Alternative titles; symbols
HGNC Approved Gene Symbol: TBK1
Cytogenetic location: 12q14.2 Genomic coordinates (GRCh38) : 12:64,452,120-64,502,114 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 12q14.2 | {Encephalopathy, acute, infection-induced (herpes-specific), susceptibility to, 8} | 617900 | Autosomal dominant | 3 |
| Autoinflammation with arthritis and vasculitis | 620880 | Autosomal recessive | 3 | |
| Frontotemporal dementia and/or amyotrophic lateral sclerosis 4 | 616439 | Autosomal dominant | 3 |
TBK1 is a ubiquitously expressed serine/threonine kinase signaling molecule that is activated by pattern recognition receptors (PRRs) upon viral infection, resulting in type I interferon production. It also inhibits RIPK1 (603453) and regulates selective autophagy (summary by Gu et al., 2016; Brenner et al., 2024).
NFKB1 (164011) or NFKB2 (164012) is bound to REL (164910), RELA (164014), or RELB (604758) to form the NFKB complex. The NFKB complex is inhibited by I-kappa-B proteins (NFKBIA, 164008, or NFKBIB, 604495), which inactivate NF-kappa-B by trapping it in the cytoplasm. Phosphorylation of serine residues on the I-kappa-B proteins by kinases (IKBKA, 600664, or IKBKB, 603258) marks them for destruction via the ubiquitination pathway, thereby allowing activation of the NFKB complex. Activated NFKB complex translocates into the nucleus and binds DNA at kappa-B-binding motifs, such as 5-prime-GGGRNNYYCC-3-prime or 5-prime-HGGARNYYCC-3-prime (where H is A, C, or T; R is an A or G purine; and Y is a C or T pyrimidine). Using degenerate primers based on sequences common to IKBKA and IKBKB, followed by 5-prime RACE and screening of fetal brain cDNA library, Tojima et al. (2000) obtained a cDNA corresponding to NAK. The cDNA encodes a deduced 730-amino acid protein that contains a leucine zipper and a helix-loop-helix motif within its C-terminal half. Unlike IKBKA and IKBKB, which each contain 2 serines in their respective activation loops, NAK contains a glutamic acid (glu168) and a serine, which must be phosphorylated for activation. Northern blot analysis revealed ubiquitous expression of a 2.2-kb transcript, with highest expression in testis.
Using PCR to screen an arrayed human spleen cDNA library, Pomerantz and Baltimore (1999) isolated a cDNA encoding TBK1, or TANK (603893)-binding kinase. The authors also cloned mouse Tbk1, the amino acid sequence of which is 94% identical to that of human TBK1. Sequence analysis revealed that TBK1 contains a kinase domain in its N terminus and 2 putative coiled-coil regions within its C-terminal region.
Using immunohistochemistry on sagittal sections of human donor eye tissues, Fingert et al. (2011) demonstrated expression of TBK1 in ganglion cells, the retinal nerve fiber layer, and the microvasculature, indicating that TBK1 protein is present in tissues affected by glaucoma (see MOLECULAR GENETICS).
By coimmunoprecipitation analyses, Pomerantz and Baltimore (1999) showed that the C-terminal 42 amino acids of Tbk1 associated with the N-terminal 190-amino acid stimulatory domain of TANK. The same region of Tbk1 also associates with TRAF2 (601895) in a TANK-dependent manner.
By functional and mutational analyses, Tojima et al. (2000) showed that NAK could phosphorylate only 1 of the 2 serines of I-kappa-B, but it could phosphorylate both serines in the activation loop of IKBKB and stimulate its I-kappa-B kinase activity. The results suggested that NAK is a specific upstream regulator of I-kappa-B kinases and particularly of IKBKB rather than IKBKA. In addition, NAK appeared to be more involved in NFKB activation downstream of PKC-epsilon (176975), an antiapoptotic factor, rather than PKC-alpha (176960) or PKC-theta (600448).
Sharma et al. (2003) demonstrated that IKKE (605048) and TANK-binding kinase-1 are components of the virus-activated kinase (VAK) that phosphorylate IRF3 (603734) and IRF7 (605047). Sharma et al. (2003) demonstrated an essential role for an IKK-related kinase pathway in triggering the host antiviral response to viral infection. Sharma et al. (2003) demonstrated that expression of IKKE or TBK1 is sufficient to induce phosphorylation of IRF3 and IRF7. This modification permits IRF3 dimerization and translocation to the nucleus, where it induces transcription of interferon and ISG56 genes.
By yeast 2-hybrid, mutation, binding, and coimmunoprecipitation analyses, Fujita et al. (2003) determined that residues 158 to 270 of NAP1 (AZI2; 609916) interacted with NAK. Binding of NAP1 to NAK increased NAK kinase activity, resulting in phosphorylation of ser536 of RELA, and activated NFKB. RNA interference analysis showed that NAP1 depletion impaired TNF (191160)-induced NFKB activation and promoted TNF-induced apoptosis. Fujita et al. (2003) concluded that the NAK-NAP1 complex may protect cells from TNF-induced apoptosis by promoting NFKB activation.
Using normal and tumorigenic human epithelial cell lines, Chien et al. (2006) found that a RALB (179551)/SEC5 (EXOC2; 615329) effector complex specifically supported tumor cell survival by directly recruiting and activating TBK1. In cancer cell lines, constitutive engagement of this pathway, via chronic RALB activation, restricted initiation of apoptotic programs typically engaged in the context of oncogenic stress. Although dispensable for survival of nontumorigenic human epithelial cells in culture, this pathway helped mount an innate immune response to double-stranded RNA or Sendai virus exposure. Chien et al. (2006) concluded that the RALB/SEC5 effector complex is a component of TBK1-dependent innate immune signaling and that this pathway is required to support pathologic survival in the context of a tumorigenic regulatory environment.
Production of type I interferon is a critical host defense triggered by PRRs of the innate immune system. Kayagaki et al. (2007) demonstrated that reduction of DUBA (300713) augmented the PRR-induced type I interferon response in transfected HEK293 cells, whereas ectopic expression of DUBA had the converse effect. DUBA selectively cleaved the lys63-linked polyubiquitin chains on TRAF3 (601896), an E3 ubiquitin ligase essential for type I interferon response, resulting in its dissociation from the downstream signaling complex containing TBK1. A discrete ubiquitin interaction motif within DUBA was required for efficient deubiquitination of TRAF3 and optimal suppression of type I interferon. Kayagaki et al. (2007) concluded that their data identified DUBA as a negative regulator of innate immune responses.
Ishii et al. (2008) demonstrated in vivo that TBK1, a noncanonical I-kappa-B kinase, mediates the adjuvant effect of DNA vaccines and is essential for its immunogenicity in mice. Plasmid DNA-activated TBK1-dependent signaling and the resultant type I interferon receptor-mediated signaling was required for induction of antigen-specific B and T cells, which occurred even in the absence of innate immune signaling through a well-known CpG DNA sensor, Toll-like receptor-9 (TLR9; 605474), or Z-DNA binding protein-1 (ZBP1; 606750). Moreover, bone marrow transfer experiments revealed that TBK1-mediated signaling in hematopoietic cells was critical for the induction of antigen-specific B and CD4+ T cells, whereas in nonhematopoietic cells TBK1 was required for CD8+ T-cell induction. Ishii et al. (2008) concluded that TBK1 is a key signaling molecule for DNA vaccine-induced immunogenicity, by differentially controlling DNA-activated innate immune signaling through hematopoietic and nonhematopoietic cells.
Using yeast 2-hybrid screens, Morton et al. (2008) identified TBK1 as a binding partner for optineurin (OPTN; 602432); the interaction was confirmed by overexpression/immunoprecipitation experiments in HEK293 cells and by coimmunoprecipitation of endogenous OPTN and TBK1 from cell extracts. A TBK1-binding site was detected between residues 1 and 127 of optineurin; residues 78 through 121 were found to display striking homology to the TBK1-binding domain of TANK. The OPTN-binding domain was localized to residues 601 to 729 of TBK1; residues 1 to 688 of TBK1, which do not bind to TANK, did not interact with OPTN. The OPTN mutant E50K (602432.0001), known to cause open angle glaucoma (GLC1E; 137760), displayed markedly enhanced binding to TBK1, suggesting that this interaction may contribute to familial glaucoma caused by this mutation.
From lysates of transfected HEK293T cells, using tandem affinity purification and polyacrylamide gel electrophoresis, Seo et al. (2013) isolated 4 proteins that associate with TBK1: NAP1, TANK, TBKBP1 (608476), and TBK1 itself.
Barbie et al. (2009) used systematic RNA interference to detect synthetic lethal partners of oncogenic KRAS (190070) and found that the noncanonical I-kappa-B kinase TBK1 was selectively essential in cells that contain mutant KRAS. Suppression of TBK1 induced apoptosis specifically in human cancer cell lines that depend on oncogenic KRAS expression. In these cells, TBK1 activated NF-kappa-B (see 164011) antiapoptotic signals involving c-REL (164910) and BCLXL (BCL2L1; 600039) that were essential for survival, providing mechanistic insights into this synthetic lethal interaction. Barbie et al. (2009) concluded that their observations indicated that TBK1 and NF-kappa-B signaling are essential in KRAS mutant tumors, and established a general approach for the rational identification of codependent pathways in cancer.
By small interfering RNA-mediated knockdown of Rab factors in a murine macrophage line, Pilli et al. (2012) showed that inhibition of Rab8b (613532) caused a decrease in conversion of Mycobacterium bovis BCG phagosomes to degradative compartments after the induction of autophagy and autophagic killing of mycobacteria. Knockdown of Rab8b-interacting partners showed that Tbk1 was critical for autophagic killing of BCG by suppressing the maturation of autophagosomes. Coimmunoprecipitation, proximity ligation in situ analysis, and confocal microscopy revealed that Tbk1 associated with Rab8b on autophagic organelles. High-content imaging analysis showed that Tbk1 was required in bone marrow macrophages for phosphorylation of p62 (SQSTM1; 601530) on ser403, which was in turn required for autophagic function and clearance of p62 and associated cargo. Further analysis revealed that Il1b (147720) was necessary for the induction of autophagy in mycobacteria-infected macrophages and that Tbk1 was required for Il1b-induced autophagic elimination of M. tuberculosis. Pilli et al. (2012) concluded that TBK1 Is important for the conversion of autophagic organelles into mature and bactericidal organelles for both starvation- and IL1B-induced autophagy.
Harman et al. (2015) had previously shown that dendritic cells (DCs) and macrophages failed to produce type I IFN in response to human immunodeficiency virus (HIV)-1 (see 609423), but that the failure was not mediated through HIV-1 targeting IRF3, as occurs in T cells. Harman et al. (2015) found that cells exposed to HIV-1, but not herpes simplex-2 or Sendai virus, failed to induce expression of either type I or type III IFNs, in spite of sensing the virus and inducing PRR signaling. Phosphorylation of TBK1 was completely inhibited through binding of HIV-1 Vpr and Vif proteins to TBK1. HIV-1 lacking either protein induced IFNB (147640) expression. Harman et al. (2015) concluded that inhibition of TBK1 autophosphorylation due to binding of Vpr and Vif proteins is the principal mechanism by which HIV-1 blocks type I and type III IFN induction in myeloid cells.
Using immunoprecipitation and kinase assays, Gu et al. (2016) showed that mouse Rkip (PEBP1; 604591) physically associated with Tbk1 and regulated its activation by promoting Tbk1 autophosphorylation at ser172. In turn, Tbk1 phosphorylated Rkip at ser109, thereby increasing type I interferon production in antiviral innate immune responses. Mutation analyses demonstrated that Rkip and Tbk1 formed a positive-feedback loop, as phosphorylation of Rkip at ser109 by Tbk1 strengthened its interaction with Tbk1 and enhanced Tbk1 activation.
Shao et al. (2022) studied the interplay of the frontotemporal dementia-amyotrophic lateral sclerosis (FTD-ALS; see 616439)-associated genes C9ORF72 (614260), TBK1, and TDP43 (605078). Shao et al. (2022) found that TBK1 is phosphorylated in response to C9ORF72 poly(gly-ala; GA) aggregation and sequestered into inclusions, resulting in decreased TBK1 activity and contributing to neurodegeneration. Reducing Tbk1 activity in mice using a knockin mutation exacerbated poly(GA)-induced phenotypes, including increased Tdp43 pathology and the accumulation of defective endosomes in poly(GA)-positive neurons. The authors postulated a disruption of the endosomal-lysosomal pathway in FTD-ALS, leading to increased susceptibility to protein aggregation, driving TDP43 proteinopathy and neurodegeneration.
Cryoelectron Microscopy
Zhang et al. (2019) presented the cryoelectron microscopy structure of human TBK1 in complex with cGAMP-bound, full-length chicken STING (TMEM173; 612374). The structure revealed that the C-terminal tail of STING adopts a beta-strand-like conformation and inserts into a groove between the kinase domain of one TBK1 subunit and the scaffold and dimerization domain of the second subunit in the TBK1 dimer. In this binding mode, the phosphorylation site ser366 in the STING tail cannot reach the kinase-domain active site of bound TBK1, which suggests that STING phosphorylation by TBK1 requires the oligomerization of both proteins. Mutational analyses validated the interaction mode between TBK1 and STING and supported a model in which high-order oligomerization of STING and TBK1, induced by cGAMP, leads to STING phosphorylation by TBK1.
Crystal Structure
Zhao et al. (2019) showed that a conserved PLPLRT/SD motif within the C-terminal tail of STING mediates the recruitment and activation of TBK1. Crystal structures of TBK1 bound to STING revealed that the PLPLRT/SD motif binds to the dimer interface of TBK1. Cell-based studies confirmed that the direct interaction between TBK1 and STING is essential for induction of IFN-beta after cGAMP stimulation. Zhao et al. (2019) showed that full-length STING oligomerizes after it binds cGAMP, and highlighted this as an essential step in the activation of STING-mediated signaling.
In affected individuals from 2 families and 1 sporadic patient with adult-onset open angle glaucoma (GLC1P; 177700) and normal intraocular pressures, Fingert et al. (2011) identified 3 overlapping duplications on chromosome 12q14, all of which included the TBK1 gene. Microarray studies showed significant differential expression of TBK1 between patients and controls, and Northern blot analysis of RNA from patient fibroblasts showed that expression of TBK1 was 1.48-fold greater than in controls.
Using quantitative PCR, Kawase et al. (2012) identified a 300-kb duplication, chr12:64,803,839-65,098,981 (GRCh37), in 1 (0.40%) of 252 Japanese probands with normal tension glaucoma (NTG). This duplication encompassed TBK1 as well as the XPOT (603180) and RASSF3 (607019) genes, and was similar in extent to the 300-kb duplication previously reported in a sporadic NTG patient by Fingert et al. (2011). No duplications were found in 57 NTG patients from the United States or in 202 Japanese controls.
Using real-time quantitative PCR, Awadalla et al. (2015) investigated CNVs on chromosome 12q14, including the TBK1 gene, in a large, well-characterized Australian cohort of patients with NTG or high tension glaucoma (HTG). Four (1.2%) of 334 NTG cases were found to carry novel CNVs that differed from but overlapped with those previously reported. The CNVs, which were duplications in 3 cases and a triplication in 1, were confirmed by custom comparative genomic hybridization arrays. The CNVs segregated with NTG in all 4 families, showing an autosomal dominant pattern of inheritance. No CNVs were detected in 1,045 Australian patients with HTG or in 254 unaffected controls.
Frontotemporal Dementia and/or Amyotrophic Lateral Sclerosis 4
In a whole-exome sequencing analysis of 2,869 patients with amyotrophic lateral sclerosis (ALS; see 105400) and 6,405 controls, Cirulli et al. (2015) found evidence to implicate TBK1 as an ALS gene (discovery p = 1.12 x 10(-5), replication p = 5.78 x 10(-7), combined p = 3.60 x 10(-11)). Cirulli et al. (2015) concluded that their results revealed a key role of the autophagic pathway in ALS.
In affected members from 13 European Caucasian families with frontotemporal dementia and/or amyotrophic lateral sclerosis-4 (FTDALS4; 616439), Freischmidt et al. (2015) identified 8 different heterozygous loss-of-function mutations in the TBK1 gene (see, e.g., 604834.0001-604834.0005). There was evidence of incomplete penetrance. Mutations in the first 9 families were found by whole-exome sequencing of 252 European probands with familial ALS, and accounted for about 4% of cases overall. In vitro studies performed on most of the mutations indicated that they resulted in haploinsufficiency. Nine missense variants of unknown significance were also identified (see, e.g., E696K, 604834.0006), 4 of which were found to result in impaired TBK1 function. Although the patients were ascertained because of ALS, a high proportion (about 50%) showed cognitive impairment, often progressing to fulminant frontotemporal dementia.
In 3 unrelated patients with FTDALS4, Pottier et al. (2015) identified heterozygous missense mutations in the TBK1 gene (see, e.g., 604834.0006 and 604834.0007). The mutations were was found by whole-genome sequencing of 107 deceased patients with FTD. Western blot analysis of patient cells showed decreased levels of the mutant protein in 2 of the patients.
Acute Infection-Induced (Herpes-Specific) Encephalopathy-8, Susceptibility to
In 2 unrelated patients with herpes simplex encephalitis (HSE) (IIAE8; 617900), Herman et al. (2012) identified heterozygous missense mutations in the TBK1 gene (G159A, 604834.0008 and D50A, 604834.0009). In vitro functional expression assays showed that the G159A mutation had a dominant-negative effect, whereas the D50A mutation resulted in haploinsufficiency. Patient fibroblasts showed enhanced viral replication and cell death caused by TLR3-dependent viruses, HSV-1 and VSV. Interferon production to TLR3-independent agonists and viruses tested were maintained in patient fibroblasts and peripheral blood mononuclear cells, which explained the clinical phenotype in these patients being limited to HSE.
In a Danish woman (P10) with adult-onset herpes simplex encephalitis, Mork et al. (2015) identified a heterozygous missense mutation in the TBK1 gene (I207V; 604834.0010). The mutation was found by whole-exome sequencing of a cohort of 16 patients with adult-onset HSE and confirmed by Sanger sequencing. Peripheral blood mononuclear cells showed impaired induction of CXCL10 (147310) and TNF-alpha (TNFA; 191160) after HSV-1 infection compared to controls. However, interferon-beta (IFNB1; 147640) production was significantly increased in response to poly(I:C). The findings suggested abnormal and impaired responses to viral infection in this patient. The findings also suggested that TBK1 variants may contribute to HSE susceptibility in adults.
Autoinflammation With Arthritis And Vasculitis
In 4 patients from 3 unrelated consanguineous families with autoinflammation with arthritis and vasculitis (AIARV; 620880), Taft et al. (2021) identified homozygous mutations in the TBK1 gene (604834.0011-604834.0013). The mutations, which were found by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the families. There were 2 nonsense and 1 missense mutations. Detailed in vitro studies of fibroblasts derived from some of the patients were consistent with a complete loss of function (in those with nonsense mutations) or a hypomorphic allele (in the patient with a missense variant). TBK1-deficient cells were able to react to cytoplasmic, but not endosomal, poly(I:C) stimulation as measured by induction of IFN-beta and IL6 (147620). These findings were consistent with adequate antiviral immunity mediated through the IFN-I system, as observed in patients, and suggested that the mutations had specific effects on different downstream signaling pathways. TBK1 deficiency caused increased cellular sensitivity to TNF-induced RIPK1 (603453)-dependent cell death (RCD), which may underlie the autoinflammation observed in the patients.
McWhirter et al. (2004) showed that purified recombinant IKKE and TBK1 directly phosphorylate the critical serine residues in IRF3. They also examined the expression of IRF3-dependent genes in mouse embryonic fibroblasts derived from Tbk1-null (-/-) mice, and showed that Tbk1 is required for the activation and nuclear translocation of Irf3 in these cells. Moreover, mouse embryonic fibroblasts with the Tbk1 knockout showed marked defects in expression of IFN-alpha (147660), IFN-beta (147640), IP10 (147310), and RANTES (187011) after infection with either Sendai or Newcastle disease viruses. They concluded that TBK1 is essential for IRF3-dependent antiviral gene expression.
Brenner et al. (2024) found that the E696K mutation (604834.0006) resulted in decreased TBK1 protein expression both in primary cortical neurons from heterozygous E696K mutant mice and in heterozygous human-derived induced motor neurons, suggesting instability of the mutant protein. The E696K mutant TBK1 protein retains kinase activity and the ability to activate interferon transcription, but abolishes binding to the autophagy adaptor protein optineurin (OPTN; 602432), thus conferring a partial and specific loss of function. In contrast to mice with homozygous complete loss-of-function mutations or deletion of the Tbk1 gene, mice homozygous for E696K/E696K did not show shortened lifespan, liver necroptosis, autoimmune disease, glial activation, or neuroinflammation, arguing against a role for neuroinflammation and activation of the RIPK/TNFA pathway in the pathogenesis of FTDALS4. However, heterozygous mutant male mice showed age-dependent progressive motor neuron degeneration and loss of spinal cord motor neurons that was exacerbated in homozygous mice. Homozygous mutant male mice also showed impaired social interactions. In homozygous mutant animals, there was evidence of failure of the autophago/lysosomal system in spinal motor neurons and other cells, which contained p62 (601530) inclusions. Brenner et al. (2024) concluded that disruptions in autophagy or lysophagy, rather than immune-linked functions of TBK1, underlie the cause of FTDALS4. The authors postulated a possible dominant-negative effect of the E696K mutation.
In affected members of 2 families from Denmark and Sweden, respectively, with frontotemporal dementia and/or amyotrophic lateral sclerosis-4 (FTDALS4; 616439), Freischmidt et al. (2015) identified a heterozygous 4-bp deletion (c.1343_1346delAATT, NM_013254.3) in the TBK1 gene, resulting in a frameshift and premature termination (Ile450LysfsTer15). The mutation, which was found by whole-exome sequencing, segregated with the disorder in the families and was not found in 827 German controls or in 3,101 in-house exomes. However, there was evidence of incomplete penetrance in both families. Analysis of patient cells showed about 50% reduction in TBK1 expression, consistent with haploinsufficiency.
In a Swedish proband with frontotemporal dementia and/or amyotrophic lateral sclerosis-4 (FTDALS4; 616439), Freischmidt et al. (2015) identified a heterozygous 2-bp deletion (c.1434_1435delTG, NM_013254.3) in the TBK1 gene, resulting in a frameshift and premature termination (Val479GlufsTer4). The mutation, which was found by whole-exome sequencing, was not detected in 827 German controls or in 3,101 in-house exomes. The patient had a family history of the disorder, but segregation analysis was not possible. Expression of the mutation in HEK293T cells showed that it resulted in virtual absence of protein expression, consistent with a loss of function.
In patients from 2 families with frontotemporal dementia and/or amyotrophic lateral sclerosis-4 (FTDALS4; 616439), Freischmidt et al. (2015) identified a heterozygous c.2138+2T-C transition (c.2138+2T-C, NM_013254.3) in the TBK1 gene, resulting in an in-frame 72-bp deletion in exon 20 (p.690_713del) in the C-terminal CCD2 domain. Expression of the corresponding protein in patient cells was confirmed by Western blot analysis. In vitro functional expression studies showed that the mutation rendered TBK1 unable to bind optineurin (OPTN; 602432); kinase activity of the mutant TBK1 protein was retained. The mutation, which was found by whole-exome sequencing, was not detected in 827 German controls or in 3,101 in-house exomes. The mutation segregated with the phenotype in the families, with evidence of incomplete penetrance. The families, which were from Sweden and Denmark, were found to have a remote common ancestor.
In a Swedish patient with frontotemporal dementia and/or amyotrophic lateral sclerosis-4 (FTDALS4; 616439), Freischmidt et al. (2015) identified a heterozygous 1-bp deletion (c.958delA, NM_013254.3) in the TBK1 gene, resulting in a frameshift and premature termination (Thr320GlnfsTer40). The mutation, which was found by whole-exome sequencing, was not found in 827 German controls or in 3,101 in-house exomes. The patient had a family history of the disorder, but segregation analysis was not possible. Expression of the mutation in HEK293T cells showed that it resulted in virtual absence of protein expression, consistent with a loss of function.
In 4 unrelated Swedish patients with frontotemporal dementia and/or amyotrophic lateral sclerosis-4 (FTDALS4; 616439), Freischmidt et al. (2015) identified a heterozygous c.1340+1G-A transition (c.1340+1G-A, NM_013254.3) in the TBK1 gene, resulting in an ala417-to-ter (A417X) substitution. The mutation in the first patient, which was found by whole-exome sequencing, was not found in 827 German controls or in 3,101 in-house exomes. The mutation in the 3 additional patients was found by targeted sequencing of 500 Swedish and 510 German patients with sporadic ALS. The variant was also found in 1 of 650 Swedish controls, consistent with incomplete penetrance. Analysis of patient cells showed about 50% reduction in TBK1 expression, consistent with haploinsufficiency.
In 2 unrelated Swedish patients with frontotemporal dementia and/or amyotrophic lateral sclerosis-4 (FTDALS4; 616439), Freischmidt et al. (2015) identified a heterozygous c.2086G-A transition (c.2086G-A, NM_013254.3) in the TBK1 gene, resulting in a glu696-to-lys (E696K) substitution at a highly conserved residue in the CCD2 domain. The mutation in the first patient was found by whole-exome sequencing. In vitro functional expression studies showed that the mutation impaired TBK1 binding to OPTN (602432), consistent with a loss of function.
Pottier et al. (2015) identified a heterozygous E696K mutation in a woman (case C) with FTDALS4. The mutation, which was found by whole-genome sequencing of 107 patients with FTD, was present at a low frequency (0.00001654) in the Exome Aggregation Consortium database. Pottier et al. (2015) noted that the mutation occurred in the OPTN-binding domain. Western blot analysis of patient cells showed decreased levels of the mutant protein. The patient had onset of symptoms at age 78 and died at age 84. A pathologic diagnosis was consistent with FTD and ALS with TDP43 (605078) inclusions.
Variant Function
Brenner et al. (2024) found that the E696K mutation resulted in decreased TBK1 protein expression both in primary cortical neurons from heterozygous E696K mutant mice and in heterozygous human-derived induced motor neurons, suggesting instability of the mutant protein. The E696K mutant TBK1 protein retains kinase activity and the ability to activate interferon transcription, but abolishes binding to the autophagy adaptor protein optineurin (OPTN; 602432), thus conferring a partial and specific loss of function. In contrast to mice with homozygous complete loss-of-function mutations or deletion of the Tbk1 gene, mice homozygous for E696K/E696K did not show shortened lifespan, liver necroptosis, autoimmune disease, glial activation, or neuroinflammation, arguing against a role for neuroinflammation and activation of the RIPK/TNFA pathway in the pathogenesis of FTDALS4. However, heterozygous mutant male mice showed age-dependent progressive motor neuron degeneration and loss of spinal cord motor neurons that was exacerbated in homozygous mice. Homozygous mutant male mice also showed impaired social interactions. In homozygous mutant animals, there was evidence of failure of the autophago/lysosomal system in spinal motor neurons and other cells, which contained p62 (601530) inclusions. Brenner et al. (2024) concluded that disruptions in autophagy or lysophagy, rather than immune-linked functions of TBK1, underlie the cause of FTDALS4. The authors postulated a possible dominant-negative effect of the E696K mutation.
In a woman (case E) with frontotemporal dementia and/or amyotrophic lateral sclerosis-4 (FTDALS4; 616439), Pottier et al. (2015) identified a c.1201A-G transition (c.1201A-G, NM_013254.3) in the TBK1 gene, resulting in a lys401-to-glu (K401E) substitution. The mutation, which was found by whole-genome sequencing of 107 patients with FTD, was present at a low frequency (0.00001227) in the Exome Aggregation Consortium database. The patient had a clinical diagnosis of Alzheimer disease with onset at age 80 and died at age 90. Postmortem tissue showed features of FTD with TDP43 (605078) inclusions and greatly reduced TBK1 protein levels.
In a 17-year-old Polish patient (P1) who had onset of herpes simplex encephalitis (IIAE8; 617900) at age 7 years, Herman et al. (2012) identified a heterozygous c.476G-C transversion in exon 5 of the TBK1 gene, resulting in a gly159-to-ala (G159A) substitution at a highly conserved residue. The patient's unaffected mother did not carry the variant; DNA from the unaffected father was not available. The mutation was not found in the dbSNP (build 135) database or in 1,050 control human DNA samples. Patient fibroblasts showed normal levels of TBK1 mRNA and protein. In vitro functional expression assays showed that the G159A mutant had no enzyme activity, and transfection of the mutation into TBK1-null cells failed to restore poly(I:C)-induced interferon production via the TLR3 (603029) pathway. The findings were consistent with a loss of function. Studies of patient fibroblasts, which were heterozygous for the mutation, showed no interferon response upon stimulation with extracellular poly(I:C), and no interferon response after infection with HSV-1. These findings suggested a dominant-negative effect. Patient fibroblasts also showed increased viral replication and cell death compared to controls in response to HSV-1.
In a 26-year-old French patient (P2) with herpes simplex encephalitis (IIAE8; 617900) with onset at age 11 months, Herman et al. (2012) identified a heterozygous c.149A-C transversion in exon 3 of the TBK1 gene, resulting in an asp50-to-ala (D50A) substitution at a highly conserved residue in the kinase domain. The patient's unaffected mother also carried the mutation, indicating incomplete penetrance. The mutation was not found in the dbSNP (build 135) database or in 1,050 control human DNA samples. Patient fibroblasts showed decreased levels of TBK1 mRNA and protein compared to controls. In vitro functional expression assays showed that the D50A mutant had no enzyme activity, and transfection of the mutation into TBK1-null cells failed to restore poly(I:C)-induced interferon production via the TLR3 (603029) pathway. The findings were consistent with a loss of function and haploinsufficiency. However, studies of patient fibroblasts, which were heterozygous for the mutation, showed no detectable impairment of TLR3-dependent extracellular poly(I:C) responses, although there was increased viral replication and cell death for HSV-1.
In a Danish woman (P10) with herpes simplex encephalitis (IIAE8; 617900), Mork et al. (2015) identified a heterozygous c.619A-G transition (c.619A-G, NM_013254.3) in the TBK1 gene, resulting in an ile207-to-val (I207V) substitution. The mutation, which was found by whole-exome sequencing of a cohort of 16 patients with adult-onset HSE and confirmed by Sanger sequencing, was not found in the ExAC database. Peripheral blood mononuclear cells showed impaired induction of CXCL10 (147310) and TNF-alpha (TNFA; 191160) after HSV-1 infection compared to controls. However, interferon-beta (IFNB1; 147640) production was significantly increased in response to poly(I:C). The findings suggested abnormal and impaired responses to viral infection in this patient. The findings also suggested that TBK1 variants may contribute to HSE susceptibility in adults.
Frontotemporal Dementia and/or Amyotrophic Lateral Sclerosis 4
In affected members of a French family (family 13) with with frontotemporal dementia and/or amyotrophic lateral sclerosis-4 (FTDALS4; 616439), Freischmidt et al. (2015) identified a heterozygous c.1318C-T transition (c.1318C-T, NM_013254.3) in the TBK1 gene, resulting in an arg440-to-ter (R440X) substitution that segregated with the disorder in the family. Functional studies were not performed, but the mutation was predicted to result in haploinsufficiency.
Autoinflammation With Arthritis and Vasculitis
In an 8-year-old Turkish girl (P4), born of consanguineous parents (family 3), with autoinflammation with arthritis and vasculitis (AIARV; 620880), Kosukcu et al. (2021) and Taft et al. (2021) identified a homozygous R440X mutation in the TBK1 gene. The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, was heterozygous in the unaffected parents, who were both less than 40 years of age. The heterozygous R440X mutation was also present in the maternal grandmother of the proband, who had early-onset dementia. The mutation was not found in the gnomAD database. Transfection of the mutation into HEK293 cells showed absence of TBK1 mRNA and protein, suggesting that it caused nonsense-mediated mRNA decay and a complete loss of function.
In 2 sibs (P1 and P2), born of consanguineous Moroccan parents (family 1), with autoinflammation with arthritis and vasculitis (AIARV; 620880), Taft et al. (2021) identified a homozygous G-to-A transition in the TBK1 gene (chr12.64890825G-A, GRCh37) that resulted in a trp619-to-ter (W619X) substitution in the helix-loop-helix domain of the protein. The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. It was not present in the gnomAD database. Patient fibroblasts showed decreased TBK1 mRNA and undetectable TBK1 protein levels, consistent with nonsense-mediated mRNA decay and a complete loss of function. Detailed in vitro studies showed that TBK1-null cells were able to react to cytoplasmic, but not endosomal, poly(I:C) stimulation as measured by induction of IFN-beta (147640) and IL6 (147620). These findings were consistent with adequate antiviral immunity mediated through the IFN1 system, as observed in patients. Additional in vitro studies showed that TBK1 deficiency results in increased sensitivity to TNF (191160)-induced RIPK1 (603453)-dependent cell death (RCD), which may underlie the autoinflammation observed in the patients.
In a 7-year-old boy (P3), born of consanguineous Indian parents (family 2), with autoinflammation with arthritis and vasculitis (AIARV; 620880), Taft et al. (2021) identified a homozygous T-to-G transversion (chr12.64868103T-G, GRCh37) in the TBK1 gene, resulting in a tyr212-to-asp (Y212D) substitution at a highly conserved residue in the kinase domain. The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. The mutation was not present in the gnomAD database. Transfection of the mutation into HEK293 cells showed that it was expressed at normal levels, but did not trigger downstream signaling in functional studies, suggesting that it is a severely hypomorphic or loss-of-function variant. TBK1-null cells expressing the Y212D mutation showed muted type I interferon gene stimulation and IL6 (147620) mRNA expression following endosomal p(I:C) stimulation, but behaved similar to wildtype in response to cytoplasmic stimulation, suggesting that the mutation has specific effects on different downstream signaling pathways.
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