Key Points• Somatic CDKN1B (p27) mutations were identified in 16% (13/81) of HCL patients and coexist with BRAFV600E mutations.• CDKN1B is the second most common mutated gene in HCL implicating altered cell cycle regulation and/or senescence in HCL.Hairy cell leukemia (HCL) is marked by near 100% mutational frequency of BRAFV600E mutations. Recurrent cooperating genetic events that may contribute to HCL pathogenesis or affect the clinical course of HCL are currently not described. Therefore, we performed whole exome sequencing to explore the mutational landscape of purine analog refractory HCL. In addition to the disease-defining BRAFV600E mutations, we identified mutations in EZH2, ARID1A, and recurrent inactivating mutations of the cell cycle inhibitor CDKN1B (p27). Targeted deep sequencing of CDKN1B in a larger cohort of HCL patients identify deleterious CDKN1B mutations in 16% of patients with HCL (n 5 13 of 81). In 11 of 13 patients the CDKN1B mutation was clonal, implying an early role of CDKN1B mutations in the pathogenesis of HCL. CDKN1B mutations were not found to impact clinical characteristics or outcome in this cohort. These data identify HCL as having the highest frequency of CDKN1B mutations among cancers and identify CDNK1B as the second most common mutated gene in HCL. Moreover, given the known function of CDNK1B, these data suggest a novel role for alterations in regulation of cell cycle and senescence in HCL with CDKN1B mutations. (Blood. 2015;126(8):1005-1008) IntroductionHairy-cell leukemia (HCL) is a rare, mature B-cell malignancy presenting with slow progressing pancytopenia and splenomegaly. Classical HCL is successfully treated with chemotherapy, but eradication of minimal residual disease is rarely achieved. 1 Standard treatment fails in a minority of patients, with a potentially fatal outcome.Gain-of-function mutations of the BRAF serine/threonine protein kinase (BRAFV600E) have been identified in nearly all cases of classical HCL, and mitogen-activated protein kinase signaling is considered the key oncogenic pathway in HCL.2 Chung et al 3 recently identified hematopoietic stem cells as the cell of origin of HCL by demonstrating that hematopoietic stem cells, and subsequently cells along the hematopoietic hierarchy, contain mutated BRAF. Currently, however, no other recurrently mutated genes are known to coexist with BRAFV600E mutations in HCL. It is unclear if BRAFV600E mutations alone are sufficient to induce HCL. Moreover, it is also not known if additional mutations may be acquired in BRAFV600E-mutant HCL cells, resulting in acquired resistance to therapies commonly administered to patients with HCL such as purine analogs. Therefore, we performed whole-exome sequencing (WES) in 3 HCL patients who were refractory to purine analog treatment and received the BRAF inhibitor (BRAFi) vemurafenib followed by recurrence testing of novel mutations in a larger cohort of HCL patients. Study designClinical samples were provided by

SummaryThe genome of pluripotent stem cells adopts a unique three-dimensional architecture featuring weakly condensed heterochromatin and large nucleosome-free regions. Yet, it is unknown whether structural loops and contact domains display characteristics that distinguish embryonic stem cells (ESCs) from differentiated cell types. We used genome-wide chromosome conformation capture and super-resolution imaging to determine nuclear organization in mouse ESC and neural stem cell (NSC) derivatives. We found that loss of pluripotency is accompanied by widespread gain of structural loops. This general architectural change correlates with enhanced binding of CTCF and cohesins and more pronounced insulation of contacts across chromatin boundaries in lineage-committed cells. Reprogramming NSCs to pluripotency restores the unique features of ESC domain topology. Domains defined by the anchors of loops established upon differentiation are enriched for developmental genes. Chromatin loop formation is a pervasive structural alteration to the genome that accompanies exit from pluripotency and delineates the spatial segregation of developmentally regulated genes.

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The benefit of molecularly-informed therapies in cancer of unknown primary (CUP) is unclear. Here, we use comprehensive molecular characterization by whole genome/exome, transcriptome and methylome analysis in 70 CUP patients to reveal substantial mutational heterogeneity with TP53, MUC16, KRAS, LRP1B and CSMD3 being the most frequently mutated known cancer-related genes. The most common fusion partner is FGFR2, the most common focal homozygous deletion affects CDKN2A. 56/70 (80%) patients receive genomics-based treatment recommendations which are applied in 20/56 (36%) cases. Transcriptome and methylome data provide evidence for the underlying entity in 62/70 (89%) cases. Germline analysis reveals five (likely) pathogenic mutations in five patients. Recommended off-label therapies translate into a mean PFS ratio of 3.6 with a median PFS1 of 2.9 months (17 patients) and a median PFS2 of 7.8 months (20 patients). Our data emphasize the clinical value of molecular analysis and underline the need for innovative, mechanism-based clinical trials.