Evaluation of Hi-C sequencing for the detection of gene fusions in hematologic and solid pediatric cancer samples.

HiC sequencing is a DNA-based next-generation sequencing method that preserves the 3D conformation of the genome and has shown promise in detecting genomic rearrangements in translational research studies. To evaluate HiC as a potential clinical diagnostic platform, analytical concordance with routine laboratory testing was assessed using primary pediatric leukemia and sarcoma specimens previously positive for clinically significant genomic rearrangements. Archived specimen types tested included viable and nonviable frozen leukemic cells, as well as formalin-fixed paraffin-embedded (FFPE) tumor tissues. Initially, pediatric acute myeloid leukemia (AML) and alveolar rhabdomyosarcoma (A-RMS) specimens with known genomic rearrangements were subjected to HiC analysis to assess analytical concordance. Subsequently, a discovery cohort consisting of AML and acute lymphoblastic leukemia (ALL) cases with no known genomic rearrangements based on prior clinical diagnostic testing were evaluated to determine whether HiC could detect rearrangements. Using a standard sequencing depth of 50 million raw read-pairs per sample, or approximately 5X raw genomic coverage, 100% concordance was observed between HiC and previous clinical cytogenetic and molecular testing. In the discovery cohort, a clinically relevant gene fusion was detected in 45% of leukemia cases (5/11). This study demonstrates the value of HiC sequencing to medical diagnostic testing as it identified several clinically significant rearrangements, including those that might have been missed by current clinical testing workflows. Key points: HiC sequencing is a DNA-based next-generation sequencing method that preserves the 3D conformation of the genome, facilitating detection of genomic rearrangements.HiC was 100% concordant with clinical diagnostic testing workflows for detecting clinically significant genomic rearrangements in pediatric leukemia and rhabdomyosarcoma specimens.HiC detected clinically significant genomic rearrangements not previously detected by prior clinical cytogenetic and molecular testing.HiC performed well with archived non-viable and viable frozen leukemic cell samples, as well as archived formalin-fixed paraffin-embedded tumor tissue specimens.

3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma.

Ependymoma is a tumor of the brain or spinal cord. The two most common and aggressive molecular groups of ependymoma are the supratentorial ZFTA-fusion associated and the posterior fossa ependymoma group A. In both groups, tumors occur mainly in young children and frequently recur after treatment. Although molecular mechanisms underlying these diseases have recently been uncovered, they remain difficult to target and innovative therapeutic approaches are urgently needed. Here, we use genome-wide chromosome conformation capture (Hi-C), complemented with CTCF and H3K27ac ChIP-seq, as well as gene expression and DNA methylation analysis in primary and relapsed ependymoma tumors, to identify chromosomal conformations and regulatory mechanisms associated with aberrant gene expression. In particular, we observe the formation of new topologically associating domains ('neo-TADs') caused by structural variants, group-specific 3D chromatin loops, and the replacement of CTCF insulators by DNA hyper-methylation. Through inhibition experiments, we validate that genes implicated by these 3D genome conformations are essential for the survival of patient-derived ependymoma models in a group-specific manner. Thus, this study extends our ability to reveal tumor-dependency genes by 3D genome conformations even in tumors that lack targetable genetic alterations.

Synthesis, structure and magnetism of homodinuclear complexes of Co, Ni and Cu supported by a novel bitriazine scaffold.

Btzn (1), an amine-functionalized bi(1,3,5-triazine) 4,4'-(NH(2))(2)-6,6'-(NHC(6)H(5))(2)-2,2'-(1,3,5-C(3)N(3))(2), is reported, and its coordination with Co, Ni and Cu is explored. Reactions of metal salts (2 equiv) with Btzn (1 equiv) result in dimeric species [(Btzn)Co(2)(NCS)(4)(EtOH)(2)(DMF)(2)], (2), [(Btzn)Ni(2)(η(1)-ONO(2))(2)(MeOH)(4)(DMF)(2)]·2[NO(3)], (3), [(Btzn)Cu(2)Cl(4)(DMF)(2)], (4), and [(Btzn)Cu(2)(η(2)-O(2)NO)(2)(OH(2))(2)(DMF)(2)]·2[NO(3)], (5). These complexes are the first examples of the coordination of transition metals with bi(1,3,5-triazine) ligands. Their structures display a bridging bis-bidentate coordination mode for Btzn. Variable-temperature magnetic susceptibility of the complexes reveals antiferromagnetic exchange between the spin carriers, with calculated exchange coupling values (J) of -4.7 cm(-1) for 3, -18.2 cm(-1) for 4, and -5.5 cm(-1) for 5. An in-depth evaluation of the metal geometry highlights the inefficient overlap of the magnetic d-orbitals through the bridging ligand, most likely leading to reduced delocalization and coupling.