G2C::Proteomics

The synapse is the connection between nerve cells (neurons). The function of the synapse is to transmit the electrical activity from one neuron to the next thus passing information through the nervous system. Inside synapses there are over a thousand proteins and they are the components from which the neurotransmission machinery is built. The organisation of these hundreds of proteins is an important issue since proteins bind and interact to form multiprotein complexes, which are molecular machines. Understanding the composition of these multiprotein complexes may shed light on diseases as well as fundamental biology of learning and other forms of behaviour.

Isolating protein complexes from cells and tissues is technically demanding and particularly from the brain, which is a very complex organ. New methods are required for complex tissues, and in this study we have further developed a system employed in yeast. Our objective was to isolate the core components of the synapse, particularly those involving proteins bound to PSD-95, which is a key molecule required for learning and memory.

We combined proteomic and mouse genetic engineering methods to isolate multiprotein complexes from the mouse brain. A Tandem Affinity Purification tag was integrated into the genomic locus of PSD-95 so that PSD-95 could be readily isolated with other proteins attached to it. This method combined with mass spectrometry analysis describes a core complex of 118 proteins that comprise containing key proteins involved in the neurotransmission.

Protein interaction network of PSD-95 interacting proteins.

PSD-95/Dlg4 is shown in red, it's primary interactors are shown in blue and secondary interactors are shown in yellow. Click on circles to view genetic and genomic information in G2Cdb.

The medical importance of this complex is revealed since 49 proteins are involved with a range of important common brain diseases including epilepsy, depression, schizophrenia, bipolar disease, mental retardation and neurodegenerative diseases including Alzheimer's and Huntington's diseases.

Details of the mice generation and protein purification conditions are described in Fernandez et. al. The principal datasets for the synapses complex(es) are found in Table 1 and Table 2. These datasets are also integrated in Supplementary Table 1 with links to G2Cdb resources as well as the comparison with other proteomic datasets. G2Cdb access enables one to identify the functional roles for individual proteins/genes in knockout mice and human genetics.

UnMASCing diseases of the brain provides discussion of the papers principal findings and their relevance to brain disease.

Data resources

• Table 1. Functional classification of PSD-95-associated proteins in at least three out of four tandem purifications.
• Table 2. Functional classification of PSD-95-associated proteins in one or two tandem purifications.
• Table 3. Genes associated with neurological and psychiatric diseases.

• Supplementary Table 1. Proteins identified in the single step and tandem purifications by LC-MS/MS.
• Supplementary Table 2. Proteins identified by LC-MS/MS in three tandem purifications from wild type mice.
• Supplementary Table 3. Known PSD-95 primary interactors extracted from UniHI database and manually curated.
• Supplementary Table 4. EmPAI values from single step and tandem purifications.
• Supplementary Table 5. Comparison to proteins found in receptor complexes and synaptic lists.
• Supplementary Table 6. Protein nodes of the interaction network's MCC.
• Supplementary Table 7. Gene targeting and genotyping primers.

FAQs

1. What is the Tandem Affinity Purification (TAP) method?

The Tandem Affinity Purification method consists of a genetic modification of the protein of interest by fusion with a TAP (two different tags separated by a protease site) tag into the C- or N- terminal end of the protein (10504710). The tagged protein is isolated (with its associated proteins) in a tandem procedure: a first purification is followed by a protease cleavage and the complex is recovered in a second purification that ends with the elution in native conditions.

2. What advantages does the TAP method offer?

The TAP method allows a more stringent purification removing weak interactors and potential contaminants. The TAP method also has technical advantages over immunoprecipitation that is limited by i) the availability of suitable antibodies and their cross reaction with other proteins, ii) the possibility that the antibody-protein interaction is affected by either posttranslational modifications or by the binding with other proteins, iii) the antibody may disrupt interacting partners, and iv) the harsh conditions for the complex elution may result in protein degradation.

3. Which proteins belong to the core set of postsynaptic proteins?

Table 1 lists the proteins identified in at least three of four Tandem Affinity Purifications that are considered as the core of the postsynaptic terminal of excitatory synapses. Table 2 shows the synaptic proteins that have been purified once or twice and could be weak or non-abundant PSD-95 interactors. These proteins should not be considered as part of the PSD-95 core complex.

4. Has this protein been identified in any PSD purification and/or in the MASC complex, PSD or other neuronal complex before?

Go to Supplementary Table 1 and identify the gene name or the protein ID. Follow the G2Cdb link and the G2Cdb gene report is shown. Other gene lists containing this gene are reported.

5. Does this protein directly bind PSD-95?

PSD-95 binary interactors that belong to the PSD-95 complex are listed in Supplementary Table 3. Literature reference are provided directly to PubMed for inspection.

6. What is the G2C database?

G2Cdb is an integrated database for neurobiologists that contains data linking gene function to cognition. The datasets include gene and protein expression, synaptic physiology, mouse and human behaviour data with synapse proteomics. The datasets includes that generated by members of the Genes to Cognition program and literature mined data.

7. Is this gene related to any disorder?

PSD-95 interactors involved in mental disease are shown in the Table 3. Following the G2Cdb ID in the Supplementary Table 1 you have access to the G2Cdb gene report that links to behavioural and physiological data in knockout mice.

References

Table 1. Functional classification of PSD-95-associated proteins in at least three out of four tandem purifications.

Approved gene symbols and protein names, and UniProt accession numbers are shown. Number of approved peptides for each protein identified by LC-MS/MS in the four tandem purifications are indicated as T1, T2, T3 and T4. More information of these proteins is listed in Supplementary Table 1.

Adaptor / Regulatory Proteins

			Number of peptides
MGI Symbol	Approved Name	UniProt Acc	T1	T2	T3	T4	Cluster
Anks1	ankyrin repeat and SAM domain containing 1	P59672		4	3	3
Anks1b	ankyrin repeat and sterile alpha motif domain containing 1B	Q8BZM2	17	5	10	10
Baiap2	brain-specific angiogenesis inhibitor 1-associated protein 2	Q8BKX1	20	12	13	13	d
Begain	brain-enriched guanylate kinase-associated	Q68EF6	4	8	12	16	a
Dlg1	Synapse-associated protein 97	Q3UP61	24	42	34	42	a
Dlg2	Postsynaptic density protein 93	Q91XM9	49	67	69	80	a
Dlg3	Synapse-associated protein 102	Q52KF7	27	17	14	22	a
Dlg4	Postsynaptic density protein 95	Q62108	42	57	64	64	a
Dlgap1	SAP90/PSD-95-associated protein 1	Q9D415	11	9	14	24	a
Dlgap2	SAP90/PSD-95-associated protein 2	Q8BJ42	18	12	19	24	a
Dlgap3	SAP90/PSD-95-associated protein 3	A2A7T7	16	8	7	15	a
Dlgap4	SAP90/PSD-95-associated protein 4	A2BDU3	14	9	7	14	a

Receptors / Channels / Transporters Proteins

			Number of peptides
MGI Symbol	Approved Name	UniProt Acc	T1	T2	T3	T4	Cluster
Gria1	glutamate receptor, ionotropic, AMPA 1	Q5NBY1	2	3	5	13	b
Gria2	glutamate receptor, ionotropic, AMPA 2	P23819	4	8	10	20	b
Gria3	glutamate receptor, ionotrophic, AMPA 3	Q9Z2W9		2	9	18	b
Gria4	glutamate receptor, ionotrophic, AMPA 4	Q9Z2W8	2	2	5	9	b
Grik2	glutamate receptor, ionotropic, kainate 2 (beta 2)	P39087		2	4	6	b
Grik5	glutamate receptor, ionotropic, kainate 5 (gamma 2)	Q61626		2	3	7	b
Grin1	glutamate receptor, ionotropic, NMDA1 (zeta 1)	A2AI21	29	40	50	55	a
Grin2a	glutamate receptor, ionotropic, NMDA2A (epsilon 1)	P35436	24	31	36	46	a
Grin2b	glutamate receptor, ionotropic, NMDA2B (epsilon 2)	Q01097	44	54	67	78	a
Grin2d	glutamate receptor, ionotropic, NMDA2D (epsilon 4)	Q03391	3	6	9	10	a
Gpr123	G protein-coupled receptor 123	Q52KJ6	2	3	3	3
Cacng2	calcium channel, voltage-dependent, gamma subunit 2	O88602	2	2	2	3	b
Kcna1	K+ voltage-gated channel, shaker-related subfamily, member 1	P16388	6	5	5	6	c
Kcna2	K+ voltage-gated channel, shaker-related subfamily, member 2	P63141	4	5	7	6	c
Kcna3	K+ voltage-gated channel, shaker-related subfamily, member 3	P16390	3	4	6	5	c
Kcna4	K+ voltage-gated channel, shaker-related subfamily, member 4	Q8CBF8	2	3	5	5	c
Kcnab1	K+ voltage-gated channel, shaker-related subfamily, beta member 1	P63143	3	3	4	6	c
Kcnab2	K+ voltage-gated channel, shaker-related subfamily, beta member 2	P62482	5	6	10	11	c
Kcnj10	K+ inwardly-rectifying channel, subfamily J, member 10	Q9JM63	3	3	4	6	a
Kcnj4	K+ inwardly-rectifying channel, subfamily J, member 4	P52189	4	6	6	8	a
Vdac1	voltage-dependent anion channel 1	Q60932	4	4	5	5	f
Vdac2	voltage-dependent anion channel 2	Q60930	4	2	3	4
Atp1b1	ATPase, Na+/K+ transporting, beta 1 polypeptide1	P14094	3	3	6	3
Atp6v0d1	ATPase, H+ transporting, V0 subunit d isoform 1	P51863	3	3	4	2
Sfxn3	sideroflexin 3	Q91V61	3	3	4	3
Slc1a2	solute carrier family, member 2	P43006	3	2	4	4
Slc25a4	ADP/ATP translocase 1	P48962	2		3	6	g
Slc25a5	ADP/ATP translocase 2	P51881	2	2	3	6	g
Slc4a4	solute carrier family 4 (anion exchanger), member 4	O88343		3	6	4

Cytoskeletal / Structural / Cell adhesion Proteins

			Number of peptides
MGI Symbol	Approved Name	UniProt Acc	T1	T2	T3	T4	Cluster
Ablim1	actin binding LIM protein 1	Q8K4G5	20	10	18	22
Adam22	a disintegrin and metallopeptidase domain 22	Q9R1V6	12	16	24	31	e
Arc	activity regulated cytoskeletal-associated protein	Q9WV31	8	13	20	19
Arpc4	actin related protein 2/3 complex, subunit 4	P59999		2	2	4
Capza2	capping protein (actin filament) muscle Z-line, alpha 2	P47754		2	2	2
Cfl1	cofilin 1, non-muscle	P18760	2	2	3	4
Dstn	destrin	Q9R0P5	2	5	6	6
Fscn1	fascin homolog 1, actin bundling protein (Strongylocentrotus purpuratus)	Q61553	2	2		3	f
Lgi1	leucine-rich repeat LGI family, member 1	Q9JIA1	6	12	19	15	e
Nefl	neurofilament, light polypeptide 68kDa	P08551	3		3	6	a
Nrxn1	neurexin 1	Q9CS84	8	17	12	23
Plp1	proteolipid protein (myelin) 1	P60202	2	3	4	5
Sept11	septin 11	Q8C1B7	2	2	2	2
Sept5	septin 5	Q9Z2Q6	2		2	4
Spnb2	spectrin beta 2	Q62261	2		2	5	a
Tuba1a*	tubulin, beta polypeptide	P05213,	11	14	20	20
Tubb2b*	tubulin, beta 2b	Q7TMM9	19	21	24	27
Tubb6	tubulin, beta 6	Q922F4	8	8	13	13

Vesicular / Trafficking / Transport Proteins

			Number of peptides
MGI Symbol	Approved Name	UniProt Acc	T1	T2	T3	T4	Cluster
Arf3	ADP-ribosylation factor 3	P61205	2	2	3	4
Cltc	clathrin, heavy chain (Hc)	Q5SXR6	10		4	12	a
Cpne4*	copine IV	Q8BLR2	4	2		3
Cpne7	copine VII7	Q0VE82	4	3	2	3
Iqsec1	IQ motif and Sec7 domain 1	Q8R0S2	11	7	6	15
Iqsec2	IQ motif and Sec7 domain 2	Q5DU25	34	25	24	36
Nsf	N-ethylmaleimide sensitive fusion protein	P46460	4	4	7	9
Stx1b2	syntaxin 1B2	P61264	3	4	3	2
Stxbp1	syntaxin binding protein 1	O08599	5	3	4	4
Syt1	synaptotagmin I	P46096	5	2	2	2
Vamp2*	Synaptobrevin 2	P63024	2		4	2

Enzyme Proteins

			Number of peptides
MGI Symbol	Approved Name	UniProt Acc	T1	T2	T3	T4	Cluster
Acat1	acetyl-Coenzyme A acetyltransferase 1	Q8QZT1	2		3	3
Aco2	aconitase 2, mitochondrial	Q99KI0	3		3	2
Acot7	acyl-CoA thioesterase 7	Q91V12	3	3	3	4
Aldoc	aldolase C, fructose-bisphosphate	P05063	4	2		4
Atp5c1	ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1	Q91VR2	3	3		4	g
Atp5b	ATP synthase, H+ transporting mitochondrial F1 complex, beta subunit	P56480	2		6	5	g
Atp5o	ATP synthase, H+ transporting, mitochondrial F1 complex, O subunit	Q9DB20	2	2	4	4	g
Atp5a1	ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 1	Q03265	5	10	14	11	g
Cnp	2',3'-cyclic nucleotide 3' phosphodiesterase	P16330	10	3	11	10
Gapdh	glyceraldehyde-3-phosphate dehydrogenase	P16858	9	8	9	10	f
Gda	guanine deaminase	Q9R111	29	26	29	31	a
Glul	glutamate-ammonia ligase (glutamine synthetase)	P15105	5	17	21	19
Gpx4	glutathione peroxidase 4	O70325		2	2	2
Msrb2	methionine sulfoxide reductase B2	Q78J03		2	7	4
Pdha1	pyruvate dehydrogenase E1 alpha 1	P35486	4	3	8	5
Pdhb	pyruvate dehydrogenase (lipoamide) beta	Q9D051	4	4	4	6
Pgk1	phosphoglycerate kinase 1	P09411	2	3	13	8	f
Pkm2	pyruvate kinase, muscle	P52480	7	6	11	12
Ppap2b	phosphatidic acid phosphatase type 2B	Q99JY8		2	2	5
Prdx1	peroxiredoxin 1	P35700	4	7	10	14
Prdx2	peroxiredoxin 2	Q61171		2	2	3
Sdha	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	Q8K2B3	7	6	8	6
Sucla2	succinate-CoA ligase, ADP-forming, beta subunit	Q9Z2I9	4	2	5	6

Kinase Proteins

			Number of peptides
MGI Symbol	Approved Name	UniProt Acc	T1	T2	T3	T4	Cluster
Camk2a	calcium/calmodulin-dependent protein kinase II alpha	P11798	11	3	4	11	a
Camk2b	calcium/calmodulin-dependent protein kinase II beta	Q5SVI3	10	5	5	7	a
Mapk1	mitogen activated protein kinase 1	P63085	3	3	4	9
Phosphatases
Ppap2b	phosphatidic acid phosphatase type 2B	Q99JY8		2	2	5
Ppp3ca	protein phosphatase 3, catalytic subunit, alpha isoform	P63328	12	6	7	11	a
Ppp3cb	protein phosphatase 3, catalytic subunit, beta isoform	P48453	7	3	2	4

G-protein signaling Proteins

			Number of peptides
MGI Symbol	Approved Name	UniProt Acc	T1	T2	T3	T4	Cluster
Abr	active BCR-related gene	Q6PCY1	2		2	6
Gnao1	guanine nucleotide binding protein, alpha o	P18872	8	7	15	16
Kalrn	kalirin, RhoGEF kinase	A2CG52	2	3	2	8
Rac1	RAS-related C3 botulinum substrate 1	Q3TLP8	2	2	3	3	d
Syngap1	synaptic Ras GTPase activating protein 1 homolog (rat)	Q9QUH6	21	15	17	38	a

Transcription / Translation Proteins

			Number of peptides
MGI Symbol	Approved Name	UniProt Acc	T1	T2	T3	T4	Cluster
Park7	Parkinson disease (autosomal recessive, early onset) 7	A2A817		3	3	3
Rps14	ribosomal protein S14	P62264		2	3	2
Rps3	ribosomal protein S3	P62908	2		3	4
Uba52*	ubiquitin A-52 residue ribosomal protein fusion product 1	Q66JP1	3	3	5	6

Signal transduction Proteins

			Number of peptides
MGI Symbol	Approved Name	UniProt Acc	T1	T2	T3	T4	Cluster
Btbd11	BTB (POZ) domain containing 11	Q6GQW0	5	3	2	3
Phb2	prohibitin 2	O35129	2		5	4
Ywhae	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide	P62259	3		2	2
Pcbp1	poly(rC) binding protein 1	P60335		3	3	5

Unclassified Proteins

			Number of peptides
MGI Symbol	Approved Name	UniProt Acc	T1	T2	T3	T4	Cluster
Fam81a	family with sequence similarity 81, member A	Q3UXZ6	7	6	21	18
AI662250	expressed sequence AI662250	Q3UKV2	2	2	2
B630019K06Rik	RIKEN cDNA B630019K06 gene	Q7TNS5	6	7	8	9
Frmpd3	FERM and PDZ domain containing 3	Q8BXG0		2	5	5
Pgam5	phosphoglycerate mutase family member 5	Q3UK19	7	7	8	10
Prrt1	proline-rich transmembrane protein 1	O35449	2	2	2	3
Slc9a3r1	solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 1	P70441	4	3	7	2

Genes marked with an asterisk represent genes whose peptides are common to other genes:

Cpne5*

Cpne4, Cpne8.

Tuba1a*

Tuba1b, Tuba4c, Tuba1b.

Tubb2b*

Tubb5, Tubb2a, Tubb2c, Tubb4.

Uba52*

Ubc, Ubb.

Vamp2*

Vamp3.

Table 2. Functional classification of PSD-95-associated proteins in one or two tandem purifications.

Adaptor / Regulatory Proteins

			Number of peptides
MGI Symbol	Approved Name	UniProt Acc	T1	T2	T3	T4
Ap2a1	adaptor protein complex AP-2, alpha 1 subunit	P17426				3
Grb2	growth factor receptor bound protein 2	Q60631	2	4

Receptors / Channels / Transporters Proteins

			Number of peptides
MGI Symbol	Approved Name	UniProt Acc	T1	T2	T3	T4
Atp2b1	ATPase, Ca++ transporting, plasma membrane 1	Q05CJ5		2		4
Grin2c	glutamate receptor, ionotropic, NMDA2C (epsilon 3)	Q01098				5
Grm3	glutamate receptor, metabotropic 3	Q9QYS2				2
Kcnj16	potassium inwardly-rectifying channel, subfamily J, member 16	Q9Z307				7
Lrp1	low density lipoprotein receptor-related protein 1	Q91ZX7		2		3
Lrrtm1	leucine rich repeat transmembrane neuronal 1	Q8K377				2
Slc1a3	Sodium-dependent glutamate/aspartate transporter 1	P56564			3	3
Slc2a1	solute carrier family 2 (facilitated glucose transporter), member 1	P17809			2	2
Vdac3	voltage-dependent anion channel 3	Q60931	2			5

Cytoskeletal / Structural / Cell adhesion Proteins

			Number of peptides
MGI Symbol	Approved Name	UniProt Acc	T1	T2	T3	T4
Mtap1a	microtubule-associated protein 1 A	Q9QYR6	3			2
Nlgn2	neuroligin 2	Q69ZK9				2
Nlgn3	neuroligin 3	A2AGI2				2
Syn2	synapsin II	Q64332			3	4
Shank1	SH3/ankyrin domain gene 1	XP_001474960	4

Enzyme Proteins

			Number of peptides
MGI Symbol	Approved Name	UniProt Acc	T1	T2	T3	T4
Cit	citron	P49025				11
Crym	crystallin, mu	O54983			3	3
Csmd2	CUB and Sushi multiple domains 2	A2A8D7				5
Dusp10	dual specificity phosphatase 10	Q8R3L3			3	2
Jak3	Janus kinase 3	Q62137				2
Mapk3	mitogen activated protein kinase 3	Q63844				4
Ube2v1	ubiquitin-conjugating enzyme E2 variant 1	Q9CZY3		2	5
Ube2v2	ubiquitin-conjugating enzyme E2 variant 2	Q9D2M8		2	4

G-protein signaling Proteins

			Number of peptides
MGI Symbol	Approved Name	UniProt Acc	T1	T2	T3	T4
Gna13	guanine nucleotide binding protein, alpha 13	Q8C5L2			2	2
Gnb1	guanine nucleotide binding protein (G protein), beta 1	P62874	3			3
Rab6	RAB6, member RAS oncogene family	P35279				4

Signalling Proteins

			Number of peptides
MGI Symbol	Approved Name	UniProt Acc	T1	T2	T3	T4
Fbxo2	F-box protein 2	Q80UW2				4
Fbxo6	F-box protein 6	Q9QZN4			3	4
Nxph3	neurexophilin 3	Q91VX5				2
Pcbp2	poly(rC) binding protein 2	Q61990			3	3
Traf3	Tnf receptor-associated factor 3	Q3UHJ1			3	3

Chaperone / Protein folding / Signalling Proteins

			Number of peptides
MGI Symbol	Approved Name	UniProt Acc	T1	T2	T3	T4
Hspa12a	heat shock protein 12A	Q8K0U4				2
DNA binding
Hist1h2bj*	histone 1, H2bb	Q8CGP2			3	3

Transcription / Translation Proteins

			Number of peptides
MGI Symbol	Approved Name	UniProt Acc	T1	T2	T3	T4
Eef1a1*	eukaryotic translation elongation factor 1 alpha 1	P10126	2	2
Lsm11	U7 snRNP-specific Sm-like protein LSM11	Q8BUV6			2	3

Unclassified Proteins

			Number of peptides
MGI Symbol	Approved Name	UniProt Acc	T1	T2	T3	T4
Clu	clusterin	Q06890			2	3
Lancl1	LanC (bacterial lantibiotic synthetase component C)-like 1	O89112				4
Mog	myelin oligodendrocyte glycoprotein	Q61885	2			2
Neto1	neuropilin (NRP) and tolloid (TLL)-like 1	Q8R4I7	2			2

⁺ indicates NCBI accession number.

Genes marked with an asterisk represent genes whose peptides are common to other genes:

Hist1h2bj*

Hist1h2bm Hist1h2be Hist1h2bn Hist1h2bg Hist1h2bp Hist1h2bh Hist1h2bf Hist1h2bb Hist3h2bb Hist1h2bc Hist1h2bl Hist2h2bb.

Table 3. Genes associated with neurological and psychiatric diseases.

Disease association data for proteins in the tandem purification was mined from the Genetic Association Database, CiteXplore and manually curated. References are provided below.

Adam22

Epilepsy¹

Acot7

Schizophrenia³

Atp1b1

Rett syndrome⁵

Neurodegeneration⁷

Atp5a1

Alzheimer's⁹

Atp5c1

Bipolar afective disorder^{11, 12}

Cacng2

Bipolar disorder¹³

CamKIIa

Bipolar disorder¹⁴

CamKIIb

Schizophrenia¹⁷

Depression¹⁷

Capza2

Mental retardation¹⁹

Cltc

Mental retardation²¹

Cnp1

Schizophrenia^{3, 22}

Dlg1

Schizophrenia²⁴

Dlg2

Schizophrenia²²

Dlg3

Schizophrenia^{23, 24}

Bipolar disorder²³

Depression²³

X-Mental retardation³¹

Dlg4

Schizophrenia³³

Bipolar disorder²³

Dlgap1

Schizophrenia³⁵

Gapdh

Alzheimer's³⁹

Gda

Schizophrenia³⁷

Gnao1

Schizophrenia⁴¹

Gria1

Schizophrenia^46-50

Alzheimer's^55-59

Epilepsy^{61, 62}

Gria2

Schizophrenia^{4, 64}

Epilepsy^66-71

Gria3

Schizophrenia⁴⁷

X-Mental retardation⁷³

Gria4

Schizophrenia²²

Grik2

Mental retardation⁷⁵

Schizophrenia²²

Grin1

Attention disorder⁷⁸

Bipolar afective disorder⁸⁰

Schizophrenia⁸¹

Seizure⁸²

Grin2a

Alzheimer's⁸³

Huntington disease⁸⁴

Schizophrenia³³

Grin2b

Schizophrenia^{22, 23}

Bipolar afective disorder^86-88

Epilepsy^{11, 89}

Huntington disease^{84, 90}

Grin2d

Schizophrenia²

Kcnj4

Schizophrenia⁴

Kcna1

Episodic ataxia, type 1⁶

Kcnj10

Epilepsy⁸

Seizure¹⁰

Lgi1

Epilepsy¹

Mapk1

Schizophrenia^{15, 16}

Depression¹⁸

Msrb2

Bipolar afective disorder¹¹

Nefl

CMT1²⁰

Schizophrenia³

Bipolar²³

CMT^{225, 26}

ALS^{27, 28}

Nrxn1

Autism²⁹

Schizophrenia²²

Nsf

Schizophrenia³⁰

Pdha1

Depression³²

Pgk1

Parkinson's⁵

Mental retardation³⁴

Bipolar disorder³⁶

Plp1

Pelizaeus-Merzbacher disease³⁸

Depression⁴⁰

Multiple sclerosis^42-45

Demyelinating disease^51-54

Spastic paraplegia⁶⁰

Pppp3ca

Schizophrenia⁶³

Prdx1

Alzheimer's⁶⁵

Prdx2

Parkinson's⁷²

Sl1a2

Schizophrenia²²

ALS⁷⁴

Slc25a4

Bipolar afective disorder¹²

Ophtalmoplegia⁷⁶

Stxbp1

Schizophrenia⁷⁷

Vdac1

Alzheimer's⁹

Schizophrenia³

Bipolar afective disorder¹²

Vdac2

Bipolar afective disorder¹²

Ywhae

Miller-Dieker lissencephaly⁸⁵

References

1. Fukata, Y. et al. Epilepsy-related ligand/receptor complex LGI1 and ADAM22 regulate synaptic transmission. Science 313, 1792-5 (2006).
2. Makino, C., Shibata, H., Ninomiya, H., Tashiro, N. & Fukumaki, Y. Identification of single-nucleotide polymorphisms in the human N-methyl-D-aspartate receptor subunit NR2D gene, GRIN2D, and association study with schizophrenia. Psychiatr Genet 15, 215-21 (2005).
3. Hakak, Y. et al. Genome-wide expression analysis reveals dysregulation of myelination-related genes in chronic schizophrenia. Proc Natl Acad Sci U S A 98, 4746-51 (2001).
4. Le-Niculescu, H. et al. Towards understanding the schizophrenia code: an expanded convergent functional genomics approach. Am J Med Genet B Neuropsychiatr Genet 144B, 129-58 (2007).
5. Delgado, I. J., Kim, D. S., Thatcher, K. N., LaSalle, J. M. & Van den Veyver, I. B. Expression profiling of clonal lymphocyte cell cultures from Rett syndrome patients. BMC Med Genet 7, 61 (2006).
6. Browne, D. L. et al. Identification of two new KCNA1 mutations in episodic ataxia/myokymia families. Hum Mol Genet 4, 1671-2 (1995).
7. Weber, P., Bartsch, U., Schachner, M. & Montag, D. Na,K-ATPase subunit beta1 knock-in prevents lethality of beta2 deficiency in mice. J Neurosci 18, 9192-203 (1998).
8. Lenzen, K. P. et al. Supportive evidence for an allelic association of the human KCNJ10 potassium channel gene with idiopathic generalized epilepsy. Epilepsy Res 63, 113-8 (2005).
9. Zhang, J. et al. Inhibition of the dopamine D1 receptor signaling by PSD-95. J Biol Chem 282, 15778-89 (2007).
10. Buono, R. J. et al. Association between variation in the human KCNJ10 potassium ion channel gene and seizure susceptibility. Epilepsy Res 58, 175-83 (2004).
11. Conti, L. et al. Niche-independent symmetrical self-renewal of a mammalian tissue stem cell. PLoS Biol 3, e283 (2005).
12. Konradi, C. et al. Molecular evidence for mitochondrial dysfunction in bipolar disorder. Arch Gen Psychiatry 61, 300-8 (2004).
13. Silberberg, G. et al. Stargazin involvement with bipolar disorder and response to lithium treatment. Pharmacogenet Genomics 18, 403-12 (2008).
14. Xing, G. et al. Decreased prefrontal CaMKII alpha mRNA in bipolar illness. Neuroreport 13, 501-5 (2002).
15. Kyosseva, S. V. Differential expression of mitogen-activated protein kinases and immediate early genes fos and jun in thalamus in schizophrenia. Prog Neuropsychopharmacol Biol Psychiatry 28, 997-1006 (2004).
16. Kyosseva, S. V. et al. Mitogen-activated protein kinases in schizophrenia. Biol Psychiatry 46, 689-96 (1999).
17. Novak, G., Seeman, P. & Tallerico, T. Increased expression of calcium/calmodulindependent protein kinase IIbeta in frontal cortex in schizophrenia and depression. Synapse 59, 61-8 (2006).
18. Dwivedi, Y. et al. Reduced activation and expression of ERK1/2 MAP kinase in the post-mortem brain of depressed suicide subjects. J Neurochem 77, 916-28 (2001).
19. Gulesserian, T., Kim, S. H., Fountoulakis, M. & Lubec, G. Aberrant expression of centractin and capping proteins, integral constituents of the dynactin complex, in fetal down syndrome brain. Biochem Biophys Res Commun 291, 62-7 (2002).
20. Jordanova, A. et al. Mutations in the neurofilament light chain gene (NEFL) cause early onset severe Charcot-Marie-Tooth disease. Brain 126, 590-7 (2003).
21. Holmes, S. E. et al. Disruption of the clathrin heavy chain-like gene (CLTCL) associated with features of DGS/VCFS: a balanced (21;22)(p12;q11) translocation. Hum Mol Genet 6, 357-67 (1997).
22. Carter, C. J. eIF2B and oligodendrocyte survival: where nature and nurture meet in bipolar disorder and schizophrenia? Schizophr Bull 33, 1343-53 (2007).
23. Clinton, S. M. & Meador-Woodruff, J. H. Abnormalities of the NMDA Receptor and Associated Intracellular Molecules in the Thalamus in Schizophrenia and Bipolar Disorder. Neuropsychopharmacology 29, 1353-62 (2004).
24. Toyooka, K. et al. Selective reduction of a PDZ protein, SAP-97, in the prefrontal cortex of patients with chronic schizophrenia. J Neurochem 83, 797-806 (2002).
25. Georgiou, D. M. et al. A novel NF-L mutation Pro22Ser is associated with CMT2 in a large Slovenian family. Neurogenetics 4, 93-6 (2002).
26. Miltenberger-Miltenyi, G. et al. Clinical and electrophysiological features in Charcot- Marie-Tooth disease with mutations in the NEFL gene. Arch Neurol 64, 966-70 (2007).
27. Cluskey, S. & Ramsden, D. B. Mechanisms of neurodegeneration in amyotrophic lateral sclerosis. Mol Pathol 54, 386-92 (2001).
28. Lee, I. et al. A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans. Nat Genet 40, 181-8 (2008).
29. Szatmari, P. et al. Mapping autism risk loci using genetic linkage and chromosomal rearrangements. Nat Genet 39, 319-28 (2007).
30. Mirnics, K., Middleton, F. A., Marquez, A., Lewis, D. A. & Levitt, P. Molecular characterization of schizophrenia viewed by microarray analysis of gene expression in prefrontal cortex. Neuron 28, 53-67 (2000).
31. Tarpey, P. et al. Mutations in the DLG3 gene cause nonsyndromic X-linked mental retardation. Am J Hum Genet 75, 318-24 (2004).
32. Koene, S. et al. Major depression in adolescent children consecutively diagnosed with mitochondrial disorder. J Affect Disord (2008).
33. Dracheva, S. et al. N-methyl-D-aspartic acid receptor expression in the dorsolateral prefrontal cortex of elderly patients with schizophrenia. Am J Psychiatry 158, 1400-10 (2001).
34. Svaasand, E. K., Aasly, J., Landsem, V. M. & Klungland, H. Altered expression of PGK1 in a family with phosphoglycerate kinase deficiency. Muscle Nerve 36, 679-84 (2007).
35. Pickard, B. S. et al. Candidate psychiatric illness genes identified in patients with pericentric inversions of chromosome 18. Psychiatr Genet 15, 37-44 (2005).
36. Matigian, N. et al. Expression profiling in monozygotic twins discordant for bipolar disorder reveals dysregulation of the WNT signalling pathway. Mol Psychiatry 12, 815-25 (2007).
37. Pennington, K. et al. Prominent synaptic and metabolic abnormalities revealed by proteomic analysis of the dorsolateral prefrontal cortex in schizophrenia and bipolar disorder. Mol Psychiatry 13, 1102-17 (2008).
38. Kutsuwada, T. et al. Impairment of suckling response, trigeminal neuronal pattern formation, and hippocampal LTD in NMDA receptor epsilon 2 subunit mutant mice. Neuron 16, 333-44 (1996).
39. Yao, W. D. et al. Identification of PSD-95 as a regulator of dopamine-mediated synaptic and behavioral plasticity. Neuron 41, 625-38 (2004).
40. Sokolov, B. P. Oligodendroglial abnormalities in schizophrenia, mood disorders and substance abuse. Comorbidity, shared traits, or molecular phenocopies? Int J Neuropsychopharmacol 10, 547-55 (2007).
41. Vawter, M. P. et al. Microarray screening of lymphocyte gene expression differences in a multiplex schizophrenia pedigree. Schizophr Res 67, 41-52 (2004).
42. Jamain, S. et al. Mutations of the X-linked genes encoding neuroligins NLGN3 and NLGN4 are associated with autism. Nat Genet 34, 27-9 (2003).
43. Trotter, J. L., Hickey, W. F., van der Veen, R. C. & Sulze, L. Peripheral blood mononuclear cells from multiple sclerosis patients recognize myelin proteolipid protein and selected peptides. J Neuroimmunol 33, 55-62 (1991).
44. Klein, L., Klugmann, M., Nave, K. A., Tuohy, V. K. & Kyewski, B. Shaping of the autoreactive T-cell repertoire by a splice variant of self protein expressed in thymic epithelial cells. Nat Med 6, 56-61 (2000).
45. Chou, Y. K. et al. Frequency of T cells specific for myelin basic protein and myelin proteolipid protein in blood and cerebrospinal fluid in multiple sclerosis. J Neuroimmunol 38, 105-13 (1992).
46. O'Connor, J. A. & Hemby, S. E. Elevated GRIA1 mRNA expression in Layer II/III and V pyramidal cells of the DLPFC in schizophrenia. Schizophr Res 97, 277-88 (2007).
47. Magri, C. et al. Study on GRIA2, GRIA3 and GRIA4 genes highlights a positive association between schizophrenia and GRIA3 in female patients. Am J Med Genet B Neuropsychiatr Genet 147B, 745-53 (2008).
48. Eastwood, S. L. et al. Decreased expression of mRNAs encoding non-NMDA glutamate receptors GluR1 and GluR2 in medial temporal lobe neurons in schizophrenia. Brain Res Mol Brain Res 29, 211-23 (1995).
49. Komiyama, N. H. et al. SynGAP regulates ERK/MAPK signaling, synaptic plasticity, and learning in the complex with postsynaptic density 95 and NMDA receptor. J Neurosci 22, 9721-32 (2002).
50. Ibrahim, H. M. et al. Ionotropic glutamate receptor binding and subunit mRNA expression in thalamic nuclei in schizophrenia. Am J Psychiatry 157, 1811-23 (2000).
51. Whitham, R. H. et al. Lymphocytes from SJL/J mice immunized with spinal cord respond selectively to a peptide of proteolipid protein and transfer relapsing demyelinating experimental autoimmune encephalomyelitis. J Immunol 146, 101-7 (1991).
52. Bongarzone, E. R. et al. Identification of a new exon in the myelin proteolipid protein gene encoding novel protein isoforms that are restricted to the somata of oligodendrocytes and neurons. J Neurosci 19, 8349-57 (1999).
53. Bruno, R. et al. Multiple sclerosis candidate autoantigens except myelin oligodendrocyte glycoprotein are transcribed in human thymus. Eur J Immunol 32, 2737-47 (2002).
54. Jewtoukoff, V., Amzazi, S., Lebar, R., Bach, M. A. & Marche, P. N. T-cell receptor identification of an oligodendrocyte-specific autoreactive cytotoxic T-cell clone without self restriction. Scand J Immunol 36, 893-8 (1992).
55. Wakabayashi, K. et al. Phenotypic down-regulation of glutamate receptor subunit GluR1 in Alzheimer's disease. Neurobiol Aging 20, 287-95 (1999).
56. Pellegrini-Giampietro, D. E., Bennett, M. V. & Zukin, R. S. AMPA/kainate receptor gene expression in normal and Alzheimer's disease hippocampus. Neuroscience 61, 41-9 (1994).
57. Yasuda, R. P. et al. Reduction of AMPA-selective glutamate receptor subunits in the entorhinal cortex of patients with Alzheimer's disease pathology: a biochemical study. Brain Res 678, 161-7 (1995).
58. Aronica, E., Dickson, D. W., Kress, Y., Morrison, J. H. & Zukin, R. S. Non-plaque dystrophic dendrites in Alzheimer hippocampus: a new pathological structure revealed by glutamate receptor immunocytochemistry. Neuroscience 82, 979-91 (1998).
59. Eder, P., Reinprecht, I., Schreiner, E., Skofitsch, G. & Windisch, M. Increased density of glutamate receptor subunit 1 due to Cerebrolysin treatment: an immunohistochemical study on aged rats. Histochem J 33, 605-12 (2001).
60. Gorman, M. P. et al. Steroid-responsive neurologic relapses in a child with a proteolipid protein-1 mutation. Neurology 68, 1305-7 (2007).
61. Grigorenko, E. et al. Changes in glutamate receptor subunit composition in hippocampus and cortex in patients with refractory epilepsy. J Neurol Sci 153, 35-45 (1997).
62. Babb, T. L. et al. Glutamate AMPA receptors in the fascia dentata of human and kainate rat hippocampal epilepsy. Epilepsy Res 26, 193-205 (1996).
63. Gerber, D. J. et al. Evidence for association of schizophrenia with genetic variation in the 8p21.3 gene, PPP3CC, encoding the calcineurin gamma subunit. Proc Natl Acad Sci U S A 100, 8993-8 (2003).
64. Beveridge, N. J. et al. Dysregulation of miRNA 181b in the temporal cortex in schizophrenia. Hum Mol Genet 17, 1156-68 (2008).
65. Cumming, R. C., Dargusch, R., Fischer, W. H. & Schubert, D. Increase in expression levels and resistance to sulfhydryl oxidation of peroxiredoxin isoforms in amyloid beta-resistant nerve cells. J Biol Chem 282, 30523-34 (2007).
66. Ganor, Y. et al. Antibodies to glutamate receptor subtype 3 (GluR3) are found in some patients suffering from epilepsy as the main disease, but not in patients whose epilepsy accompanies antiphospholipid syndrome or Sneddon's syndrome. Autoimmunity 38, 417-24 (2005).
67. Watson, R. et al. Absence of antibodies to glutamate receptor type 3 (GluR3) in Rasmussen encephalitis. Neurology 63, 43-50 (2004).
68. Levite, M., Fleidervish, I. A., Schwarz, A., Pelled, D. & Futerman, A. H. Autoantibodies to the glutamate receptor kill neurons via activation of the receptor ion channel. J Autoimmun 13, 61-72 (1999).
69. Levite, M. & Hermelin, A. Autoimmunity to the glutamate receptor in mice--a model for Rasmussen's encephalitis? J Autoimmun 13, 73-82 (1999).
70. Moga, D. E. et al. Glutamate receptor subunit 3 (GluR3) immunoreactivity delineates a subpopulation of parvalbumin-containing interneurons in the rat hippocampus. J Comp Neurol 462, 15-28 (2003).
71. Rembach, A. et al. Antisense peptide nucleic acid targeting GluR3 delays disease onset and progression in the SOD1 G93A mouse model of familial ALS. J Neurosci Res 77, 573-82 (2004).
72. Fang, J., Nakamura, T., Cho, D. H., Gu, Z. & Lipton, S. A. S-nitrosylation of peroxiredoxin 2 promotes oxidative stress-induced neuronal cell death in Parkinson's disease. Proc Natl Acad Sci U S A 104, 18742-7 (2007).
73. Wu, Y. et al. Mutations in ionotropic AMPA receptor 3 alter channel properties and are associated with moderate cognitive impairment in humans. Proc Natl Acad Sci U S A 104, 18163-8 (2007).
74. Julien, J. P. Amyotrophic lateral sclerosis. unfolding the toxicity of the misfolded. Cell 104, 581-91 (2001).
75. Motazacker, M. M. et al. A defect in the ionotropic glutamate receptor 6 gene (GRIK2) is associated with autosomal recessive mental retardation. Am J Hum Genet 81, 7928 (2007).
76. Kaukonen, J. et al. Role of adenine nucleotide translocator 1 in mtDNA maintenance. Science 289, 782-5 (2000).
77. Behan, A., Byrne, C., Dunn, M. J., Cagney, G. & Cotter, D. R. Proteomic analysis of membrane microdomain-associated proteins in the dorsolateral prefrontal cortex in schizophrenia and bipolar disorder reveals alterations in LAMP, STXBP1 and BASP1 protein expression. Mol Psychiatry (2008).
78. Bickel, S., Lipp, H. P. & Umbricht, D. Impaired attentional modulation of auditory evoked potentials in N-methyl-D-aspartate NR1 hypomorphic mice. Genes Brain Behav 6, 558-68 (2007).
79. Potkin, S. G. et al. A genome-wide association study of schizophrenia using brain activation as a quantitative phenotype. Schizophr Bull 35, 96-108 (2009).
80. Mundo, E. et al. Evidence that the N-methyl-D-aspartate subunit 1 receptor gene (GRIN1) confers susceptibility to bipolar disorder. Mol Psychiatry 8, 241-5 (2003).
81. Begni, S. et al. Association between the G1001C polymorphism in the GRIN1 gene promoter region and schizophrenia. Biol Psychiatry 53, 617-9 (2003).
82. Suh, J. G., Ryoo, Z. W., Won, M. H., Oh, Y. S. & Kang, T. C. Differential alteration of NMDA receptor subunits in the gerbil dentate gyrus and subiculum following seizure. Brain Res 904, 104-11 (2001).
83. Smith, R. E., Haroutunian, V., Davis, K. L. & Meador-Woodruff, J. H. Expression of excitatory amino acid transporter transcripts in the thalamus of subjects with schizophrenia. Am J Psychiatry 158, 1393-9 (2001).
84. Arning, L. et al. NR2A and NR2B receptor gene variations modify age at onset in Huntington disease in a sex-specific manner. Hum Genet 122, 175-82 (2007).
85. Cardoso, C. et al. Refinement of a 400-kb critical region allows genotypic differentiation between isolated lissencephaly, Miller-Dieker syndrome, and other phenotypes secondary to deletions of 17p13.3. Am J Hum Genet 72, 918-30 (2003).
86. Martucci, L. et al. N-methyl-D-aspartate receptor NR2B subunit gene GRIN2B in schizophrenia and bipolar disorder: Polymorphisms and mRNA levels. Schizophr Res 84, 214-21 (2006).
87. Abdolmaleky, H. M., Thiagalingam, S. & Wilcox, M. Genetics and epigenetics in major psychiatric disorders: dilemmas, achievements, applications, and future scope. Am J Pharmacogenomics 5, 149-60 (2005).
88. Fallin, M. D. et al. Bipolar I disorder and schizophrenia: a 440-single-nucleotide polymorphism screen of 64 candidate genes among Ashkenazi Jewish case-parent trios. Am J Hum Genet 77, 918-36 (2005).
89. Knuesel, M. et al. Identification of novel protein-protein interactions using a versatile mammalian tandem affinity purification expression system. Mol Cell Proteomics 2, 1225-33 (2003).
90. Arzberger, T., Krampfl, K., Leimgruber, S. & Weindl, A. Changes of NMDA receptor subunit (NR1, NR2B) and glutamate transporter (GLT1) mRNA expression in Huntington's disease--an in situ hybridization study. J Neuropathol Exp Neurol 56, 440-54 (1997).

Supplementary tables.

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