Alternative titles; symbols
HGNC Approved Gene Symbol: TYMS
Cytogenetic location: 18p11.32 Genomic coordinates (GRCh38): 18:657,653-673,578 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 18p11.32 | Dyskeratosis congenita, digenic | 620040 | Digenic dominant | 3 |
The TYMS gene encodes thymidylate synthase (TYMS, or TS; EC 2.1.1.45) which catalyzes the reductive methylation of dUMP to form dTMP in the de novo nucleotide synthesis pathway (summary by Tummala et al., 2022).
Thymidylate synthase uses the 5,10-methylenetetrahydrofolate (methylene-THF) as a cofactor to maintain the dTMP (thymidine-5-prime monophosphate) pool critical for DNA replication and repair. The enzyme has been of interest as a target for cancer chemotherapeutic agents. It is considered to be the primary site of action for 5-fluorouracil, 5-fluoro-2-prime-deoxyuridine, and some folate analogs.
Takeishi et al. (1985) cloned TYMS from a human fibroblast cDNA library. The deduced 313-amino acid protein has a calculated molecular mass of 35.7 kD. Several sequences of TYMS are invariant between human, E. coli, L. casei, and T4 phage, including 7 tripeptides, a tetrapeptide, and an octapeptide. One of these sequences, thr75-thr76-lys77, is within the folylpolyglutamate-binding sites of the L. casei sequence. Cys195 of the tripeptide pro194-cys195-his196 is known to bind 5-fluoro-2-prime deoxyuridylate. Takeishi et al. (1985) also identified 2 polyadenylation signals that give rise to 2 mRNA species of 1.6 and 1.4 kb.
The rTS gene (607427), which overlaps the 3-prime end of the TS gene, produces 2 mRNAs, rTS-alpha and rTS-beta, through alternative splicing. Chu and Dolnick (2002) analyzed the function of rTS-alpha, which is partially complementary, or antisense, to TS mRNA near its 3-prime end, including exon 7. They found that rTS-alpha RNA and TS mRNA levels varied inversely when the growth of HEp2 cells progressed from a late-log phase to plateau phase. Transfection and expression of the antisense region of rTS-alpha alone was sufficient to downregulate TS mRNA. Downregulation was also associated with increased site-specific cleavage of TS mRNA.
By cDNA microarray, Western blot analysis, and luciferase reporter assay, Yoo et al. (2009) identified the transcription factor LSF (TFCP2; 189889) as a positive regulator of TYMS.
Takeishi et al. (1985) and Takeishi et al. (1989) described unique structural features within the 5-prime untranslated region of the TYMS gene. This region has an 80% GC content and contains triple tandemly repeated elements of a 28-bp sequence and an inverted sequence of the same length. The repeats have the sequence CGCCGCG, and consequently this region can form 3 interconvertible secondary structures, each of which contains a stem-loop structure formed by the association of 2 CGCCGCG sequences. Takeishi et al. (1989) determined that the TYMS gene spans 23 kb. They also deduced 2 major mRNA cap sites within the inverted sequence.
Kaneda et al. (1990) determined that the TYMS gene contains 7 exons and spans about 30 kb. The 5-prime flanking region does not contain a TATA or CAAT box, nor does it have a GC box for SP1 (189906) binding. Intron 1 has 3 CG boxes.
Ledbetter et al. (1984) isolated TS-deficient Chinese hamster cells and by hybridization with a human lymphoblast line showed that the TS gene is located on human chromosome 18. By Southern blot analysis of a panel of human/hamster cell hybrids probed with cDNA from mouse TS, Nussbaum et al. (1985) localized the TS gene to the segment 18q21.31-qter.
By nonisotopic in situ hybridization, Hori et al. (1990) refined the location of the gene to 18p11.32. Silverman et al. (1993) used YACs as probes and fluorescence in situ hybridization to map the TS gene to 18p11.32. The same YAC contained the YES1 gene (164880); the 2 genes were less than 50 kb apart.
TYMS Polymorphism
There is a common tandem repeat polymorphism in the 5-prime untranslated region of TYMS, and the number of tandem repeats affects TYMS activity levels, mediated through effects of the repeats on translation efficiency (Kawakami et al. (1999, 2001)). Triple-repeat (3) and double-repeat (2) alleles are the most common (Marsh et al., 1999), of which the triple-repeat allele results in higher TYMS expression (Kawakami et al., 2001). Marsh et al. (1999) reported the prevalence of the 3/3 genotype as 67% in Chinese and about 40% in whites and southwest Asians.
TYMS competes with 5,10-methylenetetrahydrofolate reductase (MTHFR; 607093) for the availability of methylene-THF. Therefore, Trinh et al. (2002) hypothesized that polymorphisms in TYMS that influence enzyme activity would affect plasma folate levels and, thereby indirectly, plasma homocysteine levels. They investigated the relationship between TYMS genotype and plasma concentrations of homocysteine and folate in a cohort of 505 Chinese in Singapore. The TYMS 3/3 genotype was associated with reduced plasma folate and, among individuals with low dietary folate intake, with elevated plasma homocysteine levels. These associations were independent of the well-established effect of the MTHFR 677C-T genotype (607093.0003) on plasma folate and homocysteine levels. The results suggested that TYMS and MTHFR compete for limited supplies of folate required for the remethylation of homocysteine. Trinh et al. (2002) suggested that these genetic determinants of plasma folate and homocysteine levels may be useful in identifying individuals at increased risk for cardiovascular disease.
Krajinovic et al. (2002) focused on the possibility that interindividual variability in response to methotrexate could be caused by variable concentrations of thymidylate synthase. They investigated the possible association between the triple-repeat polymorphism in the TYMS promoter and outcome of acute lymphoblastic leukemia (ALL) in 205 children treated with methotrexate. They obtained DNA samples from buccal epithelial cells, peripheral blood, or bone marrow in remission, and analyzed them for the polymorphism by PCR amplification. Individuals who were homozygous for the triple repeat had a poorer outlook than those with other genotypes (odds ratio 4.1, p = 0.001). Genotyping of TYMS might make it possible to individualize treatment for patients with ALL.
Resistance to chemotherapy is a major cause of mortality in advanced cancer patients. Wang et al. (2004) used digital karyotyping to search for genomic alterations in liver metastases that were clinically resistant to 5-fluorouracil (5-FU). In 2 of 4 patients, they identified amplification of a region of approximately 100 kb on 18p11.32 that was of particular interest because it contains the TYMS gene, a molecular target of 5-FU. Analysis of TYMS by FISH identified TYMS gene amplification in 7 of 31 (23%) 5-FU-treated cancers, whereas no amplification was observed in metastases of patients who had not been treated with 5-FU. Patients with metastases containing TYMS amplification had a substantially shorter median survival (329 days) than those without amplification (1,021 days, P less than 0.01). These data suggested that genetic amplification of TYMS is a major mechanism of 5-FU resistance in vivo and have important implications for the management of colorectal cancer patients with recurrent disease. In patients with TYMS gene amplification, 5-FU would likely add toxicity without efficacy. Wang et al. (2004) stated that detection of TYMS gene amplification is straightforward by the methods they described and can be performed on routinely fixed and paraffin-embedded samples.
Kealey et al. (2005) analyzed the impact of the TYMS 3-prime UTR ins/del polymorphism on folate and homocysteine levels in 444 young (20 to 26 years old) individuals from Northern Ireland. Among nonsmokers only, the TYMS 3-prime UTR ins/del polymorphism was significantly associated with red blood cell folate (p = 0.002) and homocysteine (p = 0.03) concentrations. In nonsmokers in the highest quartile of RBC folate concentration, median RBC folate concentration was much higher and serum homocysteine much lower for del/del individuals compared with either ins/ins or ins/del individuals. Kealey et al. (2005) suggested that the TYMS 3-prime UTR del/del genotype is a significant determinant of elevated RBC folate concentration in northwestern European nonsmokers.
Digenic Dyskeratosis Congenita
In 6 patients from 5 unrelated families (families 1-5) with digenic dyskeratosis congenita (DKCD; 620040), Tummala et al. (2022) identified heterozygous mutations in the TYMS gene (188350.0001-188350.0004). The mutations, which were found by exome sequencing and confirmed by Sanger sequencing, were inherited from an unaffected parent in all cases. Patient cells showed decreased TYMS protein levels compared to controls and to the unaffected parents. Patient cells, and not parental cells, demonstrated hypersensitivity to 5-FU, which is a known inhibitor of TYMS activity. Cells derived from patient 1 showed altered nucleotide metabolism with increased dUMP and decreased dTMP due to TYMS deficiency affecting the de novo pathway for nucleotide synthesis. There was also evidence for genomic instability. Cells from 3 probands showed a decrease in telomere length and reduced telomerase activity. Due to the observed hypersensitivity of DKCD patient cells to 5-FU, the authors screened the ENOSF1 gene (607427) and identified a common haplotype in all patients that was inherited from the unaffected parent who did not have the TYMS mutation. This haplotype, 'C-A-ins' (rs699517, rs2790, and rs11280056), has been associated with both reduced TYMS and increased ENOSF1 expression. Patient cells showed a marked increase in the ratio of ENOSF1 to TYMS expression compared to parents and controls. The authors noted that ENOSF1 has been shown to modify TYMS expression at the RNA level by acting as an antisense molecular inhibitor of TYMS expression, which was supported by the findings in patient cells. Expression of wildtype TYMS rescued the TYMS expression and ameliorated the ENOSF1 antisense effect, presumably by outcompeting ectopically expressed TYMS RNA. Silencing ENOSF1 by RNA interference rescued TYMS expression at both the RNA and protein levels. These results were consistent with a digenic epistatic relationship between the TYMS and ENOSF1 alleles. In addition, sequencing identified heterozygous intronic variants in the ENOSF1 or TYMSOS (TYMS opposite strand) genes in 4 of the 5 probands (and in the affected sib from family 4), that were inherited from an unaffected parent and may have contributed to the phenotype. Of note, the proband in family 1 did not have additional variants besides the TYMS mutation and the 3-SNP haplotype. Three additional probands (P6, P7, and P8) with DKC without genetic information from the parents carried heterozygous putative loss-of-function mutations in the TYMS gene; these patients did not carry the haplotype. P6 additionally carried a heterozygous variant in intron 4 of the ENOSF1 gene, and P8 additionally carried a heterozygous variant in intron 3 of the TYMS gene, both of which may have influenced the phenotype. P7 carried only a heterozygous splice site mutation in the TYMS gene. Tummala et al. (2022) concluded that the molecular pathogenesis of DKCD involves posttranscriptional inhibition of TYMS translation through ENOSF1-TYMS RNA-RNA interactions, which causes severe TYMS deficiency, genotoxic stress, and abnormal telomere maintenance, resulting in the features of DKC.
In 2 unrelated boys (family 1 and 2) with digenic dyskeratosis congenita (DKCD; 620040), Tummala et al. (2022) identified a heterozygous 2-bp deletion (c.486_487delAA, NM_001071.4) in the TYMS gene, predicted to result in a frameshift and premature termination (Arg163SerfsTer3). The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, was inherited from an unaffected parent in each case. Patient cells showed decreased TYMS protein levels compared to the parents and to controls. Due to the observed hypersensitivity of patient cells to 5-FU, the authors screened the ENOSF1 gene (607427) and identified a common haplotype in both boys that was inherited from the unaffected parent who did not have the TYMS mutation. This C-A-ins haplotype (rs699517, rs2790, and rs11280056) has been associated with both reduced TYMS and increased ENOSF1 expression. Patient cells showed a marked increase in the ratio of ENOSF1 to TYMS expression compared to parents and controls. Sequencing also identified a heterozygous variant in intron 1 of the ENOSF1 gene in patient 2 that was inherited from the mother, who did not carry the TYMS mutation; this ENOSF1 variant may have influenced the phenotype. Patient 1 did not have additional variants besides the TYMS mutation and the haplotype.
In a 3-year-old boy (family 3) with digenic dyskeratosis congenita (DKCD; 620040), Tummala et al. (2022) identified a heterozygous c.343C-T transition (c.343C-T, NM_001071.4) in the TYMS gene, resulting in an arg115-to-ter (R115X) substitution. The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, was inherited from the unaffected father. Patient cells showed decreased TYMS protein levels compared to the parents and to controls. Due to the observed hypersensitivity of patient cells to 5-FU, the authors screened the ENOSF1 gene (607427) and identified a common haplotype that was inherited from the unaffected mother, who did not have the TYMS mutation. This C-A-ins haplotype (rs699517, rs2790, and rs11280056) had been associated with both reduced TYMS and increased ENOSF1 expression. Sequencing also identified a heterozygous variant in intron 3 of the ENOSF1 gene (MAF of 0.0009 in gnomAD) from the unaffected mother that may have influenced the phenotype.
In 2 sibs (family 4) with digenic dyskeratosis congenita (DKCD; 620040), Tummala et al. (2022) identified a heterozygous 2-bp insertion (c.534_535insTG, NM_001071.4) in the TYMS gene, resulting in a frameshift and premature termination (Met179Ter). The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, was inherited from the unaffected father. The sibs also carried a common haplotype in the ENOSF1 gene that was inherited from the unaffected mother who did not have the TYMS mutation. This C-A-ins haplotype (rs699517, rs2790, and rs11280056) had been associated with both reduced TYMS and increased ENOSF1 expression. Sequencing also identified a heterozygous variant in intron 1 of the TYMSOS (TYMS opposite strand) gene in both sibs that was inherited from the unaffected mother (MAF of 0.00026 in gnomAD) and may have influenced the phenotype.
In a 26-year-old woman (family 5) with digenic dyskeratosis congenita (DKCD; 620040), Tummala et al. (2022) identified a heterozygous c.480A-T transversion (c.480A-T, NM_001071.4) in the TYMS gene, resulting in a gln160-to-his (Q160H) substitution at a highly conserved residue. The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, was inherited from the unaffected father. The proband also carried a common haplotype in the ENOSF1 gene (607427) that was inherited from the unaffected mother who did not have the TYMS mutation. This C-A-ins haplotype (rs699517, rs2790, and rs11280056) has been associated with both reduced TYMS and increased ENOSF1 expression. She also carried a heterozygous variant in intron 3 of the ENOSF1 gene (MAF of 0.0013 in gnomAD) that was inherited from the mother and may have influenced the phenotype. The patient was noted to have a severe adverse response to treatment with topical 5-FU when undergoing treatment for squamous cell carcinoma and melanoma in her leg.
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Tummala, H., Walne, A., Buccafusca, R., Alnajar, J., Szabo, A., Robinson, P., McConkie-Rosell, A., Wilson, M., Crowley, S., Kinsler, V., Ewins, A.-M., Madapura, P. M., Patel, M., Pontikos, N., Codd, V., Vulliamy, T., Dokal, I. Germline thymidylate synthase deficiency impacts nucleotide metabolism and causes dyskeratosis congenita. Am. J. Hum. Genet. 109: 1472-1483, 2022. [PubMed: 35931051] [Full Text: https://doi.org/10.1016/j.ajhg.2022.06.014]
Wang, T.-L., Diaz, L. A., Jr., Romans, K., Bardelli, A., Saha, S., Galizia, G., Choti, M., Donehower, R., Parmigiani, G., Shih, I.-M., Iacobuzio-Donahue, C., Kinzler, K. W., Vogelstein, B., Lengauer, C., Velculescu, V. E. Digital karyotyping identifies thymidylate synthase amplification as a mechanism of resistance to 5-fluorouracil in metastatic colorectal cancer patients. Proc. Nat. Acad. Sci. 101: 3089-3094, 2004. [PubMed: 14970324] [Full Text: https://doi.org/10.1073/pnas.0308716101]
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