. 2016 Mar 22;22(3):384–395. doi: 10.1038/mp.2016.27

Table 2. Significantly changed proteins identified using label-based LC-SRM (targeted proteomics) in the PFC and HPC of the Df(16)A ^+/− mouse compared with wild-type mice (PFC=20 vs 20, HPC=11 vs 10).

							Prefrontal cortex							Hippocampus
							Proteomics							Proteomics
						Discovery (D)			Targeted proteomics (SRM)					D	Targeted proteomics (SRM)
					Transcriptomics	10 vs 10	12 vs 10	20 vs 20	20 vs 21				Transcriptomics	10 vs 10	11 vs 10
Uniprot	Acc. no.	Protein	Gene	Label					Ratio		P	P*			Ratio		P	P*
22q11.2 critical gene products+vector construct
Sep-05	Q9Z2Q6	Septin-5	Sep-05	22q11.2	⇓	▾	▾	▾	▾	0.78	5.2E-11	1.1E-09	⇓	▾	▾	0.85	1.8E-04	4.9E-04
RANG	P34022	Ran-specific GTPase-activating protein	Ranbp1	22q11.2	⇓	—	—	—	▾	0.55	<E-15	<E-15	⇓	—	▾	0.47	<E-15	<E-15
Q8JZU2	Q8JZU2	Protein Slc25a1	Slc25a1	22q11.2	⇓	—	—	—	▾	0.79	4.8E-08	7.5E-07	⇓	—	▾	0.64	6.7E-10	5.9E-09
PROD	Q9WU79	Proline dehydrogenase 1, mitochondrial	Prodh	22q11.2	⇓	—	—	—	▾	0.62	3.5E-07	4.4E-06	⇓	—	▾	0.90	0.26	0.30
COMT	O88587	Catechol O-methyltransferase	Comt	22q11.2	⇓	—	—	—	▾	0.76	1.4E-06	1.4E-05	⇓	—	▾	0.71	1.6E-03	3.6E-03
HPRT	P00493	Hypoxanthine-guanine phosphoribosyltransferase	Hprt1	Vector construct	*	▴	—	—	▴	1.56	<E-15	<E-15	—	—	▾	1.77	<E-15	<E-15

miRNA targets
GSK3B	Q9WV60	Glycogen synthase kinase-3 beta	Gsk3b	miRNA target (2/4)	⇑	NS	—	▾	▴	1.14	4E-06	3.2E-05	NS	—	▴	1.16	6.1E-04	1.5E-03
OGT1	Q8CGY8	O-GlcNAc transferase subunit p110	Ogt	miRNA target (1/4) + Figure 1d	⇑	▴	—	—	▴	1.22	1.3E-02	3.5E-02	NS	—	▴	1.20	8.9E-03	1.6E-02
KIF5A	P33175	Kinesin heavy chain isoform 5A	Kif5a	miRNA target (1/4)	NS	—	—	▴	▴	1.22	3.6E-02	0.09	⇑	—	NS	1.15	0.18	0.22
A4	P12023	Amyloid beta A4 protein	App	miRNA target (1/4)	NS	—	—	—	NS	1.13	6.5E-02	0.13	NS	—	NS	1.11	0.16	0.21
KDM2A	P59997	Lysine-specific demethylase 2A	Kdm2a	miRNA target (2/4)	NS	—	—	—	NS	1.02	0.77	0.86	NS	—	NS	1.06	0.71	0.74
RHOA	Q9QUI0	Transforming protein RhoA	Rhoa	miRNA target, Liu et al.,¹¹⁵	NS	NS	NS	NS	NS	1.05	0.37	0.48	NS	▾	NS	1.08	0.05	0.08
MBOA5	Q91V01	Lysophospholipid acyltransferase 5	Lpcat3	miRNA target (1/4) + Figure 1d	NS	—	—	—	NS	1.09	0.13	0.21	NS	—	NS	—	—	—
ADA10	O35598	Disintegrin metalloproteinase domain-containing protein 10	Adam10	miRNA target (3/4)	NS	(▴)	—	—	NS	1.03	0.59	0.73	NS	NS	NS	1.04	0.696	0.7443
ANFY1	Q810B6	Ankyrin repeat and FYVE domain-containing protein 1	Ankfy1	miRNA target (1/4)	NS	—	—	—	NS	1.02	0.85	0.91	NS	NS	NS	1.22	0.05	0.07

Discovery
PP2BC	P48455	Serine/threonine-protein phosphatase 2B catalytic γ isoform	Ppp3cc	Figure 1d	NS	▴	▴	▴	▴	1.06	1.1E-02	3.1E-02	NS	NS	▴	1.21	4.7E-10	4.8E-09
PP2BB	P48453	Serine/threonine-protein phosphatase 2B catalytic β isoform	Ppp3cb		NS	NS	NS	NS	▴	1.16	5.8E-04	2.4E-03	NS	NS	▴	1.16	8.9E-03	1.6E-02
NFL	P08551	Neurofilament light polypeptide (NF-L)	Nefl	Figure 1d	NS	▴	-	▴	▴	1.09	1.8E-03	6.3E-03	NS	NS	▴	1.15	1.6E-04	4.9E-04
AINX	P46660	Alpha-internexin (Alpha-Inx)	Ina	Figure 1d	NS	▴	—	▴	NS	0.96	0.31	0.42	NS	NS	▴	1.21	3.0E-08	2.3E-07
NRDC	Q8BHG1	Nardilysin (EC 3.4.24.61)	Nrd1	Figure 1d	NS	—	▾	▾	NS	1.02	0.60	0.73	NS	NS	NS	0.99	0.89	0.90
VGLU1	Q3TXX4	Vesicular glutamate transporter 1 (VGluT1)	Slc17a7	Transcriptomics⁵	⇑	NS	—	—	▴	1.16	1.6E-06	1.4E-05	⇑	NS	▴	1.19	1.5E-04	4.8E-04

Implicated pathways
mTOR–autism spectrum disorders and mental retardation
MTOR	Q9JLN9	Serine/threonine-protein kinase mTOR	Mtor		NS	—	—	—	▴	1.28	4.8E-04	2.1E-03	NS	NS	NS	1.10	0.30	0.34
MK03	Q63844	Mitogen-activated protein kinase 3 (ERK-1)	Mapk3		NS	▴	—	—	▴	1.16	2.3E-05	1.5E-04	NS	NS	▴	1.23	3.7E-05	1.3E-04
MK01	P63085	Mitogen-activated protein kinase 1 (ERK-2)	Mapk1		NS	▴	—	—	▴	1.11	5.9E-05	3.0E-04	NS	NS	▴	1.07	6.3E-03	1.2E-02
PEA15	Q62048	Astrocytic phosphoprotein PEA-15	Pea15		NS	▴	—	—	▴	1.15	5.0E-05	2.8E-04	NS	—	▾	0.91	2.8E-02	4.4E-02
KPCG	P63318	Protein kinase C gamma type	Prkcg		⇑	(▴)	NS	NS	▴	1.11	1.2E-03	4.6E-03	NS	NS	▴	1.21	6.2E-07	2.9E-06

Glutamatergic signalling—schizophrenia and affective disorders
NMDZ1	P35438	Glutamate receptor ionotropic, NMDA 1 (NMD-R1)	Grin1	Hippocampus network⁵	NS	—	—	—	▴	1.15	0.015	3.8E-02	⇑	NS	▴	1.86	1.1E-12	2.3E-11
GRIA1	P23818	Glutamate receptor 1 (GluR-1)	Gria1	Hippocampus network⁵	⇑	NS	—	—	NS	1.08	0.18	0.26	⇑	NS	▴	1.43	2.7E-06	1.0E-05
GRIA2	P23819	Glutamate receptor 2 (GluR-2)	Gria2		NS	—	NS	(▴)	▴	1.12	4E-04	2E-03	NS	▾	▴	1.25	1.9E-12	2.9E-11
GRIA3	Q9Z2W9	Glutamate receptor 3 (GluR-3)	Gria3	Hippocampus network⁵	NS	—	NS	—	NS	1.03	0.64	0.76	⇑	—	▴	1.30	1.1E-03	2.6E-03
KCC2A	P11798	Calcium/calmodulin-dependent protein kinase type II α	Camk2a	Hippocampus network⁵	⇑	NS	▴	—	NS	1.05	0.20	0.28	⇑	NS	▴	1.27	1.6E-07	1.1E-06
KCC2G	Q923T9	Calcium/calmodulin-dependent protein kinase type II γ	Camk2g		NS	NS	NS	NS	NS	1.05	0.11	0.20	NS	NS	▴	1.25	1.7E-04	4.9E-04
SYT1	P46096	Synaptotagmin-1	Syt1	Hippocampus network⁵	NS	NS	▾	▴	NS	1.05	0.07	0.13	⇑	NS	NS	1.08	0.05	0.08
DLG4	Q62108	Disks large homolog 4	Dlg4	Hippocampus network⁵	⇑	—	—	NS	NS	1.00	0.81	0.88	⇑	NS	▴	1.17	7.6E-05	2.6E-04
NCDN	Q9Z0E0	Neurochondrin (Norbin)	Ncdn		⇑	NS	NS	▴	(▴)	1.09	0.05	0.10	NS	NS	▴	1.27	3.0E-03	6.2E-03

Housekeeping
RL8	P62918	60S ribosomal protein L8	Rpl8		⇓	—	—	—	NS	1.05	0.35	0.46	NS	NS	—	—	—	—
MAP2	O08663	Methionine aminopeptidase 2	Metap2		NS	NS	NS	NS	NS	1.04	0.21	0.29	NS	NS	NS	1.06	0.04	0.06
RS3A	P97351	40S ribosomal protein S3a	Rps3a		NS	—	—	—	NS	1.04	0.11	0.20	NS	NS	(▴)	1.12	0.04	0.06

Abbreviations: HFC, hippocampus; NS, not significant. Significantly (P*<0.05) downregulated and upregulated in proteomic profiling (▾▴) or transcriptomic profiling^{5, 8} (⇑⇓), in brackets if only P<0.05; PFC, prefrontal cortex; —, not detected.

Findings are compared with label-free LC-MS^E proteomic discovery profiling and transcriptomic profiling results. Italicized cells indicates consistency across the studies. Column ‘Label' indicates implication of protein (for example, predicted miRNA target by Xof4 bioinformatic prediction tools). P-values were determined using SRMstats and corrected for multiple hypothesis testing (P*).¹⁸

Table 2. Significantly changed proteins identified using label-based LC-SRM (targeted proteomics) in the PFC and HPC of the Df(16)A +/− mouse compared with wild-type mice (PFC=20 vs 20, HPC=11 vs 10).

Table 2. Significantly changed proteins identified using label-based LC-SRM (targeted proteomics) in the PFC and HPC of the Df(16)A ^+/− mouse compared with wild-type mice (PFC=20 vs 20, HPC=11 vs 10).