine than just fludarabine alone.  Add in the rituxan (ie. FCR described here) and you overcome some of the negative prognosis associated with 11q.

BIRC3

BIRC3 is another new marker of considerable importance and guess where it lives in the genome?  It lives at the far end of the same 11q deletion that knocks out ATM.  Interesting not all 11q deletions are created equal.  Most include BIRC3 but not all do – so it is possible to have an 11q deletion and have either normal or deleted BIRC3 depending on the size of the deletion.  Sadly FISH doesn’t tell us which is which because BIRC3 is a bad thing to go wrong.

Since BIRC3 is one of the newest abnormalities, we know less about how it interacts with all the permutations of 11q / ATM etc.  For now I think we can just summarize that having a mutated BIRC3 puts you in a high risk category even if everything else appears normal or favorable such as 13q deleted.

BIRC3 is a protein from a family known as IAP or “inhibitor of apoptosis.”  BIRC3 therefore helps regulate cell death and influences another very important protein known as NF-kB.  BIRC3 is another way cells can become resistant to fludarabine.

SF3B1

This is a new marker that burst onto the scene just about two years ago.  Right now, we do not routinely test for it (catch a theme here?). 

When you make an RNA copy of DNA it often consists of long segments of RNA called “introns” that need to be cut out of the final RNA strand (I remember it by saying “introns interrupt”).  Once all the introns have been removed you are left with the “exons.”  When all the exons are lined up end to end it can be copied (translated) into a protein.  We used to think this was just a bunch of cellular waste from millennia of evolution, but now we know that these introns have a bunch of important functions.

SF3B1 has the task of cutting out all those introns and creating the uninterrupted sequence of exons.  Right now, I don’t think we totally understand what happens at a cellular level when SF3B1 is mutated but we do understand some of the clinical implications.   Patients with SF3B1 mutations are resistant to fludarabine.  The other thing about SF3B1 mutations is that it makes you “high risk.”  It isn’t as bad as 17P deletion or P53 mutation but you are still worse off with it than you are without it.

SF3B1 can be sneaky, it can hide in the background of cases with normal chromosomes or even in the 13q deletions where you might otherwise expect a patient to do fairly well. There are now several markers for fludarabine resistance and including P53, BIRC3, and SF3B1. In my mind it would be pretty helpful to know a patient’s markers when they are first diagnosed or when you are picking out a treatment. 

There are several other important new molecules such as XPO1, MYD88, etc.  I have not really seen good data yet that indicates that they influence treatment choice or prognosis.  I wouldn’t be surprised if we learn more about them in the next 1-2 years.

It is an alphabet soup out there but right now these markers are not readily available.  I anticipate we might have a test for them soon and it will be helpful but unfortunately it will add a whole new dimension to the way so many patients worry about their future.  In the future people will now no longer say, “phew, I am a 13q, BCR mutated CLL.”  Instead they may say, “I am 13q deleted, BCR mutated, P53/BIR3 normal, SF3B1 6% subclone mutated.”  It is going to get very complicated very soon!

p53 matters in DLBCL too.

I've written about 17p deletion in CLL previously.  You may recall that this is the chromosomal home of TP53 - the gene which encodes the p53 protein- one of the most important determinants of chemotherapy success.  P53 is mutated with lower frequency in many of the lymphoid cancers than it is in solid tumors (such as pancreatic, esophageal, etc) which may partially explain the success we enjoy in treating diseases like DLBCL.

A recent paper has evaluated the impact of p53 mutations on survival of patients with DLBCL treated with R-CHOP chemotherapy.  They found a mutation in about 1/5 patients.  It was important!  Those without a mutation survived about twice as long as those in whom it was not mutated.

I've attached a link to an editorial / summary I wrote on behalf of Clinical Oncology News for the interested reader:  p53 Is a biomarker in patients with DLBCL on R-CHOP.  Below is a copy of the text.  It is written for an audience of oncologists so the writing might be a little more technical than what I usually put here in the blog.  Hopefully it is still worth the read.


Personalized medicine is the goal of detecting unique characteristics of an individual’s cancer and appropriately modifying therapeutic interventions to maximize efficacy and minimize side effects. A growing number of molecular diagnostics offer multiplex analysis of many oncologic targets bundled within one commercial assay. With the explosive progress in genome sequencing technology, a thorough understanding of molecular biomarkers is imperative if the goal of personalized medicine is to be reached.

p53 is one of the most important molecular markers in cancer. Known as the “guardian of the genome,” p53 determines cell fate in response to a variety of cellular stresses by regulating transcription of important proteins resulting in cell cycle arrest or activation of pro-apoptotic machinery. Loss of p53 activity is therefore a common mechanism by which cancer cells avoid cell death in response to chemotherapy.

The article by Xu-Monette et al highlights the importance and complexity of p53 analysis in patients with DLBCL. Despite histopathologic similarities, patients with DLBCL can be clustered into distinct subgroups based on gene expression profiling. Beyond RNA expression differences, DNA mutational analysis adds further insight into the prognosis of these patients.

This study evaluates a large multi-institutional cohort of patients with de novo DLBCL (excluding patients with transformed disease), treated in uniform manner according to p53 status, using a variety of molecular techniques including sequencing, expression profiling, fluorescence in situ hybridization and immunohistochemistry.

p53 mutation is shown to be an adverse molecular finding in the 21.9% of patients with abnormalities. Overall survival in patients with wild-type p53 was nearly twice as great as it was for those patients with mutated p53, with similar effect on PFS. This effect was independent of germinal center (GC) or activated B-cell subtype, which differs from the prior analysis of DLBCL patients treated with CHOP alone (pre-rituximab) where the effect was limited to patients with GC subtype DLBCL. This highlights the importance of re-evaluation of prognostic markers as standards of care change.

One concern is the incredible complexity of p53 alterations. This study highlights the multitude of ways p53 can be altered in gene sequencing. Although there are hotspots for recurring abnormalities, not all mutations are created equally. Some mutations may not affect amino acid sequence, whereas others cause an amino acid substitution or premature termination of the coding sequence.

It is tempting to consider p53 changes in a binary “yes/no” manner but that probably oversimplifies the biology. As personalized diagnostics emerge, the interpretation of such abnormalities may be as important as the detection of the change in the first place.

Identification of a high-risk cohort may enable therapeutic intensification, but such trials are difficult to design and execute. As the molecular taxonomy of cancer advances more quickly than our ability to know what to do with the data, clinical research remains a vital link in advancing the care of these patients.

Richter's Syndrome / Histologic Transformation

Patients with CLL or indolent NHL occasionally experience a significant clinical change in their disease where it becomes a lot more aggressive.  When this happens, the formerly "slow growing" cancer becomes a lot more nasty and in many cases the prognosis gets a lot worse.  In a number of publications, NHL, CLL) the average survival when this happens is about a year.  A number of those are older articles (retrospective / in pre-rituximab era) which may have been confounded by patient selection bias.  My own impression is that many patients do quite a bit better but that is at least what the literature reports.

In CLL/SLL this is called "Richter's Transformation (RT)" while in the indolent NHL's this is called, "Histologic Transformation (HT)."  Sometimes docs jumble these terms and call it "Richter's Syndrome" or "transformation" regardless of which disease it started out as.  There is a different discussion about what we call Grade 3 follicular lymphoma.  Sometimes these can be confused by the patient.  I will save the discussion of Grade 3 until an upcoming post.  In follicular lymphoma HT occurs at a rate of about 3%/year.  While that is a pretty small number, it is cumulative so by 10 years it may be as high as 30%. In CLL the rate appears to be a fair bit lower so that the cumulative risk is only about 10-15%.

The best clue that a patient has undergone RT/HT is when the disease acquires a bad attitude.  Instead of just involving blood and lymph nodes, you see it in new places like liver, lung, intestine, bone nodules, sometimes even brain.  Patients might experience increasing fevers, night sweats, weight loss.  Laboratory changes are notable for a significant rise in a blood marker known as LDH (we are not talking about subtle changes, but 2-4x higher).  If you get a PET scan (which measures metabolic activity of tissues), you might get one spot which is disproportionately "hot."

Traditional risk factors for developing this in CLL include an increasing number of prior therapies, CLL diagnosis at a younger age (longer exposure to risk), and more advanced disease.  A number of newer studies show that pre-existing NOTCH mutations, "stereotyped B-cell receptors (a topic for a future post)," 17p deletions etc. also increase the risk.  In indolent NHL, risk factors include the diagnosis of grade III follicular NHL, advanced disease, high flipi scores, and several lab variables (LDH, B2 microglobulin).

Under the microscope, the new disease most commonly resembles the "intermediate grade" Diffuse Large B Cell Lymphoma.  Less commonly it can look like Hodgkin's Disease, and extremely rarely it may look like Burkitt's or Lymphoblastic Lymphoma.  In any case, it goes from "indolent" to aggressive, or even the highly aggressive.

Because it is so easy to get samples of cancer cells from patients with CLL (blood draw), we know a lot more about transformation in CLL than we do in low grade lymphoma.  It is probably worth while therefore writing about what occurs in CLL and then highlighting the differences that we know about in NHL.

In CLL there are two main and one uncommon way of experiencing RT.  The most common way (80%)  is for the dominant CLL clone to acquire more and more genomic mutations over time.  Typically these involve several important genes including p53, Myc, and NOTCH.  The second most common way (20%) is for a patient with CLL to "spontaneously" develop an entirely new diffuse large B cell lymphoma that is clonally unrelated to the original CLL. You might think no patient should ever have such bad luck, but in a prior post about 13q, I detailed how some genomic deletions can predisopose to lymphoid malignancies.  Some patients who develop CLL may in fact be predisoposed to the spontaneous development of DLBCL.

The difference is significant.  In the first case, you have a highly resistant clone - often with a p53 mutation - giving rise to an aggressive lymphoid malignancy.  When p53 mutations are present, chemotherapy often does not work well.  Just like every other cancer we have ever studied, p53 is a BAD THING to have mutated in DLBCL.  Conversely, when DLBCL develops spontaneously, it is often a curable cancer.  This plays out with regard to prognosis of the transformation.  In the former, survival averages about a year, whereas in the latter a good number of patients are cured.  Once again, I would point out that it is frustrating that we have no way to tell which one a patient has with testing that we would consider readily available.  In indolent lymphoma, it seems far more likely that the new DLBCL is clonally related and p53 mutations are as high as 80%!

Treatment often consists of R-CHOP chemotherapy regardless of which sort of RT you have.  While this is typically a well tolerated treatment, it is harder on the patient if they have already been exposed to a bunch of chemotherapy previously.  You only get to beat up the bone marrow so many times (chemo) before it starts telling you it can't accept more flogging.  It is not uncommon to run into dose delays, or reduced dosing, etc.  Add this to more resistant disease and you can probably figure why it is less effective.  Furthermore, a lot of patients with follicular lymphoma have been previously treated with the "H" in R-CHOP and you can only give so many doses of that drug before the heart starts to complain.  Since treatment is less effective, some patients will be treated with an "auto" stem cell transplant but a lot depends on how robust the patient is at that point and how well they responded to therapy.

In the future, I think this may be one situation where the "engineered T cells" could become an important therapy.  NOTCH antibodies have recently entered clinical trials and might be appealing.  We have used brentuximab vedotin in one clinical trial and been pleased with the results for some of our patients.  Hopefully these newer approaches will give a more favorable outlook to patients with RS/HT sometime soon.

Here is a video I did with Brian Koffman describing it all:  Richters Transformation

CLL Prognosis

Many CLL patients identify themselves by their prognostic markers when writing in social media outlets.  "Diagnosis age 63, unmutated, trisomy 12, treated FCR age 67, still in remission 2 years later"  is the sort of "tag line" I've seen people write.  For individuals who visit social sites frequently it is a way to tell your story in a few words.  For individuals who are new to CLL, it can all seem very confusing.  Well it is about to get a whole lot more complicated for everyone very soon.

A lot of what follows is very technical but I wanted to get it all written in one place.  I hope patients actually read and re-read this material several times.  For people who are prone to sleeping every time they read one of my posts, here are two videos I did with Brian Koffman in Sept 2013 that goes over the same material in video format:

Part 1: New Prognostic Markers
Part 2: Another on New Prognostic Markers

I've been wanting to write this post for a while but a recent paper has really brought this to the forefront of management of our CLL patients.  Unfortunately the names are strange and I worry this post may fall toward the technical side - sorry.  I will create a separate post that specifically defines many of these terms.

Integrated mutational and cytogenetic analysis identifies new prognostic subgroups in chronic lymphocytic leukemia

For people who have read all my posts on FISH testing, you are probably aware that it is an antiquated technology that has served us well for 20 years but needs desperately to be replaced. Sequencing technology has advanced incredibly quickly and is now poised to refine our understanding of CLL risk groups with new molecular detail.

While most patients are aware of the incredible advances in CLL therapies (ibrutinib, CAL-101, GA-101, ABT-199), fewer are aware of the really important advances in molecular markers that have been recently discovered.  Once these are rolled out to the general public we will be able to understand with much more precision how a patients disease will behave.  Pretty soon, folks will not only be talking about 13q, 17p without also talking about BIRC3, SF3B1, and NOTCH.

In the last 24 months, genomic sequencing has been applied to cases of CLL with pretty remarkable results (see New England Journal of Medicine article or Journal of Experimental Medicine article)

Several key findings have emerged from these data sets.

1) CLL has a relatively simple genome.  While some "smart cancers" (cancers that quickly gain resistance to our treatments and are far more aggressive) like small cell lung cancer may have 50,000 mutations per tumor, CLL (a comparatively dumb cancer - which is typically slow, responds well to most treatments, does not gain resistance all that fast) may have fewer than 100 mutations per case and only a small fraction of those (around 10-20) affect important proteins (the enzymes that make all things happen inside a cell).

2) Certain mutations seem to be observed fairly commonly in CLL and have some defined prognostic or predictive value.  For instance BIRC3 turns out to be a really bad thing to have - it is the new 17p.  NOTCH probably is one way to get to Richter's and helps sort out the trisomy 12 cases, SF3B1 makes you resistant to fludarabine chemotherapy.

3) Certain mutations are seen early in the disease, while others seem to accumulate with time.  Furthermore, some of the ones present later on are actually present early but only emerge through "clonal selection."

4) Some cases of "familial CLL" (ie those cases that run in families) have an unifying genomic explanation that point toward things we already knew were important.


With all of this new information, it was only a matter of time before someone took on the herculean effort to figure out which of these were most important and what they all mean when you analyze them simultaneously in a large group of patients (1300 of them to make this model).

The old risk groups were:
High risk: 17p changes (home of the p53 protein)
Intermediate risk: 11q changes
Low risk; normal cytogenetics & trisomy 12
Very Low Risk: Isolated 13q changes

Unfortunately, there is a lot of biologic diversity that FISH testing misses since it only looks at large chunks of missing or added DNA.  Using sequencing technology (think microscope compared to telescope) as an adjunct to FISH we can now help sort all of these out.

The new risk groups
Very high risk: 17p deletions, p53 mutations, or BIRC3 mutations (10 year survival 29%)
High risk: 11q deletions, SF3B1 mutations, NOTCH mutations (10 year survival 37%)
Low Risk: Normal cytogenetics, trisomy 12 (without NOTCH mutations) (10 year survival 57%)
Very low risk: Isolated 13q deletions (10 year survival same as age matched controls).



There are some really interesting observations contained within this.

1)  It is not a surprise that 17p deletion and p53 mutation are both really bad - we've known that for a long time.  They commonly run together (ie. most 17p deletions also have p53 mutations - but not all cases).

2) BIRC3 is a new kid on the block.  It has only been recognized for about 18 months.  Turns out it is really bad to have.  It confers chemotherapy resistance and is often very discrete from p53 alterations (i.e., if you have one, your probably don't have the other).  We've known for a while that p53 doesn't explain all cases of chemotherapy resistance - BIRC3 explains a lot of them.

3)  We have known for a while that 11q deletions often associate with bulky lymph nodes, unmutated B-cell receptors, faster growth kinetics, requirement for alkylating drugs (cytoxan, bendamustine).  It has often been considered a poor risk feature.  SF3B1 and NOTCH are totally new though and we didn't know where these fit in terms of hierarchy.  Turns out, they are about equal.

4)  Last year the relationship between NOTCH and trisomy 12 was identified.  About half of trisomy 12 cases carry a NOTCH mutation - particularly those with unmutated BCR (ie. cases with unmutated BCR and trisomy 12 have high frequency of NOTCH mutations - sorry if this gets confusing).  We have been aware that trisomy 12 was a bit of a wild card - some did fine, some did poorly.  Turns out that NOTCH mutations can sort the two apart.  Those with mutations do worse, those without mutations are now considered "low risk."  I am very eager to learn if the new NOTCH antibodies turn into personalized medicines for patients with the NOTCH (or even FBXW7 changes).

5)  Our good old friend 13q is still "good risk."  The surprise here is that 25% of 13q cases get put into higher risk categories when you do the mutation analysis.  They might have an SF3B1 mutation or BIRC3 mutation you would have otherwise never known about.  By carving out the bad players, it makes the good group even better.  "Matching age controls" does have some limitations because the model is built upon typical CLL cases.  There are probably not sufficient number of 42 year olds with 13q in the model to say that they necessarily match their peers.

6)  This model holds true no matter when you evaluate a patient.  In other words, if clonal evolution occurs and you go from very low risk to high risk by molecular definition - your clinical outcome changes too.

There are some important questions in all of this.

1) The most obvious is - how do I know what I am?  Right now - you can't easily tell.  There really are not commercial tests to sort this out - I'm trying to make one but seem to running into more walls than doors.  If anyone out there wants to finance this idea, let me know!

2) What defines "positive" for mutation?  For 17p by FISH we do not define a patient as positive until 20% of their cells are positive.  With ultrasensitive testing you may find 0.07% of cells have a BIRC3 mutation.  That patient isn't "positive" but I would be very concerned that clone may evolve in the future.  Do you therefore do anything different when you choose to treat them?

3)  This analysis may miss some of the subtlety of different FISH abnormalities.  We already know there are type I and type II deletions on chromosome 13 with different prognostic value.  We also know that the overall percent of cells with 11q or 13q makes a difference.  This model does not capture that degree of subtlety.

4)  Mutated vs unmutated is not included necessarily in this model - I would like to know if it "sub-stratifies" amongst the various different risk groups (although it is more common to see unmutated with 17p and 11q than the 13q cases so perhaps the model was just not big enough to take it all into account)

5) How do these markers hold up in the face of the new drugs.  ABT-199, ibrutinib, CAL-101, GA-101 are so remarkable.  Will traditional markers hold up in the "new era?"  It is important to note that this model is based upon cases that have already been followed for quite a few years.  Some didn't get rituxan with their first line of therapy.  Presumably none were able to take advantage (since it is an Italian study) of the new drugs.  By definition, this is a backwards looking model and does not capture what I see as a very optimistic future. For example, 29% 10 year survival for poor risk does not reflect the impressive durable control obtained in front line 17p patients treated with ibrutinib.


Though there are questions, the authors of this paper are to be thanked profusely for their remarkable effort to create a single predictive model of this magnitude.  I would imagine that there were thousands of hours put into creating and analyzing the data.  This paper will serve as a landmark for quite a few years and will help guide countless numbers of patients.

17p Deletion in CLL

17p is the genomic alteration in CLL that triggers the greatest concern in most patients.  It can have a tremendous impact on CLL prognosis and the FDA has recently extended approval to ibrutinib in this population (even without prior treatment) and the European equivalent of the FDA (the EMA) will do the same for idelalisib in combination with rituximab.  A lot of patients know that 17p deletions is one of the high risk markers in CLL  – but there are a lot of things to consider about CLL with 17p deletion before completely tearing your hair out.

When we say 17p deletion CLL, what we mean is that the short (petit) arm of chromosome 17 is missing.  You have 23 pairs of chromosomes (46 total) and as you get higher in the numbering, the chromosomes get smaller and smaller.  It is probably an excessive simplification to say that the biology of 17p is all about one particular protein called p53 – but for the time being that is most of the story.

P53 is affectionately called “the guardian of the genome.”  Every time I read about p53 I discover some new function of the protein that I didn’t know about before.  One of the most important though is that it will bind to DNA in a bunch of places and turn on / off the genes at those locations.  In this role it is known as a “transcription factor.”  Many of the proteins that are regulated by p53 have to do with cell survival or cell death.  When P53 decides it is time for a cell to die – very few things can stop that.  The most important signal that turns on p53 is DNA damage (hence – guardian of the genome). 

When DNA damage occurs the cells have a lot of repair mechanisms to try to fix the problem (including the ATM protein on chromosome 11q).   P53 will halt cell proliferation until that DNA damage is fixed.  Some DNA damage cannot be easily fixed and when that is the case, p53 triggers a cell death cascade called apoptosis (one of several ways that cells can die).

I mentioned above that you have two copies of every chromosome – so you ought to have two copies of P53.  We have been good at detecting absence of chromosome 17p for quite some time (via routine cytogenetics or FISH), but we have not always been very good at detecting p53 mutations which have been far more difficult to measure until recently.  With new sequencing technology, it is relatively easy to look for mutations and an increasing number of laboratories are offering that service. 

This is important because patients with 17P deletion are not the only individuals who have to be concerned about it.  About 30 percent of patients with abnormality in P53 have a mutation BUT NO DELETION.  Those have just as bad a prognosis but are not currently detected by FISH testing (nor SNP arrays which are one newer technology that is gaining popularity).   There is a strong association between loss of chromosome 17p on one chromosome and mutation of the other copy (about 85% of cases with 17P deletion will also have P53 mutation on the other chromosome).  

Another common misunderstanding has to do with “how many deleted cells does it take to call a patient 17p deleted?”  In other words, FISH will report the percentage of cells lacking one copy of 17p.  That can range from 1% to 100%.  In simple terms, the more abnormal cells, the worse.  For research purposes we say that 20% of cells lacking one copy of 17p calls that person “17p deleted.”  Some labs have lower thresholds (7%).  Occasionally I will hear from a patient that has 2% of cells with 17p deletion who is worried about their future.  By convention we would not group that patient into a 17p deletion category.

I think the 20% distinction is important – but gets more emphasis than it deserves.  We have prior posts talking about clonal evolution and this is a topic that is very important to understand (also covered in my "watch and wait" post.  If you have a small percentage of 17p deleted cells and you get chemotherapy that damages DNA – requiring p53 to transmit death signals – guess which cells are going to survive.  We know that one out of five patients will have a high risk molecular abnormality at relapse (11q/17p).  If we look hard enough we can see that it was often there to begin with – but below our typical levels of detection.  By giving therapy that removes the more sensitive cells, the resistant ones remain.  On the other hand, if you have a large number of 17p deleted cells, you are less likely to respond to chemotherapy in the first place.

The question becomes, what to do clinically when a patient has a 17p deletion.  There are not a lot of standard regimens that are particularly active when a patient has a high load of 17p deleted cells.  FCR and BR are not very effective.  Indeed, perhaps the most important clinical trial in this population right now is the frontline study of idelalisib in combination with rituximab.  It is available here and here (can be opened at any of these locations)

Campath (an antibody that does not damage DNA) can work well, but does not clear bulky lymph nodes which are common with 17p deletion.  High dose steroids can shift cells into the circulation where they can be removed by campath.  Rituxan also does not damage DNA both rituxan and campath combine well with high doses of steroids.

The new drugs CAL-101 (aka GS 1101), ibrutinib (aka PCI-32765), and ABT-199 (AKA GDC-0199) appear in preliminary reports to be quite active in 17p deleted CLL.  Multiple clinical trials are available for those drugs.  For untreated CLL with 17P, I think it is worth trying to get into this study

I have a particularly memorable patient who presented to my clinic with bad stage IV 17p deleted disease.  He had bulky nodes, WBC count of 200, platelets of 20k and hemoglobin of 8.  His FISH showed 100% 17p deleted.  Two cycles of FCR did nothing except get him transfused every few days.  I switched him to campath with rituximab and got his marrow into better shape but he still had bulky nodes.  He was young enough for transplant, but not eligible because he still had bulky nodes.  I sequentially gave him R-ESHAP, bendamustine rituxan, revlimid rituxan, ofatumumab all without much benefit.  I started him on CAL-101 and his disease melted away.  His disease control lasted nearly two years.

When a patient is young enough, they should definitely consider a stem cell transplant for 17p deleted disease.  The challenge though is that CLL more commonly affects patients too old for transplant.  The engineered T cells hold some promise for being active in this setting.

I also have a lower threshold for starting treatment in previously untreated CLL with 17p deletion (see "when to treat CLL").  Since those cells are likely to be resistant, I don’t see value in getting too far behind before getting started.   When I start, I might avoid FCR though some would argue it is still the right choice (NCCN lists this as first choice but I do not agree).  In Europe, you would typically get steroids with campath and I tend to think that is the right option.  Unfortunately, not enough sound data to tell us one regimen is better than another in this situation.  If a patient has access to ibrutinib in this setting that may be preferable.

Finally – one more biologic consideration.  Richter’s transformation is the name given to CLL that changes behavior and becomes a lot more aggressive – a different entity we call diffuse large B cell lymphoma.  It appears that p53 abnormalities are one of several key steps to getting to Richters (the other possibly being abnormalities in Myc or a protein that turns on Myc called NOTCH).  This is part of the reason Richter’s can be so difficult – it has intrinsic resistance to chemotherapy.

We are lucky to have a host of new drugs working through the system.  I will be very interested to see if drugs work out in this setting!

Thanks for reading - I also discuss this in a video done by Brian Koffman.  For anyone still interested, here is the link:   High risk CLL