Genetics and Epigentics

By Drs. Ghia and Smith

Chronic Lymphocytic Leukemia (CLL) is a disease that causes uncontrollable growth of body’s white blood cells, called B-lymphocytes or B cells. Patients with aggressive disease experience a rapid increase in white blood cells counts over a relatively short period of time and will require treatment soon after diagnosis. On the other hand, in patients with indolent disease, the rise white blood cell counts occurs more slowly. Unfortunately, indolent forms of CLL invariably transition to aggressive CLL, necessitating treatment. Understanding this transition from indolent to aggressive disease, known as CLL progression, is one Emanuela Ghia, Ph.D.’s primary research interests.

Dr. Ghia, an Assistant Project Scientist in Dr. Thomas Kipps’ laboratory, has been researching the mechanisms that drive the progression of CLL, collaborating with Erin Smith, Ph.D., from the Genome Information Sciences Division, led by Kelly Frazer, Ph.D., at the UC San Diego Moores Cancer Center. More specifically, they are working to identify the genetic and epigenetic changes that drive CLL progression.

What are genetic and epigenetic changes? 

Genetic changes are mutations that occur in DNA. Interestingly, depending on their location and type, some mutations may have no negative consequences on our health while others can facilitate cancer growth. For example, in CLL some mutations may accelerate the growth of B-lymphocytes. Epigenetic changes are due to alterations in what genes are actually expressed. Such control of gene expression allows for different cell types, such your as skin cells or blood cells, to have striking differences in what proteins they use even though both have the same blueprint DNA, which codes for these proteins. An important process that turns on or turns off genes is called “methylation”.

Drs. Ghia and Smith are evaluating leukemia cells from patients who progressed from indolent to aggressive disease and required treatment. Leukemia cells are collected at two time points: (1) within 1 year from diagnosis and (2) after 4 or more years from diagnosis and within 1 year of requiring therapy. The collection of these leukemia cells allow Drs. Ghia and Smith to perform whole-genome sequencing* to study genetic changes and to perform methylation analyses** to study epigenetic changes.

This study is designed to allow researchers in the field of CLL to understand the genetic and epigenetic changes that are the key players driving CLL progression. Moreover, this important study should provide hope for patients with CLL because it will enable the development of new therapies specifically designed to target the genetic and epigenetic changes determined to play an important role in CLL progression.

*Whole-genome sequencing is an efficient method to selectively sequence the coding regions of the genome and also to calculate allele frequency. Exons are short, functionally important sequences of DNA which represent the regions in genes that are translated into protein. In the human genome there are about 180,000 exons: these constitute about 1% of the human genome, which translates to about 30 megabases (Mb) in length.

**DNA methylation array is designed to interrogate whether known DNA CpG islands are methylated or not. CpG islands are genomic regions that contain a high frequency of cytosine and guanine next to each other. DNA methylation is one of several epigenetic mechanisms that cells use to control gene expression.

Drs. Ghia and Smith are working with the UC San Diego’s Moores Cancer Center “My Answer to Cancer” Program**. This initiative is working to pinpoint the root cause of several cancers, ranging from chronic lymphocytic leukemia to breast.

The UC San Diego Moores Cancer Center is poised to implement genomic sequencing and personalized care for all of our patients and transform the way we treat cancer. Sharing space with researchers and clinical trials means that the Moores Cancer Center can quickly deliver new discoveries from the laboratory to our patients. Simply put, UC San Diego Moores Cancer Center is the perfect place for the MY ANSWER TO CANCER initiative. Please visit “My Answer to Cancer” at to learn more about this initiative.

Removing the Block and ABT199


By Michael Choi, M.D. 

Chronic Lymphocytic Leukemia (CLL) has been described as a relentless accumulation of leukemic cells due to an imbalance of excessive cell proliferation and defective cell death. In other words, CLL cells have both “pro-survival” and “anti-death” mechanisms. In a previous article, we described the pathways on the pro-survival side, such as the B-cell receptor associated tyrosine kinases, and clinical trials of agents that block those pathways. In this article, we will focus on the opposite side of the equation: the mechanism by which CLL cells escape cell death, and how new therapies can overcome it.

Cell death is normally tightly regulated by proteins in the B-cell lymphoma/ leukemia 2 (BCL-2) family. BCL-2 sequesters and disables the proteins BAX and BAK, which when left free of BCL-2, signal a cell to die. When normal cells or their DNA are damaged, BCL-2 is bound and occupied by other signals, thus freeing BAX and BAK to trigger cell death. CLL cells (and other cancerous cells) have extremely high levels of BCL-2, to the point that its grasp on BAX and BAK cannot be overcome.

In recent years, therapies that inhibit BCL-2 have been designed and largely pioneered by our group and collaborators in the CLL Research Consortium. The pharmaceutical company Abbott has developed and refined drugs that inhibit BCL-2, including ABT-737, ABT-263, and ABT-199. In a phase 1 study treating patients with relapsed CLL, ABT-263 was strikingly effective: 90% of patients experienced a significant decrease in lymphocyte counts and the median progression-free interval was over 2 years. (Roberts, Seymour, Brown, Wierda, Kipps, et al. JCO, 2011)

Although very well tolerated overall, the most common adverse effect of ABT- 263 was a decrease in platelet counts due to the inhibition of one particular BCL-2 family member that is important for platelet function. Due to this, ABT-199 was developed to avoid this effect on platelets. Trials of this oral drug are ongoing, both alone and combined with other agents. Although these are early phase studies (phase 1 and 2), our years of experience with Abbott compounds and the clinical proof that blocking BCL-2 is an effective treatment make us confident that these new agents will represent a significant step towards our goal of curing this disease.

MicroRNAs in Chronic Lymphocytic Leukemia

 By Dr. Marek Mraz 

Chronic lymphocytic leukemia (CLL) is the most common leukemia among adults in the Western world and remains an “enigma” in modern hematology. The B-cell receptor (BCR) signaling pathway of CLL cells is known to affect the pathogenesis of CLL. The BCR signaling pathway is a complex network of proteins that regulate the response of normal and malignant B cells to the stimulation of the BCR by antigens. Morever, some of the prognostic markers used today in the treatment of CLL, such as ZAP-70 and mutation status of the immunoglobulin heavy chain gene (IGVH), are involved in BCR signaling pathways. A key research question, then, is what regulates the BCR in CLL cells? What makes a CLL cell so receptive to BCR stimulation?

Interestingly, a recently discovered group of molecules called MicroRNAs (miRNAs) was found to affect the BCR signaling pathway. MiRNAs are small sequences of RNA (one of the two types of nucleic acids present in the cells), which do not encode for proteins, but rather work to regulate the expression of other genes (see graphic). MiRNAs have been found to be uniquely expressed in almost all types of human cancers and are key players in the development of tumors. They also belong to a larger family of RNAs, called non-coding RNAs, whose expression is also deregulated in cancer.

Dr. Marek Mraz’s previous work described aberrant expression of miRNAs in the most aggressive CLL subtype (p53 aberration), and found that microRNA expression was associated with immunoglobulin structure. Presently, Dr. Mraz is investigating the role that a specifc miRNA, called miR-150, plays in the regulation of BCR signaling pathways in CLL. As part of this project, he is performing a large-scale search for the proteins regulated by this molecule. His results suggest that this miRNA might contribute to the deregulation of BCR signaling of CLL cells and thus contributes to their aggressive and cancerous behavior. The novel data on this miRNA’s contribution to BCR signaling in CLL will be presented at the American Society of Hematology (ASH) Annual Meting in December 2012. More importantly, Dr. Mraz’s work and research identifying relevant miRNAs, will ultimately be used to develop miRNA-based therapeutics.