Sunday, February 24, 2013

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 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.”


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.


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 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 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.


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!