Katheleen Gardiner, PhD
Work in my laboratory focuses on the molecular basis of the cognitive deficits seen in Down syndrome. Down syndrome (Trisomy 21) is the most common cause of intellectual disability, and is due to an extra copy of human chromosome 21 and the increased expression of some number of the ~500 genes encoded by it. We seek to identify the subset of genes whose increased expression perturbs normal cellular pathways relevant to learning and memory and to construct gene-pathway and pathway-phenotype correlations.
The specific goals of our work are to: (i) determine the functions of chromosome 21 proteins and non-coding genes, (ii) identify the pathways in which they function, (iii) describe perturbations in these pathways in trisomy that are relevant to learning and behavior, and (iv) identify methods to eliminate the perturbations and correct the deficits in learning and behavior. We integrate two approaches in pursuing these goals: (1) a molecular approach analyzing perturbations of signaling pathways in brains of mouse models of Down syndrome, and (2) a bioinformatics-based approach using chr21 gene/protein structure, function, expression and evolutionary information.
1. Molecular analysis of mouse models of Down syndrome
Functional data implicate chromosome 21 protein-coding genes as modulators
of many pathways, complexes and cellular processes. Our interests focus
on the inter-related pathways of MAP kinase, calcineurin and NMDA receptor
signaling, adenosine-to-inosine pre-mRNA editing, and adult neurogenesis,
and through these to the regulation of “learning and memory genes” BDNF,
CREB, Elk, and estrogen and glucocorticoid receptors (ER, GR). In general,
chromosome 21 proteins are not central players in these processes, but
impact them peripherally. For example, the chromosome 21 proteins DSCR1
and ITSN1 inhibit calcineurin and activate MAP kinase, respectively; SUMO3
inhibits Elk and GR; NRIP1 inhibits ER and GR; and Synaptojanin, ITSN1,
TIAM1 and DSCR1 (through inhibition of TIAM1, Rac and calcineurin) modulate
NMDA receptor activity. Therefore, increased expression of chromosome
21 proteins is predicted to produce perturbations that may be modest and
subtle, and yet still give rise to specific deficits in learning and memory.
This also makes clear that a pathway, and not a candidate gene, approach
to studying cognition in DS is necessary.
We use mouse models as the system in which to assay the molecular consequences
of increased gene dosage. Available mouse models of Down syndrome include
segmental trisomies of chromosome 16, single gene knockouts, and single
gene overexpressing transgenics. These include mice made by others and
in our lab, and allow for studying mouse models with different complements
of trisomic genes. Because many chromosome 21 proteins mutually interact
and/or impact the same pathways, it is critical to have models that are
trisomic for defined sets of chromosome 21 orthologs. Thus, we plan to
create additional models as BAC transgenics and by breeding of knockouts
to segmental trisomies.
To define the perturbations, we analyze the levels, activities and distributions
of selected chromosome 21 and non-chromosome 21 proteins in brain regions,
typically hippocampus, cortex and cerebellum. Non-chromosome 21 targets
currently of particular interest include phosphorylated forms of Erk1/2,
Elk, CREB, Akt, CAMKII, GSK3B and NMDAR. We perturb the systems further
and assess the molecular phenotypes at timed intervals after mice have
been exposed to tests of learning and behavior (Contextual Fear Conditioning)
and to drugs that modulate behavior (for example, the NMDA receptor antagonists,
MK801 and memantine). By these methods, we have recently demonstrated
that two major mouse models of Down syndrome have abnormal basal levels
of phosphorylated Erk1/2, Elk, GSK3B and Akt, and abnormal dynamic responses
to treatment with MK-801. Because we need to vary the trisomic gene content
and the age of mice, plus use drugs that target different pathways and
behavioral tests that require different pathways and brain regions, we
have recently implemented the new, moderate-scale method of Reverse Phase
Protein Arrays to speed these analyses. As comprehensive data accumulate,
they will be analyzed in collaboration with bioinformaticians using techniques
of Inductive Machine learning, neural networks and Fuzzy Cognitive Maps.
By these methods, we will be able to define key points in pathways that
are perturbed in Down syndrome and where therapeutic interventions may
have maximal effect.
2. Bioinformatics of chr21 genes and pathways
In an ongoing project, we continue to collect, correlate and reanalyze
information on chromosome 21 genes and their orthologs in model organisms.
We integrate data from individual gene-specific literature reports, from
large scale functional genomics and proteomics experiments, and from organism-specific
databases. We provide these data in a publicly available database: “Chromosome
21 Gene Function and Pathway Database” (http://chr21db.cudenver.edu).
Currently, the database contains information on the structures of chromosome
21 genes, their protein domain compositions, conservation in model organisms,
protein interactions and basic expression data. We have also developed
and provide a number of tools that aid in identification and prediction
of protein networks based on human and conserved model organism experimental
data, and in text mining from functional genomics/proteomics reports.
While the database is focused on human chr21, the tools are of general
applicability.
Additional projects include: (1) to determine the role of natural expression
variation in the DS phenotype by mining chr21 mouse ortholog data from
WebQTL (http://www.webqtl.org). This is a database correlating information
on brain region gene expression levels, SNPs, and behavioral phenotypes
from 78 lines of C57BL/6J X DBA Recombinant Inbred mouse strains; (2)
to identify and predict the expression and functional consequences of
polymorphisms in all chr21 genes by mining data from dbSNP and correlating
SNPs with coding and regulatory regions; (3) to extract additional functional
data for chr21 genes by a chr21-relevant reanalysis of the “Connectivity
Map” (Lamb et al Science 2006), a database of results from microarray
analysis of human cell lines treated with more than 100 drugs and small
molecules; data will be used to identify drugs that affect chr21 gene
expression; and (4) to predict drugs and drug targets for potential treatment
of cognitive deficits in DS by integrating datasets from 1-3.
Selected Recent Publications
-Siddiqui A, Lacroix T, Scott-McKean J, Stasko M, Costa AC, Gardiner
K. (2008). Molecular response of the Ts65Dn and Ts1Cje mouse models
of Down syndrome to the NMDA receptor antagonist, MK-801, Genes, Brain
Behav, 7:810-819.
-Voronov SV, Frere SG, Giovedi S, Pollina EA, Borel C, Zhang H, Schmidt
C, Akeson E, Wenk M, Cimasoni L, Antonarakis SE, Arancio O, Davisson MT,
Gardiner K, De Camilli P, Di Paolo G. (2008) SYNJ1-linked phosphoinositide
dyshomeostasis and cognitive deficits in mouse models of Down Syndrome,
Proc Natl Acad Sci, 105:9415-9420
-Kuhn DE, Nuovo GJ, Martin MM, Malana GE, Pleister AP, Gardiner K,
Terry Jr AV, Head E, Lott L, Elton TE, Feldman DS. Chromosome 21-derived
mir-155 provides an etiological basis for aberrant protein expression
in Down syndrome brain, Biochem Biophys Res Commun (2008) 370:473-477.
-Pritchard M, Reeves RH, Dierssen M, Patterson D, Gardiner K. (2008)
Down syndrome and the genes of human chromosome 21: current knowledge
and future potentials. Cyto Genet Genome Res, 121:67-77.
-Nguyen CD, Mannino M, Gardiner K, Cios KJ. (2008) ClusFCM Algorithm for
Prediction of Protein Functions Using Homologies and Protein Interactions,
J Bioinform Comp Biol 6:203-222.
-Nguyen CD, Gardiner K, Cios KJ. A Hidden Markov Model for Prediction of Protein-Protein
Interaction Sites (2007) J Bioinform Comp Biol 5:739-753.
-Du Y, Stasko M, Costa AC, Davisson, MT and Gardiner, KJ. (2007) Editing of
the serotonin 2C receptor pre-mRNA: effects of the Morris Water Maze, GENE, 39:186-197.
Gardiner, K, Du, Y. (2006) A-to-I editing of the 5HT2C receptor and behavior.
Briefings Funct Genom Proteom. 5:37-42.
-Nguyen C, Thaicharoen S, Lacroix T, Gardiner K, Cios K. (2007) A
Comprehensive Chromosome 21 Database. IEEE EMB, 26:86093
-Du Y, Davisson MT, Kafadar K, Gardiner K. (2006) A-to-I pre-mRNA
editing of the serotonin 2C receptor: Comparisons among inbred mouse strains. GENE 382:39-46
-Gardiner,K, Costa, AC. (2006) The genes of human chromosome 21: choosing
candidates for relevance to intellectual disability. Am J Med Genet, 142:196-205.
-Ma'ayan A, Gardiner K, Iyengar R. (2006) The Cognitive Phenotype of Down
syndrome: Insights from Intracellular Network Analysis, NeuroRx 3:396-406.
-Gardiner, K, Du, Y. (2006) A-to-I editing of the 5HT2C receptor and behavior.
Briefings Funct Genom Proteom. 5:37-42.
-Gardiner, K. (2006) Transcriptional deregulation in Down syndrome: predicting
effects on CREB, ELK, GR and ER. Behav Genet. 36:439-453
-Nikolaienko O, Nguyen C, Crnic LS, Cios K, Gardiner K. (2005) A chromosome 21/Down
syndrome database. GENE 364:90-98.
-Gardiner K. (2004) Gene-dosage effects in Down syndrome and trisomic mouse models. Genome Biol. 5:244.
-Gardiner K, Davisson MT and Crnic LS (2004) Building protein interaction maps for
Down syndrome. Briefings Funct Genom Proteom 3:142-156.
-Tsyba L, Skripkina I, Rynditch A, Nikolaenko O, Fortna A, Gardiner K. (2004)
Alternative splicing of mammalian Intersectin 1: domain associations and tissue specificities. Genomics 84:106-13.
-Gardiner K. (2003). Predicting pathway perturbations in Down syndrome. J Neural Transm 67:21-37
-Gardiner K, Fortna A, Bechtel L and Davisson M. (2003). Mouse models of Down
syndrome: how useful can they be? Comparison of the gene content of human chromosome 21
with orthologous mouse genomic regions. GENE 318:137-147.
