Allele | asilomar | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Mutation Type | missense | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Chromosome | 4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Coordinate | 151,014,331 bp (GRCm39) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Base Change | T ⇒ C (forward strand) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Gene | Tnfrsf9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Gene Name | tumor necrosis factor receptor superfamily, member 9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Synonym(s) | Cd137, CDw137, 4-1BB, ILA, Ly63, A930040I11Rik | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Chromosomal Location | 151,004,612-151,030,561 bp (+) (GRCm39) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a member of the TNF-receptor superfamily. This receptor contributes to the clonal expansion, survival, and development of T cells. It can also induce proliferation in peripheral monocytes, enhance T cell apoptosis induced by TCR/CD3 triggered activation, and regulate CD28 co-stimulation to promote Th1 cell responses. The expression of this receptor is induced by lymphocyte activation. TRAF adaptor proteins have been shown to bind to this receptor and transduce the signals leading to activation of NF-kappaB. [provided by RefSeq, Jul 2008] PHENOTYPE: Homozygous mutation of this gene results in enhanced T cell proliferation, decreased B cell IgG production, decreased cytotoxic T cell activity, and increased numbers of erythrocytes, granulocyte macrophages, and multipotential progenitor cells in the bone marrow, blood, and spleen. [provided by MGI curators] |
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Accession Number | NCBI RefSeq: NM_011612, NM_001077508, NM_001077509; MGI:1101059 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Mapped | Yes | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Amino Acid Change | Valine changed to Alanine | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Institutional Source | Beutler Lab | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Gene Model | predicted gene model for protein(s): [ENSMUSP00000030808] [ENSMUSP00000059684] [ENSMUSP00000101296] [ENSMUSP00000101297] [ENSMUSP00000111961] [ENSMUSP00000122917] [ENSMUSP00000120761] [ENSMUSP00000117860] | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AlphaFold | P20334 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Structure | STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A M4-1BB PEPTIDE [X-RAY DIFFRACTION] | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SMART Domains |
Protein: ENSMUSP00000030808 Gene: ENSMUSG00000028965 AA Change: V10A
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Predicted Effect | probably benign
PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79) |
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SMART Domains |
Protein: ENSMUSP00000059684 Gene: ENSMUSG00000028965 AA Change: V10A
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Predicted Effect | probably benign
PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79) |
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SMART Domains |
Protein: ENSMUSP00000101296 Gene: ENSMUSG00000028965 AA Change: V10A
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Predicted Effect | probably benign
PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79) |
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SMART Domains |
Protein: ENSMUSP00000101297 Gene: ENSMUSG00000028965 AA Change: V10A
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Predicted Effect | probably benign
PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79) |
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SMART Domains |
Protein: ENSMUSP00000111961 Gene: ENSMUSG00000028965 AA Change: V10A
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Predicted Effect | probably benign
PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79) |
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SMART Domains |
Protein: ENSMUSP00000122917 Gene: ENSMUSG00000028965 AA Change: V10A
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Predicted Effect | probably benign
PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79) |
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SMART Domains |
Protein: ENSMUSP00000120761 Gene: ENSMUSG00000028965 AA Change: V10A
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Predicted Effect | probably benign
PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79) |
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SMART Domains |
Protein: ENSMUSP00000117860 Gene: ENSMUSG00000028965 AA Change: V10A
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Predicted Effect | probably benign
PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79) |
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Meta Mutation Damage Score | 0.0898 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Is this an essential gene? | Probably nonessential (E-score: 0.095) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Phenotypic Category | Autosomal Recessive | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Candidate Explorer Status | loading ... | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Single pedigree Linkage Analysis Data |
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Penetrance | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Alleles Listed at MGI | All Mutations and Alleles(23) : Endonuclease-mediated(2) Gene trapped(12) Targeted(9) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Lab Alleles |
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Mode of Inheritance | Autosomal Recessive | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Local Stock | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Repository | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Last Updated | 2019-09-04 9:39 PM by Anne Murray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Record Created | 2017-08-29 9:50 AM by Bruce Beutler | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Record Posted | 2018-09-07 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Phenotypic Description |
The asilomar phenotype was identified among N-ethyl-N-nitrosourea (ENU)-mutagenized G3 mice of the pedigree R5596, some of which showed in increase in the B to T cell ratio (Figure 1) due to reduced frequencies of CD8+ T cells (Figure 2), naïve CD4 T cells in CD4 T cells (Figure 3) and naïve CD8 T cells in CD8 T cells (Figure 4) with concomitant increased frequencies of B cells (Figure 5), IgD+ B cells (Figure 6), IgM+ B cells (Figure 7), effector memory CD4 T cells in CD4 T cells (Figure 8), and effector memory CD8 T cells in CD8 T cells (Figure 9). |
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Nature of Mutation |
Whole exome HiSeq sequencing of the G1 grandsire identified 44 mutations. All of the above anomalies were linked by continuous variable mapping to a mutation in Tnfrsf9: a T to C transition at base pair 150,929,874 (v38) on chromosome 4, or base pair 9,720 in the GenBank genomic region NC_000070 encoding Tnfrsf9. The strongest association was found with a recessive model of inheritance to the normalized B:T ratio, wherein two variant homozygotes departed phenotypically from nine homozygous reference mice and 10 heterozygous mice with a P value of 1.53 x 10-7 (Figure 10). The mutation corresponds to residue 160 in the mRNA sequence NM_011612 within exon 1 of 8 total exons.
The mutated nucleotide is indicated in red. The mutation results in a valine to alanine substitution at position 10 (V10A) in the CD137 protein, and is strongly predicted by PolyPhen-2 to be benign (score = 0.015). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Illustration of Mutations in Gene & Protein |
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Protein Prediction |
Tnfrsf9 encodes CD137 (alternatively, 4-1BB, TNFRSF9 [tumor necrosis factor receptor (TNFR) superfamily member 9], or ILA [induced by lymphocyte activation]). CD137 is a member of the TNFR family, which also includes Fas (alternatively, TNFR6; see the record for cherry), CD40 (see the record for bluebonnet), and lymphotoxin β receptor (LTβR; see the record for kama). Similar to other members of the TNFR family, CD137 is a single-pass type-I transmembrane-spanning protein. CD137 has a signal peptide, four cysteine-rich domains (CRDs) in the extracellular domain, and a C-terminal cytoplasmic region [Figure 11 & 12; (1); PDB:5WJF (2); PDB:6BWV (3)]. Mouse CD137 has two TNF receptor-associated factor (TRAF)-binding sites within the cytoplasmic region that can recruit TRAF1 and TRAF2 (4). Human CD137 can also recruit TRAF3 (see the record for hulk) (5). The extracellular region of CD137 has an elongated jellyroll β-sandwich fold consisting of two β-sheets (Figure 12) (3). The CRDs (namely CRD1, CRD2, and CRD3) mediate ligand binding (2;3;6). The cysteine residues within the CRDs participate in intradomain disulfide bridges (CRD1 and CRD4 have two each, CRD2 and CRD3 have 3 each) that promote the stability of the ectodomain (2;7). CD137 is N-linked glycosylated at Asn128 and Asn138 within CRD4 (2). CD137 glycosylation mediates binding to galectin-9, which putatively functions in regulating CD137 signaling (2). Tnfrsf9 produces two isoforms through alternative splicing: the canonical transmembrane-spanning protein (CD137) and a soluble form (sCD137) (8). Human sCD137 is released by activated lymphocytes and putatively negatively regulates immune responses by either competitive binding to the CD137 ligand or by inserting into CD137 trimers/dimers on the cell surface (9;10). Increased levels of sCD137 have been noted in the sera of patients with chronic lymphocytic leukemia (11), rheumatoid arthritis (12), multiple sclerosis (13;14), systemic lupus erythematosus, and Behcet’s disease [reviewed in (15)]. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Expression/Localization | CD137 is expressed by activated T cells (not resting T cells) (16), regulatory T cells (17), activated natural killer T cells (18), B cells (19), dendritic cells (20-22), monocytes (23), eosinophils (24), neutrophils (25;26), activated NK cells (27;28), mast cells (29), vascular endothelial cells (30), and chondrocytes (6) [reviewed in (31)]. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Background | The ligand for CD137, CD137L (alternatively, 4-1BBL or TNFSF9), is a type II transmembrane protein and member of the TNF (see the record for Panr1) superfamily. CD137L is expressed on antigen-presenting cells (APCs; e.g., B cells dendritic cells, and macrophages). CD137/CD137L-associated signaling mediates the activation, proliferation, survival, apoptosis, and differentiation of several immune cell types as well as preventing activation-induced cell death, promoting cell cycle progression, enhancing cytotoxicity and the production of type 1 cytokines (Table 1). More information about CD137-associated signaling is detailed, below. Table 1. CD137/CD137L-associated functions
Binding of CD137L to CD137 activates the non-canonical NF-κB (NF-κB2; see the record for xander) signaling pathway (Figure 13) (4;5). The non-canonical NF-κB pathway drives the post-translational processing of p100 to mature p52 through IKK-1 and NIK, and results in the activation of p52/RelB heterodimers. The receptors involved in non-canonical signaling (e.g., lymphotoxin-β receptor [LTβR; see the record for kama], B cell activating receptor [BAFFR; see the record for tannin], CD40 [see the record for bluebonnet], receptor activator of NF-κB [RANK] and TNF-related weak inducer of apoptosis [TWEAK]) are involved in secondary lymphoid organogenesis (SLO), B cell differentiation, survival and homeostasis, osteoclastogenesis, and angiogenesis (43), and bind to TNF receptor associated factors (TRAFs) to regulate NIK activity. Downstream of the receptors, TRAF2 and TRAF3 form a complex with NIK to mediate NIK degradation (44-47). After receptor stimulation, the complex is destabilized by TRAF2/3 degradation, permitting the release of NIK from the complex (45-47). After NIK is activated, it is able to bind to and phosphorylate several substrates including IKK-1 and p100, and serves as a docking molecule between IKK-1 and p100 (48-50). Phosphorylation of p100 by IKK-1 results in polyubiquitination and processing to p52 (49). NIK also activates mitogen‐associated protein kinases (MAPKs) through MAP/ERK kinase kinases and MAPK kinases. The NF-κB signaling pathway functions in essentially all mammalian cell types and is activated in response to injury, infection, inflammation and other stressful conditions requiring rapid reprogramming of gene expression. Typically, the rapid and transient activation of NF-κB complexes in response to a wide range of stimuli such as proinflammatory cytokines tumor necrosis factor (TNF)-α, interleukin (IL)-1β, IL-6, and CD40L (see the record for walla). CD137-associated NF-κB activation promotes an increase in the expression of anti-apoptotic proteins including Bcl-2 and Bcl-XL. CD137L/CD137 activation also leads to activation of the extracellular signal regulated kinase (ERK), c‐Jun N‐terminal kinase (JNK), and p38 MAPK signaling cascades (4;32;33;51;52). CD137 activation results in recruitment of TRAF1 and TRAF2, which activates the ERK, JNK, and p38 MAPK pathways. TRAF2 promotes ASK1 (Apoptosis Signal-Regulating Kinase-1) recruitment and activation. ASK1 activates the JNK and MAPK pathways. Activation of the ERK, JNK, and p38 MAPK pathways promotes cell cycle progression and cell survival. CD137L/CD137 participate in bidirectional signaling (Figure 13). Several signaling factors involved in CD137L reverse signaling have been identified, including p38, ERK1/2, PI3K, and PKA (53). Reverse signaling results in cytokine production as well as survival, proliferation, migration, and differentiation of APCs. In humans, CD137L-associated signaling activates Src tyrosine kinases, p38 MAPK, MEK1/2, ERK1/2, PI3K, and NF-κB, leading to antigen presenting cell activation and differenation. In the mouse, CD137L-associated signaling induces M-CSF and IL-1β secretion through Src tyrosine kinase/mTOR/p70S6K and Src tyrosine kinase/AKT pathways. CD137 is an inducer of antitumor immune responses (54-56), and CD137 agonists used with cancer vaccines and immune checkpoint inhibitors boost anticancer immune responses (57;58). CD137 antibodies can increase anti-pathogen immune responses and transplant rejections as well as improve several mouse model autoimmune diseases, including systemic lupus erythematosus (59), collagen-induced arthritis (60), uveoretinitis (61), experimental autoimmune encephalomyelitis (62), allergic airway inflammation and asthma (63;64), inflammatory bowel disease (65), and chronic graft vs. host disease (66). Some Tnfrsf9-deficient (Tnfrsf9-/-) mice exhibited preweaning lethality (MGI). Tnfrsf9-/- mice exhibited insulitis in non-diabetic female mice at 30 weeks (67). Tnfrsf9-/- mice showed reduced levels of IgG2a and IgG3 in response to KLH immunization, increased levels of IgA, IgG2a, and IgG2b in naïve mice, and increased absolute numbers of granulocyte-macrophage, erythroid, and multipotential progenitor cells in the bone marrow, blood, and spleen (68;69). The Tnfrsf9-/- mice showed reduced IL-2 and IL-4 secretion from T cells, increased T cell proliferation after stimulation with anti-CD3 and ConA, and reduced cytotoxic T lymphocyte activity to vesicular stomatitis virus (68). Tnfrsf9-/- mice also showed increased dendritic cell frequencies and reduced dendritic cell survival rates as well as reduced NK/NK T cell numbers and functions (18). Tnfrsf9-/- mice showed increased effector CD4 T cell responses to OVA protein in adjuvant (70). Heterozygous mice (Tnfrsf9+/-) mice show increased bone mineral content and bone mineral density (MGI). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Putative Mechanism | The phenotype of the asilomar mice indicates loss of CD137asilomar function mediating T cell survival. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Primers |
PCR Primer asilomar_pcr_F: AGAATGACACTTGTGAGATATCCC asilomar_pcr_R: GGCTGCTTTGTTGGATTCAA Sequencing Primer asilomar_seq_F: TGGGGTTACAGCATCCACTAC asilomar_seq_R: AGTCGGTGCTCTTAACCAAAGTC |
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Genotyping | PCR program 1) 94°C 2:00 The following sequence of 910 nucleotides is amplified (chromosome 4, + strand): 1 agaatgacac ttgtgagata tccccctctt ttagagacag ggtttcatgt agctcaggtt Primer binding sites are underlined and the sequencing primers are highlighted; the mutated nucleotide is shown in red. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
References | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Science Writers | Anne Murray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Illustrators | Diantha La Vine | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Authors | Xue Zhong, Jin Huk Choi, and Bruce Beutler |