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SummaryAberrant enhancer activation has been identified as a key mechanism driving oncogene expression in many cancers. Here we use TOPmentation (Transcription factor-OPtimized ChIPmentation) to probe enhancer usage in primary MLL-rearranged acute lymphoblastic leukemia. We find that MLL-AF4, commonly held to promote transcription by binding to gene promoters, is also present at many active enhancers, where it assembles a complex of transcriptional co-activators normally found in the gene body. This includes DOT1L, ENL, PAF1, and a newly identified interaction with the histone chaperone FACT. By chemical degradation, we demonstrate that PAF1 and FACT are required for enhancer activity, including maintaining histone H3K27 acetylation, enhancer RNA transcription and enhancer-promoter interactions. This work identifies novel roles for PAF1 and FACT in enhancer function, and reveals an enhancer-targeting mechanism by which MLL-AF4 upregulates transcription, recruiting transcription machinery through a network of multivalent interactions to control enhancer activity and gene expression in acute leukemias.

The BCR-ABL tyrosine kinase produced by the t(9;22)(q34;q11) translocation, also known as the Philadelphia chromosome, is the initiating event in chronic myeloid leukemia (CML) and Ph+ acute lymphoblastic leukemia (ALL). Targeting of BCR-ABL with tyrosine kinase inhibitors (TKIs) has resulted in rapid clinical responses in the vast majority of patients with CML and Philadelphia chromosome+ ALL. However, long-term use of TKIs occasionally results in emergence of therapy resistance, in part through the selection of clones with mutations in the BCR-ABL kinase domain. We present here an overview of the current practice in monitoring for such mutations, including the methods used, the clinical and laboratory criteria for triggering mutational analysis, and the guidelines for reporting BCR-ABL mutations. We also present a proposal for a public database for correlating mutational status with in vitro and in vivo responses to different TKIs to aid in the interpretation of mutation studies.

Splenic marginal zone cell lymphomas (SMZCLs) are low-grade B-cell lymphomas that usually present with massive splenomegaly and subtle (subleukemic) peripheral blood involvement. Polymerase chain reaction (PCR) analysis of peripheral blood from a patient with subleukemic SMZCL showed evidence of two clonal immunoglobulin heavy chain (IgH) gene rearrangements. IgH PCR analysis of DNA derived from the patient's splenic neoplasm demonstrated a single clonal IgH rearrangement, which had a different electrophoretic mobility from either of the two PCR products detected in the patient's peripheral blood. Additional characterization of these PCR products by DNA sequencing demonstrated two independent IgH rearrangements in the peripheral blood, one of which used IgH joining region 6c (JH6C) and the other JH4. A different IgH rearrangement was present in the splenic tumor, which used JH4a. No sequences from the splenic neoplasm were detected in the peripheral blood and vice versa. This case illustrates that PCR might reveal monoclonal populations in peripheral blood unrelated to the presence of lymphoma in other anatomic compartments.

Nasal T-lymphocyte/natural killer cell lymphomas (nT/NKLs) are a distinct group of neoplasms highly associated with Epstein-Barr virus (EBV), with a high prevalence in Asia but rare in Western countries. Recent studies indicate that these neoplasms are of cytotoxic T- or NK-cell derivation. Previous studies identifying a characteristic 30-base pair deletion within the 3' end of latent membrane protein-1 (del-LMP-1) in other EBV-associated lymphomas suggested a pathogenetic role for del-LMP-1 in those neoplasms. We examined 23 cases of nT/NKL from Mexico for expression of the cytolytic granular proteins TIA-1 and perforin (PRF), and for the presence of EBV by in situ hybridization (ISH). Polymerase chain reaction was performed to identify the EBV (EBNA-2) strain type and the status of the LMP-1 gene (del-LMP-1). Controls consisted of 11 sinonasal B-cell lymphomas (nBLs) and 30 reactive tonsils (RTs) from healthy Mexican individuals. The nT/NKLs expressed TIA-1 in 21 (91%) of 23 cases and PRF in 15 (65%) of 23 cases. In contrast, all of the nBLs were negative for TIA-1 and PRF. Twenty-two (96%) of 23 nT/NKLs were positive for EBV by ISH. In contrast, only 2 (18%) of 11 nBLs were positive for EBV by ISH. EBV strain Type A was identified in 21 (91%) of 23 cases, whereas strain Type B was present in 2 (9%) of the 23 nT/NKLs. A similar percentage (80%) of Type A was noted in 12 of the 15 RTs. del-LMP-1 was detected in 6 (26%) of 23 nT/NKLs, comprising 4 cases of Type A and 2 of Type B. del-LMP-1 was detected in 9 (45%) of 20 RTs. Our results indicated that TIA-1 and PRF were sensitive markers of nT/NKL. The presence of del-LMP-1 in comparable frequencies in the RTs and nT/NKLs suggested to us that this genotype was common in the Mexican population and argued against a definite pathogenetic role for del-LMP-1 in nT/NKL.

We report two cases of extramedullary myeloid cell tumor that arose in patients with chronic myelomonocytic leukemia. In both cases, the tumors were difficult to recognize histologically because the neoplasms lacked cytological evidence of granulocyte maturation, such as cytoplasmic granulation or eosinophilic myelocytes, and the Leder stains for chloroacetate esterase were negative. Immunohistochemical studies were necessary to establish the correct diagnosis. The neoplastic cells in both tumors expressed myeloperoxidase, lysozyme, and CD43 and were negative for B-cell, T-cell, and other nonhematopoietic antigens tested. We report these cases to emphasize that extramedullary myeloid cell tumors may rarely precede transformation to acute myeloid leukemia in patients with chronic myelomonocytic leukemia. Extramedullary myeloid cell tumors of monocytic lineage may be difficult to recognize in routine and Leder-stained sections, and immunohistochemical studies may be essential for establishing the diagnosis.

Extramedullary myeloid cell tumors (EMCTs) may be unsuspected clinically and difficult to recognize histologically. Fresh or frozen tissue is often not available for analysis. We studied 29 cases of EMCT using routinely fixed and processed paraffin-embedded tissue, an immunohistochemical method, and a panel of antibodies.We studied 29 patients with EMCTs: 22 males and 7 females, with a median age of 48 years (range, 5 to 80 years). Histologically, 9 tumors were well differentiated, 16 were poorly differentiated, and 4 were blastic.The Leder stain (napthol-ASD-chloroacetate esterase) was positive in 21 (77.7%) of 27 tumors. Immunohistochemically, the following antibodies reacted with the greatest number of cases: Leu-22 or MT1 (CD43) in 28 (96.6%) of 29, antilysozyme in 27 (96.4%) of 28, and antimyeloperoxidase (MP07) in 21 (91.3%) of 23 cases. Other myeloid lineage-associated antibodies were positive in a subset of cases: antineutrophil elastase (NP57) in 10 (62.5%) of 16, Leu-M1 (CD15) in 7 (46.6%) of 15, and Mac-387 in 6 (40.0%) of 15 cases. The well-differentiated EMCTs reacted with most myeloid-associated antibodies; poorly differentiated and blastic tumors were more often negative. The pan-leukocyte antibody LCA (CD45RB) reacted with 15 (60%) of 25 neoplasms. Three (16.6%) of 18 tumors contained numerous p53-positive cells, ranging from 10% to 50% of the tumor cell population. In 10 cases, exons 5 through 8 of the p53 gene were analyzed using the polymerase chain reaction and single-stranded conformational polymorphism analysis. Gel shifts consistent with mutations were identified in exon 8 of one tumor (10%) that exhibited abundant p53 immunostaining.Immunohistochemical studies using fixed, paraffin-embedded sections are very useful in the diagnosis of EMCTs. The most sensitive antibodies are anti-CD43, antilysozyme, and antimyeloperoxidase. Immunohistochemical methods are more sensitive than the Leder stain. We found p53 staining in a small subset of cases, in which we were able to confirm evidence of p53 gene mutation using the polymerase chain reaction and single-stranded conformational polymorphism analysis in one case; p53 gene mutations appear to be uncommon in EMCTs.

Low-grade follicle center lymphoma (LGFCL) is characterized genetically by the t(14;18) translocation and an indolent clinical course. Histologic progression from LGFCL to an aggressive diffuse large B-cell lymphoma (DLCL) occurs in 60% to 80% of cases, and this transformation is associated with the accumulation of secondary genetic alterations. Using 10 polymorphic microsatellite markers spanning the chromosome 9p21 region harboring the p15 (p15(INK4B)/MTS-2/CDKN2B) and p16 (p16(INK4A)/MTS-1/CDKN2) tumor-suppressor gene loci, we analyzed 11 matched pairs of LGFCL and their corresponding progressed DLCL biopsies for loss of heterozygosity and homozygous deletions at 9p21. A comparative multiplex polymerase chain reaction assay was also used for the detection of homozygous deletions. Deletions were identified in 8 of the 11 cases studied (73%): 6 homozygous (54%) and 2 hemizygous (18%). The deletions were identified exclusively in the progressed DLCL biopsies. Immunohistochemical studies showed an excellent correlation with the results from the genetic analyses. Of the 9 matched pairs of LGFCL and progressed DLCL with interpretable immunohistochemical staining, 9 of 9 (100%) of the LGFCL showed diffuse reactivity for p16. Four of the 9 (44%) immunohistochemically evaluable cases of progressed DLCL showed loss of or, in 1 case, markedly diminished p16 expression. All 4 of these cases correspondingly showed homozygous deletions at 9p21. Five of the 9 progressed DLCL cases showed p16 expression and demonstrated retention of one or both 9p21 alleles by genetic analysis. This is the first longitudinal series examining sequential biopsy specimens of low-grade and progressed FCL for genetic loss at 9p21 encompassing the p16 and p15 loci. The high frequency and exclusive occurrence of deletions involving p16 in the progressed DLCLs suggests that genetic loss at 9p21 targeting p16 and/or p15 is an important secondary genetic event in the histologic progression of FCL.