Quantitative proteomics reveal a feedforward mechanism for mitochondrial PARKIN translocation and ubiquitin chain synthesis.

Phosphorylation is often used to promote protein ubiquitylation, yet we rarely understand quantitatively how ligase activation and ubiquitin (UB) chain assembly are integrated with phosphoregulation. Here we employ quantitative proteomics and live-cell imaging to dissect individual steps in the PINK1 kinase-PARKIN UB ligase mitochondrial control pathway disrupted in Parkinson's disease. PINK1 plays a dual role by phosphorylating PARKIN on its UB-like domain and poly-UB chains on mitochondria. PARKIN activation by PINK1 produces canonical and noncanonical UB chains on mitochondria, and PARKIN-dependent chain assembly is required for accumulation of poly-phospho-UB (poly-p-UB) on mitochondria. In vitro, PINK1 directly activates PARKIN's ability to assemble canonical and noncanonical UB chains and promotes association of PARKIN with both p-UB and poly-p-UB. Our data reveal a feedforward mechanism that explains how PINK1 phosphorylation of both PARKIN and poly-UB chains synthesized by PARKIN drives a program of PARKIN recruitment and mitochondrial ubiquitylation in response to mitochondrial damage.

A direct GABAergic output from the basal ganglia to frontal cortex.

The basal ganglia are phylogenetically conserved subcortical nuclei necessary for coordinated motor action and reward learning. Current models postulate that the basal ganglia modulate cerebral cortex indirectly via an inhibitory output to thalamus, bidirectionally controlled by direct- and indirect-pathway striatal projection neurons (dSPNs and iSPNs, respectively). The basal ganglia thalamic output sculpts cortical activity by interacting with signals from sensory and motor systems. Here we describe a direct projection from the globus pallidus externus (GP), a central nucleus of the basal ganglia, to frontal regions of the cerebral cortex (FC). Two cell types make up the GP-FC projection, distinguished by their electrophysiological properties, cortical projections and expression of choline acetyltransferase (ChAT), a synthetic enzyme for the neurotransmitter acetylcholine (ACh). Despite these differences, ChAT(+) cells, which have been historically identified as an extension of the nucleus basalis, as well as ChAT(-) cells, release the inhibitory neurotransmitter GABA (γ-aminobutyric acid) and are inhibited by iSPNs and dSPNs of dorsal striatum. Thus, GP-FC cells comprise a direct GABAergic/cholinergic projection under the control of striatum that activates frontal cortex in vivo. Furthermore, iSPN inhibition of GP-FC cells is sensitive to dopamine 2 receptor signalling, revealing a pathway by which drugs that target dopamine receptors for the treatment of neuropsychiatric disorders can act in the basal ganglia to modulate frontal cortices.

RNAi screening identifies a mechanosensitive ROCK-JAK2-STAT3 network central to myofibroblast activation.

Myofibroblasts play key roles in wound healing and pathological fibrosis. Here, we used an RNAi screen to characterize myofibroblast regulatory genes, using a high-content imaging approach to quantify α-smooth muscle actin stress fibers in cultured human fibroblasts. Screen hits were validated on physiological compliance hydrogels, and selected hits tested in primary fibroblasts from patients with idiopathic pulmonary fibrosis. Our RNAi screen led to the identification of STAT3 as an essential mediator of myofibroblast activation and function. Strikingly, we found that STAT3 phosphorylation, while responsive to exogenous ligands on both soft and stiff matrices, is innately active on a stiff matrix in a ligand/receptor-independent, but ROCK- and JAK2-dependent fashion. These results demonstrate how a cytokine-inducible signal can become persistently activated by pathological matrix stiffening. Consistent with a pivotal role for this pathway in driving persistent fibrosis, a STAT3 inhibitor attenuated murine pulmonary fibrosis when administered in a therapeutic fashion after bleomycin injury. Our results identify novel genes essential for the myofibroblast phenotype, and point to STAT3 as an important target in pulmonary fibrosis and other fibrotic diseases.

Genome-wide RNAi screen for nuclear actin reveals a network of cofilin regulators.

Nuclear actin plays an important role in many processes that regulate gene expression. Cytoplasmic actin dynamics are tightly controlled by numerous actin-binding proteins, but regulation of nuclear actin has remained unclear. Here, we performed a genome-wide RNA interference (RNAi) screen in Drosophila cells to identify proteins that influence either nuclear polymerization or import of actin. We validate 19 factors as specific hits, and show that Chinmo (known as Bach2 in mammals), SNF4Aγ (Prkag1 in mammals) and Rab18 play a role in nuclear localization of actin in both fly and mammalian cells. We identify several new regulators of cofilin activity, and characterize modulators of both cofilin kinases and phosphatase. For example, Chinmo/Bach2, which regulates nuclear actin levels also in vivo, maintains active cofilin by repressing the expression of the kinase Cdi (Tesk in mammals). Finally, we show that Nup98 and lamin are candidates for regulating nuclear actin polymerization. Our screen therefore reveals new aspects of actin regulation and links nuclear actin to many cellular processes.

Identification of genes that promote or antagonize somatic homolog pairing using a high-throughput FISH-based screen.

The pairing of homologous chromosomes is a fundamental feature of the meiotic cell. In addition, a number of species exhibit homolog pairing in nonmeiotic, somatic cells as well, with evidence for its impact on both gene regulation and double-strand break (DSB) repair. An extreme example of somatic pairing can be observed in Drosophila melanogaster, where homologous chromosomes remain aligned throughout most of development. However, our understanding of the mechanism of somatic homolog pairing remains unclear, as only a few genes have been implicated in this process. In this study, we introduce a novel high-throughput fluorescent in situ hybridization (FISH) technology that enabled us to conduct a genome-wide RNAi screen for factors involved in the robust somatic pairing observed in Drosophila. We identified both candidate "pairing promoting genes" and candidate "anti-pairing genes," providing evidence that pairing is a dynamic process that can be both enhanced and antagonized. Many of the genes found to be important for promoting pairing are highly enriched for functions associated with mitotic cell division, suggesting a genetic framework for a long-standing link between chromosome dynamics during mitosis and nuclear organization during interphase. In contrast, several of the candidate anti-pairing genes have known interphase functions associated with S-phase progression, DNA replication, and chromatin compaction, including several components of the condensin II complex. In combination with a variety of secondary assays, these results provide insights into the mechanism and dynamics of somatic pairing.

A genetic screen identifies interferon-α effector genes required to suppress hepatitis C virus replication.

BACKGROUND & AIMS: Hepatitis C virus (HCV) infection is a leading cause of end-stage liver disease. Interferon-α (IFNα) is an important component of anti-HCV therapy; it up-regulates transcription of IFN-stimulated genes, many of which have been investigated for their antiviral effects. However, all of the genes required for the antiviral function of IFNα (IFN effector genes [IEGs]) are not known. IEGs include not only IFN-stimulated genes, but other nontranscriptionally induced genes that are required for the antiviral effect of IFNα. In contrast to candidate approaches based on analyses of messenger RNA (mRNA) expression, identification of IEGs requires a broad functional approach. METHODS: We performed an unbiased genome-wide small interfering RNA screen to identify IEGs that inhibit HCV. Huh7.5.1 hepatoma cells were transfected with small interfering RNAs incubated with IFNα and then infected with JFH1 HCV. Cells were stained using HCV core antibody, imaged, and analyzed to determine the percent infection. Candidate IEGs detected in the screen were validated and analyzed further. RESULTS: The screen identified 120 previously unreported IEGs. From these, we more fully evaluated the following: asparagine-linked glycosylation 10 homolog (yeast, α-1,2-glucosyltransferase); butyrylcholinesterase; dipeptidyl-peptidase 4 (CD26, adenosine deaminase complexing protein 2); glucokinase (hexokinase 4) regulator; guanylate cyclase 1, soluble, ß 3; MYST histone acetyltransferase 1; protein phosphatase 3 (formerly 2B), catalytic subunit, ß isoform; peroxisomal proliferator-activated receptor-γ-DBD-interacting protein 1; and solute carrier family 27 (fatty acid transporter), member 2; and demonstrated that they enabled IFNα-mediated suppression of HCV at multiple steps of its life cycle. Expression of these genes had more potent effects against flaviviridae because a subset was required for IFNα to suppress dengue virus but not influenza A virus. In addition, many of the host genes detected in this screen (92%) were not transcriptionally stimulated by IFNα; these genes represent a heretofore unknown class of non-IFN-stimulated gene IEGs. CONCLUSIONS: We performed a whole-genome loss-of-function screen to identify genes that mediate the effects of IFNα against human pathogenic viruses. We found that IFNα restricts HCV via actions of general and specific IEGs.

An image-based RNAi screen identifies SH3BP1 as a key effector of Semaphorin 3E-PlexinD1 signaling.

Extracellular signals have to be precisely interpreted intracellularly and translated into diverse cellular behaviors often mediated by cytoskeletal changes. Semaphorins are one of the largest families of guidance cues and play a critical role in many systems. However, how different cell types translate extracellular semaphorin binding into intracellular signaling remains unclear. Here we developed and performed a novel image-based genome-wide functional RNAi screen for downstream signaling molecules that convert the interaction between Semaphorin 3E (Sema3E) and PlexinD1 into cellular behaviors. One of the genes identified in this screen is a RhoGAP protein, SH3-domain binding protein 1 (SH3BP1). We demonstrate that SH3BP1 mediates Sema3E-induced cell collapse through interaction with PlexinD1 and regulation of Ras-related C3 botulinum toxin substrate 1 (Rac1) activity. The identification and characterization of SH3BP1 as a novel downstream effector of Sema3E-PlexinD1 provides an explanation for how extracellular signals are translated into cytoskeletal changes and unique cell behavior, but also lays the foundation for characterizing other genes identified from our screen to obtain a more complete picture of plexin signaling.

Differential determinants of cancer cell insensitivity to antimitotic drugs discriminated by a one-step cell imaging assay.

Cancer cells can be drug resistant due to genetic variation at multiple steps in the drug response pathway, including drug efflux pumping, target mutation, and blunted apoptotic response. These are not discriminated by conventional cell survival assays. Here, we report a rapid and convenient high-content cell-imaging assay that measures multiple physiological changes in cells responding to antimitotic small-molecule drugs. Our one-step, no-wash assay uses three dyes to stain living cells and is much more accurate for scoring weakly adherent mitotic and apoptotic cells than conventional antibody-based assays. We profiled responses of 33 cell lines to 8 antimitotic drugs at multiple concentrations and time points using this assay and deposited our data and assay protocols into a public database (http://lincs.hms.harvard.edu/). Our data discriminated between alternative mechanisms that compromise drug sensitivity to paclitaxel and revealed an unexpected bell-shaped dose-response curve for BI2536, a highly selective inhibitor of Polo-like kinases. Our approach can be generalized, is scalable, and should therefore facilitate identification of molecular biomarkers for mechanisms of drug insensitivity in high-throughput screens and other assays.

Rapid induction of apoptosis during Kinesin-5 inhibitor-induced mitotic arrest in HL60 cells.

Small molecule inhibitors of Kinesin-5 (K5Is) that arrest cells in mitosis with monopolar spindles are promising anti-cancer drug candidates. Clinical trials of K5Is revealed dose-limiting neutropenia, or loss of neutrophils, for which the molecular mechanism is unclear. We investigated the effects of a K5I on HL60 cells, a human promyelocytic leukemia cell line that is often used to model dividing neutrophil progenitors in cell culture. We found K5I treatment caused unusually rapid death of HL60 cells exclusively during mitotic arrest. This mitotic death occurred via the intrinsic apoptosis pathway with molecular events that include cytochrome c leakage into the cytoplasm, caspase activation, and Parp1 cleavage. Bcl-2 overexpression protected from death. We probed mitochondrial physiology to find candidate triggers of cytochrome c release, and observed a decrease of membrane potential (ΔΨm) before mitochondrial outer membrane permeabilization (MOMP). Interestingly, this loss of ΔΨm was not blocked by overexpressing Bcl-2, suggesting it might be a cause of Bax/Bak activation, not a consequence. Taken together, these results show that K5I induces intrinsic apoptosis during mitotic arrest in HL60 with loss of ΔΨm as an upstream event of MOMP.

An intermittent live cell imaging screen for siRNA enhancers and suppressors of a kinesin-5 inhibitor.

Kinesin-5 (also known as Eg5, KSP and Kif11) is required for assembly of a bipolar mitotic spindle. Small molecule inhibitors of Kinesin-5, developed as potential anti-cancer drugs, arrest cell in mitosis and promote apoptosis of cancer cells. We performed a genome-wide siRNA screen for enhancers and suppressors of a Kinesin-5 inhibitor in human cells to elucidate cellular responses, and thus identify factors that might predict drug sensitivity in cancers. Because the drug's actions play out over several days, we developed an intermittent imaging screen. Live HeLa cells expressing GFP-tagged histone H2B were imaged at 0, 24 and 48 hours after drug addition, and images were analyzed using open-source software that incorporates machine learning. This screen effectively identified siRNAs that caused increased mitotic arrest at low drug concentrations (enhancers), and vice versa (suppressors), and we report siRNAs that caused both effects. We then classified the effect of siRNAs for 15 genes where 3 or 4 out of 4 siRNA oligos tested were suppressors as assessed by time lapse imaging, and by testing for suppression of mitotic arrest in taxol and nocodazole. This identified 4 phenotypic classes of drug suppressors, which included known and novel genes. Our methodology should be applicable to other screens, and the suppressor and enhancer genes we identified may open new lines of research into mitosis and checkpoint biology.

Termolecular kinetics for the Mu + CO + M recombination reaction: A unique test of quantum rate theory.

The room-temperature termolecular rate constants, k0, for the Mu + CO + M<==>MuCO + M (M = He, N2, Ar) recombination reaction have been measured by the muSR technique, and are reported for moderator gas pressures of up to approximately 200 bar (densities less, similar 0.4 x 10(22) molec cm(-3)). The experimental relaxation rates reveal an unusual signature, in being dominated by the electron spin-rotation interaction in the MuCO radical that is formed in the addition step. In N2 moderator, k0 = 1.2+/-0.1 x 10(-34) cm(6) s(-1), only about 30% higher than found in Ar or He. The experimental results are compared with theoretical calculations carried out on the Werner-Keller-Schinke (WKS) surface [Keller et al., J. Chem. Phys. 105, 4983 (1996)], within the framework of the isolated resonance model (IRM). The positions and lifetimes of resonance states are obtained by solving the complex Hamiltonian for the nonrotating MuCO system, using an L2 method, with an absorbing potential in the asymptotic region. Accurate values of the vibrational bound and resonance states of MuCO reveal unprecedented isotope effects in comparisons with HCO, due to the remarkable effect of replacing H by the very light Mu atom (m(Mu) approximately (1/9)m(H)). Due to its pronounced zero-point energy shift, there are only two (J = 0) bound states in MuCO. Contributions from nonzero J states to the termolecular rate constants are evaluated through the J-shifting approximation, with rotational constants evaluated at the potential minimum. The value of the important A constant (181 cm(-1)) used in this approximation was supported by accurate J = K = 1 calculations, from which A = 180 cm(-1) was obtained by numerical evaluation. The calculations presented here, with a "weak collision factor" beta c = 0.001, indicative of the very sparse density of MuCO states, give a very good account of both the magnitude and pressure dependence of the experimental rates, but only when the fact that the two initially bound (J = 0) states become resonances for J > 0 is taken into account. This is the first time in IRM calculations of atom-molecule recombination reactions where J not equal to 0 states have proven to be so important, thus providing a truly unique test of quantum rate theory.

Quantum and quasiclassical studies of the O(3P)+HCl-->OH+Cl(2P) reaction using benchmark potential surfaces.

We have performed quantum mechanical (QM) dynamics calculations within the independent-state approximation with new benchmark triplet A" and A' surfaces [B. Ramachandran et al., J. Chem. Phys. 119, 9590 (2003)] for the rovibronic state-to-state measurements of the reaction O(3P)+HCl(v=2,j=1,6,9)-->OH(v'j')+Cl(2P) [Zhang et al., J. Chem. Phys. 94, 2704 (1991)]. The QM and experimental rotational distributions peak at similar OH(j') levels, but the QM distributions are significantly narrower than the measurements and previous quasiclassical dynamics studies. The OH(low j) populations observed in the measurements are nearly absent in the QM results. We have also performed quasiclassical trajectory with histogram binning (QCT-HB) calculations on these same benchmark surfaces. The QCT-HB rotational distributions, which are qualitatively consistent with measurements and classical dynamics studies using other surfaces, are much broader than the QM results. Application of a Gaussian binning correction (QCT-GB) dramatically narrows and shifts the QCT-HB rotational distributions to be in very good agreement with the QM results. The large QCT-GB correction stems from the special shape of the joint distribution of the classical rotational/vibrational action of OH products. We have also performed QM and QCT calculations for the transition, O+HCl(v=0,T=300 K)-->OH(v'j')+Cl from threshold to approximately 130 kcal mol(-1) collision energy as a guide for possible future hyperthermal O-atom measurements. We find in general a mixed energy release into translation and rotation consistent with a late barrier to reaction. Angular distributions at high collision energy are forward peaked, consistent with a stripping mechanism. Direct collisional excitation channel cross sections, O+HCl(v=0,T=300 K)-->O+HCl(v'=1), in the same energy range are large, comparable in magnitude to the reactive channel cross sections. Although the (3)A" state dominates most collision processes, above approximately 48 kcal mol(-1), the (3)A' state plays the major role in collisional excitation.

A reduced dimensionality quasiclassical and quantum study of the proton transfer reaction H3O(+)+H2O-->H2O+H3O(+).

We report quantum and quasiclassical calculations of proton transfer in the reaction H(3)O(+)+H(2)O in three degrees of freedom, the two OH(+) bond lengths and the OH(+)O angle. The reduced dimensional potential energy surface is obtained from the full dimensional OSS3(p) energy function of H(5)O(2) (+) [L. Ojamae, I. Shavitt, and S. J. Singer, J. Chem. Phys. 109, 5547 (1998)], with an additional long-range correction to reproduce the correct ion-molecule interaction. This surface is used to perform both quasiclassical trajectory and quantum reactive scattering calculations of the zero total angular momentum cumulative reaction probability and cross sections for initial rotational states 0, 1, and 2. Comparison of these quantities are made to assess the importance of quantum effects in this reduced dimensional reaction. Additional quasiclassical cross sections are calculated to obtain the thermal rate constant for the reaction.