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New funding accelerates research on B-cell lymphomas

Grants and philanthropic donations -- the fiscal engine of cancer research -- fuel scientific discoveries in the lab and new therapies in the clinic that might otherwise remain stalled. Recently, researchers in the DF/HCC Lymphoma and Myeloma Program gained greater traction on the battlefield against B-cell lymphomas from three sources: the competitive renewal of an NCI program project grant, a new Specialized Center of Research (SCOR) grant from the Leukemia and Lymphoma Society, and a generous gift from a private donor.

The interrelated projects made possible by this funding reflect a collaborative approach to lymphoma research that spans disciplines and institutions, and captures the expertise of veteran and junior investigators alike. Program leader Margaret Shipp, MD, (DFCI) is quick to acknowledge the power of the collaborative research model, especially in light of current constraints on the federal budget. “It’s a way of harnessing different types of expertise that reside in multiple institutions to achieve synergies that no one group could accomplish,” says Shipp.

Renewal Rewards Collaboration, Expands Research

Renewed immediately, the PO1 grant, titled “Molecular Targets of Germinal Center B-cell Lymphomas,” joins basic, translational and clinical investigators with pathologists and biostatisticians from four DF/HCC institutions -- BWH, CHB, DFCI, and HMS -- as well as colleagues from the Broad Institute of Harvard and MIT and the CBR Institute for Biomedical Research.

During the first five years, investigators developed informative mouse models, identified critically important pathways and rational targets, and differentiated specific subtypes of germinal center B-cell lymphomas. Projects in the renewal expand this work to better understand the underlying pathogenetic events in these diseases, the incidence of which has increased dramatically over a decade, and to develop more effective therapeutic interventions.

According to project leader Frederick Alt, PhD (CHB), scientific director of the CBR, germinal centers are a “dangerous environment.” A critical part of the immune system, germinal centers are where B cells mature into antibody-forming cells and memory cells. When activated by antigen, mature B cells deliberately break the chromosomes that contain immunoglobulin (Ig) genes, explains Alt, and rearrange the genes to create the specific class of antibodies needed. If the DNA gets broken in both strands – and this double-strand break is not repaired – however, chromosomal translocations can occur. Since Ig genes are naturally expressed at very high levels to produce ample antibodies, if an oncogene happens to fuse with Ig genes during translocation, it too becomes overexpressed and can cause transformation. “That happens frequently in mature B-cell tumors,” adds Alt.

To more closely mimic these lymphomas, Alt and colleagues are creating sophisticated mouse models with defects in DNA damage repair and deregulated Ig gene rearrangements that predispose to oncogenic translocations. His lab has already shown that inactivating this repair pathway in mature B cells undergoing gene rearrangement causes genetic instability, but does not produce a high rate of cancer because checkpoint proteins cause the damaged cells to die. “When we eliminate both types of proteins in mature B cells,” explains Alt, “every mouse develops tumors.” Thus his new project involves inactivating one DNA repair protein at a time (there are several in the pathway) in combination with checkpoint deficiencies to model more types of germinal center B-cell lymphoma. “We’ll study the models to further elucidate particular pathways and discover new characteristics of these tumors,” says Alt.


Profiling Human Tumors

Another new component of the renewal, according to Shipp, is combining the genetic analysis of human tumors with the transcriptional profiles developed during the first phase of the grant. Platform-based approaches including high-density SNP arrays – so-called “SNP chips” – can scan an individual’s genome for variations (single nucleotide polymorphisms) in DNA sequence and copy numbers, while RNA transcriptional profiles reveal the differential expression of an individual’s genes. Together, these analyses compare the basic tumor blueprint and associated operating instructions to create a more comprehensive profile of which pathways or sets of genes are driving the growth of tumors. In the first phase, platform-based approaches -- which rely heavily on collaboration with investigators in the DNA Microarray/Bioinformatics Core, directed by Todd Golub, MD, of the Broad -- helped delineate different subtypes of tumors and led to improvement in diagnosis and identification of promising treatment targets, notes Shipp.

Providing the samples of well-characterized human tumors for genetic analysis is the domain of pathologist Jon Aster, MD, PhD (BWH), director of the DF/HCC Specialized Histopathology Services Core. “As the stewards of the lymphoma bank,” says Aster, “we are the liaison between clinical diagnosis and translational research. Once markers are identified, we also examine archival tissues to see how effectively they predict outcome and responsiveness to therapy. In addition, because we diagnose human lymphomas every day, we judge how closely a particular mouse model resembles its human counterpart.”


Blockbusting Proteins

In the renewal, investigators will also expand the clinical component of the grant by designing inhibitors against a short list of high-priority targets, identified in the first term, and taking them into clinical trials over the next 5 years. One example is a PKC-beta inhibitor, which showed promising results in a recently completed Phase II trial in patients with relapsed or refractory diffuse large B-cell lymphoma. A multinational Phase III trial is now under way, evaluating the effect of the inhibitor in early-stage disease. The Histopathology Core played a key role in validating PKC-beta as a potential target and will perform this vital function in upcoming clinical trials.

Another innovative approach to lymphoma therapy has emerged from a young investigator, Loren Walensky, MD, PhD (DFCI), whom Shipp recruited because of his novel technique for making peptides with new, potent pharmacological properties. Walensky will use this technique to try to target and neutralize cardinal proteins that drive the development of lymphoma.

“The longstanding challenge has been to identify or create small molecules that can block cancer-causing proteins, some of which have large and complex interaction surfaces,” explains Walensky. Theoretically, peptides, because of their natural complexity and greater surface area, are better suited than small molecules for the job of blocking these intricate surfaces. In many cases, the point of contact between proteins involves an alpha-helical peptide, a short stretch of amino acids arranged in a three-dimensional coiled motif. Although such peptide fragments can be made in the laboratory, they can lose their architecture because other structural components of the natural protein are absent.

“If the amino acids are not properly configured in three-dimensional space, the binding target may be presented with a piece of spaghetti instead of a slinky, such that the peptide loses its biological activity,” explains Walensky. His technique reinforces the alpha helices by inserting a “hydrocarbon-staple” that firmly braces the naturally coiled architecture. Chemical stapling also renders the compounds cell-permeable, remedying a common shortcoming of peptides and enabling them to reach the many critical cancer targets inside the cell.   

SCOR Grant Extends the Reach of B-cell Lymphoma Research

Last year, as investigators were writing the PO1 renewal application, they realized there was much more research to be done in B-cell lymphomas than could be supported by the NCI grant alone. So Alt submitted a separate application to the Leukemia and Lymphoma Society for a SCOR grant titled “Pathogenetic Mechanisms and Therapeutic Targets in B-cell Lymphoma.” Scheduled for funding in late October, this new grant taps investigators from four DF/HCC institutions who will explore the basic biology of tumors in mice and humans to elucidate oncogenic B-cell receptor signaling (a project led by Shipp) and DNA repair-associated genetic abnormalities (a project headed by principal investigator Alt); Tony Letai, MD, PhD, and Glenn Dranoff, MD, (DFCI) are leading other projects. Like the PO1, the SCOR grant requires the expertise and support of the DF/HCC Hematopathology Core, directed by Aster, and also involves a project, co-led by Walensky and Klaus Rajewsky, MD (CBR), to evaluate and attempt to inhibit other potential lymphoma targets using stapled peptides.

New Testing Center Links Donor Desire to Research Need

Facilitating the success of these projects and other research efforts across the consortium is a new DF/HCC Lymphoma Target Testing Center (TTC), a collaboration of investigators from BWH, DFCI, HMS, MGH, and the Broad. The start-up of the TTC was sponsored by a private donor in search of a way to finance and advance lymphoma research. The timing was just right.

“We had identified a testing center as a high priority to short-track the time it took from basic discovery to clinical therapies,” says Shipp. “Investigators needed access to well-characterized cell lines and models that reflect the biology of specific lymphoid malignancies.”

The TTC will help DF/HCC investigators rapidly identify and credential rational therapeutic targets and assess the efficacy of candidate target inhibitors. Overseen by a Steering Committee including Shipp, Golub, Aster, Nancy Harris, MD (MGH), and Andrew Kung, MD, PhD (DFCI), the Center will provide cell lines with extensive background information regarding underlying genetic lesions and transcriptional profiles; it will also generate tissue microarrays of the cell lines for use in immunohistochemical analyses, and develop murine models to evaluate the growth of the lymphoma cell lines in vivo.

“We believe this Center will have the highest impact on the greatest number of investigators,” adds Shipp.

Image above: A chromosome paint on a dividing cell from a mouse model of mature B-cell lymphoma, revealing translocations that will be characterized as part of the SCOR grant. [from Frederick Alt, PhD (CHB)]