By Peter Martin, MD and Olivier Elemento, PhD
Based on multiple randomized phase 3 studies initiated over a decade ago, R-CHOP chemotherapy is the standard of care for first-line treatment of patients with diffuse large B-cell lymphoma (DLBCL). However, sometimes R-CHOP is not successful. Fortunately, our understanding of lymphoma has evolved over the past decade.
It is increasingly clear that “DLBCL” is a heterogeneous group of related tumors. Studies using gene expression profiling , have revealed that DLBCL can be divided into three subgroups based on the probable cell of origin (i.e., the cell from which the lymphoma was derived): activated B-cell like DLBCL (ABC), germinal center-like DLBCL (GCB), and a third group, termed “type 3”, that doesn’t possess any specific characteristics (click here to read the abstract). So far, the clinical relevance of differentiating between the ABC and GCB subtypes of DLBCL remains somewhat unclear. Nonetheless, studies done at Weill Cornell Medical College and elsewhere have suggested that certain treatments might preferentially benefit one subtype (see here and here). As a result, ongoing clinical trials are evaluating newer therapies targeted to the appropriate subgroup.
Just as we are beginning to understand the significance of DLBCL gene expression profiles, recent technological advances in DNA sequencing are making the rapid, high-resolution sequencing of a tumor’s entire genome (DNA code) possible and affordable . Two recently published papers describe the results of long-term efforts by two different groups to sequence the genome of DLBCL tumors.
A Groundbreaking Study
In a paper entitled “Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma” published in the journal Nature, Gascoyne, Marra and colleagues describe the results of a groundbreaking study. The researchers sequenced the entire DNA code from lymphoma tumors and compared the results to normal DNA obtained from the same patients. They were able to identify several genes that were mutated in the tumors but not in the normal DNA. Using these data, they were able to identify 109 genes with a potential role in lymphoma. Importantly, they found that the MLL2 gene was mutated in 32% of DLBCL tumors and MEF2B was mutated in 11.4%. Both of these genes play crucial roles in the epigenetic modulation of chromatin . The fact that the mutations were common but not present in every case suggests that some DLBCL subtypes may be more or less dependent on epigenetic dysregulation. Importantly, the findings also suggest a role for epigenetic therapies. Click here and here for examples of clinical trials at Weill Cornell that work through epigenitic modification.
In a second paper entitled “Analysis of the coding genome of diffuse large B-cell lymphoma” published in Nature Genetics, Dr. Dalla-Favera and colleagues reported the results of a study to sequence the entire coding genome of paired DLBCL tumor and normal DNA from six untreated individuals. The researchers identified 93 genes that were commonly mutated, 26 of which had never been implicated in cancer. Included in the list of mutated genes was MLL2, providing support to the findings reported by Marra and Gascoyne.
These two studies provide critical information regarding the complexity of DLBCL tumors. In the short term, researchers will use the data to develop a better understanding of the various pathways that work to promote development and survival of lymphoma cells. These discoveries may lead to new classification systems, in the same way that gene expression profiling identified the ABC and GCB subtypes. In the medium term, the data will be used to identify key targets for development of novel lymphoma therapies. These discoveries will lead to new, and hopefully better, drugs that are more specific to lymphoma cells and have fewer side effects. In the long term, the goal is to be able to sequence each patient’s tumor, identify all mutated genes in that tumor, and construct a regimen of drugs and dosages that is most likely to be effective. This goal is the goal of personalized medicine, that is, a medicine informed by the genetic makeup of each patient’s tumor and normal tissue.
Personalized medicine is probably years away from becoming a practical reality, but these two papers demonstrate that we are moving quickly in the right direction. For example, the Human Genome Project (an international research project to determine the sequence of the human genome) began in 1990 and was completed in 2003. We can now sequence an entire human genome in a couple of weeks.
A New Era of Cancer Medicine
At Weill Cornell Medical College, we are on the forefront of these technological advances. The Melnick lab is one of the few labs in the country able to rapidly and cost-effectively sequence DLBCL genomes with high resolution. The Melnick lab uses the same sequencing technology to determine which genes are aberrantly expressed in each tumor and to find non-genetic (epigenetic) differences between normal cells and tumor cells. The Melnick lab is working in close collaboration with the Elemento lab, a lab that specializes in bioinformatics and has specific expertise in analyzing the large amounts of genetic data coming from these experiments.
At Weill Cornell, we are preparing to embark on a new era of cancer medicine. Beginning shortly, we will be working to sequence every lymphoma tumor for every new patient seen here. We hope to pilot the use of this information to select individual drugs targeted to treat individual patients not eligible for other clinical trials. We also expect to provide vital information to ongoing international clinical and genomic research projects.
1. Gene expression profiling is a laboratory test that describes the degree to which certain genes are expressed (turned on or off) in a given tissue sample. Specifically, a piece of tissue (DLBCL tumor tissue in this case) is broken apart and the RNA is extracted. RNA is like DNA—it contains important information that is used by a cell to make proteins. Unlike DNA, however, which is essentially a complete copy of the genetic code and is the same in all cells in an organism (e.g., lung cells, gut cells, blood cells, etc.), RNA represents only those genes that are of particular importance to a given tissue (i.e., white blood cells make a different set of RNA than skin cells).
2. Sequencing is a technique that allows researchers to determine the genetic code of cells within a given sample, tissue or tumor. DNA sequencing generates massive amounts of data that need to be crunched by powerful computers and interpreted by cross-disciplinary teams of clinicians, scientists and computer experts .
3. Epigenetics is the study of changes in gene expression that are not due to changes in gene sequences. For example, all cells in a body share identical genes (except for tumors). Nonetheless, some cells become skin cells while others become lung cells and others become brain cells. Cells are able to differentiate into different tissue types as genes get turned on or off; i.e., the gene sequences are the same but only some of the genes are actually being used in a given tissue type. The mechanisms that are responsible for turning, and maintaining, a gene on or off are called epigenetic mechanisms. Currently, we believe the DNA methylation and histone modification are the two most important epigenetic modifications.