Genomics of CLL: New Developments

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Transcript: 

Dr. George Calin: So, thank you very much. Of course, it’s all the time a pleasure to talk about what you like more, to talk in front of colleagues, and most importantly, to talk in front of patients and the ones who are affected. So, this is my scientific title, but this is a true title. So, basically, what I will tell you today, it’s a little different of what you heard. I will not talk about proteins. I will talk about non-coding RNA, and I will not talk about too much how we are doing it, but how we use your samples and how we use your donation in order to do a type of science that you cannot really do before in publications, because we are the first one to discover the thing.

So, I start from the story, and, in fact, my colleague and friend Sabrina Bertilaccio introduced very nicely this concept of very short RNAs that never, never produce proteins, and also, you learn about BCL-2, MCL-1, BTK, and so-and-so about proteins, but regulates the protein expressions. The name, it’s microRNAs, and I will tell you also about very long RNAs all have one characteristic, have nothing to do with the codifying on proteins, but regulates the activity of proteins.

I know that my life was quite difficult before, because a lot of people were saying, “Calin’s loving the graded RNAs without importance,” really? Nobel Prize 2024 was for discoveries of microRNAs. So, job done, are extremely important. Are we lucky? Of course, and I’m one of the luckiest in the world.

Why? Because I work with a great scientist, Carlo Croce, who is very, very, very skilled scientist, and we were exactly the No. 1 who in 2002 for the first time said, “MicroRNAs are important in any type of disease,” and not any type of disease, but chronic lymphocytic leukemia, and this was done starting from two samples, one from Michael Keating, one from Kanti Rai with 13q deletion. Digging into the genome of these two patients, only two, two patient samples, we identify that these two microRNAs are going down, and they regulate BLC-2 protein. Is this important?

Yes. A lot of you know better as me, CLL, it’s a bipolar disease. Most of you survive a decade or longer. Why? Because low miR16, expression increase BCL-2 expression and venetoclax (Venclexta), it’s working, as Varsha Gandhi showed in the others. Venetoclax is working better with ibrutinib (Imbruvica) as itself, but it target the protein which is regulated by microRNAs. But what we are doing with the five, 10 percent Richter transformation as the one who relapse high, aggressive CLL. To be frank , we cannot tell you what we are doing. You know why?

Because we don’t know the mechanism. How can we give to the patients a very thoughtful therapeutic if we don’t know the mechanism? The concept is, when the world works on a disease and doesn’t find with usual tools, the mechanism, something different should be the true mechanism. And I will tell you the story, and here is a Richter transformation, a very nice image where the disease was located in heart, very, very, very rarely, and you can see very nicely the difference between the cells in non-aggressive, indolent CLL and the cells in the Richter transformation which are located not in blood but in tissues, who proliferate and looks very ugly. Not anymore.

The quite decent round, the malignant cells who are indolent. And we start from a concept. How come bacteria are not smarter as human beings? Why? Because exomes are producing proteins. Bacteria, over 90 percent of the genome produce proteins, not non-coding genome who do not produce proteins. In the humans, you see down, right, quite 2 percent of the genome produce proteins, and all other non-coding. Really, can you believe as patients, we believe as scientists, and you guys believe as clinicians that focusing on 2 percent of the genome will solve the diseases in humans? It’s wrong, because most of the diseases will have the mechanism is hiding in 97 percent of the human genome.

And I will tell you a story, funded very much from CLL Global, from the CLL moon shot, a story about how we dig into this 97 percent of the genome, and we identify a completely new therapeutics combination for patient with very aggressive CLL. And here is, of course, a nicely shown stuff of what we are focusing and what we tell you day by day. Let’s give us the genome, and we’ll do whole exome sequencing. We’ll check the proteins. Really checking the proteins will make the difference? I don’t think so. Checking all the genome will make a difference. And, in fact, this is my first paper when I step in MD Anderson in which I was looking to something that is very strange. In that moment was a peculiarity of the human genome.

Five percent of our human genome never change in evolution between human, mouse, and rat. Can you believe that 300 million years of evolution are focusing on a part of the genome who make no sense? I don’t think so. We publish in that moment something that I think was published well. The fact that this ultra conserved element of the human genome produce RNAs who do not codify for proteins, because they are located in between genes.

And here, I start the story, and I will show you during my presentation, also, faces of the people in the lab, because I think they are the important one who should believe, should trust us and should develop, at best, our thinking. One was Linda Fabris. I give her this region name, Ultra Conserved Element 206. Look very strange, no? The 206 element in all the human genome, and I give to her because what we identify, we identify that in Richter patients, it is a dichotomy between the part of the genome who amplify this region of UCE 206 and the part of the genome who lost P16. P16, it’s an essential protein for the patient with Richter transformation.

Not only, but one of patients give us a wonderful sample, a sample from Richter in which the malignant cells were not hiding in the ganglia or in the bone marrow, but were present in the blood. It was that very short period of time when the cells tried to migrate to other lymph node and so on. What we found in this patient with 65 percent malignant cells in the blood, Richter, we found these genes that we name TRUC-16, thousand of times over-expressed versus all other CLL. For me, this was in 2022, something like that, the bingo moment, like in 2000 when we discover microRNAs in cancer.

TRUC-16 is this region. It is extremely important that you know why, because one of you, the patients, in his blood samples of Richter show us the reality. One thousand times over-expression of our gene of interest who never codify for protein and come from the part of the genome which is the same in me, you, rat, and mouse. And then, Linda worked a lot about six years on the project, about six years, and look what we found. I want you to focus only on the right side. We found that this long, long coding RNAs, RNAs is on who didn’t codify for proteins bind to the p16 and block protein p16 expression. This inducing a high level of two important proteins, CDK4 and CDK6. What are these? Are proteins to induce proliferation.

Make your cells to proliferate quicker, while the indolent CLL cells don’t proliferate, they don’t die, because they have high BCL-2, because they have low miR15-16. The aggressive CLL and the Richter cells proliferate a lot because they have the amplification of this piece of the genome, which produce a long, long coding RNA who bind a very important protein, which we know is, it’s low expressed in Richter, but never the genome is deleted, and this protein lost the regulation of CDK4 and 6.

Of course, we use models in order to find out that this is the truth, and yeah, we found that this, this treatment with palbociclib (Ibrance), a CDK-4, 6 inhibitor, who, by the way, it’s used like standard of therapy in breast cancer. So, this is a therapy that is already of the approved. It’s working also in cells of CLL with high level of this gene that we discover and clone in my lab. Now, here is Linda [Fabris], here is Sam Akanksha what they are doing? They took appendix from Richter patients, and they will do the therapeutics on the mice in order to see if it happened, what already Linda and Sam prove to happen in a cell and with high TRUC-16.

Here is the data. Basically, mice treated by gavaje with palbociclib, CDK4/6, inhibitor. You can go please to your cell phone and check, CDK4/6 inhibitor in CLL Richter transformation, NIH.gov. You know how many results you will find? Zero. Nobody was thinking to this, because nobody knew the mechanism, because nobody was looking for this mechanism, which is completely new. And in fact, if you check here very carefully, you will see that the treatment, three out of eight mice survived over 250 days. We stopped the experiment because we said, “Enough is enough. We have to publish it in a paper,” and in fact, what you see here is not just a therapy wipe out the malignant cells. I don’t want to sell you dreams.

The therapy blocks the proliferation of the cells. No cure, CDK5, PAX5, little, very little clusters of two, three, four malignant cells. So, hyper-proliferation is wiped out. Now, is this enough for a scientist? No, is not enough. Here, Kinga, Zara, Erik and Swati create a mouse, a mouse in which we over-express this long, long coding RNA. The mouse developed, surprise, surprise. No, for us is no surprise, developed Richter transformation. Look here. The mouse have a huge boost in plasma LDH during the evolution, about 16 to 18 months of it.

So, not only we have an idea, not only we have cell lines, but we have a model in order to exploit what we are seeing and to use your cells and to use the drugs in order to see if this is a good therapeutic, and finishing, we took lymph nodes from these mice. And with a colleague named Humam Kadara, from translational molecular pathology, we use this very new technology to map the geographic of the lymph nodes in wild type and transgenic mice for what type of cells you find. No surprise for us, but happiness for us. Why? The transgenic mice was Richter, have high proliferating B-cell compartment. So, CDK4, 6, it’s really a major component, because induce the proliferation in these mice. Now, you will tell me, “You are a dreamer.”

No, I’m not a dreamer. I like to read, in fact. In MD Anderson, it’s already a clinical trial with the ibrutinib and palbociclib. What we are doing now, we will connect with people from analytic to do a BTK inhibitor plus a CDK4, 6 inhibitor for the first time in the patient with CLL. We don’t have to go to FDA. This already an FDA-approved drug. What is new is the use of this combinatorial therapeutics who was done for other type of cancer in patients with Richter or highly aggressive CLL. So, in some of you, sometime in the next month, if you are lucky, there’s a company agree with the deal, this type of therapeutics will move forward.

So, what I wanted to tell you, I wanted to tell you that having strange ideas in science for the first time, nobody could really in 2016, when I give to Linda Fabris a project about ultra conservation in CLL, because nobody was looking for, as nobody can in 2025 read about CDK4, 6 inhibitor and ibrutinib in CLL, because nobody is giving, but this is telling what have to happen when we are using the money that you are giving us in a very kind way, with young people who think in science, and also something very important. Good science means to open the door for everybody.

The door should be closed in front of you before. With this said, thank you, of course, to all the patients, all the families, and also to all my colleagues. I think the science is what makes this world better, and why not to say thanks to CLL Global, thanks to Michael Keating deal with the same place, because this is exactly a wonderful place to be and to do science. With this, thank you to all the patients, thank you who are listening, and remember. You are never working alone, because we scientists, we clinicians are close to you in order to cure CLL. Thank you very much.