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Proteomic-Based Profiling of Lymphomas: Chromatin Proteomics; Composition and Modification of Histone and Non-Histone Chromosomal Proteins

18 Years
Not Enrolling
Lymphoma, Leukemia, Lymphoid Hyperplasia

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Trial Information

Proteomic-Based Profiling of Lymphomas: Chromatin Proteomics; Composition and Modification of Histone and Non-Histone Chromosomal Proteins


Lymphomas are comprised of a diversity of tumors with different pathologic and clinical
features. While distinct differences in gene expression profiles have been elucidated in
different lymphomas, there has been inconsistent correlation with the few published
proteomic studies.

Greater insights into the biology of lymphomas may be achieved by integrating current
genomic information with additional studies focused on the interrelationships in tumors of
the patterns of chromatin protein expression, chromatin protein modification, and RNA
expression profiling (both within bulk tumor and within specific microscopic tumor niches
accessible by microdissection and cell sorting approaches).


The goals of this protocol are to identify the global levels of all histones (including
variant histones) and non-histone chromosomal proteins, and to measure the relative levels
of most known covalent modifications on histone and non-histone chromosomal proteins.

For a limited number of cases illustrative of selected pathological entities, we propose to
map the genome-wide distribution of those modifications judged to be biochemically


This work will involve the analysis of a broad panel of lymphoma and lymphoid samples, which
were previously procured under multiple protocols at the NIH, and for which there is excess
tissue available for research. We also request permission to extend this analysis to surplus
materials to be accrued under existing protocols, upon completion of all superseding
diagnostic tests and medical/scientific studies. The criteria for inclusion in this study
are subsumed under the enveloping protocols. The number of cases to be included is dependent
upon the size of these protocols; because statistical significance improves with increasing
numbers. We hope to include up to 300 cases.


Lysates from surplus samples will be prepared and arrayed onto microarrays.

These arrays will be probed with panels of protein and modification specific antibodies.

The antibody reactivity will be quantified and samples will be subjected to statistical
analysis, especially hierarchical clustering to correlate patterns of reactivity with
clinical and histological features.

Representative cases for which sufficient surplus tissue remains will be subjected to
ChIP-Seq to map the distribution of modifications across the genome.

Inclusion Criteria


We propose to analyze the histone and chromatin modifications from several classes of
patients: 1) patients bearing the diagnosis of lymphoid malignancies made or confirmed at
the NIH. Solid tumors of the lymphoid system would constitute the major source of these
tissues, however tissue samples from patients with malignant diagnoses that involve
circulating malignant cells (Mycosis fungoides, Sezary syndrome, etc.) would also be
appropriate for analysis; 2) non-malignant lymphoid tissue obtained for diagnostic
purposes or normal lymphoid tissue obtained incidentally during surgery (in all cases only
residual and surplus tissue will be used, only with the express approval of the
appropriate clinical investigator(s). Primarily included among these tissues would be
hyperplastic lymphoid tissue especially tonsils. Other hyperplastic and non-malignant
lymph node samples showing proliferative responses or sinus histiocytosis would also be
appropriate to compare with the malignant samples.


Only cases with sufficient frozen biopsy material from initial biopsy and/or biopsies at
relapse of disease to obtain adequate tissues lysates for proteomic-based analyses and in
selected cases for ChIPSeq following analysis of RNA expression as performed under
superceding protocols. In some cases, for some histone modifications, it may be possible
to recover appropriate tissue from paraffin embedded blocks, however no such samples will
be used for this study without prior consultation and approval from the clinical
investigator and hematopathologist associated with the superceding protocols. Samples from
minors < 18 years old will not be used.

Type of Study:


Study Design:

Time Perspective: Retrospective

Principal Investigator

David L Levens, M.D.

Investigator Role:

Principal Investigator

Investigator Affiliation:

National Cancer Institute (NCI)


United States: Federal Government

Study ID:




Start Date:

May 2009

Completion Date:

Related Keywords:

  • Lymphoma
  • Leukemia
  • Lymphoid Hyperplasia
  • Antibodies
  • Reverse Phase Microarrays
  • Epigenetics
  • Acetylation
  • Methylation
  • Lymphoma
  • Hyperplasia
  • Leukemia
  • Lymphoma



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