* 606652

HEPATITIS A VIRUS CELLULAR RECEPTOR 2; HAVCR2


Alternative titles; symbols

T-CELL IMMUNOGLOBULIN AND MUCIN DOMAINS-CONTAINING PROTEIN 3; TIM3


HGNC Approved Gene Symbol: HAVCR2

Cytogenetic location: 5q33.3     Genomic coordinates (GRCh38): 5:157,085,832-157,109,044 (from NCBI)


Gene-Phenotype Relationships
Location Phenotype Phenotype
MIM number
Inheritance Phenotype
mapping key
5q33.3 T-cell lymphoma, subcutaneous panniculitis-like 618398 AR 3

TEXT

Description

The HAVCR2 gene encodes a critical negative regulator in the immune system, acting as a negative checkpoint in peripheral tolerance and innate immune and inflammatory responses (summary by Gayden et al., 2018).

CD4 (186940)-positive T helper lymphocytes can be divided into types 1 (Th1) and 2 (Th2) on the basis of their cytokine secretion patterns. Th1 cells and their associated cytokines are involved in cell-mediated immunity to intracellular pathogens and delayed-type hypersensitivity reactions, whereas Th2 cells are involved in the control of extracellular helminthic infections and the promotion of atopic and allergic diseases. The 2 types of cells also cross-regulate the functions of the other. TIM3 is a Th1-specific cell surface protein that regulates macrophage activation and enhances the severity of experimental autoimmune encephalomyelitis in mice (summary by Monney et al., 2002).


Cloning and Expression

By immunoscreening Th1 and Th2 cells with monoclonal antibodies derived from mouse Th1 cell-immunized rats, followed by gene-expression cloning, Monney et al. (2002) obtained a cDNA encoding mouse Tim3. By genomic database searching and RT-PCR, the authors isolated a cDNA encoding human TIM3. The deduced 301-amino acid type I membrane protein, 63% identical overall and 77% identical in the cytoplasmic domain, has an Ig variable-like domain, a mucin-like domain consisting of 31% serine and threonine residues, and a cytoplasmic domain with a tyrosine phosphorylation motif. Monney et al. (2002) noted that TIM3 is related to the hepatitis A virus cellular receptor (HAVCR1; 606518), also known as TIM1 or Kim1.

Sabatos et al. (2003) identified an 800-bp cDNA encoding a soluble isoform of mouse Tim3 lacking the mucin and transmembrane domains. The truncated form contains only exons 1, 2, 6, and 7, while the full-length protein contains all 7 exons.


Gene Function

Using flow cytometric and RT-PCR analysis, Monney et al. (2002) detected Tim3 only on activated Th1 cells and CD11b+ (ITGAM; 120980) macrophages. Cells expressing Tim3 predominate in the central nervous system of mice at the onset of experimental autoimmune encephalomyelitis (EAE), a Th1-mediated autoimmune disease. Anti-Tim3 treatment enhanced the clinical and pathologic severity of EAE and increased the number and activation level of macrophages. Monney et al. (2002) proposed that anti-Tim3 may trigger the production of proinflammatory cytokines in vivo and induce macrophage activation possibly by enhancing the migration of Th1 cells into the brain or by blocking an interaction between Tim3 and an inhibitory ligand.

By flow cytometric analysis using full-length and soluble mouse Tim3 fusion proteins, Sanchez-Fueyo et al. (2003) demonstrated that a putative ligand for Tim3 exists on resting CD4-positive T cells, but not on CD8 (see 186910)-positive T cells, B cells, or CD11b-positive leukocytes. Some expression was detected on splenic CD11c (ITGAX; 151510)-positive dendritic cells. Expression of the ligand was downregulated on activated CD4-positive/CD25 (147730)-negative effector T cells but persisted on CD4-positive/CD25-positive regulatory T cells.

Independently, Sabatos et al. (2003) also demonstrated the lack of expression of a mouse Tim3 ligand on non-CD4-positive T cells and B cells. Limited expression was detected on CD11c-positive dendritic cells and CD11b-positive macrophages. Treatment with a Tim3-Ig fusion protein induced hyperproliferation of CD3 (see 186740)-positive T cells, but not other leukocyte types, and induced expression of Th1-type cytokines.

Using real-time RT-PCR, Khademi et al. (2004) found that human Th1 cell lines expressed higher levels of TIM3, whereas Th2 lines expressed higher levels of TIM1. Mononuclear cells from cerebrospinal fluid (CSF) of patients with multiple sclerosis (MS; 126200) expressed higher TIM1 mRNA levels than controls. Moreover, higher TIM1 expression was associated with low IFNG (147570) expression in CSF mononuclear cells and with clinical remissions. In contrast, TIM3 expression correlated well with high expression of IFNG and TNF (191160). Khademi et al. (2004) concluded that differential expression of TIMs by Th1 and Th2 cells may be implicated in different phases of an autoimmune disease.

Using RT-PCR and ELISA, Koguchi et al. (2006) showed that T-cell clones from CSF of patients with multiple sclerosis (MS; see 126200) secreted more IFNG than did clones from CSF of control subjects, but they expressed less TIM3 and TBET (TBX21; 604895). The reduced levels of TIM3 correlated with resistance to T-cell tolerance induced by costimulatory blockade. Small interfering RNA-mediated reduction of TIM3 expression on ex vivo CD4-positive T cells enhanced proliferation and IFNG secretion. Koguchi et al. (2006) concluded that TIM3 expression is dysregulated in MS CSF clones, and that TIM3 expression on T cells regulates proliferation and IFNG secretion.

Anderson et al. (2007) found that TIM3 is constitutively expressed on cells of the innate immune system in both mice and humans, and that it can synergize with Toll-like receptors. Moreover, an antibody agonist of Tim3 acted as an adjuvant during induced immune responses, and Tim3 ligation induced distinct signaling events in T cells and dendritic cells; the latter finding could explain the apparent divergent functions of Tim3 in these cell types. Thus, Anderson et al. (2007) concluded that by virtue of differential expression on innate versus adaptive immune cells, Tim3 can either promote or terminate TH1 immunity and may be able to influence a range of inflammatory conditions.

Huang et al. (2015) showed that TIM3 was coexpressed and interacted directly with carcinoembryonic antigen cell adhesion molecule-1 (CEACAM1; 109770), another molecule expressed on activated T cells and involved in T-cell inhibition. The interaction involved the membrane-distal immunoglobulin-variable (IgV)-like N-terminal domains of the proteins. The presence of CEACAM1 endowed TIM3 with inhibitory function. In a mouse adoptive transfer colitis model, Ceacam1-deficient T cells were hyperinflammatory with reduced cell surface expression of Tim3 and regulatory cytokines, and this was restored by T-cell-specific Ceacam1 expression. During chronic viral infection and in a tumor environment, Ceacam1 and Tim3 marked exhausted T cells. Co-blockade of Ceacam1 and Tim3 led to enhancement of antitumor immune responses with improved elimination of tumors in mouse colorectal cancer models. Huang et al. (2015) concluded that CEACAM1 serves as a ligand for TIM3 that is required for its ability to mediate T-cell inhibition, and that this interaction has a crucial role in regulating autoimmunity and antitumor immunity. In an erratum, Huang et al. (2015) withdrew the crystallographic model of a heterodimer between the IgV domains of CEACAM1 and TIM3 originally presented in their report and replaced it with a more accurate CEACAM1-CEACAM1 homodimer model. They noted that additional solution-based NMR and surface-based SPR studies independently provided biochemical evidence to support direct interaction between CEACAM1 and TIM3 via their N-terminal IgV domains. However, after withdrawal of their crystallographic model, they could no longer state the stoichiometry, describe the molecular details, or differentiate between cis/trans modes of IgV domain interaction, as claimed in their original report.

Using flow cytometric analysis, Yi et al. (2016) showed that TBET and TIM3 were constitutively expressed in resting CD14 (158120)-positive monocyte/macrophages. TBET and TIM3 expression was significantly upregulated in individuals with chronic hepatitis C virus (HCV; see 609532) infection. Coculture with HCV-infected hepatocytes resulted in upregulation of TBET. The HCV core protein alone could mediate upregulation of TBET and TIM3 by acting through its receptor, GC1QR (C1QBP; 601269), and inducing JNK (MAPK8; 601158) signaling. Knockdown of TBET in THP1 monocytes via small interfering RNA resulted in decreased TIM3 production and increased IL12 (see 161560) production and STAT1 (600555) phosphorylation in response to stimulation with HCV core protein. Yi et al. (2016) proposed that TBET is an upstream regulator of TIM3 that impairs IL12 production during HCV infection.


Biochemical Features

Cao et al. (2007) reported the crystal structure of the murine Tim3 IgV domain to 2-angstrom resolution. The structure revealed that 4 cysteines form 3 noncanonical disulfide bonds, resulting in a unique surface that mediates a previously unidentified galectin-9 (LGALS9; 601879)-independent binding process. Cao et al. (2007) proposed that the multiple TIM3 binding activities contribute to the regulated assembly of signaling complexes required for effective Th1-mediated immunity.


Gene Structure

The mouse Tim3 gene contains 7 exons (Sabatos et al., 2003).


Mapping

By screening congenic mouse T-cell lines for reduced Th2 responsiveness, McIntire et al. (2001) identified a segment of chromosome 11 homologous to human chromosome 5q23-q35 that they termed the 'T-cell and airway hyperreactivity phenotype regulator' (Tapr) locus. They mapped the mouse Tims, including Tim3, to the Tapr locus on chromosome 11 and the human homologs to chromosome 5q33.2.


Molecular Genetics

In 9 patients from 7 unrelated families of East Asian origin with subcutaneous panniculitis-like T-cell lymphoma (SPTCL; 618398), Gayden et al. (2018) identified a germline homozygous missense variant in the HAVCR2 gene (Y82C; 606652.0001). Homozygosity for Y82C was found in tumor tissue from the patients for whom tumor tissue was available. A homozygous Y82C variant was found in tumor tissue from 3 additional patients of East Asian descent, but germline DNA was not available for study. A germline homozygous I97M variant (606652.0002) was found in 2 unrelated patients of European descent (patients P13 and P14), one of whom was shown to carry the I97M variant in homozygosity in tumor tissue. A heterozygous I97M variant was found in the germline and tumor tissue of a third patient (P15) of European descent. One patient of North African descent (P16) was compound heterozygous for these 2 mutations in her tumor; additional DNA was not available for germline analysis. The variants, which were found by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in 5 families from whom DNA was available. In patient panniculitis biopsies, mutant HAVCR2 showed abnormal intracellular aggregate staining in the peri-Golgi apparatus with limited plasma expression compared to wildtype. Peripheral monocytes from several patients showed absent HAVCR2 expression, and there was absent protein expression on activated CD4+ and CD8+ lymphocytes. Heterozygous carriers had an intermediate level of membrane protein expression. Decreased membrane expression of the mutant proteins was confirmed after transfection of the mutations in HEK293 cells. In vitro functional expression studies indicated that the mutant proteins were improperly folded and had disrupted posttranslational glycosylation, resulting in decreased or absent expression at the cell surface. In vitro studies of T lymphocytes and macrophages derived from 3 patients (P3, P4, and P11) with the Y82C mutation showed increased secretion of the inflammatory cytokines TNFA (191160), IL2 (147680), and IL1B (147720) compared to controls, and this response was increased with stimulation by lipopolysaccharide (LPS) and an NLRP3 (606416) agonist. There was also a decrease in FOXP3 (300292)+ CD4+ regulatory T cells. The findings suggested that misfolding of HAVCR2 promotes secretion of inflammatory cytokines and activation of the NLRP3 inflammasome, and that the disorder results from uncontrolled immune activation. These mutations were found in 16 (60%) of 27 patients with the disorder who were studied.

Polprasert et al. (2019) identified a homozygous Y82C mutation in 10 unrelated patients from Thailand or Japan with SPTCL. Another patient was compound heterozygous for Y82C and T101I (606652.0003). The mutations were found by whole-exome sequencing and confirmed by deep sequencing. The Y82C variant had a mean allele frequency of 3.6 x 10(-3) in the gnomAD database, with enrichment among East Asians (2.1 x 10(-2)). The T101I variant had a mean allele frequency of 6.6 x 10(-3) in gnomAD, and was enriched among South Asians (1.8 x 10(-3)). Functional studies of the variants and studies of the effects of the mutation on HAVCR2 in patient cells were not performed. Analysis of patient SPTCL cells identified somatic mutations in genes associated with epigenetic regulation and signal transduction.


Animal Model

Sanchez-Fueyo et al. (2003) found that blockade of Tim3 by anti-Tim3 or a full-length Tim3 fusion protein appeared to enhance the capacity of Th1 cells to mediate tissue damage after induction of diabetes in a nonobese diabetic-severe combined immunodeficiency mouse model (see 222100). Anti-Tim3 also prevented the acquisition of transplantation tolerance induced by blockade of costimulatory molecules by dampening the antigen-specific immunosuppressive function of CD4-positive/CD25-positive regulatory T cells.

Sabatos et al. (2003) found that Tim3-deficient mice were refractory to the induction of high-dose immunologic tolerance.


ALLELIC VARIANTS ( 3 Selected Examples):

.0001 T-CELL LYMPHOMA, SUBCUTANEOUS PANNICULITIS-LIKE, SUSCEPTIBILITY TO

HAVCR2, TYR82CYS (rs184868814)
  
RCV000768411...

In 9 patients from 7 unrelated families of East Asian origin with subcutaneous panniculitis-like T-cell lymphoma (SPTCL; 618398), Gayden et al. (2018) identified a homozygous germline c.245A-G transition (c.245A-G, NM_032782) in the HAVCR2 gene, resulting in a tyr82-to-cys (Y82C) substitution at a highly conserved residue in the IgV domain, which is critical for terminating immune responses. The variant, which was found by whole-exome sequencing and confirmed by targeted sequencing, was found at a low frequency (0.0036) in the gnomAD database, with a higher prevalence among East Asians (minor allele frequency of 0.02104). The mutation segregated in the families from whom parental DNA was available, and heterozygous carriers were unaffected. Four individuals in the ExAC database were homozygous for the variant (3 East Asian and 1 Latino), but it was not possible to contact these individuals for phenotypic information. Heterozygosity for the variant was found in 8 of 107 control individuals from Tahiti (Polynesia) (allele frequency of 4 x 10(-2)). Haplotype analysis showed at least 12 distinct chromosomal backgrounds carrying the variant, suggesting that it is recurrent, although several patients carried a haplotype with evidence of a founder effect in the East Asian population. In patient panniculitis biopsies, mutant HAVCR2 showed abnormal intracellular aggregate staining in the peri-Golgi apparatus with limited plasma expression compared to wildtype. Peripheral monocytes from several patients showed absent HAVCR2 expression, and there was absent expression on activated CD4+ and CD8+ lymphocytes. Heterozygous carriers had an intermediate level of membrane expression. Decreased membrane expression of the mutant protein was confirmed after transfection of the mutation in HEK293 cells. In vitro functional expression studies indicated that the mutant protein was improperly folded and had disrupted posttranslational glycosylation, resulting in improper expression at the cell surface.

Polprasert et al. (2019) identified a homozygous Y82C mutation in 10 unrelated patients from Thailand or Japan with SPTCL. Another patient was compound heterozygous for Y82C and a c.302C-T transition in the HAVCR2 gene, resulting in a thr101-to-ile (T101I; 606652.0003) substitution at a highly conserved residue in the IgV-like domain. The mutations were found by whole-exome sequencing and confirmed by deep sequencing. The Y82C variant had a mean allele frequency of 3.6 x 10(-3) in the gnomAD database, with enrichment among East Asians (2.1 x 10(-2)). The T101I variant had a mean allele frequency of 6.6 x 10(-3) in gnomAD, and was enriched among South Asians (1.8 x 10(-3)). Functional studies of the variants and studies of the effects of the mutation on HAVCR2 in patient cells were not performed.


.0002 T-CELL LYMPHOMA, SUBCUTANEOUS PANNICULITIS-LIKE, SUSCEPTIBILITY TO

HAVCR2, ILE97MET (rs35960726)
  
RCV000768412...

In 2 unrelated patients with subcutaneous panniculitis-like T-cell lymphoma (SPTCL; 618398), Gayden et al. (2018) identified a homozygous germline c.291A-G transition (c.291A-G, NM_032782) in the HAVCR2 gene, resulting in an ile97-to-met (I97M) substitution at a highly conserved residue in the IgV domain, which is critical for terminating immune responses. The mutation, which was found by whole-exome sequencing and confirmed by targeted sequencing, was found at a low frequency (0.002908) in the ExAC/gnomAD database. In patient panniculitis biopsies, mutant HAVCR2 showed abnormal intracellular aggregate staining in the peri-Golgi apparatus with limited plasma expression compared to wildtype. Decreased membrane expression of the mutant protein was confirmed after transfection in HEK293 cells. In vitro functional expression studies indicated that the mutant protein was improperly folded and had disrupted posttranslational glycosylation, resulting in improper expression at the cell surface.


.0003 T-CELL LYMPHOMA, SUBCUTANEOUS PANNICULITIS-LIKE, SUSCEPTIBILITY TO

HAVCR2, THR101ILE (rs147827860)
  
RCV000768413...

For discussion of the c.302C-T transition (c.302C-T, NM_032782) in the HAVCR2 gene, resulting in a thr101-to-ile (T101I) substitution at a highly conserved residue in the IgV-like domain, that was found in compound heterozygous state in a patient with subcutaneous panniculitis-like T-cell lymphoma (SPTCL; 618398) by Polprasert et al. (2019), see 606652.0001.


REFERENCES

  1. Anderson, A. C., Anderson, D. E., Bregoli, L., Hastings, W. D., Kassam, N., Lei, C., Chandwaskar, R., Karman, J., Su, E. W., Hirashima, M., Bruce, J. N., Kane, L. P., Kuchroo, V. K., Hafler, D. A. Promotion of tissue inflammation by the immune receptor Tim-3 expressed on innate immune cells. Science 318: 1141-1143, 2007. [PubMed: 18006747, related citations] [Full Text]

  2. Cao, E., Zang, X., Ramagopal, U. A., Mukhopadhaya, A., Fedorov, A., Fedorov, E., Zencheck, W. D., Lary, J. W., Cole, J. L., Deng, H., Xiao, H., DiLorenzo, T. P., Allison, J. P., Nathenson, S. G., Almo, S. C. T cell immunoglobulin mucin-3 crystal structure reveals a galectin-9-independent ligand-binding surface. Immunity 26: 311-321, 2007. [PubMed: 17363302, related citations] [Full Text]

  3. Gayden, T., Sepulveda, F. E., Khuong-Quang, D.-A., Pratt, J., Valera, E. T., Garrigue, A., Kelso, S., Sicheri, F., Mikael, L. G., Hamel, N., Bajic, A., Dali, R., and 32 others. Germline HAVCR2 mutations altering TIM-3 characterize subcutaneous panniculitis-like T cell lymphomas with hemophagocytic lymphohistiocytic syndrome. Nature Genet. 50: 1650-1657, 2018. Note: Erratum: Nature Genet. 51: 196 only, 2019. [PubMed: 30374066, related citations] [Full Text]

  4. Huang, Y.-H., Zhu, C., Kondo, Y., Anderson, A. C., Gandhi, A., Russell, A., Dougan, S. K., Petersen, B.-S., Melum, E., Pertel, T., Clayton, K. L., Raab, M., and 12 others. CEACAM1 regulates TIM-3-mediated tolerance and exhaustion. Nature 517: 386-390, 2015. Note: Erratum: Nature 536: 359 only, 2016. [PubMed: 25363763, images, related citations] [Full Text]

  5. Khademi, M., Illes, Z., Gielen, A. W., Marta, M., Takazawa, N., Baecher-Allan, C., Brundin, L., Hannerz, J., Martin, C., Harris, R. A., Hafler, D. A., Kuchroo, V. K., Olsson, T., Piehl, F., Wallstrom, E. T cell Ig- and mucin-domain-containing molecule-3 (TIM-3) and TIM-1 molecules are differentially expressed on human Th1 and Th2 cells and in cerebrospinal fluid-derived mononuclear cells in multiple sclerosis. J. Immun. 172: 7169-7176, 2004. [PubMed: 15153541, related citations] [Full Text]

  6. Koguchi, K., Anderson, D. E., Yang, L., O'Connor, K. C., Kuchroo, V. K., Hafler, D. A. Dysregulated T cell expression of TIM3 in multiple sclerosis. J. Exp. Med. 203: 1413-1418, 2006. [PubMed: 16754722, images, related citations] [Full Text]

  7. McIntire, J. J., Umetsu, S. E., Akbari, O., Potter, M., Kuchroo, V. K., Barsh, G. S., Freeman, G. J., Umetsu, D. T., DeKruyff, R. H. Identification of Tapr (an airway hyperreactivity regulatory locus) and the linked Tim gene family. Nature Immun. 2: 1109-1116, 2001. [PubMed: 11725301, related citations] [Full Text]

  8. Monney, L., Sabatos, C., Gaglia, J. L., Ryu, A., Waldner, H., Chernova, T., Manning, S., Greenfield, E. A., Coyle, A. J., Sobel, R. A., Freeman, G. J., Kuchroo, V. K. Th1-specific cell surface protein regulates macrophage activation and severity of an autoimmune disease. Nature 415: 536-541, 2002. [PubMed: 11823861, related citations] [Full Text]

  9. Polprasert, C., Takeuchi, Y., Kakiuchi, N., Yoshida, K., Assanasen, T., Sitthi, W., Bunworasate, U., Pirunsarn, A., Wudhikarn, K., Lawasut, P., Uaprasert, N., Kongkiatkamon, S., and 14 others. Frequent germline mutations of HAVCR2 in sporadic subcutaneous panniculitis-like T-cell lymphoma. Blood Adv. 3: 588-595, 2019. [PubMed: 30792187, related citations] [Full Text]

  10. Sabatos, C. A., Chakravarti, S., Cha, E., Schubart, A., Sanchez-Fueyo, A., Zheng, X. X., Coyle, A. J., Strom, T. B., Freeman, G. J., Kuchroo, V. K. Interaction of Tim-3 and Tim-3 ligand regulates T helper type 1 responses and induction of peripheral tolerance. Nature Immun. 4: 1102-1110, 2003. [PubMed: 14556006, related citations] [Full Text]

  11. Sanchez-Fueyo, A., Tian, J., Picarella, D., Domenig, C., Zheng, X. X., Sabatos, C. A., Manlongat, N., Bender, O., Kamradt, T., Kuchroo, V. K., Gutierrez-Ramos, J.-C., Coyle, A. J., Strom, T. B. Tim-3 inhibits T helper type 1-mediated auto- and alloimmune responses and promotes immunological tolerance. Nature Immun. 4: 1093-1101, 2003. [PubMed: 14556005, related citations] [Full Text]

  12. Yi, W., Zhang, P., Liang, Y., Zhou, Y., Shen, H., Fan, C., Moorman, J. P., Yao, Z. Q., Jia, Z., Zhang, Y. T-bet-mediated Tim-3 expression dampens monocyte function during chronic hepatitis C virus infection. Immunology 150: 301-311, 2016. [PubMed: 27809352, related citations] [Full Text]


Cassandra L. Kniffin - updated : 04/23/2019
Paul J. Converse - updated : 11/22/2017
Matthew B. Gross - updated : 08/24/2017
Ada Hamosh - updated : 03/03/2015
Ada Hamosh - updated : 2/14/2008
Paul J. Converse - updated : 7/31/2007
Paul J. Converse - updated : 2/2/2007
Paul J. Converse - updated : 11/11/2005
Paul J. Converse - updated : 11/12/2003
Paul J. Converse - updated : 7/24/2002
Creation Date:
Paul J. Converse : 1/30/2002
alopez : 04/24/2019
ckniffin : 04/23/2019
mgross : 11/22/2017
mgross : 08/24/2017
carol : 07/31/2017
alopez : 03/03/2015
alopez : 2/15/2008
terry : 2/14/2008
mgross : 8/24/2007
terry : 7/31/2007
mgross : 2/2/2007
mgross : 5/4/2006
mgross : 11/14/2005
terry : 11/11/2005
alopez : 11/25/2003
alopez : 11/13/2003
mgross : 11/12/2003
mgross : 11/12/2003
mgross : 7/24/2002
mgross : 7/24/2002
alopez : 1/30/2002
alopez : 1/30/2002

* 606652

HEPATITIS A VIRUS CELLULAR RECEPTOR 2; HAVCR2


Alternative titles; symbols

T-CELL IMMUNOGLOBULIN AND MUCIN DOMAINS-CONTAINING PROTEIN 3; TIM3


HGNC Approved Gene Symbol: HAVCR2

Cytogenetic location: 5q33.3     Genomic coordinates (GRCh38): 5:157,085,832-157,109,044 (from NCBI)


Gene-Phenotype Relationships

Location Phenotype Phenotype
MIM number
Inheritance Phenotype
mapping key
5q33.3 T-cell lymphoma, subcutaneous panniculitis-like 618398 Autosomal recessive 3

TEXT

Description

The HAVCR2 gene encodes a critical negative regulator in the immune system, acting as a negative checkpoint in peripheral tolerance and innate immune and inflammatory responses (summary by Gayden et al., 2018).

CD4 (186940)-positive T helper lymphocytes can be divided into types 1 (Th1) and 2 (Th2) on the basis of their cytokine secretion patterns. Th1 cells and their associated cytokines are involved in cell-mediated immunity to intracellular pathogens and delayed-type hypersensitivity reactions, whereas Th2 cells are involved in the control of extracellular helminthic infections and the promotion of atopic and allergic diseases. The 2 types of cells also cross-regulate the functions of the other. TIM3 is a Th1-specific cell surface protein that regulates macrophage activation and enhances the severity of experimental autoimmune encephalomyelitis in mice (summary by Monney et al., 2002).


Cloning and Expression

By immunoscreening Th1 and Th2 cells with monoclonal antibodies derived from mouse Th1 cell-immunized rats, followed by gene-expression cloning, Monney et al. (2002) obtained a cDNA encoding mouse Tim3. By genomic database searching and RT-PCR, the authors isolated a cDNA encoding human TIM3. The deduced 301-amino acid type I membrane protein, 63% identical overall and 77% identical in the cytoplasmic domain, has an Ig variable-like domain, a mucin-like domain consisting of 31% serine and threonine residues, and a cytoplasmic domain with a tyrosine phosphorylation motif. Monney et al. (2002) noted that TIM3 is related to the hepatitis A virus cellular receptor (HAVCR1; 606518), also known as TIM1 or Kim1.

Sabatos et al. (2003) identified an 800-bp cDNA encoding a soluble isoform of mouse Tim3 lacking the mucin and transmembrane domains. The truncated form contains only exons 1, 2, 6, and 7, while the full-length protein contains all 7 exons.


Gene Function

Using flow cytometric and RT-PCR analysis, Monney et al. (2002) detected Tim3 only on activated Th1 cells and CD11b+ (ITGAM; 120980) macrophages. Cells expressing Tim3 predominate in the central nervous system of mice at the onset of experimental autoimmune encephalomyelitis (EAE), a Th1-mediated autoimmune disease. Anti-Tim3 treatment enhanced the clinical and pathologic severity of EAE and increased the number and activation level of macrophages. Monney et al. (2002) proposed that anti-Tim3 may trigger the production of proinflammatory cytokines in vivo and induce macrophage activation possibly by enhancing the migration of Th1 cells into the brain or by blocking an interaction between Tim3 and an inhibitory ligand.

By flow cytometric analysis using full-length and soluble mouse Tim3 fusion proteins, Sanchez-Fueyo et al. (2003) demonstrated that a putative ligand for Tim3 exists on resting CD4-positive T cells, but not on CD8 (see 186910)-positive T cells, B cells, or CD11b-positive leukocytes. Some expression was detected on splenic CD11c (ITGAX; 151510)-positive dendritic cells. Expression of the ligand was downregulated on activated CD4-positive/CD25 (147730)-negative effector T cells but persisted on CD4-positive/CD25-positive regulatory T cells.

Independently, Sabatos et al. (2003) also demonstrated the lack of expression of a mouse Tim3 ligand on non-CD4-positive T cells and B cells. Limited expression was detected on CD11c-positive dendritic cells and CD11b-positive macrophages. Treatment with a Tim3-Ig fusion protein induced hyperproliferation of CD3 (see 186740)-positive T cells, but not other leukocyte types, and induced expression of Th1-type cytokines.

Using real-time RT-PCR, Khademi et al. (2004) found that human Th1 cell lines expressed higher levels of TIM3, whereas Th2 lines expressed higher levels of TIM1. Mononuclear cells from cerebrospinal fluid (CSF) of patients with multiple sclerosis (MS; 126200) expressed higher TIM1 mRNA levels than controls. Moreover, higher TIM1 expression was associated with low IFNG (147570) expression in CSF mononuclear cells and with clinical remissions. In contrast, TIM3 expression correlated well with high expression of IFNG and TNF (191160). Khademi et al. (2004) concluded that differential expression of TIMs by Th1 and Th2 cells may be implicated in different phases of an autoimmune disease.

Using RT-PCR and ELISA, Koguchi et al. (2006) showed that T-cell clones from CSF of patients with multiple sclerosis (MS; see 126200) secreted more IFNG than did clones from CSF of control subjects, but they expressed less TIM3 and TBET (TBX21; 604895). The reduced levels of TIM3 correlated with resistance to T-cell tolerance induced by costimulatory blockade. Small interfering RNA-mediated reduction of TIM3 expression on ex vivo CD4-positive T cells enhanced proliferation and IFNG secretion. Koguchi et al. (2006) concluded that TIM3 expression is dysregulated in MS CSF clones, and that TIM3 expression on T cells regulates proliferation and IFNG secretion.

Anderson et al. (2007) found that TIM3 is constitutively expressed on cells of the innate immune system in both mice and humans, and that it can synergize with Toll-like receptors. Moreover, an antibody agonist of Tim3 acted as an adjuvant during induced immune responses, and Tim3 ligation induced distinct signaling events in T cells and dendritic cells; the latter finding could explain the apparent divergent functions of Tim3 in these cell types. Thus, Anderson et al. (2007) concluded that by virtue of differential expression on innate versus adaptive immune cells, Tim3 can either promote or terminate TH1 immunity and may be able to influence a range of inflammatory conditions.

Huang et al. (2015) showed that TIM3 was coexpressed and interacted directly with carcinoembryonic antigen cell adhesion molecule-1 (CEACAM1; 109770), another molecule expressed on activated T cells and involved in T-cell inhibition. The interaction involved the membrane-distal immunoglobulin-variable (IgV)-like N-terminal domains of the proteins. The presence of CEACAM1 endowed TIM3 with inhibitory function. In a mouse adoptive transfer colitis model, Ceacam1-deficient T cells were hyperinflammatory with reduced cell surface expression of Tim3 and regulatory cytokines, and this was restored by T-cell-specific Ceacam1 expression. During chronic viral infection and in a tumor environment, Ceacam1 and Tim3 marked exhausted T cells. Co-blockade of Ceacam1 and Tim3 led to enhancement of antitumor immune responses with improved elimination of tumors in mouse colorectal cancer models. Huang et al. (2015) concluded that CEACAM1 serves as a ligand for TIM3 that is required for its ability to mediate T-cell inhibition, and that this interaction has a crucial role in regulating autoimmunity and antitumor immunity. In an erratum, Huang et al. (2015) withdrew the crystallographic model of a heterodimer between the IgV domains of CEACAM1 and TIM3 originally presented in their report and replaced it with a more accurate CEACAM1-CEACAM1 homodimer model. They noted that additional solution-based NMR and surface-based SPR studies independently provided biochemical evidence to support direct interaction between CEACAM1 and TIM3 via their N-terminal IgV domains. However, after withdrawal of their crystallographic model, they could no longer state the stoichiometry, describe the molecular details, or differentiate between cis/trans modes of IgV domain interaction, as claimed in their original report.

Using flow cytometric analysis, Yi et al. (2016) showed that TBET and TIM3 were constitutively expressed in resting CD14 (158120)-positive monocyte/macrophages. TBET and TIM3 expression was significantly upregulated in individuals with chronic hepatitis C virus (HCV; see 609532) infection. Coculture with HCV-infected hepatocytes resulted in upregulation of TBET. The HCV core protein alone could mediate upregulation of TBET and TIM3 by acting through its receptor, GC1QR (C1QBP; 601269), and inducing JNK (MAPK8; 601158) signaling. Knockdown of TBET in THP1 monocytes via small interfering RNA resulted in decreased TIM3 production and increased IL12 (see 161560) production and STAT1 (600555) phosphorylation in response to stimulation with HCV core protein. Yi et al. (2016) proposed that TBET is an upstream regulator of TIM3 that impairs IL12 production during HCV infection.


Biochemical Features

Cao et al. (2007) reported the crystal structure of the murine Tim3 IgV domain to 2-angstrom resolution. The structure revealed that 4 cysteines form 3 noncanonical disulfide bonds, resulting in a unique surface that mediates a previously unidentified galectin-9 (LGALS9; 601879)-independent binding process. Cao et al. (2007) proposed that the multiple TIM3 binding activities contribute to the regulated assembly of signaling complexes required for effective Th1-mediated immunity.


Gene Structure

The mouse Tim3 gene contains 7 exons (Sabatos et al., 2003).


Mapping

By screening congenic mouse T-cell lines for reduced Th2 responsiveness, McIntire et al. (2001) identified a segment of chromosome 11 homologous to human chromosome 5q23-q35 that they termed the 'T-cell and airway hyperreactivity phenotype regulator' (Tapr) locus. They mapped the mouse Tims, including Tim3, to the Tapr locus on chromosome 11 and the human homologs to chromosome 5q33.2.


Molecular Genetics

In 9 patients from 7 unrelated families of East Asian origin with subcutaneous panniculitis-like T-cell lymphoma (SPTCL; 618398), Gayden et al. (2018) identified a germline homozygous missense variant in the HAVCR2 gene (Y82C; 606652.0001). Homozygosity for Y82C was found in tumor tissue from the patients for whom tumor tissue was available. A homozygous Y82C variant was found in tumor tissue from 3 additional patients of East Asian descent, but germline DNA was not available for study. A germline homozygous I97M variant (606652.0002) was found in 2 unrelated patients of European descent (patients P13 and P14), one of whom was shown to carry the I97M variant in homozygosity in tumor tissue. A heterozygous I97M variant was found in the germline and tumor tissue of a third patient (P15) of European descent. One patient of North African descent (P16) was compound heterozygous for these 2 mutations in her tumor; additional DNA was not available for germline analysis. The variants, which were found by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in 5 families from whom DNA was available. In patient panniculitis biopsies, mutant HAVCR2 showed abnormal intracellular aggregate staining in the peri-Golgi apparatus with limited plasma expression compared to wildtype. Peripheral monocytes from several patients showed absent HAVCR2 expression, and there was absent protein expression on activated CD4+ and CD8+ lymphocytes. Heterozygous carriers had an intermediate level of membrane protein expression. Decreased membrane expression of the mutant proteins was confirmed after transfection of the mutations in HEK293 cells. In vitro functional expression studies indicated that the mutant proteins were improperly folded and had disrupted posttranslational glycosylation, resulting in decreased or absent expression at the cell surface. In vitro studies of T lymphocytes and macrophages derived from 3 patients (P3, P4, and P11) with the Y82C mutation showed increased secretion of the inflammatory cytokines TNFA (191160), IL2 (147680), and IL1B (147720) compared to controls, and this response was increased with stimulation by lipopolysaccharide (LPS) and an NLRP3 (606416) agonist. There was also a decrease in FOXP3 (300292)+ CD4+ regulatory T cells. The findings suggested that misfolding of HAVCR2 promotes secretion of inflammatory cytokines and activation of the NLRP3 inflammasome, and that the disorder results from uncontrolled immune activation. These mutations were found in 16 (60%) of 27 patients with the disorder who were studied.

Polprasert et al. (2019) identified a homozygous Y82C mutation in 10 unrelated patients from Thailand or Japan with SPTCL. Another patient was compound heterozygous for Y82C and T101I (606652.0003). The mutations were found by whole-exome sequencing and confirmed by deep sequencing. The Y82C variant had a mean allele frequency of 3.6 x 10(-3) in the gnomAD database, with enrichment among East Asians (2.1 x 10(-2)). The T101I variant had a mean allele frequency of 6.6 x 10(-3) in gnomAD, and was enriched among South Asians (1.8 x 10(-3)). Functional studies of the variants and studies of the effects of the mutation on HAVCR2 in patient cells were not performed. Analysis of patient SPTCL cells identified somatic mutations in genes associated with epigenetic regulation and signal transduction.


Animal Model

Sanchez-Fueyo et al. (2003) found that blockade of Tim3 by anti-Tim3 or a full-length Tim3 fusion protein appeared to enhance the capacity of Th1 cells to mediate tissue damage after induction of diabetes in a nonobese diabetic-severe combined immunodeficiency mouse model (see 222100). Anti-Tim3 also prevented the acquisition of transplantation tolerance induced by blockade of costimulatory molecules by dampening the antigen-specific immunosuppressive function of CD4-positive/CD25-positive regulatory T cells.

Sabatos et al. (2003) found that Tim3-deficient mice were refractory to the induction of high-dose immunologic tolerance.


ALLELIC VARIANTS 3 Selected Examples):

.0001   T-CELL LYMPHOMA, SUBCUTANEOUS PANNICULITIS-LIKE, SUSCEPTIBILITY TO

HAVCR2, TYR82CYS ({dbSNP rs184868814})
SNP: rs184868814, gnomAD: rs184868814, ClinVar: RCV000768411, RCV001785721, RCV003955498

In 9 patients from 7 unrelated families of East Asian origin with subcutaneous panniculitis-like T-cell lymphoma (SPTCL; 618398), Gayden et al. (2018) identified a homozygous germline c.245A-G transition (c.245A-G, NM_032782) in the HAVCR2 gene, resulting in a tyr82-to-cys (Y82C) substitution at a highly conserved residue in the IgV domain, which is critical for terminating immune responses. The variant, which was found by whole-exome sequencing and confirmed by targeted sequencing, was found at a low frequency (0.0036) in the gnomAD database, with a higher prevalence among East Asians (minor allele frequency of 0.02104). The mutation segregated in the families from whom parental DNA was available, and heterozygous carriers were unaffected. Four individuals in the ExAC database were homozygous for the variant (3 East Asian and 1 Latino), but it was not possible to contact these individuals for phenotypic information. Heterozygosity for the variant was found in 8 of 107 control individuals from Tahiti (Polynesia) (allele frequency of 4 x 10(-2)). Haplotype analysis showed at least 12 distinct chromosomal backgrounds carrying the variant, suggesting that it is recurrent, although several patients carried a haplotype with evidence of a founder effect in the East Asian population. In patient panniculitis biopsies, mutant HAVCR2 showed abnormal intracellular aggregate staining in the peri-Golgi apparatus with limited plasma expression compared to wildtype. Peripheral monocytes from several patients showed absent HAVCR2 expression, and there was absent expression on activated CD4+ and CD8+ lymphocytes. Heterozygous carriers had an intermediate level of membrane expression. Decreased membrane expression of the mutant protein was confirmed after transfection of the mutation in HEK293 cells. In vitro functional expression studies indicated that the mutant protein was improperly folded and had disrupted posttranslational glycosylation, resulting in improper expression at the cell surface.

Polprasert et al. (2019) identified a homozygous Y82C mutation in 10 unrelated patients from Thailand or Japan with SPTCL. Another patient was compound heterozygous for Y82C and a c.302C-T transition in the HAVCR2 gene, resulting in a thr101-to-ile (T101I; 606652.0003) substitution at a highly conserved residue in the IgV-like domain. The mutations were found by whole-exome sequencing and confirmed by deep sequencing. The Y82C variant had a mean allele frequency of 3.6 x 10(-3) in the gnomAD database, with enrichment among East Asians (2.1 x 10(-2)). The T101I variant had a mean allele frequency of 6.6 x 10(-3) in gnomAD, and was enriched among South Asians (1.8 x 10(-3)). Functional studies of the variants and studies of the effects of the mutation on HAVCR2 in patient cells were not performed.


.0002   T-CELL LYMPHOMA, SUBCUTANEOUS PANNICULITIS-LIKE, SUSCEPTIBILITY TO

HAVCR2, ILE97MET ({dbSNP rs35960726})
SNP: rs35960726, gnomAD: rs35960726, ClinVar: RCV000768412, RCV001310880

In 2 unrelated patients with subcutaneous panniculitis-like T-cell lymphoma (SPTCL; 618398), Gayden et al. (2018) identified a homozygous germline c.291A-G transition (c.291A-G, NM_032782) in the HAVCR2 gene, resulting in an ile97-to-met (I97M) substitution at a highly conserved residue in the IgV domain, which is critical for terminating immune responses. The mutation, which was found by whole-exome sequencing and confirmed by targeted sequencing, was found at a low frequency (0.002908) in the ExAC/gnomAD database. In patient panniculitis biopsies, mutant HAVCR2 showed abnormal intracellular aggregate staining in the peri-Golgi apparatus with limited plasma expression compared to wildtype. Decreased membrane expression of the mutant protein was confirmed after transfection in HEK293 cells. In vitro functional expression studies indicated that the mutant protein was improperly folded and had disrupted posttranslational glycosylation, resulting in improper expression at the cell surface.


.0003   T-CELL LYMPHOMA, SUBCUTANEOUS PANNICULITIS-LIKE, SUSCEPTIBILITY TO

HAVCR2, THR101ILE ({dbSNP rs147827860})
SNP: rs147827860, gnomAD: rs147827860, ClinVar: RCV000768413, RCV002263968, RCV003918257

For discussion of the c.302C-T transition (c.302C-T, NM_032782) in the HAVCR2 gene, resulting in a thr101-to-ile (T101I) substitution at a highly conserved residue in the IgV-like domain, that was found in compound heterozygous state in a patient with subcutaneous panniculitis-like T-cell lymphoma (SPTCL; 618398) by Polprasert et al. (2019), see 606652.0001.


REFERENCES

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  4. Huang, Y.-H., Zhu, C., Kondo, Y., Anderson, A. C., Gandhi, A., Russell, A., Dougan, S. K., Petersen, B.-S., Melum, E., Pertel, T., Clayton, K. L., Raab, M., and 12 others. CEACAM1 regulates TIM-3-mediated tolerance and exhaustion. Nature 517: 386-390, 2015. Note: Erratum: Nature 536: 359 only, 2016. [PubMed: 25363763] [Full Text: https://doi.org/10.1038/nature13848]

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Contributors:
Cassandra L. Kniffin - updated : 04/23/2019
Paul J. Converse - updated : 11/22/2017
Matthew B. Gross - updated : 08/24/2017
Ada Hamosh - updated : 03/03/2015
Ada Hamosh - updated : 2/14/2008
Paul J. Converse - updated : 7/31/2007
Paul J. Converse - updated : 2/2/2007
Paul J. Converse - updated : 11/11/2005
Paul J. Converse - updated : 11/12/2003
Paul J. Converse - updated : 7/24/2002

Creation Date:
Paul J. Converse : 1/30/2002

Edit History:
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