Genome-scale functional genomics identify genes preferentially essential for multiple myeloma cells compared to other neoplasias.

Clinical progress in multiple myeloma (MM), an incurable plasma cell (PC) neoplasia, has been driven by therapies that have limited applications beyond MM/PC neoplasias and do not target specific oncogenic mutations in MM. Instead, these agents target pathways critical for PC biology yet largely dispensable for malignant or normal cells of most other lineages. Here we systematically characterized the lineage-preferential molecular dependencies of MM through genome-scale clustered regularly interspaced short palindromic repeats (CRISPR) studies in 19 MM versus hundreds of non-MM lines and identified 116 genes whose disruption more significantly affects MM cell fitness compared with other malignancies. These genes, some known, others not previously linked to MM, encode transcription factors, chromatin modifiers, endoplasmic reticulum components, metabolic regulators or signaling molecules. Most of these genes are not among the top amplified, overexpressed or mutated in MM. Functional genomics approaches thus define new therapeutic targets in MM not readily identifiable by standard genomic, transcriptional or epigenetic profiling analyses.

An Embryonic Diapause-like Adaptation with Suppressed Myc Activity Enables Tumor Treatment Persistence.

Treatment-persistent residual tumors impede curative cancer therapy. To understand this cancer cell state we generated models of treatment persistence that simulate the residual tumors. We observe that treatment-persistent tumor cells in organoids, xenografts, and cancer patients adopt a distinct and reversible transcriptional program resembling that of embryonic diapause, a dormant stage of suspended development triggered by stress and associated with suppressed Myc activity and overall biosynthesis. In cancer cells, depleting Myc or inhibiting Brd4, a Myc transcriptional co-activator, attenuates drug cytotoxicity through a dormant diapause-like adaptation with reduced apoptotic priming. Conversely, inducible Myc upregulation enhances acute chemotherapeutic activity. Maintaining residual cells in dormancy after chemotherapy by inhibiting Myc activity or interfering with the diapause-like adaptation by inhibiting cyclin-dependent kinase 9 represent potential therapeutic strategies against chemotherapy-persistent tumor cells. Our study demonstrates that cancer co-opts a mechanism similar to diapause with adaptive inactivation of Myc to persist during treatment.

Functional Genomics Identify Distinct and Overlapping Genes Mediating Resistance to Different Classes of Heterobifunctional Degraders of Oncoproteins.

Heterobifunctional proteolysis-targeting chimeric compounds leverage the activity of E3 ligases to induce degradation of target oncoproteins and exhibit potent preclinical antitumor activity. To dissect the mechanisms regulating tumor cell sensitivity to different classes of pharmacological "degraders" of oncoproteins, we performed genome-scale CRISPR-Cas9-based gene editing studies. We observed that myeloma cell resistance to degraders of different targets (BET bromodomain proteins, CDK9) and operating through CRBN (degronimids) or VHL is primarily mediated by prevention of, rather than adaptation to, breakdown of the target oncoprotein; and this involves loss of function of the cognate E3 ligase or interactors/regulators of the respective cullin-RING ligase (CRL) complex. The substantial gene-level differences for resistance mechanisms to CRBN- versus VHL-based degraders explains mechanistically the lack of cross-resistance with sequential administration of these two degrader classes. Development of degraders leveraging more diverse E3 ligases/CRLs may facilitate sequential/alternating versus combined uses of these agents toward potentially delaying or preventing resistance.

A turn-on red-emitting fluorescent probe for determination of copper(II) ions in food samples and living zebrafish.

Herein, we developed a turn-on red-emitting fluorescent probe for the sensitive and selective detection of copper ions (Cu2+) in food samples and living zebrafish. The probe employs a hemicyanine scaffold as the fluorophore and a 2-pyridinecarbonyl group as the recognition receptor and quenching moiety. The 2-pyridinecarbonyl moiety can be specifically cleaved by Cu2+ and results in an approximately 18-fold fluorescence enhancement of the probe, thereby providing a fluorescence turn-on assay for Cu2+. Additionally, the probe exhibited excellent selectivity, high sensitivity, a broad linear relationship (0.020 to 8.0 µM), and a low limit of detection (4.0 nM, S/N = 3) for Cu2+. Concomitantly, the probe exhibited satisfactory analytical performance when used with actual food samples. Moreover, the probe could be used for in situ determination of Cu2+ in both living plant tissues and in living zebrafish.

Near-Infrared Photoluminescence and Reversible Trans-to-Cis Photoisomerization of Mononuclear and Binuclear Ytterbium(III) Complexes Functionalized by Azobenzene Groups.

Two mononuclear and one binuclear ytterbium complexes with dual near-infrared (NIR) photoluminescence and reversible trans-to-cis photoisomerization functions were synthesized and characterized. The central ytterbium(III) ion coordinates with two ß-diketonate (4,4,4-trifluoro-1-phenylbutane-1,3-dionate (tfd)) ligands and one deprotonated azobenzene-containing tetradentate ligand [(E)-4-(phenyldiazenyl)-N,N-bis(pyridin-2-ylmethyl) benzohydrazide (HL), (E)-4-((4-(dimethylamino)phenyl)diazenyl)-N,N-bis(pyridin-2-ylmethyl)benzohydrazide (HNL), or (E)-4,4'-N',N'-bis(pyridin-2-ylmethyl)benzohydrazide azobenzene (H2DL)] to form a neutral ternary complex ([Yb(tfd)2L], [Yb(tfd)2(NL)], or [Yb2(tfd)4(DL)], respectively), where the ytterbium(III) ion is eight-coordinated to N3O5 donor sets. X-ray crystallographic analysis shows that all three complexes form a trigonal dodecahedron geometry with similar -N=N- distances that are slightly longer than those of the pure azobenzene-containing ligands. The NIR luminescence properties of the Yb(III) complexes were determined at a wavelength of about 980 nm with quantum yields in the range of 0.4-0.6% in ethanol and acetonitrile solutions at room temperature, and trans-to-cis photoisomerization was determined with the quantum yields (Φt→c = 10-2) at the same level as their pure ligands. The trans-to-cis photoisomerization rates of the complexes (10-4 s-1) are slightly higher than those of the pure ligands and similar to azobenzene (10-5 to 10-4 s-1). From time-dependent density functional theory calculations of the energy levels of the first excited triplet states of the ligands, the energies of the lowest excited triplet states of all of the ligands are higher than the resonance level of Yb3+ (2F5/2, 1.2722 eV). We suggest that these azo-containing ligands may participate in energy transfer to the ytterbium ion, in addition to the main "antenna effect" ligand tfd. This is the first report of azobenzene group-functionalized ytterbium complexes with dual NIR luminescence and photoisomerization properties, indicating that azobenzene-containing lanthanide(III) complexes have potential applications as dual function materials in biological systems.

Functionalized Lanthanide(III) Complexes Constructed from Azobenzene Derivative and ß-Diketone Ligands: Luminescent, Magnetic, and Reversible Trans-to-Cis Photoisomerization Properties.

The coordination ability of ligands functionalized by azobenzene was manipulated, and two novel chelating ligands, (E)-4-(phenyldiazenyl)-N,N-bis(pyridin-2-ylmethyl) benzohydrazide (C25H22N6O, PBPM) and (E)-4-((4-(dimethylamino)phenyl)diazenyl)-N,N-bis(pyridin-2-ylmethyl) benzohydrazide (C27H27N7O, dmPBPM), were synthesized. The ligands can offer four coordinating atoms (one oxygen and three nitrogens) to act as tetradendate ligands, together with the two ß-diketonates (4,4,4-trifluoro-1-phenylbutane-1,3-dionate, tfd), and the trifluoroacetate anion presented as a ligand and a counterion to form the quaternary units with lanthanide(III) ions (La, Eu, and Gd), [Ln(tfd)2(PBPM)(CF3CO2)] (LnC47H34F9N6O7) and [Ln(tfd)2(dmPBPM)(CF3CO2)] (LnC49H39F9N7O7), where the lanthanide(III) ions are nine coordinated with N3O6 donor sets. All six complexes were structurally characterized, and four crystals were obtained and further analyzed by means of single-crystal X-ray diffraction. They all crystallized in the monoclinic P21/c space group with very similar lattice parameters, forming a monocapped twisted square antiprism. We successfully observed the photoluminescent properties of Eu(III) complexes at a wavelength of 614 nm in both solution and the solid state, as well as the trans-to-cis photoisomerization with the quantum yield (Φt→c = 10-2) of [Eu(tfd)2(PBPM)(CF3CO2)] complex that was comparable to that of PBPM. Moreover, the trans-to-cis photoisomerization rates of complexes [Ln(tfd)2(PBPM)(CF3CO2)] (La, Eu, Gd) (10-3-10-2 s -1) were also at the same level as that of PBPM and much higher than azobenzene itself (10-5-10-4 s-1). With the aid of TD-DFT calculations, the luminescence of Eu(III) complexes was found to originate from the attenuation effect of ß-diketonates. These features provide the foundation for the development of azobenzene-derived ß-diketonates lanthanide(III) complexes with photoisomerization and photoluminescence dual functions.

Azobenzene-derived tris-ß-diketonate lanthanide complexes: reversible trans-to-cis photoisomerization in solution and solid state.

Novel azobenzene-derived ß-diketonates (4,4,5,5,6,6,6-heptafluoro-1-azobenzene-1,3-hexanedione (LA), 4,4,5,5,6,6,6-heptafluoro-1-(4-dimethylamino)azobenzene-1,3-hexanedione (LB)) were designed and their complexes with lanthanide cations (La(3+), Eu(3+), Gd(3+), Yb(3+)) were prepared and characterized by (1)H NMR, FT-IR, and elemental analysis. Three of the complexes were crystallized successfully and identified by X-ray diffraction. It was significant to find that LA showed remarkably reversible trans-to-cis isomerization properties, however, LB, bearing an electron donor compared with LA, slowed down the isomerization to an extent. The presence of Ln(iii) enhanced the reversible trans-to-cis isomerization properties of both LA and LB a little upon photoirradiation in organic solvents, and amazingly increased the fatigue resistance. In addition, the complexes doped in polymethyl methacrylate (PMMA) films produced a similar phenomenon as well as when in solution. Theoretical calculations based on time dependent density functional theory (TD-DFT) were performed for geometry optimization and to determine the excitation energies of LA and LB to gain further insight into the electronic structure of the complexes, and the data were consistent with the experimental results. The excellent reversible photoisomerization properties of the newly designed Ln(iii) complexes can offer important advantages that will help with the further study of these materials to reach their full potential in applications such as molecular switching devices.

Hepatitis C virus stimulates low-density lipoprotein receptor expression to facilitate viral propagation.

UNLABELLED: Lipids play a crucial role in multiple aspects of hepatitis C virus (HCV) life cycle. HCV modulates host lipid metabolism to enrich the intracellular milieu with lipids to facilitate its proliferation. However, very little is known about the influence of HCV on lipid uptake from bloodstream. Low-density lipoprotein receptor (LDLR) is involved in uptake of cholesterol rich low-density lipoprotein (LDL) particles from the bloodstream. The association of HCV particles with lipoproteins implicates their role in HCV entry; however, the precise role of LDLR in HCV entry still remains controversial. Here, we investigate the effect of HCV infection on LDLR expression and the underlying mechanism(s) involved. We demonstrate that HCV stimulates LDLR expression in both HCV-infected Huh7 cells and in liver tissue from chronic hepatitis C patients. Fluorescence activated cell sorting and immunofluorescence analysis revealed enhanced cell surface and total expression of LDLR in HCV-infected cells. Increased LDLR expression resulted in the enhanced uptake of lipoprotein particles by HCV-infected cells. Analysis of LDLR gene promoter identified a pivotal role of sterol-regulatory element binding proteins (SREBPs), in the HCV-mediated stimulation of LDLR transcription. In addition, HCV negatively modulated the expression of proprotein convertase subtilisin/kexin type 9 (PCSK9), a protein that facilitates LDLR degradation. Ectopic expression of wild-type PCSK9 or gain-of-function PCSK9 mutant negatively affected HCV replication. Overall, our results demonstrate that HCV regulates LDLR expression at transcriptional and posttranslational level via SREBPs and PCSK9 to promote lipid uptake and facilitate viral proliferation. IMPORTANCE: HCV modulates host lipid metabolism to promote enrichment of lipids in intracellular environment, which are essential in multiple aspects of HCV life cycle. However, very little is known about the influence of HCV on lipid uptake from the bloodstream. LDLR is involved in uptake of cholesterol rich lipid particles from bloodstream. In this study, we investigated the effect of HCV on LDLR expression and the underlying mechanism triggered by the virus to modulate LDLR expression. Our observations suggest that HCV upregulates LDLR expression at both the protein and the transcript levels and that this upregulation likely contributes toward the uptake of serum lipids by infected hepatocytes. Abrogation of HCV-mediated upregulation of LDLR inhibits serum lipid uptake and thereby perturbs HCV replication. Overall, our findings highlight the importance of serum lipid uptake by infected hepatocytes in HCV life cycle.

Simultaneous detection and differentiation of three viruses in pear plants by a multiplex RT-PCR.

A multiplex RT-PCR (mRT-PCR) assay was developed for detection and differentiation of the Apple stem pitting virus (ASPV), Apple stem grooving virus (ASGV) and Apple chlorotic leaf spot virus (ACLSV), which are viruses frequently occurring in pear trees. Different combinations of mixed primer pairs were tested for their specificity and sensitivity for the simultaneous detection of the three viruses. Three primer pairs were used to amplify their fragments of 247bp, 358bp and 500bp, respectively. The primer pair for ASPV was designed in this work, while the primer pairs for ACLSV and ASGV were from previous reports. The sensitivity and specificity of the mRT-PCR assay for the three viruses were comparable to that of each uniplex RT-PCR. The mRT-PCR was applied successfully for the detection of three viruses in leaves of pear and apple plants, but was unreliable in the detection of ASGV in dormant barks. In conclusion, this mRT-PCR provides a useful tool for the routine and rapid detection and the differentiation of three pear viruses.

RKIP inhibits NF-kappaB in cancer cells by regulating upstream signaling components of the IkappaB kinase complex.

RKIP was first identified as an inhibitor of the Raf-MEK-ERK signaling pathway. RKIP was also found to play an important role in the NF-kappaB pathway. Genetic and biochemical studies demonstrated that RKIP functioned as a scaffold protein facilitating the phosphorylation of IkappaB by upstream kinases. However, contrary to what one would expect of a scaffold protein, our results show that RKIP has an overall inhibitory effect on the NF-kappaB transcriptional activities. Since NF-kappaB target gene expression is subject to negative regulation involving the optimal induction of negative regulators, our data support a hypothesis that RKIP inhibits NF-kappaB activity via the auto-regulatory feedback loop by rapidly inducing the expression and synthesis of inhibitors of NF-kappaB activation.

The RKIP (Raf-1 Kinase Inhibitor Protein) conserved pocket binds to the phosphorylated N-region of Raf-1 and inhibits the Raf-1-mediated activated phosphorylation of MEK.

The Raf-MEK-ERK pathway regulates many fundamental biological processes, and its activity is finely tuned at multiple levels. The Raf kinase inhibitory protein (RKIP) is a widely expressed negative modulator of the Raf-MEK-ERK signaling pathway. We have previously shown that RKIP inhibits the phosphorylation of MEK by Raf-1 through interfering with the formation of a kinase-substrate complex by direct binding to both Raf-1 and MEK. Here, we show that the evolutionarily conserved ligand-binding pocket of RKIP is required for its inhibitory activity towards the Raf-1 kinase mediated activation of MEK. Single amino acid substitutions of two of the conserved residues form the base and the wall of the pocket confers a loss-of-function phenotype on RKIP. Loss-of-function RKIP mutants still appear to bind to Raf-1. However the stability of the complexes formed between mutants and the N-region Raf-1 phosphopeptide were drastically reduced. Our results therefore suggest that the RKIP conserved pocket may constitute a novel phosphoamino-acid binding motif and is absolutely required for RKIP function.

Raf kinase inhibitor protein positively regulates cell-substratum adhesion while negatively regulating cell-cell adhesion.

Raf kinase inhibitor protein (RKIP) regulates a number of cellular processes, including cell migration. Exploring the role of RKIP in cell adhesion, we found that overexpression of RKIP in Madin-Darby canine kidney (MDCK) epithelial cells increases adhesion to the substratum, while decreasing adhesion of the cells to one another. The level of the adherens junction protein E-cadherin declines profoundly, and there is loss of normal localization of the tight junction protein ZO-1, while expression of the cell-substratum adhesion protein beta1 integrin dramatically increases. The cells also display increased adhesion and spreading on multiple substrata, including collagen, gelatin, fibronectin and laminin. In three-dimensional culture, RKIP overexpression leads to marked cell elongation and extension of long membrane protrusions into the surrounding matrix, and the cells do not form hollow cysts. RKIP-overexpressing cells generate considerably more contractile traction force than do control cells. In contrast, RNA interference-based silencing of RKIP expression results in decreased cell-substratum adhesion in both MDCK and MCF7 human breast adenocarcinoma cells. Treatment of MDCK and MCF7 cells with locostatin, a direct inhibitor of RKIP and cell migration, also reduces cell-substratum adhesion. Silencing of RKIP expression in MCF7 cells leads to a reduction in the rate of wound closure in a scratch-wound assay, although not as pronounced as that previously reported for RKIP-knockdown MDCK cells. These results suggest that RKIP has important roles in the regulation of cell adhesion, positively controlling cell-substratum adhesion while negatively controlling cell-cell adhesion, and underscore the complex functions of RKIP in cell physiology.