Most \u3cem\u3eCaenorhabditis elegans\u3c/em\u3e MicroRNAs are Individually Not Essential for Development or Viability

MicroRNAs (miRNAs), a large class of short noncoding RNAs found in many plants and animals, often act to post-transcriptionally inhibit gene expression. We report the generation of deletion mutations in 87 miRNA genes in Caenorhabditis elegans, expanding the number of mutated miRNA genes to 95, or 83% of known C. elegans miRNAs. We find that the majority of miRNAs are not essential for the viability or development of C. elegans, and mutations in most miRNA genes do not result in grossly abnormal phenotypes. These observations are consistent with the hypothesis that there is significant functional redundancy among miRNAs or among gene pathways regulated by miRNAs. This study represents the first comprehensive genetic analysis of miRNA function in any organism and provides a unique, permanent resource for the systematic study of miRNAs

Viroid diseases in pome and stone fruit trees and Koch s postulates: a critical assessment

[EN] Composed of a naked circular non-protein-coding genomic RNA, counting only a few hundred nucleotides, viroids¿the smallest infectious agents known so far¿are able to replicate and move systemically in herbaceous and woody host plants, which concomitantly may develop specific diseases or remain symptomless. Several viroids have been reported to naturally infect pome and stone fruit trees, showing symptoms on leaves, fruits and/or bark. However, Koch¿s postulates required for establishing on firm grounds the viroid etiology of these diseases, have not been met in all instances. Here, pome and stone fruit tree diseases, conclusively proven to be caused by viroids, are reviewed, and the need to pay closer attention to fulfilling Koch¿s postulates is emphasized. View Full-TextThis project has received funding from the European Union's Horizon 2020 Research and Innovation Scientific Exchange Program under the Marie Sklodowska-Curie grant agreement No. 734736. This publication reflects only the authors' view. The Agency is not responsible for any use that may be made of the information it contains.Di Serio, F.; Ambros Palaguerri, S.; Sano, T.; Flores Pedauye, R.; Navarro, B. (2018). Viroid diseases in pome and stone fruit trees and Koch s postulates: a critical assessment. Viruses. 10(11). https://doi.org/10.3390/v101106121011Diener, T. O. (1971). Potato spindle tuber «virus». Virology, 45(2), 411-428. doi:10.1016/0042-6822(71)90342-4Flores, R., Minoia, S., Carbonell, A., Gisel, A., Delgado, S., López-Carrasco, A., … Di Serio, F. (2015). Viroids, the simplest RNA replicons: How they manipulate their hosts for being propagated and how their hosts react for containing the infection. Virus Research, 209, 136-145. doi:10.1016/j.virusres.2015.02.027López-Carrasco, A., & Flores, R. (2016). Dissecting the secondary structure of the circular RNA of a nuclear viroid in vivo: A «naked» rod-like conformation similar but not identical to that observed in vitro. RNA Biology, 14(8), 1046-1054. doi:10.1080/15476286.2016.1223005López-Carrasco, A., & Flores, R. (2017). The predominant circular form of avocado sunblotch viroid accumulates in planta as a free RNA adopting a rod-shaped secondary structure unprotected by tightly bound host proteins. Journal of General Virology, 98(7), 1913-1922. doi:10.1099/jgv.0.000846Flores, R., Hernández, C., Alba, A. E. M. de, Daròs, J.-A., & Serio, F. D. (2005). Viroids and Viroid-Host Interactions. Annual Review of Phytopathology, 43(1), 117-139. doi:10.1146/annurev.phyto.43.040204.140243Di Serio, F., Flores, R., Verhoeven, J. T. J., Li, S.-F., Pallás, V., Randles, J. W., … Owens, R. A. (2014). Current status of viroid taxonomy. Archives of Virology, 159(12), 3467-3478. doi:10.1007/s00705-014-2200-6Di Serio, F., Li, S.-F., Matoušek, J., Owens, R. A., Pallás, V., … Randles, J. W. (2018). ICTV Virus Taxonomy Profile: Avsunviroidae. Journal of General Virology, 99(5), 611-612. doi:10.1099/jgv.0.001045Diener, T. O., Smith, D. R., & O’Brien, M. J. (1972). Potato spindle tuber viroid. Virology, 48(3), 844-846. doi:10.1016/0042-6822(72)90166-3Diener, T. O. (1972). Potato spindle tuber viroid. Virology, 50(2), 606-609. doi:10.1016/0042-6822(72)90412-6Semancik, J. S. (1970). Properties of the Infectious Forms of Exocortis Virus of Citrus. Phytopathology, 60(4), 732. doi:10.1094/phyto-60-732Semancik, J. S., Morris, T. J., & Weathers, L. G. (1973). Structure and conformation of low molecular weight pathogenic RNA from exocortis disease. Virology, 53(2), 448-456. doi:10.1016/0042-6822(73)90224-9Bos, L. (1981). Hundred years of Koch’s Postulates and the history of etiology in plant virus research. Netherlands Journal of Plant Pathology, 87(3), 91-110. doi:10.1007/bf01976645Schumacher, J., Randles, J. W., & Riesner, D. (1983). A two-dimensional electrophoretic technique for the detection of circular viroids and virusoids. Analytical Biochemistry, 135(2), 288-295. doi:10.1016/0003-2697(83)90685-1Flores, R., Duran-Vila, N., Pallas, V., & Semancik, J. S. (1985). Detection of Viroid and Viroid-like RNAs from Grapevine. Journal of General Virology, 66(10), 2095-2102. doi:10.1099/0022-1317-66-10-2095Serio, F. D., Malfitano, M., Alioto, D., Ragozzino, A., Desvignes, J. C., & Flores, R. (2001). Apple dimple fruit viroid: Fulfillment of Koch’s Postulates and Symptom Characteristics. Plant Disease, 85(2), 179-182. doi:10.1094/pdis.2001.85.2.179Pallas, V., Navarro, A., & Flores, R. (1987). Isolation of a Viroid-like RNA from Hop Different from Hop Stunt Viroid. Journal of General Virology, 68(12), 3201-3205. doi:10.1099/0022-1317-68-12-3201Navarro, B., & Flores, R. (1997). Chrysanthemum chlorotic mottle viroid: Unusual structural properties of a subgroup of self-cleaving viroids with hammerhead ribozymes. Proceedings of the National Academy of Sciences, 94(21), 11262-11267. doi:10.1073/pnas.94.21.11262De la Pena, M., Navarro, B., & Flores, R. (1999). Mapping the molecular determinant of pathogenicity in a hammerhead viroid: A tetraloop within the in vivo branched RNA conformation. Proceedings of the National Academy of Sciences, 96(17), 9960-9965. doi:10.1073/pnas.96.17.9960Bellamy, A. R., & Ralph, R. K. (1968). [104] Recovery and purification of nucleic acids by means of cetyltrimethylammonium bromide. Nucleic Acids, Part B, 156-160. doi:10.1016/0076-6879(67)12125-3Codoñer, F. M., Darós, J.-A., Solé, R. V., & Elena, S. F. (2006). The Fittest versus the Flattest: Experimental Confirmation of the Quasispecies Effect with Subviral Pathogens. PLoS Pathogens, 2(12), e136. doi:10.1371/journal.ppat.0020136Hashimoto, J., & Koganezawa, H. (1987). Nucleotide sequence and secondary structure of apple scar skin viroid. Nucleic Acids Research, 15(17), 7045-7052. doi:10.1093/nar/15.17.7045Zhu, S. F., Hadidi, A., & Hammond, R. W. (1998). AGROINFECTION OF PEAR AND APPLE WITH DAPPLE APPLE VIROID RESULTS IN SYSTEMIC INFECTION. Acta Horticulturae, (472), 613-616. doi:10.17660/actahortic.1998.472.81OSAKI, H., KUDO, A., & OHTSU, Y. (1996). Japanese Pear Fruit Dimple Disease Caused by Apple Scar Skin Viroid (ASSVd). Japanese Journal of Phytopathology, 62(4), 379-385. doi:10.3186/jjphytopath.62.379Ito, T., & Yoshida, K. (1998). REPRODUCTION OF APPLE FRUIT CRINKLE DISEASE SYMPTOMS BY APPLE FRUIT CRINKLE VIROID. Acta Horticulturae, (472), 587-594. doi:10.17660/actahortic.1998.472.78Hadidi, A., & Yang, X. (1990). Detection of pome fruit viroids by enzymatic cDNA amplification. Journal of Virological Methods, 30(3), 261-269. doi:10.1016/0166-0934(90)90068-qKyriakopoulou, P. E., & Hadidi, A. (1998). NATURAL INFECTION OF WILD AND CULTIVATED PEARS WITH APPLE SCAR SKIN VIROID IN GREECE. Acta Horticulturae, (472), 617-626. doi:10.17660/actahortic.1998.472.82Ambros, S., Desvignes, J. C., Llacer, G., & Flores, R. (1995). Pear blister canker viroid: sequence variability and causal role in pear blister canker disease. Journal of General Virology, 76(10), 2625-2629. doi:10.1099/0022-1317-76-10-2625Sano, T., Hataya, T., Terai, Y., & Shikata, E. (1989). Hop Stunt Viroid Strains from Dapple Fruit Disease of Plum and Peach in Japan. Journal of General Virology, 70(6), 1311-1319. doi:10.1099/0022-1317-70-6-1311Flores, R., Hernández, C., Desvignes, J. C., & Llácer, G. (1990). Some properties of the viroid inducing peach latent mosaic disease. Research in Virology, 141(1), 109-118. doi:10.1016/0923-2516(90)90060-vMalfitano, M., Di Serio, F., Covelli, L., Ragozzino, A., Hernández, C., & Flores, R. (2003). Peach latent mosaic viroid variants inducing peach calico (extreme chlorosis) contain a characteristic insertion that is responsible for this symptomatology. Virology, 313(2), 492-501. doi:10.1016/s0042-6822(03)00315-5Puchta, H., Luckinger, R., Yang, X., Hadidi, A., & S�nger, H. L. (1990). Nucleotide sequence and secondary structure of apple scar skin viroid (ASSVd) from China. Plant Molecular Biology, 14(6), 1065-1067. doi:10.1007/bf00019406KOGANEZAWA, H. (1985). Transmission to apple seedlings of a low molecular weight RNA extracted from apple scar skin diseased trees. Japanese Journal of Phytopathology, 51(2), 176-182. doi:10.3186/jjphytopath.51.176Koganezawa, H. (1986). FURTHER EVIDENCE FOR VIROID ETIOLOGY OF APPLE SCAR SKIN AND DAPPLE APPLE DISEASES. Acta Horticulturae, (193), 29-34. doi:10.17660/actahortic.1986.193.2Yamaguch, A., & Yanase, H. (1976). POSSIBLE RELATIONSHIP BETWEEN THE CAUSAL AGENT OF DAPPLE APPLE AND SCAR SKIN. Acta Horticulturae, (67), 249-254. doi:10.17660/actahortic.1976.67.31Desvignes, J. C., Grasseau, N., Boyé, R., Cornaggia, D., Aparicio, F., Di Serio, F., & Flores, R. (1999). Biological Properties of Apple Scar Skin Viroid: Isolates, Host Range, Different Sensitivity of Apple Cultivars, Elimination, and Natural Transmission. Plant Disease, 83(8), 768-772. doi:10.1094/pdis.1999.83.8.768Walia, Y., Dhir, S., Bhadoria, S., Hallan, V., & Zaidi, A. A. (2011). Molecular characterization of Apple scar skin viroid from Himalayan wild cherry. Forest Pathology, 42(1), 84-87. doi:10.1111/j.1439-0329.2011.00723.xDi Serio, F., Aparicio, F., Alioto, D., Ragozzino, A., & Flores, R. (1996). Identification and molecular properties of a 306 nucleotide viroid associated with apple dimple fruit disease. Journal of General Virology, 77(11), 2833-2837. doi:10.1099/0022-1317-77-11-2833Di Serio, F., Giunchedi, L., Alioto, D., Ragozzino, A., & Flores, R. (1998). IDENTIFICATION OF APPLE DIMPLE FRUIT VIROID IN DIFFERENT COMMERCIAL VARIETIES OF APPLE GROWN IN ITALY. Acta Horticulturae, (472), 595-602. doi:10.17660/actahortic.1998.472.79Roumi, V., Gazel, M., & Caglayan, K. (2017). First report of Apple dimple fruit viroid in apple trees in Iran. New Disease Reports, 35, 3. doi:10.5197/j.2044-0588.2017.035.003He, Y.-H., Isono, S., Kawaguchi-Ito, Y., Taneda, A., Kondo, K., Iijima, A., … Sano, T. (2010). Characterization of a new Apple dimple fruit viroid variant that causes yellow dimple fruit formation in ‘Fuji’ apple trees. Journal of General Plant Pathology, 76(5), 324-330. doi:10.1007/s10327-010-0258-xChiumenti, M., Torchetti, E. M., Di Serio, F., & Minafra, A. (2014). Identification and characterization of a viroid resembling apple dimple fruit viroid in fig (Ficus carica L.) by next generation sequencing of small RNAs. Virus Research, 188, 54-59. doi:10.1016/j.virusres.2014.03.026ITO, T., KANEMATSU, S., KOGANEZAWA, H., TSUCHIZAKI, T., & YOSHIDA, K. (1993). Detection of a Viroid Associated with Apple Fruit Crinkle Disease. Japanese Journal of Phytopathology, 59(5), 520-527. doi:10.3186/jjphytopath.59.520Sano, T., Yoshida, H., Goshono, M., Monma, T., Kawasaki, H., & Ishizaki, K. (2004). Characterization of a new viroid strain from hops: evidence for viroid speciation by isolation in different host species. Journal of General Plant Pathology, 70(3), 181-187. doi:10.1007/s10327-004-0105-zNakaune, R., & Nakano, M. (2008). Identification of a new Apscaviroid from Japanese persimmon. Archives of Virology, 153(5), 969-972. doi:10.1007/s00705-008-0073-2Hernandez, C., Elena, S. F., Moya, A., & Flores, R. (1992). Pear Blister Canker Viroid is a Member of the Apple Scar Skin Subgroup (apscaviroids) and also has Sequence Homology with Viroids from other Subgroups. Journal of General Virology, 73(10), 2503-2507. doi:10.1099/0022-1317-73-10-2503Lemoine, J. (1986). PROBLEMS REGARDING THE DETECTION OF GRAFT TRANSMITTED PEAR CANKER. Acta Horticulturae, (193), 251-260. doi:10.17660/actahortic.1986.193.43Ambrós, S., Llácer, G., Desvignes, J. C., & Flores, R. (1995). PEACH LATENT MOSAIC AND PEAR BLISTER CANKER VIROIDS: DETECTION BY MOLECULAR HYBRIDIZATION AND RELATIONSHIPS WITH SPECIFIC MALADIES AFFECTING PEACH AND PEAR TREES. Acta Horticulturae, (386), 515-521. doi:10.17660/actahortic.1995.386.74Flores, R., Hernandez, C., Llacer, G., & Desvignes, J. C. (1991). Identification of a new viroid as the putative causal agent of pear blister canker disease. Journal of General Virology, 72(6), 1199-1204. doi:10.1099/0022-1317-72-6-1199Desvignes, J. C., Cornaggia, D., Grasseau, N., Ambrós, S., & Flores, R. (1999). Pear Blister Canker Viroid: Host Range and Improved Bioassay with Two New Pear Indicators, Fieud 37 and Fieud 110. Plant Disease, 83(5), 419-422. doi:10.1094/pdis.1999.83.5.419SASAKI, M., & SHIKATA, E. (1977). On Some Properties of Hop Stunt Disease Agent, a Viroid. Proceedings of the Japan Academy. Ser. B: Physical and Biological Sciences, 53(3), 109-112. doi:10.2183/pjab.53.109Ohno, T., Takamatsu, N., Meshi, T., & Okada, Y. (1983). Hop stunt viroid: molecular cloning and nucleotide sequence of the complete cDNA copy. Nucleic Acids Research, 11(18), 6185-6197. doi:10.1093/nar/11.18.6185Kofalvi, S. A., Pall√°s, V., Marcos, J. F., Candresse, T., & Ca√±izares, M. C. (1997). Hop stunt viroid (HSVd) sequence variants from Prunus species: evidence for recombination between HSVd isolates. Journal of General Virology, 78(12), 3177-3186. doi:10.1099/0022-1317-78-12-3177Amari, K., Gomez, G., Myrta, A., Di Terlizzi, B., & Pallás, V. (2001). The molecular characterization of 16 new sequence variants of Hop stunt viroid reveals the existence of invariable regions and a conserved hammerhead-like structure on the viroid molecule The sequences described in this work have been deposited in the EMBL database and received accession numbers AJ297825 to AJ297840. Journal of General Virology, 82(4), 953-962. doi:10.1099/0022-1317-82-4-953SANO, T., HATAYA, T., TERAI, Y., & SHIKATA, E. (1986). Association of a viroid-like RNA from plum dapple disease occurring in Japan. Proceedings of the Japan Academy. Ser. B: Physical and Biological Sciences, 62(3), 98-101. doi:10.2183/pjab.62.98Hernandez, C., & Flores, R. (1992). Plus and minus RNAs of peach latent mosaic viroid self-cleave in vitro via hammerhead structures. Proceedings of the National Academy of Sciences, 89(9), 3711-3715. doi:10.1073/pnas.89.9.3711Ambros, S. (1998). In vitro and in vivo self-cleavage of a viroid RNA with a mutation in the hammerhead catalytic pocket. Nucleic Acids Research, 26(8), 1877-1883. doi:10.1093/nar/26.8.1877Ambrós, S., Hernández, C., & Flores, R. (1999). Rapid generation of genetic heterogeneity in progenies from individual cDNA clones of peach latent mosaic viroid in its natural host The data reported in this paper are in the EMBL nucleotide sequence database and assigned the accession nos AJ241818–AJ241850. Journal of General Virology, 80(8), 2239-2252. doi:10.1099/0022-1317-80-8-2239Fekih Hassen, I., Massart, S., Motard, J., Roussel, S., Parisi, O., Kummert, J., … Jijakli, M. H. (2007). Molecular features of new Peach Latent Mosaic Viroid variants suggest that recombination may have contributed to the evolution of this infectious RNA. Virology, 360(1), 50-57. doi:10.1016/j.virol.2006.10.021DUBÉ, A., BOLDUC, F., BISAILLON, M., & PERREAULT, J.-P. (2011). Mapping studies of the Peach latent mosaic viroid reveal novel structural features. Molecular Plant Pathology, 12(7), 688-701. doi:10.1111/j.1364-3703.2010.00703.xBussière, F., Ouellet, J., Côté, F., Lévesque, D., & Perreault, J. P. (2000). Mapping in Solution Shows the Peach Latent Mosaic Viroid To Possess a New Pseudoknot in a Complex, Branched Secondary Structure. Journal of Virology, 74(6), 2647-2654. doi:10.1128/jvi.74.6.2647-2654.2000FLORES, R., DELGADO, S., RODIO, M.-E., AMBRÓS, S., HERNÁNDEZ, C., & SERIO, F. D. (2006). Peach latent mosaic viroid: not so latent. Molecular Plant Pathology, 7(4), 209-221. doi:10.1111/j.1364-3703.2006.00332.xDesvignes, J. C. (1976). THE VIRUS DISEASES DETECTED IN GREENHOUSE AND IN FIELD BY THE PEACH SEEDLING GF 305 INDICATOR. Acta Horticulturae, (67), 315-323. doi:10.17660/actahortic.1976.67.41DESVIGNES, J. C. (1986). PEACH LATENT MOSAIC AND ITS RELATION TO PEACH MOSAIC AND PEACH YELLOW MOSAIC VIRUS DISEASES. Acta Horticulturae, (193), 51-58. doi:10.17660/actahortic.1986.193.6Flores, R., & Llácer, G. (1989). ISOLATION OF A VIROID-LIKE RNA ASSOCIATED WITH PEACH LATENT MOSAIC DISEASE. Acta Horticulturae, (235), 325-332. doi:10.17660/actahortic.1989.235.47Rodio, M.-E., Delgado, S., Flores, R., & Serio, F. D. (2006). Variants of Peach latent mosaic viroid inducing peach calico: uneven distribution in infected plants and requirements of the insertion containing the pathogenicity determinant. Journal of General Virology, 87(1), 231-240. doi:10.1099/vir.0.81356-0Rodio, M.-E., Delgado, S., De Stradis, A., Gómez, M.-D., Flores, R., & Di Serio, F. (2007). A Viroid RNA with a Specific Structural Motif Inhibits Chloroplast Development. The Plant Cell, 19(11), 3610-3626. doi:10.1105/tpc.106.049775Navarro, B., Gisel, A., Rodio, M. E., Delgado, S., Flores, R., & Di Serio, F. (2012). Small RNAs containing the pathogenic determinant of a chloroplast-replicating viroid guide the degradation of a host mRNA as predicted by RNA silencing. The Plant Journal, 70(6), 991-1003. doi:10.1111/j.1365-313x.2012.04940.xWang, L., He, Y., Kang, Y., Hong, N., Farooq, A. B. U., Wang, G., & Xu, W. (2013). Virulence determination and molecular features of peach latent mosaic viroid isolates derived from phenotypically different peach leaves: A nucleotide polymorphism in L11 contributes to symptom alteration. Virus Research, 177(2), 171-178. doi:10.1016/j.virusres.2013.08.005Zhang, Z., Qi, S., Tang, N., Zhang, X., Chen, S., Zhu, P., … Wu, Q. (2014). Discovery of Replicating Circular RNAs by RNA-Seq and Computational Algorithms. PLoS Pathogens, 10(12), e1004553. doi:10.1371/journal.ppat.1004553Serra, P., Messmer, A., Sanderson, D., James, D., & Flores, R. (2018). Apple hammerhead viroid-like RNA is a bona fide viroid: Autonomous replication and structural features support its inclusion as a new member in the genus Pelamoviroid. Virus Research, 249, 8-15. doi:10.1016/j.virusres.2018.03.001Messmer, A., Sanderson, D., Braun, G., Serra, P., Flores, R., & James, D. (2017). Molecular and phylogenetic identification of unique isolates of hammerhead viroid-like RNA from ‘Pacific Gala’ apple (Malus domestica) in Canada. Canadian Journal of Plant Pathology, 39(3), 342-353. doi:10.1080/07060661.2017.1354334Wu, Q., Wang, Y., Cao, M., Pantaleo, V., Burgyan, J., Li, W.-X., & Ding, S.-W. (2012). Homology-independent discovery of replicating pathogenic circular RNAs by deep sequencing and a new computational algorithm. Proceedings of the National Academy of Sciences, 109(10), 3938-3943. doi:10.1073/pnas.1117815109Hadidi, A., Flores, R., Candresse, T., & Barba, M. (2016). Next-Generation Sequencing and Genome Editing in Plant Virology. Frontiers in Microbiology, 7. doi:10.3389/fmicb.2016.0132

Development of an open-source, flexible framework for complex inter-institutional disparate data sharing and collaboration

Clinical information, “-omic” datasets, and tissue samples are difficult to harmonize and manage for data mining. We have developed a platform for storing clinical research data while providing access to associated data from other information stores. Data on 34 metrics from 11,000 neuroblastoma patients were instantiated into a database. The Django web framework was used to create a model for rapid development of tools and views with a front-end interface for generating complex queries. Working with Nationwide Children’s Hospital, we can now consume their tissue inventory data through an API. The end-user sees the number of patients who both match their search and have tissue available. Since initial implementation, the current tasks revolve around developing a governance structure and the necessary data use agreements. Efforts now are to (1) update the data with 5000 more patients, and (2) link to genomic data stores, facilitating disparate data acquisition for research studies

Segmental chromosomal alterations have prognostic impact in neuroblastoma: a report from the INRG project

Background: In the INRG dataset, the hypothesis that any segmental chromosomal alteration might be of prognostic impact in neuroblastoma without MYCN amplification (MNA) was tested. Methods: The presence of any segmental chromosomal alteration (chromosome 1p deletion, 11q deletion and/or chromosome 17q gain) defined a segmental genomic profile. Only tumours with a confirmed unaltered status for all three chromosome arms were considered as having no segmental chromosomal alterations. Results: Among the 8800 patients in the INRG database, a genomic type could be attributed for 505 patients without MNA: 397 cases had a segmental genomic type, whereas 108 cases had an absence of any segmental alteration. A segmental genomic type was more frequent in patients >18 months and in stage 4 disease (P<0.0001). In univariate analysis, 11q deletion, 17q gain and a segmental genomic type were associated with a poorer event-free survival (EFS) (P<0.0001, P=0.0002 and P<0.0001, respectively). In multivariate analysis modelling EFS, the parameters age, stage and a segmental genomic type were retained in the model, whereas the individual genetic markers were not (P<0.0001 and RR=2.56; P=0.0002 and RR=1.8; P=0.01 and RR=1.7, respectively). Conclusion: A segmental genomic profile, rather than the single genetic markers, adds prognostic information to the clinical markers age and stage in neuroblastoma patients without MNA, underlining the importance of pangenomic studies

International consensus for neuroblastoma molecular diagnostics: report from the International Neuroblastoma Risk Group (INRG) Biology Committee

Neuroblastoma serves as a paradigm for utilising tumour genomic data for determining patient prognosis and treatment allocation. However, before the establishment of the International Neuroblastoma Risk Group (INRG) Task Force in 2004, international consensus on markers, methodology, and data interpretation did not exist, compromising the reliability of decisive genetic markers and inhibiting translational research efforts. The objectives of the INRG Biology Committee were to identify highly prognostic genetic aberrations to be included in the new INRG risk classification schema and to develop precise definitions, decisive biomarkers, and technique standardisation. The review of the INRG database (n=8800 patients) by the INRG Task Force finally enabled the identification of the most significant neuroblastoma biomarkers. In addition, the Biology Committee compared the standard operating procedures of different cooperative groups to arrive at international consensus for methodology, nomenclature, and future directions. Consensus was reached to include MYCN status, 11q23 allelic status, and ploidy in the INRG classification system on the basis of an evidence-based review of the INRG database. Standardised operating procedures for analysing these genetic factors were adopted, and criteria for proper nomenclature were developed. Neuroblastoma treatment planning is highly dependant on tumour cell genomic features, and it is likely that a comprehensive panel of DNA-based biomarkers will be used in future risk assignment algorithms applying genome-wide techniques. Consensus on methodology and interpretation is essential for uniform INRG classification and will greatly facilitate international and cooperative clinical and translational research studies

Immunoblot analysis of the seroreactivity to recombinant Borrelia burgdorferi sensu lato antigens, including VlsE, in the long-term course of treated patients with Erythema migrans

Objective: We evaluated whether immunoblotting is capable of substantiating the posttreatment clinical assessment of patients with erythema migrans ( EM), the hallmark of early Lyme borreliosis. Methods: In 50 patients, seroreactivity to different antigens of Borrelia burgdorferi sensu lato was analyzed by a recombinant immunoblot test (IB) in consecutive serum samples from a minimum follow-up period of 1 year. Antigens in the IgG test were decorin- binding protein A, internal fragment of p41 (p41i), outer surface protein C (OspC), p39, variable major protein-like sequence expressed (VlsE), p58 and p100; those in the IgM test were p41i, OspC and p39. Immune responses were correlated with clinical and treatment-related parameters. Results: Positive IB results were found in 50% before, in 57% directly after therapy and in 44% by the end of the follow-up for the IgG class, and in 36, 43 and 12% for the IgM class. In acute and convalescence phase sera, VlsE was most immunogenic on IgG testing 60 and 70%), and p41i (46 and 57%) and OspC (40 and 57%) for the IgM class. By the end of the follow-up, only the anti-p41i lgM response was significantly decreased to 24%. Conclusions: No correlation was found between IB results and treatment-related parameters. Thus, immunoblotting does not add to the clinical assessment of EM patients after treatment. Copyright (c) 2008 S. Karger AG, Basel

Influence of segmental chromosome abnormalities on survival in children over the age of 12 months with unresectable localised peripheral neuroblastic tumours without MYCN amplification.

BACKGROUND: The prognostic impact of segmental chromosome alterations (SCAs) in children older than 1 year, diagnosed with localised unresectable neuroblastoma (NB) without MYCN amplification enrolled in the European Unresectable Neuroblastoma (EUNB) protocol is still to be clarified, while, for other group of patients, the presence of SCAs is associated with poor prognosis. METHODS: To understand the role of SCAs we performed multilocus/pangenomic analysis of 98 tumour samples from patients enrolled in the EUNB protocol. RESULTS: Age at diagnosis was categorised into two groups using 18 months as the age cutoff. Significant difference in the presence of SCAs was seen in tumours of patients between 12 and 18 months and over 18 months of age at diagnosis, respectively (P=0.04). A significant correlation (P=0.03) was observed between number of SCAs per tumour and age. Event-free (EFS) and overall survival (OS) were calculated in both age groups, according to both the presence and number of SCAs. In older patients, a poorer survival was associated with the presence of SCAs (EFS=46% vs 75%, P=0.023; OS=66.8% vs 100%, P=0.003). Moreover, OS of older patients inversely correlated with number of SCAs (P=0.002). Finally, SCAs provided additional prognostic information beyond histoprognosis, as their presence was associated with poorer OS in patients over 18 months with unfavourable International Neuroblastoma Pathology Classification (INPC) histopathology (P=0.018). CONCLUSIONS: The presence of SCAs is a negative prognostic marker that impairs outcome of patients over the age of 18 months with localised unresectable NB without MYCN amplification, especially when more than one SCA is present. Moreover, in older patients with unfavourable INPC tumour histoprognosis, the presence of SCAs significantly affects OS