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2017 Publications

Title
AuthorsReferencePMID
Contributions of individual domains to function of the HIV-1 Rev response element.O'Carroll IPThappeta YFan LRamirez-Valdez EASmith SWang YXRein A.J Virol. 2017 Aug 16. pii: JVI.00746-17. doi: 10.1128/JVI.00746-17. [Epub ahead of print]28814520

Dissection of specific binding of HIV-1 Gag to the 'packaging signal' in viral RNA.

Comas-Garcia MDatta SABaker LVarma RGudla PRRein A.Elife. 2017 Jul 20;6. pii: e27055. doi: 10.7554/eLife.27055.28726630

Long Noncoding RNA PURPL Suppresses Basal p53 Levels and Promotes Tumorigenicity in Colorectal Cancer.

Li XLSubramanian MJones MFChaudhary RSingh DKZong XGryder BSindri SMo MSchetter AWen XParvathaneni SKazandjian DJenkins LMTang WElloumi FMartindale JLHuarte MZhu YRobles AIFrier SMRigo FCam MAmbs SSharma SHarris CCDasso MPrasanth KVLal A.Cell Rep. 2017 Sep5;20(10):2408-2423. doi: 10.1016/j.celrep.2017.08.041.28877474

Prosurvival long noncoding RNA PINCR regulates a subset of p53 targets in human colorectal cancer cells by binding to Matrin 3.

Chaudhary RGryder BWoods WSSubramanian MJones MFLi XLJenkins LMShabalina SAMo MDasso MYang YWakefield LMZhu YFrier SMMoriarity BSPrasanth KVPerez-Pinera PLal A.Elife. 2017 Jun 5;6. pii: e23244. doi: 10.7554/eLife.23244.28580901

Oncogenic Activation of the RNA Binding Protein NELFE and MYC Signaling in Hepatocellular Carcinoma.

Dang HTakai AForgues MPomyen YMou HXue WRay DHa KCHMorris QDHughes TRWang XW.Cancer Cell. 2017Jul10;32(1):101-114.e8. doi: 10.1016/j.ccell.2017.06.002.28697339

The Functional Cycle of Rnt1p: Five Consecutive Steps of Double-Stranded RNA Processing by a Eukaryotic RNase III.

Song HFang XJin LShaw GXWang YXJi X.Structure. 2017 Feb 7;25(2):353-363. doi: 10.1016/j.str.2016.12.013. Epub 2017 Jan 19.28111020
Virus-Mediated Alterations in miRNA Factors and Degradation of Viral miRNAs by MCPIP1.  Happel CRamalingam DZiegelbauer JM.PLoS Biol. 2016 Nov 28;14(11):e2000998. doi: 10.1371/journal.pbio.2000998. eCollection 2016 Nov.27893764

Viral MicroRNAs Repress the Cholesterol Pathway, and 25-Hydroxycholesterol Inhibits Infection.

Serquiña AKPKambach DMSarker OZiegelbauer JM.MBio. 2017 Jul 11;8(4). pii: e00576-17. doi: 10.1128/mBio.00576-17.28698273
    
    

 

 

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pubmed: (caplen n[au] or fel...
NCBI: db=pubmed; Term=(Caplen N[AU] OR Felber B[AU] OR Franchini V[AU] OR Freed E[AU] OR Gottesman S[AU] OR Grewal S[AU] OR Harris C[AU] OR Hu W[AU] OR Huang J[AU] OR Hughes S[AU] OR Jessup J[AU] OR Ji X[AU] OR Johnson P[AU] OR Kashlev M[AU] OR KewalRamani V[AU] OR Khan J[AU] OR Kwong K[AU] OR Lal A[AU] OR Larson D[AU] OR LeGrice S[AU] OR Luo J[AU] OR Meltzer P[AU] OR Merlino G[AU] OR Mili V[AU] OR Misteli T[AU] OR Oberdoerffer S[AU] OR Pathak V[AU] OR Pavlakis G[AU] OR Rein A[AU] OR Ried T[AU] OR Shapiro B[AU] OR Singer D[AU] OR Staudt L[AU] OR Strathern J[AU] OR Wang Y[AU] OR Wang X[AU] OR Weissman A[AU] OR Young H[AU] OR Zhang Y[AU] OR Zheng ZM[AU] OR Zhurkin V[AU] OR Ziegelbauer J[AU]) AND (Bethesda OR Frederick)
A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes.
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A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes.

Molecules. 2018 Oct 19;23(10):

Authors: König G, Pickard FC, Huang J, Thiel W, MacKerell AD, Brooks BR, York DM

Abstract
Maintaining a proper balance between specific intermolecular interactions and non-specific solvent interactions is of critical importance in molecular simulations, especially when predicting binding affinities or reaction rates in the condensed phase. The most rigorous metric for characterizing solvent affinity are solvation free energies, which correspond to a transfer from the gas phase into solution. Due to the drastic change of the electrostatic environment during this process, it is also a stringent test of polarization response in the model. Here, we employ both the CHARMM fixed charge and polarizable force fields to predict hydration free energies of twelve simple solutes. The resulting classical ensembles are then reweighted to obtain QM/MM hydration free energies using a variety of QM methods, including MP2, Hartree⁻Fock, density functional methods (BLYP, B3LYP, M06-2X) and semi-empirical methods (OM2 and AM1 ). Our simulations test the compatibility of quantum-mechanical methods with molecular-mechanical water models and solute Lennard⁻Jones parameters. In all cases, the resulting QM/MM hydration free energies were inferior to purely classical results, with the QM/MM Drude force field predictions being only marginally better than the QM/MM fixed charge results. In addition, the QM/MM results for different quantum methods are highly divergent, with almost inverted trends for polarizable and fixed charge water models. While this does not necessarily imply deficiencies in the QM models themselves, it underscores the need to develop consistent and balanced QM/MM interactions. Both the QM and the MM component of a QM/MM simulation have to match, in order to avoid artifacts due to biased solute⁻solvent interactions. Finally, we discuss strategies to improve the convergence and efficiency of multi-scale free energy simulations by automatically adapting the molecular-mechanics force field to the target quantum method.

PMID: 30347691 [PubMed - indexed for MEDLINE]

Fine mapping of MHC region in lung cancer highlights independent susceptibility loci by ethnicity.
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Fine mapping of MHC region in lung cancer highlights independent susceptibility loci by ethnicity.

Nat Commun. 2018 09 25;9(1):3927

Authors: Ferreiro-Iglesias A, Lesseur C, McKay J, Hung RJ, Han Y, Zong X, Christiani D, Johansson M, Xiao X, Li Y, Qian DC, Ji X, Liu G, Caporaso N, Scelo G, Zaridze D, Mukeriya A, Kontic M, Ognjanovic S, Lissowska J, Szołkowska M, Swiatkowska B, Janout V, Holcatova I, Bolca C, Savic M, Ognjanovic M, Bojesen SE, Wu X, Albanes D, Aldrich MC, Tardon A, Fernandez-Somoano A, Fernandez-Tardon G, Le Marchand L, Rennert G, Chen C, Doherty J, Goodman G, Bickeböller H, Wichmann HE, Risch A, Rosenberger A, Shen H, Dai J, Field JK, Davies M, Woll P, Teare MD, Kiemeney LA, van der Heijden EHFM, Yuan JM, Hong YC, Haugen A, Zienolddiny S, Lam S, Tsao MS, Johansson M, Grankvist K, Schabath MB, Andrew A, Duell E, Melander O, Brunnström H, Lazarus P, Arnold S, Slone S, Byun J, Kamal A, Zhu D, Landi MT, Amos CI, Brennan P

Abstract
Lung cancer has several genetic associations identified within the major histocompatibility complex (MHC); although the basis for these associations remains elusive. Here, we analyze MHC genetic variation among 26,044 lung cancer patients and 20,836 controls densely genotyped across the MHC, using the Illumina Illumina OncoArray or Illumina 660W SNP microarray. We impute sequence variation in classical HLA genes, fine-map MHC associations for lung cancer risk with major histologies and compare results between ethnicities. Independent and novel associations within HLA genes are identified in Europeans including amino acids in the HLA-B*0801 peptide binding groove and an independent HLA-DQB1*06 loci group. In Asians, associations are driven by two independent HLA allele sets that both increase risk in HLA-DQB1*0401 and HLA-DRB1*0701; the latter better represented by the amino acid Ala-104. These results implicate several HLA-tumor peptide interactions as the major MHC factor modulating lung cancer susceptibility.

PMID: 30254314 [PubMed - indexed for MEDLINE]

Design and biological activity of novel stealth polymeric lipid nanoparticles for enhanced delivery of hydrophobic photodynamic therapy drugs.
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Design and biological activity of novel stealth polymeric lipid nanoparticles for enhanced delivery of hydrophobic photodynamic therapy drugs.

Nanomedicine. 2018 10;14(7):2295-2305

Authors: Viard M, Reichard H, Shapiro BA, Durrani FA, Marko AJ, Watson RM, Pandey RK, Puri A

Abstract
Advances in in vivo stability and preferential tumor uptake of cancer nanomedicine are warranted for effective chemotherapy. Here, we describe a novel nanoformulation using an unconventional polymeric tubule-forming phospholipid, DC8,9PC. We report that DC8,9PC transitions to stable vesicles (LNPs) in the presence of PEGylated lipid (DSPE-PEG2000); the resulting DC8,9PC:DSPE-PEG2000 LNPs efficiently included a hydrophobic PDT drug, HPPH. Remarkably, these LNPs incorporated unusually high DSPE-PEG2000 concentrations; LNP10-HPPH and LNP20-HPPH (10 & 20 mol% PEGylated lipid, respectively) exhibited >90% serum stability at 37 °C. Increased PEGylation in the LNPs correlated with enhanced tumor accumulation in intravenously injected HT29 tumor mouse xenographs. Colon-26 bearing BALB/c mice, intravenously injected with LNP20-HPPH showed superior PDT efficacy and animal survival (no tumor recurrence up to 100 days) as compared to a formulation currently used in clinical trials. Taken together, we present a simple stealth binary lipid nanosystem with enhanced efficiency of tumor accumulation and superior therapeutic efficacy.

PMID: 30059754 [PubMed - indexed for MEDLINE]

Highly Emissive Self-Assembled BODIPY-Platinum Supramolecular Triangles.
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Highly Emissive Self-Assembled BODIPY-Platinum Supramolecular Triangles.

J Am Chem Soc. 2018 06 20;140(24):7730-7736

Authors: Zhou J, Zhang Y, Yu G, Crawley MR, Fulong CRP, Friedman AE, Sengupta S, Sun J, Li Q, Huang F, Cook TR

Abstract
Light-emitting supramolecular coordination complexes (SCCs) have been widely studied for applications in the chemical and biological sciences. Herein, we report the coordination-driven self-assembly of two highly emissive platinum(II) supramolecular triangles (1 and 2) containing BODIPY-based bridging ligands. The metallacycles exhibit favorable anticancer activities against HeLa cells (IC50 of 6.41 and 2.11 μM). The characteristic ∼570 nm fluorescence of the boron dipyrromethene (BODIPY) moieties in the metallacycles permits their intracellular visualization using confocal microscopy. Additionally, the BODIPY fluorophore is an excellent photodynamic agent, making the metallacycles as ideal therapeutics for photodynamic therapy (PDT) and chemotherapy. In vitro studies demonstrate that the combination indexes against HeLa cells are 0.56 and 0.48 for 1 and 2, respectively, confirming their synergistic anticancer effect. More importantly, these SCCs also exhibit superior anticancer efficacy toward cisplatin-resistant A2780cis cell line by combining PDT and chemotherapy, showing promise in overcoming drug resistance. This study exploits a multicomponent approach to self-assembled metallacages that enables design of effective theranostic agents wherein the platinum acceptors are toxic chemotherapeutics and the BODIPY donors are imaging probes and photosensitizers. Since each piece may be independently tuned, i.e., Pt(II) polypyridyl fragment swapped for Pt(II) phosphine, the activity may be optimized without a total redesign of the system.

PMID: 29787269 [PubMed - indexed for MEDLINE]

A Cas9 transgenic Plasmodium yoelii parasite for efficient gene editing.
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A Cas9 transgenic Plasmodium yoelii parasite for efficient gene editing.

Mol Biochem Parasitol. 2018 06;222:21-28

Authors: Qian P, Wang X, Yang Z, Li Z, Gao H, Su XZ, Cui H, Yuan J

Abstract
The RNA-guided endonuclease Cas9 has applied as an efficient gene-editing method in malaria parasite Plasmodium. However, the size (4.2 kb) of the commonly used Cas9 from Streptococcus pyogenes (SpCas9) limits its utility for genome editing in the parasites only introduced with cas9 plasmid. To establish the endogenous and constitutive expression of Cas9 protein in the rodent malaria parasite P. yoelii, we replaced the coding region of an endogenous gene sera1 with the intact SpCas9 coding sequence using the CRISPR/Cas9-mediated genome editing method, generating the cas9-knockin parasite (PyCas9ki) of the rodent malaria parasite P. yoelii. The resulted PyCas9ki parasite displays normal progression during the whole life cycle and possesses the Cas9 protein expression in asexual blood stage. By introducing the plasmid (pYCs) containing only sgRNA and homologous template elements, we successfully achieved both deletion and tagging modifications for different endogenous genes in the genome of PyCas9ki parasite. This cas9-knockin PyCas9ki parasite provides a new platform facilitating gene functions study in the rodent malaria parasite P. yoelii.

PMID: 29684399 [PubMed - indexed for MEDLINE]

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Last updated by Hooper, Laura (NIH/NCI) [E] on Sep 27, 2017