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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

From: Transcriptomopathies of pre- and post-symptomatic frontotemporal dementia-like mice with TDP-43 depletion in forebrain neurons

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         
  1. 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