Characteristics and Predictive Value of Blood Transcriptome Signature in Males with Autism Spectrum Disorders

PLoS ONE

Volumn 7, Issue 12, 2012, Pages

  Kong, Sek Won ^a,b   Collins, Christin D ^a,b   Shimizu Motohashi, Yuko ^a,b   Holm, Ingrid A ^a,b,e   Campbell, Malcolm G ^a   Lee, In Hee ^a   Brewster, Stephanie J ^a,e   Hanson, Ellen ^a   Harris, Heather K ^a,e   Lowe, Kathryn R ^a,e   Saada, Adrianna ^a   Mora, Andrea ^a   Madison, Kimberly ^a   Hundley, Rachel ^a   Egan, Jessica ^a   McCarthy, Jillian ^a   Eran, Ally ^a   Galdzicki, Michal ^a   Rappaport, Leonard ^a,b   Kunkel, Louis M ^a,b,c   Kohane, Isaac S ^a,b,d,e   more..

^a BOSTON CHILDREN S HOSPITAL   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^d Harvard Medical School Center for Biomedical Informatics   (United States)

^e Autism Consortium Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NEUROTROPHIN; NOTCH RECEPTOR; TRANSCRIPTOME;

ARTICLE; AUTISM; CHILD; COHORT ANALYSIS; CONTROLLED STUDY; DIAGNOSTIC ACCURACY; DIFFERENTIAL DIAGNOSIS; FEMALE; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE STRUCTURE; GENETIC DIFFERENCE; GENETIC MODEL; GENETIC PARAMETERS; GENETIC TRAIT; GENETIC VARIABILITY; HUMAN; LONG TERM DEPRESSION; LONG TERM POTENTIATION; MAJOR CLINICAL STUDY; MALE; MEN'S HEALTH; PREDICTIVE VALUE; PRESCHOOL CHILD; RECEIVER OPERATING CHARACTERISTIC; RNA STRUCTURE; SCHOOL CHILD; SENSITIVITY AND SPECIFICITY; SEX DIFFERENCE; SIGNAL TRANSDUCTION; TRANSCRIPTOMICS; VALIDATION PROCESS;

CHILD; CHILD DEVELOPMENT DISORDERS, PERVASIVE; COHORT STUDIES; GENE EXPRESSION PROFILING; HUMANS; MALE; MODELS, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; TRANSCRIPTOME;

EID: 84870821992     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0049475     Document Type: Article

References (75)

1. American Psychiatric Association (2000) Diagnostic and statistical manual of mental disorders: DSM-IV-TR. Washington, DC: American Psychiatric Association.
2. Autism, Developmental Disabilities Monitoring Network Surveillance Year Principal I (2012) Prevalence of autism spectrum disorders- autism and developmental disabilities monitoring network, 14 sites, United States, 2008. MMWR Surveill Summ 61: 1-19.
3. Lord C, Risi S, DiLavore PS, Shulman C, Thurm A, et al. (2006) Autism from 2 to 9 years of age. Arch Gen Psychiatry 63: 694-701.
4. Howland A, Rasbury W, Heilman KM, Hammer L, (1975) The development of auditory figure-ground discrimination and ear asymmetry under nonaural stimulus presentation. Dev Med Child Neurol 17: 325-332.
5. Shattuck PT, Durkin M, Maenner M, Newschaffer C, Mandell DS, et al. (2009) Timing of identification among children with an autism spectrum disorder: findings from a population-based surveillance study. J Am Acad Child Adolesc Psychiatry 48: 474-483.
6. Wiggins LD, Baio J, Rice C, (2006) Examination of the time between first evaluation and first autism spectrum diagnosis in a population-based sample. J Dev Behav Pediatr 27: S79-87.
7. Harris SL, Handleman JS, (2000) Age and IQ at intake as predictors of placement for young children with autism: a four- to six-year follow-up. J Autism Dev Disord 30: 137-142.
8. Abrahams BS, Geschwind DH, (2008) Advances in autism genetics: on the threshold of a new neurobiology. Nat Rev Genet 9: 341-355.
9. Happe F, Ronald A, (2008) The 'fractionable autism triad': a review of evidence from behavioural, genetic, cognitive and neural research. Neuropsychol Rev 18: 287-304.
10. Shen Y, Dies KA, Holm IA, Bridgemohan C, Sobeih MM, et al. (2010) Clinical genetic testing for patients with autism spectrum disorders. Pediatrics 125: e727-735.
11. Jacquemont ML, Sanlaville D, Redon R, Raoul O, Cormier-Daire V, et al. (2006) Array-based comparative genomic hybridisation identifies high frequency of cryptic chromosomal rearrangements in patients with syndromic autism spectrum disorders. J Med Genet 43: 843-849.
12. Marshall CR, Noor A, Vincent JB, Lionel AC, Feuk L, et al. (2008) Structural variation of chromosomes in autism spectrum disorder. Am J Hum Genet 82: 477-488.
13. Shi L, Campbell G, Jones WD, Campagne F, Wen Z, et al. (2010) The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol 28: 827-838.
14. van 't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, et al. (2002) Gene expression profiling predicts clinical outcome of breast cancer. Nature 415: 530-536.
15. Ghahramani Seno MM, Hu P, Gwadry FG, Pinto D, Marshall CR, et al. (2011) Gene and miRNA expression profiles in autism spectrum disorders. Brain Res 1380: 85-97.
16. Sarachana T, Zhou R, Chen G, Manji HK, Hu VW, (2010) Investigation of post-transcriptional gene regulatory networks associated with autism spectrum disorders by microRNA expression profiling of lymphoblastoid cell lines. Genome Med 2: 23.
17. Hu VW, Nguyen A, Kim KS, Steinberg ME, Sarachana T, et al. (2009) Gene expression profiling of lymphoblasts from autistic and nonaffected sib pairs: altered pathways in neuronal development and steroid biosynthesis. PLoS One 4: e5775.
18. Hu VW, Sarachana T, Kim KS, Nguyen A, Kulkarni S, et al. (2009) Gene expression profiling differentiates autism case-controls and phenotypic variants of autism spectrum disorders: evidence for circadian rhythm dysfunction in severe autism. Autism Res 2: 78-97.
19. Enstrom AM, Lit L, Onore CE, Gregg JP, Hansen RL, et al. (2009) Altered gene expression and function of peripheral blood natural killer cells in children with autism. Brain Behav Immun 23: 124-133.
20. Gregg JP, Lit L, Baron CA, Hertz-Picciotto I, Walker W, et al. (2008) Gene expression changes in children with autism. Genomics 91: 22-29.
21. Talebizadeh Z, Butler MG, Theodoro MF, (2008) Feasibility and relevance of examining lymphoblastoid cell lines to study role of microRNAs in autism. Autism Res 1: 240-250.
22. Nishimura Y, Martin CL, Vazquez-Lopez A, Spence SJ, Alvarez-Retuerto AI, et al. (2007) Genome-wide expression profiling of lymphoblastoid cell lines distinguishes different forms of autism and reveals shared pathways. Hum Mol Genet 16: 1682-1698.
23. Baron CA, Liu SY, Hicks C, Gregg JP, (2006) Utilization of lymphoblastoid cell lines as a system for the molecular modeling of autism. J Autism Dev Disord 36: 973-982.
24. Fury W, Batliwalla F, Gregersen PK, Li W, (2006) Overlapping probabilities of top ranking gene lists, hypergeometric distribution, and stringency of gene selection criterion. Conf Proc IEEE Eng Med Biol Soc 1: 5531-5534.
25. Basu SN, Kollu R, Banerjee-Basu S, (2009) AutDB: a gene reference resource for autism research. Nucleic Acids Res 37: D832-836.
26. Castermans D, Vermeesch JR, Fryns JP, Steyaert JG, Van de Ven WJ, et al. (2007) Identification and characterization of the TRIP8 and REEP3 genes on chromosome 10q21.3 as novel candidate genes for autism. Eur J Hum Genet 15: 422-431.
27. Pinto D, Pagnamenta AT, Klei L, Anney R, Merico D, et al. (2010) Functional impact of global rare copy number variation in autism spectrum disorders. Nature 466: 368-372.
28. Piton A, Gauthier J, Hamdan FF, Lafreniere RG, Yang Y, et al. (2011) Systematic resequencing of X-chromosome synaptic genes in autism spectrum disorder and schizophrenia. Mol Psychiatry 16: 867-880.
29. Ramoz N, Cai G, Reichert JG, Silverman JM, Buxbaum JD, (2008) An analysis of candidate autism loci on chromosome 2q24-q33: evidence for association to the STK39 gene. Am J Med Genet B Neuropsychiatr Genet 147B: 1152-1158.
30. Hu VW, Frank BC, Heine S, Lee NH, Quackenbush J, (2006) Gene expression profiling of lymphoblastoid cell lines from monozygotic twins discordant in severity of autism reveals differential regulation of neurologically relevant genes. BMC Genomics 7: 118.
31. Stettner GM, Shoukier M, Hoger C, Brockmann K, Auber B, (2011) Familial intellectual disability and autistic behavior caused by a small FMR2 gene deletion. Am J Med Genet A 155A: 2003-2007.
32. Mondal K, Ramachandran D, Patel VC, Hagen KR, Bose P, et al. (2012) Excess variants in AFF2 detected by massively parallel sequencing of males with autism spectrum disorder. Hum Mol Genet.
33. Griggs BL, Ladd S, Saul RA, DuPont BR, Srivastava AK, (2008) Dedicator of cytokinesis 8 is disrupted in two patients with mental retardation and developmental disabilities. Genomics 91: 195-202.
34. Rohatgi S, Clark D, Kline AD, Jackson LG, Pie J, et al. (2010) Facial diagnosis of mild and variant CdLS: Insights from a dysmorphologist survey. Am J Med Genet A 152A: 1641-1653.
35. Badens C, Lacoste C, Philip N, Martini N, Courrier S, et al. (2006) Mutations in PHD-like domain of the ATRX gene correlate with severe psychomotor impairment and severe urogenital abnormalities in patients with ATRX syndrome. Clin Genet 70: 57-62.
36. Stenson PD, Ball EV, Mort M, Phillips AD, Shaw K, et al. (2012) The Human Gene Mutation Database (HGMD) and Its Exploitation in the Fields of Personalized Genomics and Molecular Evolution. Curr Protoc Bioinformatics Chapter 1: Unit1 13.
37. Hosack DA, Dennis G, Sherman BT, Lane HC, Lempicki RA, (2003) Identifying biological themes within lists of genes with EASE. Genome Biol 4: R70.
38. Huang da W, Sherman BT, Tan Q, Collins JR, Alvord WG, et al. (2007) The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol 8: R183.
39. Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M, (2010) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 38: D355-360.
40. Levitt P, Campbell DB, (2009) The genetic and neurobiologic compass points toward common signaling dysfunctions in autism spectrum disorders. J Clin Invest 119: 747-754.
41. Chao MV, (2003) Neurotrophins and their receptors: a convergence point for many signalling pathways. Nat Rev Neurosci 4: 299-309.
42. Dai JJ, Lieu L, Rocke D, (2006) Dimension reduction for classification with gene expression microarray data. Stat Appl Genet Mol Biol 5: Article6.
43. Nguyen DV, Rocke DM, (2002) Tumor classification by partial least squares using microarray gene expression data. Bioinformatics 18: 39-50.
44. Brodersen KH, Ong CS, Stephan KE, Buhmann JM (2010) The balanced accuracy and its posterior distribution; IStanbul, Turkey. IEEE. pp. 3121-3124.
45. Bienvenu T, Poirier K, Friocourt G, Bahi N, Beaumont D, et al. (2002) ARX, a novel Prd-class-homeobox gene highly expressed in the telencephalon, is mutated in X-linked mental retardation. Hum Mol Genet 11: 981-991.
46. Ruggieri M, Pavone P, Scapagnini G, Romeo L, Lombardo I, et al. (2010) The aristaless (Arx) gene: one gene for many "interneuronopathies". Front Biosci (Elite Ed) 2: 701-710.
47. Castensson A, Emilsson L, Sundberg R, Jazin E, (2003) Decrease of serotonin receptor 2C in schizophrenia brains identified by high-resolution mRNA expression analysis. Biol Psychiatry 54: 1212-1221.
48. Chow ML, Pramparo T, Winn ME, Barnes CC, Li HR, et al. (2012) Age-dependent brain gene expression and copy number anomalies in autism suggest distinct pathological processes at young versus mature ages. PLoS Genet 8: e1002592.
49. Voineagu I, Wang X, Johnston P, Lowe JK, Tian Y, et al. (2011) Transcriptomic analysis of autistic brain reveals convergent molecular pathology. Nature 474: 380-384.
50. Abu-Elneel K, Liu T, Gazzaniga FS, Nishimura Y, Wall DP, et al. (2008) Heterogeneous dysregulation of microRNAs across the autism spectrum. Neurogenetics 9: 153-161.
51. Garbett K, Ebert PJ, Mitchell A, Lintas C, Manzi B, et al. (2008) Immune transcriptome alterations in the temporal cortex of subjects with autism. Neurobiol Dis 30: 303-311.
52. Purcell AE, Jeon OH, Zimmerman AW, Blue ME, Pevsner J, (2001) Postmortem brain abnormalities of the glutamate neurotransmitter system in autism. Neurology 57: 1618-1628.
53. Washizuka S, Iwamoto K, Kakiuchi C, Bundo M, Kato T, (2009) Expression of mitochondrial complex I subunit gene NDUFV2 in the lymphoblastoid cells derived from patients with bipolar disorder and schizophrenia. Neurosci Res 63: 199-204.
54. Coppola G, Karydas A, Rademakers R, Wang Q, Baker M, et al. (2008) Gene expression study on peripheral blood identifies progranulin mutations. Ann Neurol 64: 92-96.
55. Padmos RC, Hillegers MH, Knijff EM, Vonk R, Bouvy A, et al. (2008) A discriminating messenger RNA signature for bipolar disorder formed by an aberrant expression of inflammatory genes in monocytes. Arch Gen Psychiatry 65: 395-407.
56. Scherzer CR, Eklund AC, Morse LJ, Liao Z, Locascio JJ, et al. (2007) Molecular markers of early Parkinson's disease based on gene expression in blood. Proc Natl Acad Sci U S A 104: 955-960.
57. Sullivan PF, Fan C, Perou CM, (2006) Evaluating the comparability of gene expression in blood and brain. Am J Med Genet B Neuropsychiatr Genet 141B: 261-268.
58. Jasinska AJ, Service S, Choi OW, DeYoung J, Grujic O, et al. (2009) Identification of brain transcriptional variation reproduced in peripheral blood: an approach for mapping brain expression traits. Hum Mol Genet 18: 4415-4427.
59. Corbett BA, Kantor AB, Schulman H, Walker WL, Lit L, et al. (2007) A proteomic study of serum from children with autism showing differential expression of apolipoproteins and complement proteins. Mol Psychiatry 12: 292-306.
60. Glatt SJ, Tsuang MT, Winn M, Chandler SD, Collins M, et al. (2012) Blood-based gene expression signatures of infants and toddlers with autism. J Am Acad Child Adolesc Psychiatry 51: 934-944 e932.
61. Vargas DL, Nascimbene C, Krishnan C, Zimmerman AW, Pardo CA, (2005) Neuroglial activation and neuroinflammation in the brain of patients with autism. Ann Neurol 57: 67-81.
62. McKusick VA (1998) Mendelian inheritance in man: a catalog of human genes and genetic disorders. Baltimore: Johns Hopkins University Press. 3 v. (various pagings) p.
63. Hennekam RC, (2006) Rubinstein-Taybi syndrome. Eur J Hum Genet 14: 981-985.
64. Kesler SR, Simensen RJ, Voeller K, Abidi F, Stevenson RE, et al. (2007) Altered neurodevelopment associated with mutations of RSK2: a morphometric MRI study of Coffin-Lowry syndrome. Neurogenetics 8: 143-147.
65. Anney R, Klei L, Pinto D, Regan R, Conroy J, et al. (2010) A genome-wide scan for common alleles affecting risk for autism. Hum Mol Genet 19: 4072-4082.
66. Affymetrix (2005) Guide to Probe Logarithmic Intensity Error (PLIER) Estimation. Available: http://media.affymetrix.com/support/technical/technotes/plier_technote.pdf. Accessed 2009 March 1.
67. Affymetrix (2005) Affymetrix User's Guide to Product Comparison Spreadsheets. Available: http://media.affymetrix.com/support/technical/manual/comparison_spreadsheets_manual.pdf. Accessed 2009 March 1.
68. Leek JT, Storey JD, (2007) Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet 3: 1724-1735.
69. Johnson WE, Li C, Rabinovic A, (2007) Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8: 118-127.
70. Storey JD, Tibshirani R, (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 100: 9440-9445.
71. Dennis G Jr, Sherman BT, Hosack DA, Yang J, Gao W, et al. (2003) DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 4: P3.
72. Varmuza K, Filzmoser P (2009) Introduction to Multivariate Statistical Analysis in Chemometrics. Boca Raton: CRC Press.
73. Ihaka R, Gentleman R, (1996) R: A language for data analysis and graphics. Journal of Computational and Graphical Statistics 5: 299-314.
74. Kuhn M, (2008) Building Predictive Models in R Using the caret Package. Journal of Statistical Software 28.
75. Witten I, Frank E (2005) Data mining: practical machine learning tools and techniques. Boston, MA: Morgan Kaufman.