Proteostasis regulators modulate proteasomal activity and gene expression to attenuate multiple phenotypes in Fabry disease

The lysosomal storage disorder Fabry disease is characterized by a deficiency of the lysosomal enzyme \u3b1-Galactosidase A. The observation that missense variants in the encoding GLA gene often lead to structural destabilization, endoplasmic reticulum retention and proteasomal degradation of the misfolded, but otherwise catalytically functional enzyme has resulted in the exploration of alternative therapeutic approaches. In this context, we have investigated proteostasis regulators (PRs) for their potential to increase cellular enzyme activity, and to reduce the disease-specific accumulation of the biomarker globotriaosylsphingosine in patient-derived cell culture. The PRs also acted synergistically with the clinically approved 1-deoxygalactonojirimycine, demonstrating the potential of combination treatment in a therapeutic application. Extensive characterization of the effective PRs revealed inhibition of the proteasome and elevation of GLA gene expression as paramount effects. Further analysis of transcriptional patterns of the PRs exposed a variety of genes involved in proteostasis as potential modulators. We propose that addressing proteostasis is an effective approach to discover new therapeutic targets for diseases involving folding and trafficking-deficient protein mutants

Comparative Genomics Of Two Leptospira Interrogans Serovars Reveals Novel Insights Into Physiology And Pathogenesis

Leptospira species colonize a significant proportion of rodent populations worldwide and produce life-threatening infections in accidental hosts, including humans. Complete genome sequencing of Leptospira interrogans serovar Copenhageni and comparative analysis with the available Leptospira interrogans serovar Lai genome reveal that despite overall genetic similarity there are significant structural differences, including a large chromosomal inversion and extensive variation in the number and distribution of insertion sequence elements. Genome sequence analysis elucidates many of the novel aspects of leptospiral physiology relating to energy metabolism, oxygen tolerance, two-component signal transduction systems, and mechanisms of pathogenesis. A broad array of transcriptional regulation proteins and two new families of afimbrial adhesins which contribute to host tissue colonization in the early steps of infection were identified. Differences in genes involved in the biosynthesis of lipopolysaccharide O side chains between the Copenhageni and Lai serovars were identified, offering an important starting point for the elucidation of the organism's complex polysaccharide surface antigens. Differences in adhesins and in lipopolysaccharide might be associated with the adaptation of serovars Copenhageni and Lai to different animal hosts. Hundreds of genes encoding surface-exposed lipoproteins and transmembrane outer membrane proteins were identified as candidates for development of vaccines for the prevention of leptospirosis.186721642172Barocchi, M.A., Ko, A.I., Ferrer, S.R., Faria, M.T., Reis, M.G., Riley, L.W., Identification of new repetitive element in Leptospira interrogans serovar Copenhageni and its application to PCR-based differentiation of Leptospira serogroups (2001) J. Clin. Microbiol., 39, pp. 191-195Barocchi, M.A., Ko, A.I., Reis, M.G., McDonald, K.L., Riley, L.W., Rapid translocation of polarized MDCK cell monolayers by Leptospira interrogans, an invasive but nonintracellular pathogen (2002) Infect. Immun., 70, pp. 6926-6932Boursaux-Eude, C., Saint Girons, I., Zuerner, R., IS1500, an IS3-like element from Leptospira interrogans (1995) Microbiology, 141, pp. 2165-2173Charon, N.W., Goldstein, S.F., Genetics of motility and chemotaxis of a fascinating group of bacteria: The spirochetes (2002) Annu. Rev. Genet., 36, pp. 47-73Chen, C.W., Huang, C.H., Lee, H.H., Tsai, H.H., Kirby, R., Once the circle has been broken: Dynamics and evolution of Streptomyces chromosomes (2002) Trends Genet., 18, pp. 522-529Colombatti, A., Bonaldo, P., Doliana, R., Type A modules: Interacting domains found in several non-fibrillar collagens and in other extracellular matrix proteins (1993) Matrix, 13, pp. 297-306De La Pena-Moctezuma, A., Bulach, D.M., Kalambaheti, T., Adler, B., Comparative analysis of the LPS biosynthetic loci of the genetic subtypes of serovar Hardjo: Leptospira interrogans subtype Hardjoprajitno and Leptospira borgpetersenii subtype Hardjobovis (1999) FEMS Microbiol. Lett., 177, pp. 319-326Delcher, A.L., Kasif, S., Fleischmann, R.D., Peterson, J., White, O., Salzberg, S.L., Alignment of whole genomes (1999) Nucleic Acids Res., 27, pp. 2369-2376Dimroth, P., Wang, H., Grabe, M., Oster, G., Energy transduction in the sodium F-ATPase of Propionigenium modestum (1999) Proc. Natl. Acad. Sci. USA, 96, pp. 4924-4929Dolata, M.M., Van Beeumen, J.J., Ambler, R.P., Meyer, T.E., Cusanovich, M.A., Nucleotide sequence of the heme subunit of flavocytochrome c from the purple phototrophic bacterium, Chromatium vinosum. A 2.6-kilobase pair DNA fragment contains two multiheme cytochromes, a flavoprotein, and a homolog of human ankyrin (1993) J. Biol. Chem., 268, pp. 14426-14431Dunne Jr., W.M., Bacterial adhesion: Seen any good biofilms lately? (2002) Clin. Microbiol. Rev., 15, pp. 155-166Durbin, R., Eddy, S.R., Krogh, A., Mitchison, G., (1998) Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, , Cambridge University Press, Cambridge, United KingdomEisen, J.A., Heidelberg, J.F., White, O., Salzberg, S.L., Evidence for symmetric chromosomal inversions around the replication origin in bacteria (2000) Genome Biol., 1. , http://genomebiology.com/2000/1/6/RESEARCH/0011, 4 December, posting date. [Online.]Faine, S., Adler, B., Bolin, C., Perolat, P., (1999) Leptospira and Leptospirosis, , MediSci, Melbourne, AustraliaFarr, R.W., Leptospirosis (1995) Clin. Infect. Dis., 21, pp. 1-6Franklin, M.J., Obman, D.E., Mutant analysis and cellular localization of the AlgI, AlgJ, and AlgF proteins required for O acetylation of alginate in Pseudomonas aeruginosa (2002) J. Bacteriol., 184, pp. 3000-3007Fraser, C.M., Casjens, S., Huang, W.M., Sutton, G.G., Clayton, R., Lathigra, R., White, O., Venter, J.C., Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi (1997) Nature, 390, pp. 580-586Fraser, C.M., Norris, S.J., Weinstock, G.M., White, O., Sutton, G.G., Dodson, R., Gwinn, M., Venter, J.C., Complete genome sequence of Treponema pallidum, the syphilis spirochete (1998) Science, 281, pp. 375-388Fukunaga, M., Mifuchi, I., Unique organization of Leptospira interrogans rRNA genes (1989) J. Bacteriol., 171, pp. 5763-5767Fulop, V., Ridout, C.J., Greenwood, C., Hajdu, J., Crystal structure of the di-haem cytochrome c peroxidase from Pseudomonas aeruginosa (1995) Structure, 3, pp. 1225-1233Galperin, M.Y., Nikolskaya, A.N., Koonin, E.V., Novel domains of the prokaryotic two-component signal transduction systems (2001) FEMS Microbiol. Lett., 203, pp. 11-21Gilges, D., Vinit, M.A., Callebaut, I., Coulombel, L., Cacheux, V., Romeo, P.H., Vigon, I., Polydom: A secreted protein with pentraxin, complement control protein, epidermal growth factor and von Willebrand factor A domains (2000) Biochem. J., 352, pp. 49-59Godfroid, F., Taminiau, B., Danese, I., Denoel, P., Tibor, A., Weynants, V., Cloeckaert, A., Letesson, J.J., Identification of the perosamine synthetase gene of Brucella melitensis 16M and involvement of lipopolysaccharide O side chain in Brucella survival in mice and in macrophages (1998) Infect. Immun., 66, pp. 5485-5493Haake, D.A., Spirochaetal lipoproteins and pathogenesis (2000) Microbiology, 146, pp. 1491-1504Haake, D.A., Champion, C.I., Martinich, C., Shang, E.S., Blanco, D.R., Miller, J.N., Lovett, M.A., Molecular cloning and sequence analysis of the gene encoding OmpL1, a transmembrane outer membrane protein of pathogenic Leptospira spp (1993) J. Bacteriol., 175, pp. 4225-4234Henneberry, R.C., Cox, C.D., Beta-oxidation of fatty acids by Leptospira (1970) Can. J. Microbiol., 16, pp. 41-45Howell, M.L., Alsabbagh, E., Ma, J.F., Ochsner, U.A., Klotz, M.G., Beveridge, T.J., Blumenthal, K.M., Hassett, D.J., AnkB, a periplasmic ankyrin-like protein in Pseudomonas aeruginosa, is required for optimal catalase B (KatB) activity and resistance to hydrogen peroxide (2000) J. Bacteriol., 182, pp. 4545-4556Hunnicutt, D.W., Kempf, M.J., McBride, M.J., Mutations in Flavobacterium johnsoniae gldF and gldG disrupt gliding motility and interfere with membrane localization of GldA (2002) J. Bacteriol., 184, pp. 2370-2378Jovanovic, T., Ascenso, C., Hazlett, K.R., Sikkink, R., Krebs, C., Litwiller, R., Benson, L.M., Rusnak, F., Neelaredoxin, an iron-binding protein from the syphilis spirochete, Treponema pallidum, is a superoxide reductase (2000) J. Biol. Chem., 275, pp. 28439-28448Ko, A.I., Galvao Reis, M., Ribeiro Dourado, C.M., Johnson Jr., W.D., Riley, L.W., Urban epidemic of severe leptospirosis in Brazil (1999) Lancet, 354, pp. 820-825. , Salvador Leptospirosis Study GroupLamothe, G.T., Jolly, L., Mollet, B., Stingele, F., Genetic and biochemical characterization of exopolysaccharide biosynthesis by Lactobacillus delbrueckii subsp. bulgaricus (2002) Arch. Microbiol., 178, pp. 218-228Levett, P.N., Leptospirosis (2001) Clin. Microbiol. Rev., 14, pp. 296-326Lombard, M., Touati, D., Fontecave, M., Niviere, V., Superoxide reductase as a unique defense system against superoxide stress in the microaerophile Treponema pallidum (2000) J. Biol. Chem., 275, pp. 27021-27026Matsunaga, J., Barocchi, M.A., Croda, J., Young, T.A., Sanchez, Y., Siqueira, I., Bolin, C.A., Ko, A.I., Pathogenic Leptospira species express surface-exposed proteins belonging to the bacterial immunoglobulin superfamily (2003) Mol. Microbiol., 49, pp. 929-945Meidanis, J., Braga, M.D., Verjovski-Almeida, S., Whole-genome analysis of transporters in the plant pathogen Xylella fastidiosa (2002) Microbiol. Mol. Biol. Rev., 66, pp. 272-299Missiakas, D., Raina, S., The extracytoplasmic function sigma factors: Role and regulation (1998) Mol. Microbiol., 28, pp. 1059-1066Palaniappan, R.U., Chang, Y.F., Jusuf, S.S., Artiushin, S., Timoney, J.F., McDonough, S.P., Barr, S.C., Mohammed, H.O., Cloning and molecular characterization of an immunogenic LigA protein of Leptospira interrogans (2002) Infect. Immun., 70, pp. 5924-5930Paton, A.W., Paton, J.C., Molecular characterization of the locus encoding biosynthesis of the lipopolysaccharide O antigen of Escherichia coli serotype O113 (1999) Infect. Immun., 67, pp. 5930-5937Paulsen, I.T., Nguyen, L., Sliwinski, M.K., Rabus, R., Saier Jr., M.H., Microbial genome analyses: Comparative transport capabilities in eighteen prokaryotes (2000) J. Mol. Biol., 301, pp. 75-100Pizza, M., Scarlato, V., Masignani, V., Giuliani, M.M., Arico, B., Comanducci, M., Jennings, G.T., Rappuoli, R., Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing (2000) Science, 287, pp. 1816-1820Rappuoli, R., Reverse vaccinology, a genome-based approach to vaccine development (2001) Vaccine, 19, pp. 2688-2691Ren, S.X., Fu, G., Jiang, X.G., Zeng, R., Miao, Y.G., Xu, H., Zhang, Y.X., Zhao, G.P., Unique physiological and pathogenic features of Leptospira interrogans revealed by whole-genome sequencing (2003) Nature, 422, pp. 888-893Santos, J.M., Lobo, M., Matos, A.P., De Pedro, M.A., Arraiano, C.M., The gene bola regulates daca (PBP5), dacC (PBP6) and ampC (AmpC), promoting normal morphology in Escherichia coli (2002) Mol. Microbiol., 45, pp. 1729-1740Springer, T.A., Folding of the N-terminal, ligand-binding region of integrin alpha-subunits into a beta-propeller domain (1997) Proc. Natl. Acad. Sci. USA, 94, pp. 65-72Tang, Y.P., Dallas, M.M., Malamy, M.H., Characterization of the Batl (Bacteroides aerotolerance) operon in Bacteroides fragilis: Isolation of a B. fragilis mutant with reduced aerotolerance and impaired growth in in vivo model systems (1999) Mol. Microbiol., 32, p. 139149Van Sluys, M.A., De Oliveira, M.C., Monteiro-Vitorello, C.B., Miyaki, C.Y., Furlan, L.R., Camargo, L.E., Da Silva, A.C., Kitajima, J.P., Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa (2003) J. Bacteriol, 185, pp. 1018-1026Vujaskovic, Z., Batinic-Haberle, I., Rabbani, Z.N., Feng, Q.F., Kang, S.K., Spasojevic, I., Samulski, T.V., Anscher, M.S., A small molecular weight catalytic metalloporphyrin antioxidant with superoxide dismutase (SOD) mimetic properties protects lungs from radiation-induced injury (2002) Free Radic. Biol. Med., 33, pp. 857-863Werts, C., Tapping, R.I., Mathison, J.C., Chuang, T.H., Kravchenko, V., Saint Girons, I., Haake, D.A., Ulevitch, R.J., Leptospiral lipopolysaccharide activates cells through a TLR2-dependent mechanism (2001) Nat. Immunol., 2, pp. 346-352Whitfield, C., Roberts, I.S., Structure, assembly and regulation of expression of capsules in Escherichia coli (1999) Mol. Microbiol., 31, pp. 1307-1319Wizemann, T.M., Heinrichs, J.H., Adamou, J.E., Erwin, A.L., Kunsch, C., Choi, G.H., Barash, S.C., Koenig, S., Use of a whole genome approach to identify vaccine molecules affording protection against Streptococcus pneumoniae infection (2001) Infect. Immun., 69, pp. 1593-1598Zuerner, R.L., Nucleotide sequence analysis of IS1533 from Leptospira borgpetersenii: Identification and expression of two IS-encoded proteins (1994) Plasmid, 31, pp. 1-11Zuerner, R.L., Huang, W.M., Analysis of a Leptospira interrogans locus containing DNA replication genes and a new IS, IS1502 (2002) FEMS Microbiol. Lett., 215, pp. 175-18

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation; analyses timings and patterns of tumour evolution; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity; and evaluates a range of more-specialized features of cancer genomes