Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

From transcriptome analysis to therapeutic anti-CD40L treatment in the SOD1 model of amyotrophic lateral sclerosis


Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by progressive loss of motor neurons. Using unbiased transcript profiling in an ALS mouse model, we identified a role for the co-stimulatory pathway, a key regulator of immune responses. Furthermore, we observed that this pathway is upregulated in the blood of 56% of human patients with ALS. A therapy using a monoclonal antibody to CD40L was developed that slows weight loss, delays paralysis and extends survival in an ALS mouse model. This work demonstrates that unbiased transcript profiling can identify cellular pathways responsive to therapeutic intervention in a preclinical model of human disease.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Co-stimulatory pathway signaling in SOD1G93A skeletal muscle, spinal cord and sciatic nerve is upregulated during disease progression and is increased in a subset of blood samples from individuals with ALS.
Figure 2: Macrophages accumulate in peripheral nerves throughout the disease course.
Figure 3: Blocking CD40L with a monoclonal antibody to CD40L improves body-weight maintenance, delays disease onset and extends survival in SOD1 mice.
Figure 4: Meta-analysis of anti-CD40L treatment compared with riluzole, apocynin and historical controls.
Figure 5: MR1 treatment lowers the frequency of CD68+ cells in sciatic nerve and CD8+ T cells in sciatic lymph node.
Figure 6: Anti-CD40L treatment decreases astrocytosis and microgliosis while reducing motor neuron loss in the spinal cord of SOD1G93A mice.
Figure 7: Treatment of SOD1G93A mice with anti-CD40L decreases the expression of genes in the co-stimulatory pathway in the spinal cord.

Accession codes




  1. Kola, I. & Landis, J. Opinion: can the pharmaceutical industry reduce attrition rates? Nat. Rev. Drug Discov. 8, 711–716 (2004).

    Article  Google Scholar 

  2. Hess, K.R. et al. Pharmacogenomic predictor of sensitivity to preoperative chemotherapy with paclitaxel and fluorouracil, doxorubicin, and cyclophosphamide in breast cancer. J. Clin. Oncol. 24, 4236–4244 (2006).

    Article  CAS  Google Scholar 

  3. Bonnefoi, H. et al. Validation of gene signatures that predict the response of breast cancer to neoadjuvant chemotherapy: a substudy of the EORTC 10994/BIG 00–01 clinical trial. Lancet Oncol. 8, 1071–1078 (2007).

    Article  CAS  Google Scholar 

  4. Cooper, C.S., Campbell, C. & Jhavar, S. Mechanisms of disease: biomarkers and molecular targets from microarray gene expression studies in prostate cancer. Nat. Clin. Pract. Urol. 4, 677–687 (2007).

    Article  CAS  Google Scholar 

  5. Lacroix, L., Commo, F. & Soria, J.C. Gene expression profiling of non-small-cell lung cancer. Expert Rev. Mol. Diagn. 8, 167–178 (2008).

    Article  CAS  Google Scholar 

  6. Kinter, J., Zeis, T. & Schaeren-Wiemers, N. RNA profiling of MS brain tissues. Int. MS J. 15, 51–58 (2008).

    CAS  PubMed  Google Scholar 

  7. Bourquin, J.P. et al. Identification of distinct molecular phenotypes in acute megakaryoblastic leukemia by gene expression profiling. Proc. Natl. Acad. Sci. USA 103, 3339–3344 (2006).

    Article  CAS  Google Scholar 

  8. Golub, T.R. et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286, 531–537 (1999).

    Article  CAS  Google Scholar 

  9. Decristofaro, M.F. & Daniels, K.K. Toxicogenomics in biomarker discovery. Methods Mol. Biol. 460, 185–194 (2008).

    Article  CAS  Google Scholar 

  10. Merrick, B.A. & Bruno, M.E. Genomic and proteomic profiling for biomarkers and signature profiles of toxicity. Curr. Opin. Mol. Ther. 6, 600–607 (2004).

    CAS  PubMed  Google Scholar 

  11. Ideker, T., Ozier, O., Schwikowski, B. & Siegel, A.F. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 18 (Suppl. 1), 233–240 (2002).

    Article  Google Scholar 

  12. Linsley, P.S., Clark, E.A. & Ledbetter, J.A. T-cell antigen CD28 mediates adhesion with B cells by interacting with activation antigen B7/BB-1. Proc. Natl. Acad. Sci. USA 87, 5031–5035 (1990).

    Article  CAS  Google Scholar 

  13. Freeman, G.J. et al. Cloning of B7–2: a CTLA-4 counter-receptor that costimulates human T cell proliferation. Science 262, 909–911 (1993).

    Article  CAS  Google Scholar 

  14. Noelle, R.J., Ledbetter, J.A. & Aruffo, A. CD40 and its ligand, an essential ligand-receptor pair for thymus-dependent B-cell activation. Immunol. Today 13, 431–433 (1992).

    Article  CAS  Google Scholar 

  15. Roy, M., Waldschmidt, T., Aruffo, A., Ledbetter, J.A. & Noelle, R.J. The regulation of the expression of gp39, the CD40 ligand, on normal and cloned CD4+ T cells. J. Immunol. 151, 2497–2510 (1993).

    CAS  PubMed  Google Scholar 

  16. Durie, F.H. et al. Prevention of collagen-induced arthritis with an antibody to gp39, the ligand for CD40. Science 261, 1328–1330 (1993).

    Article  CAS  Google Scholar 

  17. Gerritse, K. et al. CD40–CD40 ligand interactions in experimental allergic encephalomyelitis and multiple sclerosis. Proc. Natl. Acad. Sci. USA 93, 2499–2504 (1996).

    Article  CAS  Google Scholar 

  18. Mohan, C., Shi, Y., Laman, J.D. & Datta, S.K. Interaction between CD40 and its ligand gp39 in the development of murine lupus nephritis. J. Immunol. 154, 1470–1480 (1995).

    CAS  PubMed  Google Scholar 

  19. Ma, J. et al. Autoimmune lpr/lpr mice deficient in CD40 ligand: spontaneous Ig class switching with dichotomy of autoantibody responses. J. Immunol. 157, 417–426 (1996).

    CAS  PubMed  Google Scholar 

  20. Grewal, I.S. et al. Requirement for CD40 ligand in costimulation induction, T cell activation, and experimental allergic encephalomyelitis. Science 273, 1864–1867 (1996).

    Article  CAS  Google Scholar 

  21. Kirk, A.D. et al. CTLA4-Ig and anti-CD40 ligand prevent renal allograft rejection in primates. Proc. Natl. Acad. Sci. USA 94, 8789–8794 (1997).

    Article  CAS  Google Scholar 

  22. Larsen, C.P. et al. CD40-gp39 interactions play a critical role during allograft rejection. Suppression of allograft rejection by blockade of the CD40-gp39 pathway. Transplantation 61, 4–9 (1996).

    Article  CAS  Google Scholar 

  23. Monk, N.J. et al. Fc-dependent depletion of activated T cells occurs through CD40L-specific antibody rather than costimulation blockade. Nat. Med. 9, 1275–1280 (2003).

    Article  CAS  Google Scholar 

  24. Durie, F.H. et al. Prevention of collagen-induced arthritis with an antibody to gp39, the ligand for CD40. Science 261, 1328–1330 (1993).

    Article  CAS  Google Scholar 

  25. Gallon, L. et al. Differential effects of B7–1 blockade in the rat experimental autoimmune encephalomyelitis model. J. Immunol. 159, 4212–4216 (1997).

    CAS  PubMed  Google Scholar 

  26. Tan, J. et al. Role of CD40 ligand in amyloidosis in transgenic Alzheimer's mice. Nat. Neurosci. 5, 1288–1293 (2002).

    Article  CAS  Google Scholar 

  27. Goeman, J.J., Van de Geer, S.A., De Kort, F. & Van Houwelingen, J.C. A global test for groups of genes: testing association with a clinical outcome. Bioinformatics 20, 93–99 (2004).

    Article  CAS  Google Scholar 

  28. Beers, D.R., Henkel, J.S., Zhao, W., Wang, J. & Appel, S.H. CD4+ T cells support glial neuroprotection, slow disease progression, and modify glial morphology in an animal model of inherited ALS. Proc. Natl. Acad. Sci. USA 105, 15558–15563 (2008).

    Article  CAS  Google Scholar 

  29. Beers, D.R. et al. Wild-type microglia extend survival in PU.1 knockout mice with familial amyotrophic lateral sclerosis. Proc. Natl. Acad. Sci. USA 103, 16021–16026 (2006).

    Article  CAS  Google Scholar 

  30. Engelhardt, J.I., Tajti, J. & Appel, S.H. Lymphocytic infiltrates in the spinal cord in amyotrophic lateral sclerosis. Arch. Neurol. 50, 30–36 (1993).

    Article  CAS  Google Scholar 

  31. Kawamata, T., Akiyama, H., Yamada, T. & McGeer, P.L. Immunologic reactions in amyotrophic lateral sclerosis brain and spinal cord tissue. Am. J. Pathol. 140, 691–707 (1992).

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Troost, D., Van den Oord, J.J. & Vianney de Jong, J.M. Immunohistochemical characterization of the inflammatory infiltrate in amyotrophic lateral sclerosis. Neuropathol. Appl. Neurobiol. 16, 401–410 (1990).

    Article  CAS  Google Scholar 

  33. Troost, D., van den Oord, J.J., de Jong, J.M. & Swaab, D.F. Lymphocytic infiltration in the spinal cord of patients with amyotrophic lateral sclerosis. Clin. Neuropathol. 8, 289–294 (1989).

    CAS  PubMed  Google Scholar 

  34. Banerjee, R. et al. Adaptive immune neuroprotection in G93A–SOD1 amyotrophic lateral sclerosis mice. PLoS One 3, 2740 (2008).

    Article  Google Scholar 

  35. Hughes, R., Atkinson, P., Coates, P., Hall, S. & Leibowitz, S. Sural nerve biopsies in Guillain-Barre syndrome: axonal degeneration and macrophage-associated demyelination and absence of cytomegalovirus genome. Muscle Nerve 15, 568–575 (1992).

    Article  CAS  Google Scholar 

  36. Kiefer, R., Kieseier, B.C., Brück, W., Hartung, H.P. & Toyka, K.V. Macrophage differentiation antigens in acute and chronic autoimmune polyneuropathies. Brain 121, 469–479 (1998).

    Article  Google Scholar 

  37. Honey, K., Cobbold, S.P. & Waldmann, H. CD40 ligand blockade induces CD4+ T cell tolerance and linked suppression. J. Immunol. 163, 4805–4810 (1999).

    CAS  PubMed  Google Scholar 

  38. Nagelkerken, L. et al. FcR interactions do not play a major role in inhibition of experimental autoimmune encephalomyelitis by anti-CD154 monoclonal antibodies. J. Immunol. 173, 993–999 (2004).

    Article  CAS  Google Scholar 

  39. Ruderman, E & Pope, R. Co-stimulatory pathways in the therapy of rheumatoid arthritis. in New Therapeutic Targets in Rheumatoid Arthritis (ed. Tak, P.-P.) 27–43 (Birkhäuser, Basel, 2009).

  40. Noelle, R.J. et al. A 39-kDa protein on activated helper T cells binds CD40 and transduces the signal for cognate activation of B cells. Proc. Natl. Acad. Sci. USA 89, 6550–6554 (1992).

    Article  CAS  Google Scholar 

  41. Graca, L., Honey, K., Adams, E., Cobbold, S.P. & Waldmann, H. Cutting edge: anti-CD154 therapeutic antibodies induce infectious transplantation tolerance. J. Immunol. 165, 4783–4786 (2000).

    Article  CAS  Google Scholar 

  42. Kalled, S.L., Cutler, A.H. & Ferrant, J.L. Long-term anti-CD154 dosing in nephritic mice is required to maintain survival and inhibit mediators of renal fibrosis. Lupus 10, 9–22 (2001).

    Article  CAS  Google Scholar 

  43. Gill, A., Kidd, J., Vieira, F., Thompson, K. & Perrin, S. No benefit from chronic lithium dosing in a sibling-matched, gender balanced, investigator-blinded trial using a standard mouse model of familial ALS. PLoS One 4, e6489 (2009).

    Article  Google Scholar 

  44. Scott, S. et al. Design, power, and interpretation of studies in the standard murine model of ALS. Amyotroph. Lateral Scler. 9, 4–15 (2008).

    Article  CAS  Google Scholar 

  45. Harraz, M.M. et al. SOD1 mutations disrupt redox-sensitive Rac regulation of NADPH oxidase in a familial ALS model. J. Clin. Invest. 118, 659–670 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

Download references


We thank S. Appel, J. McCoy, S. Hesterlee and R. Goldstein for their thoughtful scientific discussions and contributions, R. Puchalski and the staff of the Allen Institute for Brain Science for the contribution of the in situ hybridization data, S.F. Scott, who lost his battle with ALS in 2009, for establishing the rigorous parameters required to test therapeutics in the SOD1G93A model, J. Heywood and his family for establishing ALS TDI and continuing to support our efforts and A. Nieto and L. Nieto for their dedication and financial support for the development of therapeutics for ALS. This work was supported by the Muscular Dystrophy Association/Augie's Quest, the US Department of Defense, the RGK Foundation and all our patients with ALS and their families.

Author information

Authors and Affiliations



J.M.L., F.G.V., A.G. and S.P. designed the experiments. M.Z.W. performed the immunohistochemistry and FACS experiments. R.S. and I.J.C. performed the motor neuron histology. B.A.L. oversaw and consulted on the human blood sample study. K.T., J.K. and A.M. performed all the animal studies. G.S.D.Z. consulted on the interpretation of the results. B.M.A. and S.M.S. wrote the simulation and LIMS software. A.G. performed all pharmacological statistical analysis. S.P., J.M.L., A.G. and F.G.V. wrote the paper. All authors discussed the results and commented on the manuscript.

Corresponding author

Correspondence to Steven Perrin.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–3 and Supplementary Table 4 (PDF 3784 kb)

Supplementary Table 1

Calculated Q scores of significantly different pathways in SOD1G93A mice compared to non-transgenic littermates. (XLS 27 kb)

Supplementary Table 2

RMA normalized gene expression data of all genes in five significantly changing pathways in SOD1G93A mice compared to non-transgenic littermates. (XLS 735 kb)

Supplementary Table 3

Calculated fold-change data of all genes in five significantly changing pathways in SOD1G93A mice compared to non-transgenic littermates derived from RMA normalized data. (XLS 107 kb)

Supplementary Table 5

Relative normalized transcript expression of costimulatory genes in human clinical blood samples. (XLS 142 kb)

Supplementary Note

Clinical annotation of human clinical blood samples (XLS 69 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Lincecum, J., Vieira, F., Wang, M. et al. From transcriptome analysis to therapeutic anti-CD40L treatment in the SOD1 model of amyotrophic lateral sclerosis. Nat Genet 42, 392–399 (2010).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing