Simultaneous Detection of Gene Fusions and Base Mutations in Cancer Tissue Biopsies by Sequencing Dual Nucleic Acid Templates in Unified Reaction.

BACKGROUND: Targeted next-generation sequencing is a powerful method to comprehensively identify biomarkers for cancer. Starting material is currently either DNA or RNA for different variations, but splitting to 2 assays is burdensome and sometimes unpractical, causing delay or complete lack of detection of critical events, in particular, potent and targetable fusion events. An assay that analyzes both templates in a streamlined process is eagerly needed. METHODS: We developed a single-tube, dual-template assay and an integrated bioinformatics pipeline for relevant variant calling. RNA was used for fusion detection, whereas DNA was used for single-nucleotide variations (SNVs) and insertion and deletions (indels). The reaction chemistry featured barcoded adaptor ligation, multiplexed linear amplification, and multiplexed PCR for noise reduction and novel fusion detection. An auxiliary quality control assay was also developed. RESULTS: In a 1000-sample lung tumor cohort, we identified all major SNV/indel hotspots and fusions, as well as MET exon 14 skipping and several novel or rare fusions. The occurrence frequencies were in line with previous reports and were verified by Sanger sequencing. One noteworthy fusion event was HLA-DRB1-MET that constituted the second intergenic MET fusion ever detected in lung cancer. CONCLUSIONS: This method should benefit not only a majority of patients carrying core actionable targets but also those with rare variations. Future extension of this assay to RNA expression and DNA copy number profiling of target genes such as programmed death-ligand 1 may provide additional biomarkers for immune checkpoint therapies.

Proton-Conductive Keggin-Type Clusters Decorated by the Complex Moieties of Cu(II) 2,2'-Bipyridine-4,4'-dicarboxylate/Diethyl Analogues.

Three proton-conductive decorated Keggin-type clusters, {[Cu(debpdc)(H2O)3][Cu(debpdc)(H2O)Cl][PMo12O40]} ·2CH3OH ·1.5CH3CN ·3H2O (1), {[Cu(H2bpdc)(H2O)2Cl0.5]2[PW12O40]}·10H2O (2), and {[Cu(H2bpdc)(H2O)2.5]2[SiW12O40]}·10H2O (3) (where debpdc is diethyl 2,2'-bipyridine-4,4'-dicarboxylate and H2bpdc is 2,2'-bipyridine-4,4'-dicarboxylic acid), were synthesized through electrostatic and coordination interactions between Keggin-type anions and Cu(II) H2bpdc/debpdc complex moieties. Interestingly, in the three complexes, both the H2bpdc/debpdc and the Keggin anion are covalently linked to the Cu2+ ions as polydentate organic and inorganic ligands, respectively. Notably, complexes 2 and 3 are the first examples of the functionalization of a Keggin-type cluster with Cu(II)-H2bpdc complex moieties, thereby providing a pathway to design and synthesize multifunctional hybrid materials with cluster structures based on two building units. In them, the free COOH groups of the H2bpdc ligand can act as both hydrogen bond acceptors and proton carriers. 1 has debpdc ligands with ethoxycarbonyl groups, while 2 and 3 have the H2bpdc ligands with free COOH groups; thus, the three complexes help us to understand the influence of the different substituents on the proton conductivity. The measurement results reveal that 2 and 3 have a high conductivity value of over 10-3 S cm-1 at 100 °C under 98% relative humidity, which is 2 orders of magnitude higher than that of 1 under the same conditions.

Proton-Conductive Cocrystals of Twin Isomers of Coordination Polymers in Situ Formed by Keggin Anions and Cu(II)-4,4'-Bis(hydroxymethyl)-2,2'-bipyridine Complex Moieties.

Cocrystals and isomers, two well-known unique concepts in supramolecular chemistry, are rarely put together until now. For the first time, we report three unprecedented and interesting cocrystals of twin isomers of coordination polymers (CPs) in situ formed by typical Keggin anions and Cu(II)-4,4'-bis(hydroxymethyl)-2,2'-bipyridine (Cu(II)-H2L) complex moieties. In cocrystals 1-3, the Cu(II)-H2L complex moieties are quadrisupported on Keggin-type anions through W(Mo)-Ot-Cu-Ot-W(Mo) (Ot is the terminal O atom) links in the crystal to form two twin ionic/neutral CPs with a fixed chemical stoichiometry. Cocrystals 1-2 contain ionic isomers as {[Cu1(H2L)(H2O)2]2[P1W12O40]} n n+/{[Cu2(HL)(H2O)2]2[P2W12O40]} n n- for 1 and {[Cu1(H2L)(H2O)2]2[P1Mo12O40]} n n+/{[Cu2(HL)(H2O)2]2[P2Mo12O40]} n n- for 2. Cocrystal 3 contains neutral isomers as {[Cu1(H2L)(H2O)2]2[Si1W12O40]} n and {[Cu2(H2L)(H2O)2]2[Si2W12O40]} n. Cooperation of conformation and hydrogen bond network isomerism of Cu(II)-H2L fragments and tetracoordinated mode isomerism of Keggin anion is perfectly embodied in twin isomers. Moreover, based on hydrogen-bonding interactions, twin isomers are alternately arranged in a 1:1 stoichiometric ratio to give a cocrystal. Complicated accumulation of three types of hydrogen-bonding assemblies in the same crystal may be the reason that they give conductivity values over 10-4 S·cm-1 at 100 °C under 98% relative humidity.