Prioritization of Therapeutic Targets of Inflammation Using Proteomics, Bioinformatics, and In Silico Cell-Cell Interactomics

  • Arsalan S. HaqqaniEmail author
  • Danica B. Stanimirovic
Part of the Methods in Molecular Biology book series (MIMB, volume 2024)


Protein-protein interactions play key roles in leukocyte extravasation process into the brain and have been attractive therapeutic targets for inhibiting brain inflammation using blocking (or neutralizing) antibodies. These targets include protein-protein interactions between cytokines (or chemokines) and their receptors on leukocytes and between adhesion molecules of leukocyte and brain endothelium. While a number of therapeutics against these targets are currently used in clinic for treatment of brain autoimmune and inflammatory disorders (e.g., multiple sclerosis), they are associated with side effects partly due to the off-target actions (i.e., nonspecific targets). There is a need for novel targets involved in the leukocyte extravasation process that are specific to leukocyte subsets or to individual inflammatory disorder and are amenable for drug development (i.e., druggable). We recently described the blood-brain barrier (BBB) Carta Project as a comprehensive collection of molecular “maps” consisting of multiple experimental omics (including RNA sequencing, proteomics, glycoproteomics, glycomics, metabolomics) and in silico informatics analyses on a number of mammalian species from hundreds of internal, publically available, or curated datasets. Utilizing the datasets and tools from the BBB Carta Project, we describe a methodology to identify novel “druggable” targets involving protein-protein interactions between activated leukocytes and brain endothelial cells using a combination of proteomics, bioinformatics, and in silico interactomics. The result is a prioritized list of protein-protein interactions in a network consisting of leukocyte-brain endothelial cell communication and contacts. These interactions can be further pursued for development of therapeutics such as neutralizing antibodies and their validation through preclinical testing. In addition to targeting brain inflammation, the method described here is applicable for peripheral inflammation and provides the opportunity to target important cell-cell interactions and communications that are more specific/selective for inflammatory disorders and improve currently available therapies.

Key words

Protein-protein interactions Intercellular Target prioritization Therapeutics Inflammation Extravasation Druggable Proteomics Bioinformatics 


  1. 1.
    Singer BA (2017) The role of natalizumab in the treatment of multiple sclerosis: benefits and risks. Ther Adv Neurol Disord 10:327–336CrossRefGoogle Scholar
  2. 2.
    Benucci M, Saviola G, Manfredi M, Sarzi-Puttini P, Atzeni F (2012) Tumor necrosis factors blocking agents: analogies and differences. Acta Biomed 83:72–80PubMedGoogle Scholar
  3. 3.
    Pérot S, Sperandio O, Miteva MA, Camproux A-C, Villoutreix BO (2010) Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery. Drug Discov Today 15:656–667CrossRefGoogle Scholar
  4. 4.
    Rossi B, Constantin G (2008) Anti-selectin therapy for the treatment of inflammatory diseases. Inflamm Allergy Drug Targets 7:85–93CrossRefGoogle Scholar
  5. 5.
    Engelhardt B, Wolburg H (2004) Mini-review: transendothelial migration of leukocytes: through the front door or around the side of the house? Eur J Immunol 34:2955–2963CrossRefGoogle Scholar
  6. 6.
    Coisne C, Lyck R, Engelhardt B (2007) Therapeutic targeting of leukocyte trafficking across the blood-brain barrier. Inflamm Allergy Drug Targets 6:210–222CrossRefGoogle Scholar
  7. 7.
    Wittchen ES (2009) Endothelial signaling in paracellular and transcellular leukocyte transmigration. Front Biosci (Landmark Ed) 14:2522–2545CrossRefGoogle Scholar
  8. 8.
    Haqqani AS, Stanimirovic DB (2011) Intercellular interactomics of human brain endothelial cells and th17 lymphocytes: a novel strategy for identifying therapeutic targets of CNS inflammation. Cardiovasc Psychiatry Neurol 2011:175364CrossRefGoogle Scholar
  9. 9.
    Filippi M-D (2016) Mechanism of diapedesis. Adv Immunol 129:25–53CrossRefGoogle Scholar
  10. 10.
    Ransohoff RM (2005) Natalizumab and PML. Nat Neurosci 8:1275–1275CrossRefGoogle Scholar
  11. 11.
    Scheinfeld N (2004) A comprehensive review and evaluation of the side effects of the tumor necrosis factor alpha blockers etanercept, infliximab and adalimumab. J Dermatolog Treat 15:280–294CrossRefGoogle Scholar
  12. 12.
    Cayrol R, Wosik K, Berard JL, Dodelet-Devillers A, Ifergan I, Kebir H, Haqqani AS, Kreymborg K, Krug S, Moumdjian R, Bouthillier A, Becher B, Arbour N, David S, Stanimirovic D, Prat A (2008) Activated leukocyte cell adhesion molecule promotes leukocyte trafficking into the central nervous system. Nat Immunol 9:137–145CrossRefGoogle Scholar
  13. 13.
    Haqqani AS, Stanimirovic DB (2017) Proteomes and biomarkers of the neurovascular unit. In: Caplan LR, Biller J, Leary MC, Lo EH, Thomas AJ, Yenari M, Zhang JH (eds) Primer on cerebrovascular diseases. Academic, San Diego, pp 346–350CrossRefGoogle Scholar
  14. 14.
    Haqqani AS, Stanimirovic DB (2013) Prioritization of therapeutic targets of inflammation using proteomics, bioinformatics, and in silico cell-cell interactomics. Methods Mol Biol 1061:345–360CrossRefGoogle Scholar
  15. 15.
    Weksler BB, Subileau EA, Perrière N, Charneau P, Holloway K, Leveque M, Tricoire-Leignel H, Nicotra A, Bourdoulous S, Turowski P, Male DK, Roux F, Greenwood J, Romero IA, Couraud PO (2005) Blood-brain barrier-specific properties of a human adult brain endothelial cell line. FASEB J 19:1872–1874CrossRefGoogle Scholar
  16. 16.
    Stanimirovic D, Shapiro A, Wong J, Hutchison J, Durkin J (1997) The induction of ICAM-1 in human cerebromicrovascular endothelial cells (HCEC) by ischemia-like conditions promotes enhanced neutrophil/HCEC adhesion. J Neuroimmunol 76:193–205CrossRefGoogle Scholar
  17. 17.
    Haqqani AS, Kelly J, Baumann E, Haseloff RF, Blasig IE, Stanimirovic DB (2007) Protein markers of ischemic insult in brain endothelial cells identified using 2D gel electrophoresis and ICAT-based quantitative proteomics. J Proteome Res 6:226–239CrossRefGoogle Scholar
  18. 18.
    Kebir H, Kreymborg K, Ifergan I, Dodelet-Devillers A, Cayrol R, Bernard M, Giuliani F, Arbour N, Becher B, Prat A (2007) Human TH17 lymphocytes promote blood-brain barrier disruption and central nervous system inflammation. Nat Med 13:1173–1175CrossRefGoogle Scholar
  19. 19.
    Palagi PM, Walther D, Quadroni M, Catherinet S, Burgess J, Zimmermann-Ivol CG, Sanchez J-C, Binz P-A, Hochstrasser DF, Appel RD (2005) MSight: an image analysis software for liquid chromatography-mass spectrometry. Proteomics 5:2381–2384CrossRefGoogle Scholar
  20. 20.
    Hirosawa M, Hoshida M, Ishikawa M, Toya T (1993) MASCOT: multiple alignment system for protein sequences based on three-way dynamic programming. Comput Appl Biosci 9:161–167PubMedGoogle Scholar
  21. 21.
    Haqqani AS, Kelly JF, Stanimirovic DB (2008) Quantitative protein profiling by mass spectrometry using label-free proteomics. Methods Mol Biol 439:241–256CrossRefGoogle Scholar
  22. 22.
    Saito R, Smoot ME, Ono K, Ruscheinski J, Wang P-L, Lotia S, Pico AR, Bader GD, Ideker T (2012) A travel guide to Cytoscape plugins. Nat Methods 9:1069–1076CrossRefGoogle Scholar
  23. 23.
    Barabási A-L, Oltvai ZN (2004) Network biology: understanding the cell’s functional organization. Nat Rev Genet 5:101–113CrossRefGoogle Scholar
  24. 24.
    Aßfalg A, Erdfelder E (2012) CAML—maximum likelihood consensus analysis. Behav Res Methods 44:189–201CrossRefGoogle Scholar
  25. 25.
    Abi-Haidar A, Kaur J, Maguitman A, Radivojac P, Rechtsteiner A, Verspoor K, Wang Z, Rocha LM (2008) Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks. Genome Biol 9:S11CrossRefGoogle Scholar
  26. 26.
    Melnik O, Vardi Y, Cun-Hui Zhang C-H (2004) Mixed group ranks: preference and confidence in classifier combination. IEEE Trans Pattern Anal Mach Intell 26:973–981CrossRefGoogle Scholar
  27. 27.
    Larochelle C, Uphaus T, Broux B, Gowing E, Paterka M, Michel L, Dudvarski Stankovic N, Bicker F, Lemaître F, Prat A, Schmidt MHH, Zipp F (2018) EGFL7 reduces CNS inflammation in mouse. Nat Commun 9:819CrossRefGoogle Scholar
  28. 28.
    Larochelle C, Cayrol R, Kebir H, Alvarez JI, Lécuyer M-A, Ifergan I, Viel É, Bourbonnière L, Beauseigle D, Terouz S, Hachehouche L, Gendron S, Poirier J, Jobin C, Duquette P, Flanagan K, Yednock T, Arbour N, Prat A (2012) Melanoma cell adhesion molecule identifies encephalitogenic T lymphocytes and promotes their recruitment to the central nervous system. Brain 135:2906–2924CrossRefGoogle Scholar
  29. 29.
    Ifergan I, Kebir H, Terouz S, Alvarez JI, Lécuyer M-A, Gendron S, Bourbonnière L, Dunay IR, Bouthillier A, Moumdjian R, Fontana A, Haqqani A, Klopstein A, Prinz M, Lõpez-Vales R, Birchler T, Prat A (2011) Role of ninjurin-1 in the migration of myeloid cells to central nervous system inflammatory lesions. Ann Neurol 70:751–763CrossRefGoogle Scholar
  30. 30.
    Schulze-Topphoff U, Prat A, Prozorovski T, Siffrin V, Paterka M, Herz J, Bendix I, Ifergan I, Schadock I, Mori MA, Van Horssen J, Schröter F, Smorodchenko A, Han MH, Bader M, Steinman L, Aktas O, Zipp F (2009) Activation of kinin receptor B1 limits encephalitogenic T lymphocyte recruitment to the central nervous system. Nat Med 15:788–793CrossRefGoogle Scholar
  31. 31.
    Podjaski C, Alvarez JI, Bourbonniere L, Larouche S, Terouz S, Bin JM, Lécuyer M-A, Saint-Laurent O, Larochelle C, Darlington PJ, Arbour N, Antel JP, Kennedy TE, Prat A (2015) Netrin 1 regulates blood–brain barrier function and neuroinflammation. Brain 138:1598–1612CrossRefGoogle Scholar
  32. 32.
    Haqqani AS, Hill JJ, Mullen J, Stanimirovic DB (2011) Methods to study glycoproteins at the blood-brain barrier using mass spectrometry. Methods Mol Biol 686:337–353CrossRefGoogle Scholar
  33. 33.
    Haqqani AS, Delaney CE, Brunette E, Baumann E, Farrington GK, Sisk W, Eldredge J, Ding W, Tremblay T-L, Stanimirovic DB (2018) Endosomal trafficking regulates receptor-mediated transcytosis of antibodies across the blood brain barrier. J Cereb Blood Flow Metab 38:727–740CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Human Health Therapeutics Research CentreNational Research Council of CanadaOttawaCanada

Personalised recommendations