Limited value of the FISH test
If you read our recent “Updates” article on three important blood tests, you should be able ace any pop-quiz on FISH testing.
In a nutshell, FISH test looks deep inside your CLL cells, at the very core of them, and determines if any of the more common chromosomal aberrations have occurred in the DNA of the CLL cells. Deletion of a particular snippet on the 17th chromosome, called 17p53, is known to be the most dangerous.
So, if you get your FISH test done and you see no reference to the dreaded 17p deletion, does this mean you are home free? Not so fast. FISH is an important test, but it is not the whole enchilada.
Several research papers published in recent months have identified details proving there is more to this fishy story. But before we discuss these new articles we need to fill in a bit of the background. As most of you know by now I like to use silly analogies to explain things. Here is a real-life analogy that I think is pretty nifty if I say so myself. Read on, I promise this won’t hurt one bit.
Lost, vandalized, or generally messed-up
Your home is over-run by roaches. Like most of us you dithered for awhile, hoping the nasty critters would go away all by themselves, or at the very least the problem will not get much worse than it is already. You hope. By now the roaches are eating you out of hearth and home, and it is time to do something. You are keen to get rid of the roaches; but you are not too thrilled with the idea of using off-the-shelf insecticides that may do a good job of killing roaches but are also toxic to you, your kids and pets.
You heard about this really powerful roach killer that is perfectly safe to everything else. The further good news is that you don’t have to pay some greedy pesticide company an arm and a leg to buy the stuff, you can make it yourself, it is perfectly easy to brew up a big batch of it right in your own home, provided you have accurate how-to make instructions. Sounds perfectly wonderful and you are sold!
You head to the local library to get hold of “how-to” instructions on making this wonderful “organic” roach killer. The nice lady at the front desk knows exactly the book you are looking for, in fact it is the only book in the library with the necessary instructions you need to concoct the roach killer. She directs you Isle 17, book “p”, page 53. You get it? Isle 17, book “p”, page 53 :-)
It is not your lucky day. Looks like you have to live with the roaches for quite a bit longer unless you are willing to use dangerous pesticides in order to keep them under control. Here are three possible un-lucky scenarios you may face:
- When you get to Isle 17, to your dismay some one has torn out page 53 of book “p”. Without this crucial page containing instructions, you wont know how to make the wonder roach killer.
- Or, the book is there, but some hooligan has stuck together the crucial page 53 with big wads of chewing gum. Without access to this crucial page 53 the book is next to useless since you have no hope of following the “how-to” instructions.
- Going one step further, the book is there and you check it out. But when you get home and start making the brew that is going to get rid of your roach problem, you notice someone has blacked out one or two crucial words in the instructions on page 53. It is not exactly clear what you should do. You scratch your head and decide to take a chance and guess at some of the words and make the brew anyway. But when push comes to shove, roaches continue to thrive just fine even after you sprinkle liberally the concoction you made – you just made a batch of brew that is useless as a roach killer. Bummer!
Now your only options are to live with the roaches (it may no longer be a viable option) or go to the hardware store, decide which of the available but unpleasantly toxic pesticides you are going to buy, paying through your nose in the process.
Translating this to CLL-speak
Your white blood count (WBC) has been climbing steadily, you have developed a certain ‘pregnant’ look with enlarged abdominal lymph nodes. It is getting harder to shave with the nodes around your jaw line. Watch & Worry lasted only so long, now your bone marrow is heavily infiltrated with the cancer cells, preventing proper function of stem cells and formation of healthy red blood cells, platelets etc. You are keen to get the tumor load under control but you are not too thrilled with the idea of using any of the standard issue chemotherapy drugs that kill CLL cells effectively but are also toxic to the rest of your body, healthy cells and organs.
You heard about this really powerful killer of cancer cells, a protein called TP53, that is very effective in killing CLL cells but perfectly safe to everything else. The further good news is that this is a protein your body makes by itself and you don’t have to pay some greedy drug company an arm and a leg to get treated with their latest ‘miracle’ drug with toxicity to match. It sounds like a perfect solution and you are sold!
Under normal circumstances every healthy cell in your body has the “how-to” instructions for making this wonderful protein. TP53 protein acts as a suicide pill killing the cell if it turns cancerous. The instructions on how to make this protein are located on the short “p” arm of chromosome 17, exact zip code 53 – abbreviated to 17p53 gene. When cells have access to the step by step how-to instructions located at 17p53 gene, they are able to make the tumor killing protein called TP53, as needed. When and if a particular cell turns rogue (malignant), TP53 protein is made by the cell and the cell promptly commits suicide.
Most microscopically tiny clusters of cancer cells in our bodies are killed by their own home-grown TP53 protein, before you even know there is any problem, before the tiny cluster of malignant cells can grow fangs and become a real threat to your body. TP53 protein initiates a mandatory suicide (“apoptosis”) command that few cells can disobey. Lack of robust TP53 protein function is one of the ways in which cancer cells can turn a deaf ear to suicide commands and continue living and multiplying.
Cancer cells that have managed to turn off the ability to make proper TP53 protein are that much more likely to live long and prosper, since they have learned how to get around the suicide safety switch built into every cell specifically to administer the kiss of death when cells turn cancerous. Now it is easy to see why 17p53 deletion is such a strong prognostic indicator of an aggressive variety of CLL (or any other cancer, for that matter).
Here are some possible un-lucky scenarios by which your CLL cells may have learned to turn a deaf ear to suicide signals, by virtue of forgetting how to make good TP53 protein.
- FISH test reveals you are likely to be an aggressive case, a large percentage of your CLL cells have lost the particular snippet of information contained in the 17p53 gene – your FISH test reports the dreaded 17p53 deletion. Without the right instructions found only on gene 17p53, your CLL cells cannot make TP53 protein and can therefore avoid your body’s commands to commit suicide. Such cancerous cells continue to live and produce babies with abandon, leading to a rapidly proliferating cancer.
- Your FISH test says nothing about any 17p53 deletion and everything seems to be in order at first blush. But if your CLL cells have their 17th chromosome at the crucial p53 is gunked over with excessive methyl groups, your CLL cells cannot read the DNA directions, cannot make the necessary TP53 protein and can therefore avoid committing suicide. In this instance, methyl groups are biologic versions of ugly wads of chewing gum in our roach analogy. This is called epigenetic silencing, one of the mechanisms by which cancers can initiate and progress unchecked. I strongly urge you to read our earlier article on epigentics. Better understanding of this important process may yield better therapy options in the near future. Already several de-methylating agents (scrubbers to remove the chewing gum, as it were) are in clinical trials, especially at OSU.
- Even if 17p53 gene is still there in your CLL cells, and it is not gunked over by methyl groups and therefore not epigentically silenced, it is possible that an error has crept into the DNA sequence at that particular location. A mutation has occurred that garbles up the instructions just a tad on how to make proper TP53 protein. When the how-to instruction in your genetic code have been corrupted due to mutation, your CLL cells make an equally mangled and garbled version of TP53 protein. After all, the protein made is only as good as the instructions that went into its making. Mangled TP53 protein cannot do the job it is supposed to do, namely force cancer cells to die.
If for any of the above reasons your CLL cells cannot make the correct form of TP53 protein, you are up the proverbial creek without a paddle. Without this home-grown cancer killer to keep them under check, the CLL cells can turn a deaf ear to any suicide commands. Your body has a much harder time dealing with such rebellious cancer cells on its own. You have no choice but go to your local oncology practice and choose between the various expensive and often times toxic chemotherapy options available, in order to control CLL.
One last point and we can wrap this up. The library in its infinite wisdom chose to order two identical books, two identical 17p books with the same instructions on page 53. Even if one of the two books got stolen, page stuck together or otherwise vandalized, it is possible you will get lucky and find the second copy with the necessary instructions on how to make the roach killer.
In CLL lingo, each cell in your body (including CLL cells) has a pair of #17 chromosome, each one has the precious 17p53 gene. Having both copies in pristine condition is the best case scenario, but having even just one of the pair working right is acceptable and TP53 protein can still be made correctly.
All hell breaks loose if both copies of 17p53 are lost, silenced or otherwise asleep at the dead-man switch. Such cells are very rebellious and will not commit suicide on command. When cancer cells continue to have babies but refuse to die, we have a case of rampant population explosion, a rapidly growing cancer. Cancer cells without the ability to make TP53 are also a lot harder to kill by externally administered kick in the pants and patients with this chromosomal defect are likely to have poorer response to chemotherapy.
A well conducted FISH test can only speak to the presence or absence of the 17p53 gene. It can tell you whether one or both copies of this gene are physically missing. FISH testing cannot say anything about 17p53 genes that are physically present, but buggered up or gunked over in some fashion and therefore unable to do their job.
We need this new lab test
If you are with me this far, it is obvious that what we need is a lab test that looks for properly made TP53 protein, since the protein is the business end of the whole suicide switch. When rubber meets the road, the zillion dollar question is this: can your CLL cell make this suicide protein in sufficient quantities, and make it with no mistakes?
Right now, only a few of the expert centers are able to test for the TP53 protein. Most commercial labs do not offer this test, and I am willing to bet most local oncologists will not order it even if such a test is available, not until they have a lot more CME units under their belts and there is expert consensus on the need for such a test. And a lot more patients are aware of it and ask for it.
A couple of years ago CLL Topics negotiated with Quest Diagnostics to get the company to offer a comprehensive CLL diagnostic package at reasonable cost. FISH test was included in this package. It looks like we need to get back into that game once more, get our CLL experts to develop consensus on how exactly to test for TP53 protein and then get one of the commercial labs to offer the test at an affordable cost.
After a waiting a few days for members’ questions and discussion, I will review recent papers that highlight the importance of understanding the role of TP53 protein in cancer prognostics.
Did you like my roach analogy? I must say I got a chuckle out of it. PC would have made me change it to something less gross. Hah. He is no longer here to go tut-tut and wag an editorial finger at me, so roaches it will be.
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13 comments on "How to make an effective roach killer"
Good article. I recently asked a well known New York specialist at a CLL lecture (not Rai or Furman) about p53 testing and I don’t think he got it. It is not part of the management landscape yet and it should be.
A number of recent studies seem to suggest the importance of testing p53 function in both directions. 17p del is not always that aggressive, especially if it is present at the beginning and has not developed after treatment. On the other hand, some of us without 17p del are missing functioning p53 will have a more difficult course.
Brian
I am confused. Is the test needed only for 17p deletion or for all cases?
What is actually being tested and what do you do with the results ie do the results guide treatment choices or what?
Given that we have oncs not up to speed on what is known at present, are we adding one more level of ignorance for that group?
My wish list would include a commercial test for TP53 protein. By the way, this is already done by some of the expert centers in some of their clinical trials.
The bottom line is this: FISH test results for 17p deletion do not tell the whole story. In some cases FISH may show no deletion in 17p53 gene, but the gene may be corrupted or otherwise not working and therefore not able to do its job – namely, making the TP53 protein.
Why is this important? Well, most experts now agree that lack of effective 17p53 function (ability to make proper TP53 protein) is a strong predictor of aggressive disease, and patients with this defect are most likely not going to respond to standard chemotherapy drugs such as fludarabine, or even Rituxan. People with dysfunctional 17p53 gene (whether it is actually deleted or just messed up) do not respond all that well to FCR combo either, most of them get partial responses that don’t last very long. In fact, there are very few drugs that work independent of the 17p53 pathway. Flavopiridol is one of them. Revlimd is another.
So, why should we care whether or not our CLL cells have a properly functioning 17p53 gene that can make TP53 protein correctly? Here is why. With this bit of information we can make better therapy choices. Why would we go through a therapy regimen that is not going to work, and absorb all the toxicity for no good reason?
Consensus is also emerging that people whose CLL cells cannot make TP53 protein are likely candidates for a stem cell transplant. May I suggest you read our earlier article “Catch-22” on the CLL Topics website. Making transplant decisions is not easy.
By the way, the same logic also applies to the other big & bad chromosomal abnormality, the 11q deletion. Again, FISH test can only tell us if this important tumor suppressor gene (called the ATM gene) is physically present or not. FISH does not tell us whether or not either of the two ATM genes are actully doing their job properly, making the ATM protein correctly.
Several experts I talked with suggest that in patients with a single 11q deletion to begin with, over time as a part of clonal evolution the second one can also get buggered up, even if it is not actually broken off (deleted). Tim Call of Mayo commented that people with single 11q deletion at diagnosis seem to trundle along quite nicely for the first 5-6 years because their second 11q gene is still working and doing what it is supposed to do – making the ATM protein. But things turn ugly after that time period in a majority of these patients because they lose function in that second 11q gene as well. FISH test may not be able to pick it up if the second 11q gene is not actually deleted, just messed up.
It may be a case of being lulled by a false sense of security if we depend solely on FISH test results. We need lab tests that can actually look for the proteins that 11q and 17p are supposed to make.
Let me make this a bit more personal, why relying on only FISH can be very misleading.
My husband PC had only single allele 11q deletion. That did not change over the several FISH tests he had over the course of his CLL. He went for 7 years using only Rituxan and Humax-CD20 to keep the disease under control.
Our game plan was to “save” the big gun of FCR (actually in his case FCH, since he could not use Rituxan and therefore substituted Humax-CD20) for getting a really good remission just ahead of going into a transplant. We were so sure he was going to respond well to FCR / FCH, afterall FISH test said he still had one good 11q gene!
Not so. Six cycles of struggling through FCR / FCH got him precisely nothing. The bulky nodes in his abdomen did not shrink worth a damn. It is only after he switched to Revlimid that we saw any improvement. As I sid in my comment above, Revlimid and flavopiridol are two drugs that do not need the ATM / p53 pathway. Judging from the way PC responded, after the fact it became clear his CLL cells were not just deleted in one of the two 11q (ATM) genes, they were completely dysfunctional in the other remaining 11q gene as well. But for the fact that Revlimid was able to salvage, there would have been no way to get a decent remission ahead of the transplant.
In this game what you don’t know can side-track you into dangerous scenarios.
I still recall the cold look from my doc when I asked (after treatment) how she had known that FCR would work on me without checking for the 17p deletion?
Getting them to do jjust what they already know to do is still a big problem.
I am a good example for the limited benefit that current marker testing can offer regarding prognosis or optimal treatment options. My FISH (done twice and confirmed by Byrd OSU) shows 13q del only, IgVH mutated, CD38 neg. I was also HemeScanned which revealed no other deletions but “Loss of a single BAC clone (RP11-359L2)on chromosome 22q11.2)significance unknown. I am told it is un-interpretable. I did have a ZAP-70 58%+ but it was considered probably incorrect by Dr. Hamblin after I sent copies of my blood work to him. Looks good so far but on the dark side of the balance sheet my ALC has a relentless upward curve from 23.2 in Sept.’06 to 227.3 two weeks ago. I have multiple node group involvement with 6.5cm cervical nodes, unknown internal nodes and a B2M of just under 4,000.
This makes treatment decisions more difficult. I have corresponded with 17p deleted patients with much slower disease progression than I.
The epigenetic silencing of 13q deleted folks has been found to involve miR15&16 by Carlo Croche now working at OSU. Do you have any word on progress toward therapeutics?
Can or should we advocate for stimulus money used to further in depth gene and molecular testing on the presumption that me may have many of the drugs needed to manage CLL only if we knew how to use them better? Are we not at a point where further drug development will be co-dependent on a more detailed understanding of what is actually damaged, missing or “gummed up” in each patient?
PS – I like the Roaches; go with your instincts!
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Wayne:
You are the perfect poster child for the story I was telling in this article. Just looking for the physical presence or absence of a small set of genes (13q, 11q, 17p and 12 Trisomy) is not sufficient. The age of proteomics has dawned long ago, we need to be able to measure and quantify the level of the corresponding proteins made by these genes. It is no use having the genes in question physically present if they are not doing their job and making the correct form of the protein they are supposed to make.
You are very right of course; we need money for doing the kind of fundamental research that improves our understanding of CLL. The techniques and methodology are already in place. But there has been very little money looking at basic science in the last little while. Any money coming from industry sources is all focused on short term projects that have a chance of yielding commercial success right away. In the present economic situation I am not sure how we get hold of some of that stimulus money. And of course, how we make sure the money is not wasted.
This is strictly hubris on my part: in my daydreams I fantasize winning one of those lottery jackpots with hundreds of millions of dollars. If that ever happens, I am willing to put every dime of it to good use, and (this is the hubris part), I am willing to bet we will have breakthrough therapeutic options within 5 years. I guess it will stay a daydream, since I have yet to buy a lottery ticket.
Another poster child. I was treated with 8 rounds of f then rf 2 yrs. ago on the basis of a 95k white count alone (another long story). I had a 5 week remission then a relentless march to the current 260 k white count with 98% lymphs.
I have since done my home work (Thanks Chaya). I’ve been to M.D.A. , the Hutch. , and Mayo which is my current clinic. I’ve learned I have a single 13 del., unmutated and cd38 neg. A bucket B with only a partial and short remission to an aggressive therapy. Something else is going on here.
The up side to all of the above is I am functioning well with these conditions with very little node involvement. I am 66 yrs old and I run 4 mi. a day. However I am on a watch list for salvage and go in for a check up quarterly.
Dan
Chaya,
Thank you for this article-so helpful. I know we have made progress in our understanding of the genetics of CLL but we are in early stages. You have increased my understanding of areas of chromosomes being present which many viewed with a sigh of relief, but as you point out they could be in a non-functioning state.
Chris
Chaya – the article is very interesting. I liked your roach analogy – you have a way of presenting in terms that make the issues simple to understand. I was DX Dec 2000, watch and wait. I have just started my 3rd round of chemo, after a nice long 3 year remission. In terms of disease aggressiveness, I feel very fortunate in comparison to a lot of other folks. White count rate is in excess of 6 months doubling time, and some nodes bulking up.
I had a 3 year remission after my first round also. My oncologist saw no reason to change chemo from last time (FCR), so that’s what we are doing. The only difference this time is they are giving me Neulasta 24 hours after the last session. Your comment about “saving the big gun” of FCR for just prior to transplant, caught my attention.
May or may not be worth mentioning, after my first round, I visited the Hutch for advice on salvage. I was wisely told I was not close to needing to be considered for transplant. During the process I have learned that my chromosomal aberration is trisomy-12, which I believe is relatively benign, compared to 17P deletion.
Phil
I am always impressed by your ability to explain complicated genetic concepts in clear language. The roach analogy didn’t strike a chord for me, but your clear explanation of why FISH isn’t the ultimate diagnostic tool and why we need better lab tests that look for TP53 and other proteins was good. Thanks.
amc86
as always your explanations of complicated and unexplained details (by my oncologists) are extremely helpful and wonderfully clear. please keep it up.
Hi Chaya,
Thanks so much for the FISH explanation. I can never make heads or tails out of those reports. He seems to have only the 13Q deletion and high 98% CD 38 expression. I have always suspected that FISH was not the end all since Arnie’s disease has progressed so much. (I can’t really have an in depth discussion with the onc because Arnie freaks out so much) He is currently treated at MDA with Keating. Nothing is working. Even tried OFAR. Revlimid has been a question mark because Arnie is 6″4 280 lbs. They aren’t comfortable with what dose to use. He’s scheduled to go back the 1st of April, Keating is pondering his next move. HuMax has been mentioned in combination with Revlimid. We’ll see.
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