Project description:Parkinson’s disease (PD) as a progressive neurodegenerative disorder arises from multiple genetic and environmental factors. However, underlying pathological mechanisms remain poorly understood. Using multiplexed single-cell transcriptomics, we analyze human neural precursor cells (hNPCs) from sporadic PD (sPD) patients. Alterations in gene expression appear in pathways related to primary cilia (PC). Accordingly, in these hiPSC-derived hNPCs and neurons, we observe a shortening of PC. Additionally, we detect a shortening of PC in PINK1-deficient human cellular and mouse models of familial PD. Furthermore, in sPD models, the shortening of PC is accompanied by an increased SHH signal transduction. Inhibition of this pathway rescues the alterations in PC morphology and mitochondrial dysfunction. Thus, increased SHH activity due to ciliary dysfunction is needed for the development of pathoetiological phenotypes observed in sPD, like mitochondrial dysfunction. In sum, altered PC function is part of early PD pathoetiology and inhibiting the overactive SHH signaling is a potential neuroprotective therapy.
Project description:Platinum and palladium are highly sought-after noble metals that due to their low abundance have high value and because of their stability and their roles in catalytic processes are very desirable for industrial purposes. Bacteria are able to produce nanoparticles of platinum and palladium at low temperatures and from low concentration feedstocks contrary to chemical methods and so pose a potentially untapped ‘green’ resource for nanoparticle synthesis. We have used the bacterium Desulfovibrio alaskensis G20 to reduce Pt and Pd ions to zero-valent nanoparticle forms and used differential shotgun proteomics to identify proteins responsible for this reduction . There was found to be a core set of 13 proteins common to both datasets as well as 7 proteins specific to Pt and Pd individually. Over expression of one of Pt-specific genes; the NiFe hydrogenase small subunit, resulted in the formation of larger nanoparticles. For the first time the proteins involved in the metal reduction pathway have been pinpointed and it is our hope that these target genes can then be used for nanoparticle production to tailor specific properties for industrial purposes at the genetic level rather than post-production.
Project description:Purpose:The goals of this study is to analyze the candidate genes motified by CID755674 to promote the mouse embryonic stem cell (ESC) self-renewal through RNA-seq approach. Previously, we found that MEK inhbitior PD0323901 (PD) coporates with protein kinase D inhibitor CID755673 (CID) is able to maitain mouse embryonic stem cell (mESC) self-renewal, we named this conditon is "PC". In order to find out why CID755673 can promote mouse embryonic stem cell self-renewal, we performed RNA-sequence in mESCs treated with PD or PC, and tried to identify the key mechanisms under CID
Project description:Molecular pathogenesis of posttransplant (PT) lymphoproliferative disorder, including the most prevalent diffuse large B cell lymphoma (DLBCL), is largely unknown. We have recently showed that Epstein-Barr Virus (EBV)+ and EBV- PT-DLBCL are biologically different, but gene expression profile of the latter lymphoma is similar to that of immunocompetent (IC) DLBCL. To validate these findings on a genomic level, we performed array CGH analysis of 21 EBV+ and 6 EBV- PT-DLBCL, and 11 control IC-DLBCL. Genomic and transcriptomic data were subsequently integrated. Notably, EBV+ and EBV- PT-DLBCL revealed only one shared recurrent imbalance, while EBV- PT-DLBCL displayed at least 10 aberrations recurrent in IC-DLBCL, among others gain of 3/3q and 18q, and loss of 6q23/TNFAIP3 and 9p21/CDKN2A. EBV+ PT-DLBCL showed distinct aberrations, including the most prevalent gain/amplification of 9p24.1 targeting PDCD1LG2/PDL2. Significant differential representation/expression of 3p13/FOXP1 and 9p21/CDKNA2 in EBV+ PT-DLBCL when compared with EBV- PT-/IC-DLBCL, suggests that the oncogene FOXP1 and the tumor suppressor gene CDKNA2 are not implicated in pathogenesis of EBV+ PT-DLBCL. In summary, genomic profiling of PT-/IC-DLBCL confirmed biological distinctness of EBV+ and EBV- PT-DLBCL, and relationship between EBV- PT-DLBCL and IC-DLBCL. These findings support the hypothesis that EBV- PT-DLBCL are coincidental lymphomas in transplant recipients
Project description:We used 500 melanized dopamine neurons isolated from post-mortem human substantia nigra pars compacta of each sample with laser capture microdissection. Total RNA was extracted with Arcturus PicoPure RNA extraction kit and amplified two times with Arcturus RiboAmp RNA amplification kit. the samples were then sent to the Partners Center for Genetics and Genomics (HPCGG.org) for labeling, hybridization and scanning according to standard Affymetrix protocols. Samples from a total of 16 human brains, 8 PDs (4 male and 4 female) and 8 controls (4 male and 4 female) were studied. These were selected from available material after screening total RNA extracted from a small region of the SN for integrity of 18S and 28S species using an Agilent bioanalyzer. We also matched the cases for age and post mortem interval (PMI) (PD Female age, 75 ± 4.4, PMI, 20.5 ± 2.5; PD Male age 77 ± 6.3, PMI 13.85 ± 1.7; Con Female age 68 ± 3.3, PMI 21.8 ± 0.8; Con Male age 70.2 ± 6.3, PMI 18.11 ± 3.6). Vital Statistics of the cases used in this study. PD= Parkinson disease, C= Control, F=Female, M=Male: Case Age Sex PMI Cel file Pdf1 81 F 17 459F cf1 61 f <24 515H Pdf2 84 F 24.08 515K cf2 n/a f >48 515I Pdf3 69 F <24 515J cf3 74 f 23.00 459D Pdf4 66 F <24 515F cf4 69 f 20.70 459A pdm1 68 m 17.16 515E Cm1 67 m 22.33 459C pdm2 67 m 14.5 515D Cm2 63 m 21.50 459B pdm3 94 m 9.25 515G Cm3 62 m 21.20 515L pdm4 78 m 14.50 515B Cm4 89 m 7.42 515C
Project description:Pt-ttpy (tolyl terpyridin-Pt complex) covalently binds to G-quadruplex (G4) structures in vitro and to telomeres in cellulo via its Pt moiety. Here, we identified its targets in the human genome, in comparison to Pt-tpy, its derivative without G4 affinity, and cisplatin. Pt-ttpy, but not Pt-tpy, induces the release of the shelterin protein TRF2 from telomeres concomitantly to the formation of DNA damage foci at telomeres but also at other chromosomal locations. -H2AX chromatin immunoprecipitation (ChIP-seq) after treatment with Pt-ttpy or cisplatin revealed accumulation in G- and A-rich tandemly repeated sequences, but not particularly in potential G4 forming sequences. Collectively, Pt-ttpy presents dual targeting efficiency on DNA, by inducing telomere dysfunction and genomic DNA damage at specific loci.