Research

Cancer Molecular Pathology

Dr. Frederic G. Barr, M.D., Ph.D.
Building 10, Room 2S235
(301) 480-7176

To learn more, visit Dr. Barr’s CCR website.

General Information

Mailing Address:
Cancer Molecular Pathology Section
Laboratory of Pathology, CCR
National Cancer Institute
9000 Rockville Pike
Building 10, Room 3B55
Bethesda, MD 20892-1500

Research Synopsis

1. Overview

My research laboratory uses a multidisciplinary approach involving genomics and bioinformatics along with cell culture and animal models to study recurrent chromosomal alterations, such as translocations and amplification, in cancer. Our major current focus is rhabdomyosarcoma (RMS), a family of myogenic soft tissue cancers usually occurring in children, in which we are investigating the genetic basis, biological consequences, and therapeutic implications of chromosomal alterations. In addition, my laboratory works closely with pediatric oncologists and other clinical specialists to investigate the utility of these recurrent chromosomal alterations as biomarkers for diagnosis and management.

2. Molecular genetics of alveolar rhabdomyosarcoma

During the last two decades, my research laboratory has conducted studies to unravel the fundamental events responsible for an aggressive RMS subtype known as alveolar RMS. After cytogenetic studies of this cancer identified translocations between chromosome 13 and either chromosome 2 or chromosome 1, my laboratory identified that these translocations break the PAX3 gene on chromosome 2 or the PAX7 gene on chromosome 1, and join part of these genes with part of the FOXO1 gene on chromosome 13. This process results in the formation of PAX3-FOXO1 and PAX7-FOXO1 fusion genes, which encode aberrant transcriptional regulators. My laboratory’s recent studies are investigating how these fusion proteins function in the cancer cells, and are exploring how to manipulate fusion protein expression and function with the ultimate goal of developing novel strategies for therapeutically targeting these fusion proteins.

To complement these studies of fusion proteins, my laboratory is also investigating additional changes that occur in alveolar RMS and cooperate with the fusion protein during RMS tumorigenesis. To search for such events, we performed genome-wide screens of DNA copy number changes and small DNA changes. These studies revealed that, though there are few if any recurrent small DNA changes in ARMS, there are frequent changes in which chromosome regions increase in copy number by genomic amplification and result in high expression of genes within these amplified regions. Current studies are identifying the proteins encoded by these amplified regions, the specific function of these proteins in alveolar RMS, and strategies to manipulate expression or function of these proteins. In addition, my research laboratory is also performing additional genome-wide screens to investigate changes that occur at the level of DNA methylation, a type of DNA modification that influences gene expression by altering how the DNA packages with nuclear proteins. These studies have identified numerous characteristic DNA methylation changes in alveolar RMS and are analyzing how these changes alter gene expression and function in this cancer.

3. Clinical translation in pediatric sarcomas

To investigate the clinical utility of gene fusions, amplification and other DNA changes, I also established a translational research program exploring the role of these molecular markers in the diagnosis, prognosis, and management of pediatric sarcomas. These studies are addressing both molecular approaches for detection of these changes in tumors and the correlation of these molecular findings with clinical characteristics, including patient outcome. Many of these studies are performed as part of the Soft Tissue Sarcoma Committee of the Children’s Oncology Group, an international organization devoted to translational studies of pediatric cancer. The findings of these clinical research studies are now being incorporated into the next set of clinical trials conducted by the Soft Tissue Sarcoma Committee.

Gene Regulation

Dr. David L. Levens, Head, Gene Regulation Section
Building 10, Room 2S235C
(301) 496-2176

To learn more, visit Dr. Leven's CCR website.

General Information

Mailing Address:
Gene Regulation Section 
Laboratory of Pathology, CCR
National Cancer Institute
9000 Rockville Pike
Building 10, Room 2N106
Bethesda, MD 20892

Contact Information

The Gene Regulation Section, Laboratory of Pathology, CCR, NCI studies the regulation of the transcription of the human c-myc proto-oncogene. The disregulation of this gene is implicated in the pathogenesis of a variety of human neoplasms. As a key regulator of cell growth and apoptosis, even minor perturbation of c-myc levels disturb the timing and progression of cell growth, the cell cycle, and proliferation. Despite intense and prolonged effort in many groups, the rules governing c-myc regulation have not been fully exposed. No model system including transient expression, stable transfection (either genomic or episomal) or transgenic animals has succeeded in conferring proper physiological regulation upon an exogenously introduced c-myc. Therefore either principle components or processes are missing or defective in these model systems. In addition to conventional transcription factors, the c-myc promoter binds multiple sequence specific and conformation sensitive DNA binding proteins, several of these were discovered and characterized in our group (FBPs 1-3, FIR, and hnRNPK ). The focus of the section since discovering these factors has been to elucidate the roles of these unusual proteins in the regulation of c-myc, FBP activation and FIR repression have been shown to operate through TFIIH and to delay or hasten promoter escape by paused RNA polymerase. Operation of the FBP-FIR-TFIIH system is defective in Xeroderma pigmentosum B and D, bearing mutated TFIIH subunits. Ongoing studies will relate this system to the physiological and biochemical processes and events that demand participation by these sequence and conformation sensitive nucleic acid binding proteins and to define the physiological and biochemical constraints demanding their participation.

Research Topics

• Analysis of the far upstream element (FUSE) binding protein (FBP) and its role in c-myc regulation.
• Investigation of the biological, biophysical and mechanical processes governing the generation and transmission of torsional stress in DNA and consequent changes in DNA conformation.
• Elucidation of the role and mechanism of TFIIH in the intergration of transcriptional signals during early stages of the transcription cycle.
• Analysis of the FBP Interacting Repressor (FIR) and its role in c-myc regulation and transcriptional repression.
• Identification of additional target genes and cis-elements of FBP and FIR. Role of FBP and FIR in the regulation of cell growth, proliferation and the cell-cycle.
• Structural studies of FBP-FUSE and FBP-FIR complexes.
• Characterization of the role of hnRNPK in the transcriptional control of c-myc and coupling of hnRNPK DNA binding activity with DNA topology. Structural studies of hnRNPK with the CT-element of c-myc.
• Characterization of a biological process discovered in our group which marks genes during metaphase, when transcription shuts down, scheduled to be re-expressed following mitosis. This process involves modulation of DNA conformation

Dr. Elaine S. Jaffe is Head of the Hematopathology Section at CCR. 

Dr. Jaffe's work focuses on lymphomas as tumors of the immune system. Using a combination of immunophenotypic, genomic and genetic approaches, her group is examining the pathogenesis of lymphomas, mechanisms of transformation, and signaling pathways involved in control of cellular proliferation and differentiation. 

To learn more, visit Dr. Jaffe's CCR website.

Dr. Maria J. Merino is Head of the Translational Surgical Pathology Section at the CCR.

Dr. Merino's research aim is to study and investigate the role of different tumor markers as prognostic tools in the diagnosis of breast, gynecological, and thyroid cancers, as well as other endocrine tumors and soft tissue sarcomas. 

To learn more, visit Dr. Merino's CCR website.

Experimental Pathology Laboratory (EPL)

Dr. Stephen Hewitt, Section Head, EPL
Building 10, Room 6B 
Phone: 301-496-0040

Dr. Svetlana Pack, Deputy Section Head, EPL
Building 10, Room 2N115
Phone: 301-451-2723

EPL Core Services:

Histology 

Frozen Tissue

• Cryosections
• H&Es

Fixed Tissue (Human & Animal)

• Tissue Fixation, including alternative fixatives
• Tissue Impregnation & Embedding
• Cell block preparation (agarose)
• Microtomy
• Histology Stains (H&E, PAS, Masson, additional stains with development and validation)

Immunohistochemistry  

• Non-clinical Abs on human tissue (formal menu in development)
• Animal tissue
• Double staining (with development and validation)
• Fluorescent IHC with 2ndary Abs
• IHC on Cryosections (requires assay development and validation)

In Situ Assays

• DNA (FISH)
• RNA (flourescence or chromagenic via bDNA)

Laser Capture Microdisection

• Pixel II (multiple), Veritas, and XT instruments from Arcturus/Life Technologies

Tissue Microarray

• 0.6-2.0 mm core-based TMAs

Imaging

• Whole Slide Imaging (20X and 40X)
• Whole Slide Image Hosting
• Upright fluorescent microscope imaging
• Inverted microscope with fluorescent imaging capacity

Dr. Jennifer Clare Jones is Head of the Translational Nanobiology Section at the CCR.

Tumor cells, immune cells, and irradiated tissues release large quantities of biologically active (and distinct) nanoscale extracellular vesicles (e.g., exosomes and microparticles). Dr. Jones is developing improved methods to characterize, sort, and perform functional studies of nanoparticles, and has established a translational EV analysis pipeline, with instrumentation for preparation, analysis, counting, and cytometric study of extracellular vesicles.

To learn more, visit Dr. Jones's CCR website.