Structural variation cooperates with permissive chromatin to control enhancer hijacking-mediated oncogenic transcription.

Structural variants (SVs) involving enhancer hijacking can rewire chromatin topologies to cause oncogene activation in human cancers, including hematologic malignancies; however, because of the lack of tools to assess their effects on gene regulation and chromatin organization, the molecular determinants for the functional output of enhancer hijacking remain poorly understood. Here, we developed a multimodal approach to integrate genome sequencing, chromosome conformation, chromatin state, and transcriptomic alteration for quantitative analysis of transcriptional effects and structural reorganization imposed by SVs in leukemic genomes. We identified known and new pathogenic SVs, including recurrent t(5;14) translocations that cause the hijacking of BCL11B enhancers for the allele-specific activation of TLX3 in a subtype of pediatric leukemia. Epigenetic perturbation of SV-hijacked BCL11B enhancers impairs TLX3 transcription, which are required for the growth of t(5;14) leukemia cells. By CRISPR engineering of patient-derived t(5;14) in isogenic leukemia cells, we uncovered a new mechanism whereby the transcriptional output of SV-induced BCL11B enhancer hijacking is dependent on the loss of DNA hypermethylation at the TLX3 promoter. Our results highlight the importance of the cooperation between genetic alteration and permissive chromatin as a critical determinant of SV-mediated oncogene activation, with implications for understanding aberrant gene transcription after epigenetic therapies in patients with leukemia. Hence, leveraging the interdependency of genetic alteration on chromatin variation may provide new opportunities to reprogram gene regulation as targeted interventions in human disease.

Site-specific analysis of inflammatory markers in discoid lupus erythematosus skin.

Prior studies identified T cells, B cells, and macrophages in the inflammatory infiltrate and up-regulation of their protein products in discoid lupus erythematosus (DLE) skin; however, they lacked rigorous analyses to define their specific locations in skin. Thus, we compared expressions of selected T cell, B cell, and macrophage markers in five areas of DLE, psoriasis, and normal skin. Immunostainings for CD3, CD4, CD8, CD20, CD68, CXCR3, CXCL10, and TIA-1 were performed in biopsies of 23 DLE lesional skin, 11 psoriasis lesional skin, and 5 normal skin. Three independent observers used a graded scale to rate each marker's presence in the epidermis, dermatoepidermal junction (DEJ), perivascular area, periadnexal area, and deep dermis. DLE lesional skin contained an increased abundance of CD3(+), CD8(+), and CD68(+) cells at the DEJ, and CD20(+) and CD68(+) cells in the periadnexal area versus psoriasis and normal skin. CXCR3, CXCL10, and TIA-1 were elevated in periadnexal sites of DLE lesional skin versus psoriasis lesional skin. The aggregation of T cells, B cells, macrophages, and their protein products (CXCR3, CXCL10, and TIA-1) in the DEJ and periadnexal area of DLE lesional skin may contribute to the pathology of DLE through a coordinated, sophisticated process.

Myelodysplastic syndrome (MDS)-associated cytogenetic abnormalities in pediatric chronic myelogenous leukemia.

Chronic myelogenous leukemia (CML) is very rare in the pediatric population. We report the case of a 2-year-old female with CML and concurrent myelodysplastic syndrome (MDS) associated cytogenetic abnormalities. The co-existence of t(9;22) and chromosomal deletions that are associated with MDS poses a unique diagnostic challenge. Given the reported association of t(9;22) and genomic instability, we hypothesize that the chromosomal deletions represent clonal evolution of the CML.

Automation in flow cytometry: Guidelines and review of systems.

Automation in flow cytometry has recently advanced from the partial laboratory automation and robotics islets, to more fully integrated systems. This article reviews three manufacturers' newest sample preparation systems: the Beckman CellMek, the Sysmex PS-10, and the BD FACSDuet. These three instruments are capable of performing many of the manual steps in flow cytometry sample processing (pipetting, staining, lysing, washing, fixing). General description, capabilities, advantages, and disadvantages of each system are compared. Overall, these systems have the potential to become mainstay items in today's busy clinical flow cytometry laboratories, and save a significant amount of hands-on time for laboratory staff.

An unusual case of chronic lymphocytic leukemia with trisomy 12 presenting with prolymphocytic transformation and t(8;21)(q22;q22).

First report of t(8;21)(q22;q22) in a patient with CLL. RUNX1-RUNX1T1 fusion gene resulting from the translocation may have played a role in the prolymphocytic transformation.

Myeloid and lymphoid neoplasm with abnormalities of FGFR1 presenting with trilineage blasts and RUNX1 rearrangement: a case report and review of literature.

OBJECTIVES: Myeloid and lymphoid neoplasms with abnormalities of fibroblast growth factor receptor 1 gene (FGFR1) are a rare and aggressive disease group that harbors translocations of FGFR1 with at least 14 recognized partner genes. We report a case of a patient with a novel t(17;21)(p13;q22) with RUNX1 rearrangement and trilineage blasts. METHODS: A 29-year-old man with relapsed T-lymphoblastic lymphoma in the cervical nodes showed a myeloproliferative neoplasm in his bone marrow with three separate populations of immunophenotypically aberrant myeloid, T-lymphoid, and B-lymphoid blasts by flow cytometry. Cytogenetic and fluorescent in situ hybridization studies showed unique dual translocations of t(8;13)(p11.2;q12) and t(17;21)(p13;q22) with RUNX1 rearrangement. RESULTS: The patient was initiated on a mitoxantrone, etoposide, and cytarabine chemotherapy regimen and died of complications of disease 1 month later. CONCLUSIONS: To our knowledge, this is the first reported case of a myeloid and lymphoid neoplasm with abnormalities of FGFR1 with t(17;21)(p13;q22) and trilineage blasts.

Novel r(2)(p25q31) cytogenetic abnormality in a pediatric patient with acute leukemia of ambiguous lineage.

We describe a case of acute leukemia of ambiguous lineage with a novel cytogenetic abnormality. A 1-year-old boy presented with abnormal complete blood count findings, and was found to have blasts and mild dysgranulopoiesis. The blasts showed immunophenotypic evidence of myeloid and T-lineage differentiation. Subsequent cytogenetic analysis showed r(2)(p25q31) as the sole stem line cytogenetic defect with clonal evolution. While cytogenetic abnormalities can have a critical role in the classification and prognostication of acute lymphoblastic and acute myeloid leukemia, the significance of cytogenetic abnormalities in acute leukemia of ambiguous lineage remains unclear. This finding has not been reported previously to the best of our knowledge.

Helicobacter gastritis induces changes in the oxyntic mucosa indistinguishable from the effects of proton pump inhibitors.

A causal relationship between oxyntic glands dilatation with protruding parietal cells, referred to as proton pump inhibitor (PPI) effects, and PPI use has been suspected but not established. We designed this study to evaluate the association between these changes and the use of PPIs and histamine2-receptor blockers (H2-blockers). We obtained five Sydney System-compliant biopsy specimens from patients recruited into a therapeutic trial for H. pylori. Medication history with details on PPI and H2-blockers use was collected. Two blinded pathologists graded gastritis and the intensity of putative PPI effects using a 0 to 3 scale. PPI and H2-blocker use was then disclosed and the accuracy of pathologists' assessment was analyzed. There were 138 H. pylori-negative and 104 positive patients. In H. pylori-negative patients the histologic assessment for PPI use had 77.5% sensitivity and 51.8% specificity, with a positive predictive value of 86.9% and a negative predictive value of 35.9%. In H. pylori-positive patients, sensitivity was 74.1% and specificity 26.1%. Positive and negative predictive values were 55.8% and 44.4%, respectively. Neither glandular dilatations nor parietal cell protrusions related to H2-blocker use. We conclude that these changes are associated with PPI use only in H. pylori-negative subjects. In H. pylori gastritis, so-called PPI-effects were equally prevalent in PPI-users and non-users, indicating that other factors are involved in the induction of oxyntic cell hyperplasia. We suggest that comments regarding the supposed evidence of PPI use are too often wrong to be useful and should be avoided in the diagnosis of gastric biopsy specimens.