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. 2019 Mar 29;7:50. doi: 10.1186/s40478-019-0674-x

Table 1.

The genes with altered mRNA levels in the neocortex of 3-month and 12-month-old TDP-43 cKO mice in comparison to the Ctrls are listed

Gene symbol Name RefSeq ID Log2(TDP-43 cKO/ Ctrl) Significant (q<0.05) FTLD patient White et al. [86] Other references
3 Months 12 months 3 Months 12 months 5 Months frontal cortex 20 Months frontal cortex
Common MB- Common MB-
Rabggtb Rab geranylgeranyltransferase beta subunit NM_011231 6.21 -0.14 ●
Clec7a C-type lectin domain containing 7A NM_020008 4.06 2.09 ● (Chen-Plotkin et al. [17])
Itgad Integrin alpha-D NM_001029872 2.99 1.45 ●
Brd3 bromodomain containing 3 NM_023336 2.88 0.11 ●
Atf3 activating transcription factor 3 NM_007498 2.47 1.90 ●
Slc6a3 solute carrier family 6 member 3 NM_010020 2.19 0.80 ●
Ccl9 chemokine (C-C motif) ligand 6 NM_011338 2.15 0.15 ●
Ccl6 chemokine (C-C motif) ligand 9 NM_009139 2.09 0.18 ●
Cep112 centrosomal protein 112 NM_029586 1.76 0.04 ●
Pafah2 platelet-activating factor acetylhydrolase 2 NM_001285872 1.69 1.50 ●
Tlr2 toll like receptor 2 NP_036035 1.66 0.88 ●
Oasl2 2'-5' oligoadenylate synthetase-like 2 NM_011854 1.61 0.85 ●
Lag3 lymphocyte-activation gene 3 NM_008479 1.55 0.17 ● ●
C3ar1 complement C3a receptor 1 NP_033909 1.52 0.18 ● (Chen-Plotkin et al. [17])
Lyz1,Lyz2 lysozyme 1 NM_017372 1.48 0.86 ●
Ddhd1 DDHD domain containing 1 NM_176845 1.44 0.13 ●
Myo1f myosin IF NM_053214 1.39 0.60 ● ●
Trem2 triggering receptor expressed on myeloid cells 2 NM_001272078 1.16 0.25 ● (Polymenidou et al. [58])
Ptpn6 protein tyrosine phosphatase, non-receptor type 6 NM_001077705 1.15 0.63 ● ●
Ifit3b interferon-induced protein with tetratricopeptide repeats 3B NM_001005858 1.11 0.31 ● (Polymenidou et al. [58])
C1qa complement component 1, q subcomponent, alpha polypeptide NM_007572 1.02 0.42 ● (Polymenidou et al. [58])
Tyrobp TYRO protein tyrosine kinase binding protein NM_011662 1.01 0.19 ● (Polymenidou et al. [58])
Lgals3bp lectin, galactoside-binding, soluble, 3 binding protein NM_011150 0.99 0.38 ● (Chen-Plotkin et al. [17])
C1qb complement component 1, q subcomponent, beta polypeptide NM_009777 0.96 0.41 ● ● (Polymenidou et al. [58])
C1qc complement component 1, q subcomponent, C chain NM_007574 0.90 0.39 ● ●
Fcrls Fc receptor-like S, scavenger receptor NM_030707 0.91 -0.11 ● ●
Fcgr3 Fc receptor, IgG, low affinity III NM_010188 0.83 0.53 ● ● (Polymenidou et al. [58])
Ctss cathepsin S NM_001267695 0.79 0.28 ● (Polymenidou et al. [58])
Ripor1 Rho family interacting cell polarization regulator 1 NM_001081241 -1.48 -0.28 ●
Plod3 procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3 NM_011962 -1.23 0.14 ● ●
Hist1h4m histone cluster 1, H4m NM_175654 -1.18 -0.30 ●
Zfp101 zinc finger protein 101 NM_009542 -1.02 -0.26 ● ●
Dlg3 discs large MAGUK scaffold protein 3 NM_007863 -0.87 0.00 ● (Chen-Plotkin et al. [17]) (LaClair et al. [43])
Otof otoferlin NM_001100395 -0.86 -0.34 ● ● (up)
Dock4 dedicator of cytokinesis 4 NM_172803 -0.79 -0.52 ● ● (Polymenidou et al. [58])
Abr active BCR-related gene NM_001291186 -0.79 -0.41 ● (LaClair et al. [43])
Syt17 synaptotagmin XVII NM_138649 -0.70 -0.48 ●
Unc13a unc-13 homolog A (C. elegans) NP_001025044 -0.77 -0.48 ● (Polymenidou et al. [58])
Rab11fip5 RAB11 family interacting protein 5 (class I) NM_001003955 -0.69 -0.58 ●
Fgf21 fibroblast growth factor 21 NM_020013 0.00 0.00 ●
Gfap glial fibrillary acidic protein NM_001131020 1.74 1.43 ● ● (Chen-Plotkin et al. [17]) (Polymenidou et al. [58])
Serpina3n serine (or cysteine) peptidase inhibitor, clade A, member 3N NP_035588 1.27 1.34 ● ●
C4a,C4b complement component 4a/b NM_011413 1.64 1.46 ● ● (Chen-Plotkin et al. [17])
A2m alpha-2-macroglobulin NM_175628 1.37 2.09 ● ●
Tecpr1 tectonin beta-propeller repeat containing 1 NP_081686 -1.06 -0.93 ● ● (LaClair et al. [43])
Tarsl2 threonyl-tRNA synthetase-like 2 NM_172310 -1.00 -0.90 ● ●
Pitpnm3 PITPNM family member 3 NM_001024927 -0.97 -0.96 ● ● ● (up) ● (up) (LaClair et al. [43])
Epop elongin BC and polycomb repressive complex 2 associated protein NM_175332 -0.80 -0.90 ● ●
Arc activity regulated cytoskeletal-associated protein NM_001276684 -0.84 -0.80 ● ● (Chen-Plotkin et al. [17]) (Polymenidou et al. [58])
Cry2 cryptochrome 2 (photolyase-like) NM_009963 -0.78 -0.58 ● ●
Lamp5 lysosomal-associated membrane protein family, member 5 NM_029530 -0.71 -0.96 ● ●
Fam171a2 family with sequence similarity 171, member A2 NM_199200 -0.70 -0.65 ● ● ●
Oxt oxytocin/neurophysin I prepropeptide NM_011025 1.11 2.95 ●
Plin4 perilipin 4 NM_020568 0.61 1.85 ● ●
Irs4 insulin receptor substrate 4 NP_034702 0.22 1.79 ●
Itih3 inter-alpha trypsin inhibitor, heavy chain 3 NM_008407 0.69 1.27 ●
Etnppl ethanolamine phosphate phospholyase NM_001163587 0.63 1.07 ●
AW551984 expressed sequence AW551984 NM_001199556 0.08 1.04 ●
Agt angiotensinogen (serpin peptidase inhibitor, clade A, member 8) NM_007428 0.31 0.97 ● ●
Chd1l chromodomain helicase DNA binding protein 1-like NM_026539 -0.16 0.96 ●
Uggt2 UDP-glucose glycoprotein glucosyltransferase 2 NM_001081252 0.26 0.87 ● ●
Vip vasoactive intestinal polypeptide NM_001313969 0.57 0.79 ●
Sparc secreted acidic cysteine rich glycoprotein NM_001290817 0.48 0.77 ● (Chen-Plotkin et al. [17]) ● ● (down)
Baiap3 BAI1-associated protein 3 NM_001163270 0.24 0.72 ●
Nnat neuronatin NM_001291128 0.37 0.70 ●
Fam107a family with sequence similarity 107, member A NM_183187 0.38 0.69 ●
Sdc4 syndecan 4 NM_011521 0.33 0.68 ● ● (Polymenidou et al. [58])
Ptgds prostaglandin D2 synthase (brain) NM_008963 0.27 0.65 ● (Chen-Plotkin et al. [17])
Scg2 secretogranin II NM_001310680 0.21 0.58 ● (Chen-Plotkin et al. [17])
Apod apolipoprotein D NM_001301353 0.38 0.54 ● (Chen-Plotkin et al. [17]) (Polymenidou et al. [58])
Tnnc1 troponin C1, slow skeletal and cardiac type NP_033419 -1.20 -2.38 ●
Gm10635 predicted gene 10635 NR_045336 -1.10 -2.42 ●
Mylk3 myosin light chain kinase 3 NM_175441 -1.04 -2.28 ● ●
Mecom MDS1 and EVI1 complex locus NM_007963 0.05 -1.76 ●
Rspo1 R-spondin 1 NP_619624 -0.80 -1.46 ●
Myl4 myosin, light polypeptide 4 NM_010858 -0.29 -1.36 ● (Polymenidou et al. [58])
Ddit4l DNA-damage-inducible transcript 4-like NM_030143 -0.65 -1.13 ●
Grm2 glutamate receptor, metabotropic 2 NM_001160353 -0.52 -1.12 ●
Cpne9 copine family member IX NM_170673 -0.70 -1.04 ●
Ryr1 ryanodine receptor 1 NP_033135 -0.58 -0.98 ● ● (up)
Rassf3 Ras association domain family member 3 NP_620406 -0.26 -0.91 ●
Egr1 early growth response 1 NM_007913 -0.42 -0.90 ● (Chen-Plotkin et al. [17]) ● (down)
Kcnt2 potassium channel, subfamily T, member 2 NM_001081027 -0.54 -0.89 ● ●
Rims3 regulating synaptic membrane exocytosis 3 NM_182929 -0.38 -0.84 ● ● (Polymenidou et al. [58])
Pisd-ps3 phosphatidylserine decarboxylase, pseudogene 3 NR_003518 0.10 -0.86 ●
Kcnab3 potassium voltage-gated channel, shaker-related subfamily, beta member 3 NM_010599 -0.11 -0.86 ● (Polymenidou et al. [58])
Fos FBJ osteosarcoma oncogene NM_010234 -0.77 -0.84 ●
Scube1 signal peptide, CUB domain, EGF-like 1 NM_001271472 -0.43 -0.83 ● ● (up)
Kcnh5 potassium voltage-gated channel, subfamily H (eag-related), member 5 NM_172805 -0.45 -0.83 ●
Inf2 inverted formin, FH2 and WH2 domain containing NM_198411 -0.35 -0.83 ●
Acvr1c activin A receptor, type IC NM_001111030 -0.13 -0.82 ●
Hipk4 homeodomain interacting protein kinase 4 NP_001028487 -0.51 -0.81 ●
Scrt1 scratch family zinc finger 1 NM_130893 -0.26 -0.77 ●
Hapln4 hyaluronan and proteoglycan link protein 4 NM_177900 -0.47 -0.75 ● (Polymenidou et al. [58])
Kif5a kinesin family member 5A NM_001039000 -0.52 -0.76 ●
Arhgap10 Rho GTPase activating protein 10 NP_001074833 0.00 -0.75 ●
Camk2n1 calcium/calmodulin-dependent protein kinase II inhibitor 1 NM_025451 -0.40 -0.74 ● ● ● (down)
Car10 carbonic anhydrase 10 NP_082572 -0.33 -0.73 ●
Camk4 calcium/calmodulin-dependent protein kinase IV NM_009793 -0.24 -0.73 ● ● (Polymenidou et al. [58])
Rims1 regulating synaptic membrane exocytosis 1 NM_001012623 -0.42 -0.73 ● (Chen-Plotkin et al. [17]) (Polymenidou et al. [58])
Eipr1 EARP complex and GARP complex interacting protein 1 NM_201357 -0.68 -0.73 ● (Polymenidou et al. [58])
Rgs4 regulator of G-protein signaling 4 NM_009062 -0.52 -0.73 ● (Chen-Plotkin et al. [17])
Rapgef4 Rap guanine nucleotide exchange factor (GEF) 4 NM_001204165 -0.23 -0.70 ● ● (down)
Dagla diacylglycerol lipase, alpha NM_198114 -0.43 -0.69 ●
Diras2 DIRAS family, GTP-binding RAS-like 2 NM_001024474 -0.52 -0.69 ● (Chen-Plotkin et al. [17])
Gp1bb glycoprotein Ib, beta polypeptide NM_001001999 -0.65 -0.68 ●
Ano3 anoctamin 3 NM_001128103 -0.33 -0.67 ● ●
Grm3 glutamate receptor, metabotropic 3 NM_181850 -0.26 -0.67 ●
Nefm neurofilament, medium polypeptide NM_008691 -0.53 -0.66 ● (Polymenidou et al. [58])
Gabra3 gamma-aminobutyric acid (GABA) A receptor, subunit alpha 3 NM_008067 -0.57 -0.65 ● (Polymenidou et al. [58])
Rph3a rabphilin 3A NM_001302344 -0.39 -0.65 ● (Chen-Plotkin et al. [17])
Tbr1 T-box brain gene 1 NM_009322 -0.51 -0.63 ● (Polymenidou et al. [58])
Satb1 special AT-rich sequence binding protein 1 NM_001163630 -0.39 -0.64 ●
Sh3gl2 SH3-domain GRB2-like 2 NM_019535 -0.22 -0.63 ● (Chen-Plotkin et al. [17])
Ephb6 Eph receptor B6 NM_001146351 -0.37 -0.63 ● (Chen-Plotkin et al. [17]) (Polymenidou et al. [58])
Kcnh3 potassium voltage-gated channel, subfamily H (eag-related), member 3 NM_010601 -0.43 -0.62 ●
Nrgn neurogranin NM_022029 -0.35 -0.62 ● (Chen-Plotkin et al. [17])
Cadm2 cell adhesion molecule 2 NM_001145977 -0.17 -0.61 ● ●
Camkk2 calcium/calmodulin-dependent protein kinase kinase 2, beta NM_001199676 -0.44 -0.61 ● (Chen-Plotkin et al. [17])
Rorb RAR-related orphan receptor beta NM_001043354 -0.34 -0.60 ●
Scn4b sodium channel, type IV, beta NP_001013408 0.05 -0.60 ● ●
Camk2a calcium/calmodulin-dependent protein kinase II alpha NM_001286809 -0.50 -0.60 ● (Chen-Plotkin et al. [17])
Nrn1 neuritin 1 NM_153529 -0.24 -0.60 ● (Chen-Plotkin et al. [17])
Cdk5r2 cyclin-dependent kinase 5, regulatory subunit 2 (p39) NM_009872 -0.42 -0.60 ●
Rbfox3 RNA binding protein, fox-1 homolog (C. elegans) 3 NM_001024931 -0.34 -0.60 ●
Gca grancalcin NP_663498 0.08 -0.59 ●
Osbpl1a oxysterol binding protein-like 1A NM_001252489 -0.39 -0.59 ● ●
Vsnl1 visinin-like 1 NM_012038 -0.32 -0.59 ● (Chen-Plotkin et al. [17]) ●
Adcy1 adenylate cyclase 1 NM_009622 -0.25 -0.59 ● (Chen-Plotkin et al. [17]) (Polymenidou et al. [58])
Neurod6 neurogenic differentiation 6 NM_009717 -0.41 -0.59 ● (Polymenidou et al. [58])
AI593442 expressed sequence AI593442 NM_001286641 -0.19 -0.58 ●
Stx1a syntaxin 1A (brain) NM_016801 -0.28 -0.57 ● (Chen-Plotkin et al. [17]) (Polymenidou et al. [58])
Nat8l N-acetyltransferase 8-like NP_001001985 -0.34 -0.57 ●
3110035E14Rik RIKEN cDNA 3110035E14 gene NM_178399 -0.28 -0.57 ● (Polymenidou et al. [58])
Zbtb18 zinc finger and BTB domain containing 18 NM_001012330 -0.22 -0.57 ●
Hlf hepatic leukemia factor NM_172563 -0.39 -0.56 ●
Lynx1 Ly6/neurotoxin 1 NM_011838 -0.28 -0.56 ● (Polymenidou et al. [58])
Cadps2 Ca2+-dependent activator protein for secretion 2 NM_001252105 -0.53 -0.56 ●
Psd pleckstrin and Sec7 domain containing NM_133694 -0.47 -0.56 ●
Dhcr24 24-dehydrocholesterol reductase NM_053272 -0.49 -0.54 ● ●
2900011O08Rik RIKEN cDNA 2900011O08 gene NM_144518 -0.53 -0.53 ●
Dlgap3 discs, large (Drosophila) homolog-associated protein 3 NM_001302081 -0.43 -0.52 ● (Polymenidou et al. [58])
Bhlhe40 basic helix-loop-helix family, member e40 NM_011498 -0.35 -0.53 ●
Pcp4 Purkinje cell protein 4 NM_008791 -0.04 -0.52 ● (Chen-Plotkin et al. [17]) ●
Cntnap1 contactin associated protein-like 1 NM_016782 -0.38 -0.52 ● (Chen-Plotkin et al. [17])
Cep170b centrosomal protein 170B NM_001024602 -0.42 -0.51 ●
Plcxd2 phosphatidylinositol-specific phospholipase C, X domain containing 2 NM_001134480 -0.16 -0.50 ●
Cplx2 complexin 2 NM_009946 -0.26 -0.50 ●
Phyhip phytanoyl-CoA hydroxylase interacting protein NM_145981 -0.38 -0.50 ● (Chen-Plotkin et al. [17])
Snap25 synaptosomal-associated protein 25 NM_001291056 -0.43 -0.50 ● (Chen-Plotkin et al. [17])
Slc8a2 solute carrier family 8 (sodium/calcium exchanger), member 2 NM_001347561 -0.42 -0.50 ● (Chen-Plotkin et al. [17])
D430041D05Rik RIKEN cDNA D430041D05 gene NM_001033347 -0.47 -0.49 ●
Tubb4a tubulin, beta 4A class IVA NM_009451 -0.38 -0.49 ●
Ppp3r1 protein phosphatase 3, regulatory subunit B, alpha isoform (calcineurin B, type I) NM_024459 -0.25 -0.48 ● (Chen-Plotkin et al. [17]) ●
Epdr1 ependymin related protein 1 (zebrafish) NM_134065 -0.35 -0.48 ● ● ●
Scn1b sodium channel, voltage-gated, type I, beta NM_011322 -0.20 -0.47 ●
Jph3 junctophilin 3 NM_020605 -0.39 -0.47 ● ●
Syt13 synaptotagmin XIII NM_030725 -0.33 -0.45 ● ● (Polymenidou et al. [58])
Snap91 synaptosomal-associated protein 91 NM_001277982 -0.53 -0.45 ● (Chen-Plotkin et al. [17])
Zfp365 zinc finger protein 365 NM_178679 -0.24 -0.44 ●
Atp1a1 ATPase, Na+/K+ transporting, alpha 1 polypeptide NM_144900 -0.33 -0.44 ●

The down-regulated genes are indicated by the "-" sign in the columns of Log2 (TDP-43 cKO/Ctrl). The genes that have been reported to have altered mRNA levels in the FTLD patients and in the striatum or hippocampus upon TDP-43 depletion are indicated in the far right column