Mining the transcriptome for rare disease therapies: A comparison of the efficiencies of two data mining approaches and a targeted cell-based drug screen

npj Genomic Medicine

Volumn 2, Issue 1, 2017, Pages

  Mears, A J ^a   Schock, S C ^a   Hadwen, J ^a,b   Putos, S ^a   Dyment, D ^a   Boycott, K M ^a   MacKenzie, Alex ^a,b  

^a CHILDREN S HOSPITAL OF EASTERN ONTARIO   (Canada)

^b UNIVERSITY OF OTTAWA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85042314185     PISSN: None     EISSN: 20567944     Source Type: Journal    
DOI: 10.1038/s41525-017-0018-3     Document Type: Article

References (35)

1. Chong, J. X. et al. The genetic basis of mendelian phenotypes: discoveries, challenges, and opportunities. Am. J. Hum. Genet. 97, 199-215 (2015).
2. Mazzucato, M., Visonà Dalla Pozza, L., Manea, S., Minichiello, C. & Facchin, P. A population-based registry as a source of health indicators for rare diseases: the ten-year experience of the Veneto Region's rare diseases registry. Orphanet. J. Rare. Dis. 9, 37 (2014).
3. McKusick, V. A. Mendelian inheritance in man and its online version, OMIM. Am. J. Hum. Genet. 80, 588-604 (2007).
4. Philippakis, A. A. et al. The matchmaker exchange: a platform for rare disease gene discovery. Hum. Mutat. 36, 915-921 (2015).
5. Haffner, M. E. History of orphan drug regulation-United States and beyond. Clin. Pharmacol. Ther. 100, 342-343 (2016).
6. Huang, R. et al. The NCGC pharmaceutical collection: a comprehensive resource of clinically approved drugs enabling repurposing and chemical genomics. Sci. Transl. Med. 3, 80ps16 (2011).
7. MacKenzie, A. Sense in antisense therapy for spinal muscular atrophy. doi:10.1056/NEJMcibr1114629 (2012).
8. Edgar, R., Domrachev, M. & Lash, A. E. Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic. Acids. Res. 30, 207-210 (2002).
9. Lamb, J. et al. The connectivity map : using gene-expression signatures to connect small molecules, genes, and disease. Science 313, 1929-1935 (2006).
10. Lamb, J. The connectivity map : a new tool for biomedical research. Nature. 7, 54-60 (2007).
11. Enayetallah, A. E., Ziemek, D., Leininger, M.T. et al. Modeling the mechanism of action of a DGAT1 inhibitor using a causal reasoning platform. PLoS ONE 6, e27009 (2011).
12. Chindelevitch, L. et al. Causal reasoning on biological networks: interpreting transcriptional changes. Bioinformatics. 28, 1114-1121 (2012).
13. INSERM. Prevalence and incidence of rare diseases: bibilographic data. Orphanet Rep. Ser. Rare Dis. Collect. 1, 1-55 (2015).
14. Beaulieu, C. L. et al. FORGE Canada consortium: outcomes of a 2-year national rare-disease gene-discovery project. Am. J. Hum. Genet. 94, 809-817 (2014).
15. Holler, C. J. et al. Trehalose upregulates progranulin expression in human and mouse models of GRN haploinsufficiency: a novel therapeutic lead to treat frontotemporal dementia. Mol. Neurodegener. 11, 46 (2016).
16. Albinana, V., Bernabeu-Herrero, M. E., Zarrabeitia, R., Bernabeu, C. & Botella, L. M. Estrogen therapy for hereditary haemorrhagic telangiectasia (HHT): effects of raloxifene, on Endoglin and ALK1 expression in endothelial cells. Thromb. Haemost. 103, 525-534 (2010).
17. Krawczak, M. et al. Human gene mutation database-a biomedical information and research resource. Hum. Mutat. 15, 45-51 (2000).
18. Edqvist, P.-H. D. et al. Expression of human skin-specific genes defined by transcriptomics and antibody-based profiling. J. Histochem. Cytochem. 63, 129-141 (2015).
19. Wagner, A. et al. Drugs that reverse disease transcriptomic signatures are more effective in a mouse model of dyslipidemia. Mol. Syst. Biol. 11, 791 (2015).
20. Chang, M., Smith, S., Thorpe, A., Barratt, M. J. & Karim, F. Evaluation of phenoxybenzamine in the CFA model of pain following gene expression studies and connectivity mapping. Mol. Pain. 6, 56 (2010).
21. Claerhout, S. et al. Gene expression signature analysis identifies vorinostat as a candidate therapy for gastric cancer. PLoS ONE 6, e24662 (2011).
22. Dudley, J. T. et al. Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease. Sci. Transl. Med. 3, 96ra76 (2011).
23. Kunkel, S. D. et al. mRNA expression signatures of human skeletal muscle atrophy identify a natural compound that increases muscle mass. Cell. Metab. 13, 627-638 (2011).
24. B, A. M. et al. Connectivity map-based discovery of parbendazole reveals targetable human osteogenic pathway. Proc. Natl. Acad. Sci. U. S. A. 112, 12711-12716 (2015).
25. Ishimatsu-Tsuji, Y., Soma, T. & Kishimoto, J. Identification of novel hair-growth inducers by means of connectivity mapping. FASEB. J. 24, 1489-1496 (2010).
26. Cheng, J., Yang, L., Kumar, V. & Agarwal, P. Systematic evaluation of connectivity map for disease indications. Genome. Med. 6, 540 (2014).
27. Yuen, T. et al. Disease-drug pairs revealed by computational genomic connectivity mapping on GBA1 deficient, Gaucher disease mice. Biochem. Biophys. Res. Commun. 422, 573-577 (2012).
28. Denk, F. et al. HDAC inhibitors attenuate the development of hypersensitivity in models of neuropathic pain. Pain. 154, 1668-1679 (2013).
29. Guo, Y. et al. How is mRNA expression predictive for protein expression? A correlation study on human circulating monocytes. Acta. Biochim. Biophys. Sin. 40, 426-436 (2008).
30. Gry, M. et al. Correlations between RNA and protein expression profiles in 23 human cell lines. BMC. Genomics. 10, 365 (2009).
31. Van Laer, L., Dietz, H. & Loeys, B. Loeys-dietz syndrome. Adv. Exp. Med. Biol. 802, 95-105 (2014).
32. van der Pluijm, I. et al. Defective connective tissue remodeling in Smad3 mice leads to accelerated aneurysmal growth through disturbed downstream TGF-β signaling. EbioMedicine. 12, 280-294 (2016).
33. Boycott, K. M. et al. Autosomal-recessive intellectual disability with cerebellar atrophy syndrome caused by mutation of the manganese and zinc transporter gene SLC39A8. Am. J. Hum. Genet. 97, 886-893 (2015).
34. Tuschl, K. et al. Mutations in SLC39A14 disrupt manganese homeostasis and cause childhood-onset parkinsonism.dystonia. Nat. Commun. 7, 11601 (2016).
35. Wu, Z., Wang, Y. & Chen, L. Network-based drug repositioning. Mol. Biosyst. 9, 1268-1281 (2013).