Skip to main content

Computing Longevity: Insights from Controls

  • Conference paper
Book cover Formal Methods in Macro-Biology (FMMB 2014)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 8738))

Included in the following conference series:

  • 510 Accesses

Abstract

There is a growing perception that medical treatment could be effective against aging although not as one intensive short time medication as we do with infections. It will require a precise, personalised knowledge of the genes and pathways that are perturbed during the progression to aging. Environmental factors, parental longevity and childhood are important predictors of exceptional longevity. Here we analyse molecular data (gene expression) from ”healthy” controls of different age from several studies and we identify perturbations in key pathways affecting the susceptibility to several diseases. This work is exploratory and provide a useful test on existing data and methods for future studies.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Capobianco, E., Lió, P.: Comorbidity: a multidimensional approach. Trends in Molecular Medicine 19(9), 515–521 (2013)

    Article  Google Scholar 

  2. Radner, H., Yoshida, K., Smolen, J.S., Solomon, D.H.: Multimorbidity and rheumatic conditions - enhancing the concept of comorbidity. Nature Reviews Endocrinology 10, 37–50 (2014)

    Google Scholar 

  3. Raule, N., Sevini, F., Li, S., Barbieri, A., Tallaro, F., Lomartire, L., Vianello, D., Montesanto, A., Moilanen, J.S., Bezrukov, V., Blanch, H., Hervonen, A., Christensen, K., Deiana, L., Gonos, E.S., Kirkwood, T.B., Kristensen, P., Leon, A., Pelicci, P.G., Poulain, M., Rea, I.M., Remacle, J., Robine, J.M., Schreiber, S., Sikora, E., Eline Slagboom, P., Spazzafumo, L., Antonietta Stazi, M., Toussaint, O., Vaupel, J.W., Rose, G., Majamaa, K., Perola, M., Johnson, T.E., Bolund, L., Yang, H., Passarino, G., Franceschi, C.: The co-occurrence of mtDNA mutations on different oxidative phosphorylation subunits, not detected by haplogroup analysis, affects human longevity and is population specific. Aging Cell 13(3), 401–407 (2013) (Epub. December 17, 2013), doi:10.1111/acel.12186

    Google Scholar 

  4. Garagnani, P., Pirazzini, C., Giuliani, C., Candela, M., Brigidi, P., Sevini, F., Luiselli, D., Bacalini, M.G., Salvioli, S., Capri, M., Monti, D., Mari, D., Collino, S., Delledonne, M., Descombes, P., Franceschi, C.: The three genetics (nuclear DNA, mitochondrial DNA, and gut microbiome) of longevity in humans considered as metaorganisms. Biomed Res. Int. 2014, 560340 (2014) ( Epub. April 24, 2014), doi:10.1155/2014/560340

    Google Scholar 

  5. de Magalhes, J.P., Curado, J., Church, G.M.: Meta-analysis of age-related gene expression profiles identifies common signatures of aging. Bioinformatics 25(7), 875–881 (2009)

    Article  Google Scholar 

  6. Welle, S., Brooks, A.I., Delehanty, J.M., Needler, N., et al.: Skeletal muscle gene expression profiles in 20-29 year old and 65-71 year old women. Exp. Gerontol. 39(3), 369–377 (2004), PMID: 15036396

    Google Scholar 

  7. Welle, S., Brooks, A.I., Delehanty, J.M., Needler, N., et al.: Gene expression profile of aging in human muscle. Physiol Genomics 14(2), 149–159 (2003), PMID: 12783983

    Google Scholar 

  8. Zahn, J.M., et al.: Transcriptional profiling of aging in human muscle reveals a common aging signature. PLoS Genetics 2(7), e115 (2006)

    Google Scholar 

  9. Lu, T., Pan, Y., Kao, S.Y., Li, C., et al.: Gene regulation and DNA damage in the ageing human brain. Nature 429(6994), 883–891 (2004), PMID: 15190254

    Google Scholar 

  10. Ryten, M., Trabzuni, D., Walker, R., et al.: Expression data generated from post-mortem human brain tissue originating from neurologically and neuropathologically control individuals collected from: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE46706

  11. de Jong, S., Boks, M.P., Fuller, T.F., Strengman, E., et al.: A gene co-expression network in whole blood of schizophrenia patients is independent of antipsychotic-use and enriched for brain-expressed genes. PLoS One 7(6), e39498 (2012), PMID: 22761806

    Google Scholar 

  12. Linton, P.J., Dorshkind, K.: Age-related changes in lymphocyte development and function. Nat. Immunol. 5, 133–139 (2004)

    Article  Google Scholar 

  13. Taneera, J., Lang, S., Sharma, A., Fadista, J., Zhou, Y., Ahlqvist, E., Jonsson, A., Lyssenko, V., Vikman, P., Hansson, O., Parikh, H., Korsgren, O., Soni, A., Krus, U., Zhang, E., Jing, X.J., Esguerra, J.L., Wollheim, C.B., Salehi, A., Rosengren, A., Renstrom, E., Groop, L.: A systems genetics approach identifies genes and pathways for type 2 diabetes in human islets. Cell Metabolism 16(1), 122–134 (2012)

    Article  Google Scholar 

  14. Gentleman, R., Carey, V.J., Bates, D.M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., et al.: Bioconductor: Open software development for computational biology and bioinformatics. Genome Biology 5, R80 (2004)

    Google Scholar 

  15. Smyth, G.K.: Limma: linear models for microarray data. In: Gentleman, R., Carey, V., Dudoit, S., Irizarry, R., Huber, W. (eds.) Bioinformatics and Computational Biology Solutions Using R and Bioconductor, pp. 397–420. Springer, New York (2005)

    Chapter  Google Scholar 

  16. Davis, S., Meltzer, P.S.: GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor. Bioinformatics 14, 1846–1847 (2007)

    Article  Google Scholar 

  17. Benjamini, Y., Hochberg, Y.: Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society, Series B 57(1), 289–300 (1995)

    MATH  MathSciNet  Google Scholar 

  18. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., Harris, M.A., Hill, D.P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M., Sherlock, G.: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium 25(1), 25–29 (2000)

    Google Scholar 

  19. Xie, C., et al.: KOBAS 2.0: a web server for annotation and identi cation of enriched pathways and diseases. Nucleic Acids Research 39(suppl. 2), W316–W322 (2011)

    Google Scholar 

  20. Zhang, G., Li, J., Purkayastha, S., Tang, Y., Zhang, H., Yin, Y., Li, B., Liu, G., Cai, D.: Hypothalamic Programming of Systemic Aging Involving IKK, NF-kB and GnRH. Nature 497, 211–216 (2013)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer International Publishing Switzerland

About this paper

Cite this paper

Lió, P. (2014). Computing Longevity: Insights from Controls. In: Fages, F., Piazza, C. (eds) Formal Methods in Macro-Biology. FMMB 2014. Lecture Notes in Computer Science(), vol 8738. Springer, Cham. https://doi.org/10.1007/978-3-319-10398-3_4

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-10398-3_4

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-10397-6

  • Online ISBN: 978-3-319-10398-3

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics