CTP synthase 1 explained

CTP synthase 1 is an enzyme that is encoded by the CTPS1 gene in humans.[1] [2] CTP synthase 1 is an enzyme in the de novo pyrimidine synthesis pathway that catalyses the conversion of uridine triphosphate (UTP) to cytidine triphosphate (CTP). CTP is a key building block for the production of DNA, RNA and some phospholipids.

Structure and function

CTPS1 is an asymmetrical homotetramer with only three of its four monomers contributing to the catalytic domain. The substrates required for enzymatic activity are adenosine triphosphate (ATP), UTP and the amino acid glutamine. The ATP and UTP binding domains are located at the tetramer interface, whereas the glutamine binding domain is located away from the tetramer interface.[3]

Glutamine is hydrolysed by the glutamine amidotransferase domain on the outside of the CTPS1 enzyme. The ammonia produced is channelled through to the synthase domain in the interior of the enzyme, to the tetrameric interface. ATP-dependent phosphorylation of UTP produces 4-phosphoryl UTP, which reacts with the ammonia to produce CTP. The reaction can also take place using ammonia in solution in place of the glutamine-derived ammonia. Guanosine triphosphate (GTP) is an allosteric activator of enzyme activity which stimulates the hydrolysis of glutamine. CTP is an allosteric inhibitor of enzyme activity; the CTP binding site overlaps with and impedes the UTP binding site. Thus, CTPS1 enzymatic activity is sensitive to the levels of all four essential ribonucleotides.[4] [5]

De novo pyrimidine synthesis pathway

The conversion of UTP to CTP is the final and rate limiting step in the de novo pyrimidine synthesis pathway. This step is unusual as it is catalysed by two homologous enzymes, CTPS1 and CTPS2, which share 74% homology at the protein level in humans. Human genetics suggest different cellular dependencies on CTPS1 and CTPS2 activity (see below).

Pyrimidines can also be generated by a salvage pathway that recycles DNA. Whilst the salvage pathway is sufficient for pyrimidine production in non-dividing cells, de novo pyrimidine synthesis is required for dividing cells.

Clinical significance

Inherited mutations

Inherited CTPS1 deficiency is associated with a severe immunodeficiency syndrome characterised by life-threatening varicella zoster virus (VZV) and Epstein–Barr virus (EBV) infection in the first decade of life. Several cases of Epstein–Barr virus–associated lymphoproliferative disease have also been observed, including in the central nervous system. Importantly, no phenotype has been observed outside of the blood system, suggesting that CTPS2 is able to compensate for the CTPS1 loss in other tissues.[6] [7] [8]

All individuals described to date are homozygous for the same splicing mutation in CTPS1, which results in skipping of exon 18 resulting in a severely hypomorphic enzyme. All reported families have ancestry in the North West of England, indicating a founder effect for the causative mutation.

The blood systems of individuals with inherited CTPS1 deficiency are characterised by the following:

  1. Normal numbers of T cells, normal T cell subsets
  2. Near absence of invariant NKT cells and mucosal associated invariant T cell
  3. Normal numbers of total B cells, reduced proportion of memory B cells
  4. Reduced numbers of NK cells
  5. Severely impaired T cell proliferation response and reduced IL-2 secretion following activation
  6. Impaired B cell proliferation response following activation
  7. Elevated IgG with selective deficiencies of specific antibodies
  8. Normal numbers and subset distribution of myeloid cells and dendritic cells

Inherited CTPS1 deficiency can be cured by allogeneic bone marrow transplantation.[9] [10]

Cancer

Increased expression of CTPS1 has been reported to play a role in several different cancer types.

High expression of CTPS1 has been reported to impart a worse prognosis in myeloma, pancreatic cancer and breast cancer.[11] [12] [13] [14] [15] [16]

miR-125b-5p was identified as a tumour suppressor which is down regulated in squamous cell lung cancer; CTPS1 is a potential target of miR-125b-5p, and loss of expression of this miR is predicted to result in increased expression of CTPS1.[17]

CTPS1 knock down by shRNA inhibited tumour cell growth in a breast cancer model.[18] CTPS1 knock down by CRISPR showed synergy with inhibition of ATR in a model of MYC-driven cancer.[19]

CTPS1 as a therapeutic target

Cancer therapy

The high proliferation rates and metabolic activity of cancer cells are likely to result in a critical dependency on the de novo pyrimidine synthesis pathway. This dependency is exploited therapeutically by several chemotherapy drugs that block de novo pyrimidine synthesis, including the nucleotide analogues cytosine arabinoside (ara-C) and gemcitabine.[20]

Cyclopentenyl cytosine (CPEC) is an inhibitor of both CTPS1 and CTPS2, with activity thought to be mediated by its 5'-triphosphate metabolite CPEC-TP. In phase 1 clinical studies, CPEC administration resulted in unpredictable and refractory hypotension, including fatal events, resulting in discontinuation of clinical development.[21] [22]

Recently, selective small molecule inhibitors have been described with a high degree of selectivity for CTPS1 over CTPS2. The binding mode and mechanism of CTPS1 selectivity has been resolved by cryo-EM which showed docking of the compounds to the CTP binding site of the enzyme.[23] A lead clinical candidate from this chemical series has shown efficacy in preclinical models of B and T cell neoplasia.[24]

A first in human clinical trial of a selective CTPS1 inhibitor will open to recruitment for patients with relapsed/refractory B cell lymphoma or T cell lymphoma late summer 2022 (NCT05463263).

Anti-viral therapy

Nucleoside analogues have a long history in the treatment of viral infection.[25] [26]

Specific inhibition of CTP synthase has been identified as a target for anti-viral therapies.[27] [28]

Epstein–Barr virus (EBV) upregulates the expression of both CTPS1 and CTPS2 in infected B cells, with the expression of CTPS1 increasing earlier than CTPS2. The EBV protein ENBA-LP binds to the CTPS1 promoter, along with MYC and NFκB, to enhance expression of CTPS1.[29]

SARS-CoV-2, the virus that causes COVID-19, uses CTPS1 from infected cells to drive its proliferation; inhibition of CTPS1 has been highlighted as a potential anti-viral therapy.[30]

Further reading

Notes and References

  1. Yamauchi M, Yamauchi N, Phear G, Spurr NK, Martinsson T, Weith A, Meuth M . Genomic organization and chromosomal localization of the human CTP synthetase gene (CTPS) . Genomics . 11 . 4 . 1088–1096 . December 1991 . 1783378 . 10.1016/0888-7543(91)90036-E .
  2. Web site: Entrez Gene: CTP synthase.
  3. Kursula P, Flodin S, Ehn M, Hammarström M, Schüler H, Nordlund P, Stenmark P . Structure of the synthetase domain of human CTP synthetase, a target for anticancer therapy . Acta Crystallographica. Section F, Structural Biology and Crystallization Communications . 62 . Pt 7 . 613–617 . July 2006 . 16820675 . 2242944 . 10.1107/S1744309106018136 .
  4. Lauritsen I, Willemoës M, Jensen KF, Johansson E, Harris P . Structure of the dimeric form of CTP synthase from Sulfolobus solfataricus . Acta Crystallographica. Section F, Structural Biology and Crystallization Communications . 67 . Pt 2 . 201–208 . February 2011 . 21301086 . 3034608 . 10.1107/S1744309110052334 .
  5. Lynch EM, Kollman JM . Coupled structural transitions enable highly cooperative regulation of human CTPS2 filaments . Nature Structural & Molecular Biology . 27 . 1 . 42–48 . January 2020 . 31873303 . 6954954 . 10.1038/s41594-019-0352-5 .
  6. Martin E, Palmic N, Sanquer S, Lenoir C, Hauck F, Mongellaz C, Fabrega S, Nitschké P, Esposti MD, Schwartzentruber J, Taylor N, Majewski J, Jabado N, Wynn RF, Picard C, Fischer A, Arkwright PD, Latour S . CTP synthase 1 deficiency in humans reveals its central role in lymphocyte proliferation . Nature . 510 . 7504 . 288–292 . June 2014 . 24870241 . 6485470 . 10.1038/nature13386 . 2014Natur.510..288M .
  7. Martin E, Minet N, Boschat AC, Sanquer S, Sobrino S, Lenoir C, de Villartay JP, Leite-de-Moraes M, Picard C, Soudais C, Bourne T, Hambleton S, Hughes SM, Wynn RF, Briggs TA, Patel S, Lawrence MG, Fischer A, Arkwright PD, Latour S . Impaired lymphocyte function and differentiation in CTPS1-deficient patients result from a hypomorphic homozygous mutation . JCI Insight . 5 . 5 . 133880 . March 2020 . 32161190 . 7141395 . 10.1172/jci.insight.133880 .
  8. Nademi Z, Wynn RF, Slatter M, Hughes SM, Bonney D, Qasim W, Latour S, Trück J, Patel S, Abinun M, Flood T, Hambleton S, Cant AJ, Gennery AR, Arkwright PD . Hematopoietic stem cell transplantation for cytidine triphosphate synthase 1 (CTPS1) deficiency . Bone Marrow Transplantation . 54 . 1 . 130–133 . January 2019 . 29884857 . 10.1038/s41409-018-0246-x . 46999914 .
  9. Nademi Z, Wynn RF, Slatter M, Hughes SM, Bonney D, Qasim W, Latour S, Trück J, Patel S, Abinun M, Flood T, Hambleton S, Cant AJ, Gennery AR, Arkwright PD . Hematopoietic stem cell transplantation for cytidine triphosphate synthase 1 (CTPS1) deficiency . Bone Marrow Transplantation . 54 . 1 . 130–133 . January 2019 . 29884857 . 10.1038/s41409-018-0246-x . 46999914 .
  10. Kucuk ZY, Zhang K, Filipovich L, Bleesing JJ . CTP Synthase 1 Deficiency in Successfully Transplanted Siblings with Combined Immune Deficiency and Chronic Active EBV Infection . Journal of Clinical Immunology . 36 . 8 . 750–753 . November 2016 . 27638562 . 10.1007/s10875-016-0332-z . 44209317 .
  11. Huang HY, Wang Y, Wang WD, Wei XL, Gale RP, Li JY, Zhang QY, Shu LL, Li L, Li J, Lin HX, Liang Y . A prognostic survival model based on metabolism-related gene expression in plasma cell myeloma . Leukemia . 35 . 11 . 3212–3222 . November 2021 . 33686197 . 10.1038/s41375-021-01206-4 . 232137095 .
  12. Shukla SK, Purohit V, Mehla K, Gunda V, Chaika NV, Vernucci E, King RJ, Abrego J, Goode GD, Dasgupta A, Illies AL, Gebregiworgis T, Dai B, Augustine JJ, Murthy D, Attri KS, Mashadova O, Grandgenett PM, Powers R, Ly QP, Lazenby AJ, Grem JL, Yu F, Matés JM, Asara JM, Kim JW, Hankins JH, Weekes C, Hollingsworth MA, Serkova NJ, Sasson AR, Fleming JB, Oliveto JM, Lyssiotis CA, Cantley LC, Berim L, Singh PK . MUC1 and HIF-1alpha Signaling Crosstalk Induces Anabolic Glucose Metabolism to Impart Gemcitabine Resistance to Pancreatic Cancer . Cancer Cell . 32 . 1 . 71–87.e7 . July 2017 . 28697344 . 5533091 . 10.1016/j.ccell.2017.06.004 .
  13. Conte F, Sibilio P, Grimaldi AM, Salvatore M, Paci P, Incoronato M . In silico recognition of a prognostic signature in basal-like breast cancer patients . PLOS ONE . 17 . 2 . e0264024 . 2022 . 35167614 . 8846521 . 10.1371/journal.pone.0264024 . 2022PLoSO..1764024C . free .
  14. Lin Y, Zhang J, Li Y, Guo W, Chen L, Chen M, Chen X, Zhang W, Jin X, Jiang M, Xiao H, Wang C, Song C, Fu F . CTPS1 promotes malignant progression of triple-negative breast cancer with transcriptional activation by YBX1 . Journal of Translational Medicine . 20 . 1 . 17 . January 2022 . 34991621 . 8734240 . 10.1186/s12967-021-03206-5 . free .
  15. Cao W, Jiang Y, Ji X, Guan X, Lin Q, Ma L . Identification of novel prognostic genes of triple-negative breast cancer using meta-analysis and weighted gene co-expressed network analysis . Annals of Translational Medicine . 9 . 3 . 205 . February 2021 . 33708832 . 7940929 . 10.21037/atm-20-5989 . free .
  16. Huang SP, Jiang YF, Yang LJ, Yang J, Liang MT, Zhou HF, Luo J, Yang DP, Mo WJ, Chen G, Shi L, Gan TQ . Downregulation of miR-125b-5p and Its Prospective Molecular Mechanism in Lung Squamous Cell Carcinoma . Cancer Biotherapy & Radiopharmaceuticals . 37 . 2 . 125–140 . March 2022 . 32614608 . 10.1089/cbr.2020.3657 . 220327036 .
  17. Huang SP, Jiang YF, Yang LJ, Yang J, Liang MT, Zhou HF, Luo J, Yang DP, Mo WJ, Chen G, Shi L, Gan TQ . Downregulation of miR-125b-5p and Its Prospective Molecular Mechanism in Lung Squamous Cell Carcinoma . Cancer Biotherapy & Radiopharmaceuticals . 37 . 2 . 125–140 . March 2022 . 32614608 . 10.1089/cbr.2020.3657 . 220327036 .
  18. Lin Y, Zhang J, Li Y, Guo W, Chen L, Chen M, Chen X, Zhang W, Jin X, Jiang M, Xiao H, Wang C, Song C, Fu F . CTPS1 promotes malignant progression of triple-negative breast cancer with transcriptional activation by YBX1 . Journal of Translational Medicine . 20 . 1 . 17 . January 2022 . 34991621 . 8734240 . 10.1186/s12967-021-03206-5 . free .
  19. Sun Z, Zhang Z, Wang QQ, Liu JL . Combined Inactivation of CTPS1 and ATR Is Synthetically Lethal to MYC-Overexpressing Cancer Cells . Cancer Research . 82 . 6 . 1013–1024 . March 2022 . 35022212 . 10.1158/0008-5472.CAN-21-1707 . free . 9359733 .
  20. Jordheim . Lars Petter . Durantel . David . Zoulim . Fabien . Dumontet . Charles . June 2013 . Advances in the development of nucleoside and nucleotide analogues for cancer and viral diseases . Nature Reviews. Drug Discovery . 12 . 6 . 447–464 . 10.1038/nrd4010 . 1474-1784 . 23722347. 39842610 .
  21. Schimmel KJ, Gelderblom H, Guchelaar HJ . Cyclopentenyl cytosine (CPEC): an overview of its in vitro and in vivo activity . Current Cancer Drug Targets . 7 . 5 . 504–509 . August 2007 . 17691910 . 10.2174/156800907781386579 .
  22. Politi PM, Xie F, Dahut W, Ford H, Kelley JA, Bastian A, Setser A, Allegra CJ, Chen AP, Hamilton JM . Phase I clinical trial of continuous infusion cyclopentenyl cytosine . Cancer Chemotherapy and Pharmacology . 36 . 6 . 513–523 . 1995 . 7554044 . 10.1007/BF00685802 . 799892 .
  23. Lynch EM, DiMattia MA, Albanese S, van Zundert GC, Hansen JM, Quispe JD, Kennedy MA, Verras A, Borrelli K, Toms AV, Kaila N, Kreutter KD, McElwee JJ, Kollman JM . Structural basis for isoform-specific inhibition of human CTPS1 . Proceedings of the National Academy of Sciences of the United States of America . 118 . 40 . e2107968118 . October 2021 . 34583994 . 8501788 . 10.1073/pnas.2107968118 . 2021PNAS..11807968L . free .
  24. Asnagli H, Minet N, Pfeiffer C, Hoeben E, Lane R, Laughton D, Birch L, Jones G, Novak A, Parker AE, Ludwig H, Fischer A, Latour S, Beer PA . CTP Synthase 1 Is a Novel Therapeutic Target in Lymphoma . HemaSphere . 7 . 4 . e864 . April 2023 . 37008165 . 10060080 . 10.1097/HS9.0000000000000864 .
  25. De Clercq E . 1994-07-01 . Antiviral Activity Spectrum and Target of Action of Different Classes of Nucleoside Analogues . Nucleosides and Nucleotides . 13 . 6–7 . 1271–1295 . 10.1080/15257779408012151 . 0732-8311.
  26. Jordheim LP, Durantel D, Zoulim F, Dumontet C . Advances in the development of nucleoside and nucleotide analogues for cancer and viral diseases . Nature Reviews. Drug Discovery . 12 . 6 . 447–464 . June 2013 . 23722347 . 10.1038/nrd4010 . 39842610 .
  27. De Clercq E, Bernaerts R, Shealy YF, Montgomery JA . Broad-spectrum antiviral activity of carbodine, the carbocyclic analogue of cytidine . Biochemical Pharmacology . 39 . 2 . 319–325 . January 1990 . 1689159 . 7111205 . 10.1016/0006-2952(90)90031-f .
  28. De Clercq E, Murase J, Marquez VE . Broad-spectrum antiviral and cytocidal activity of cyclopentenylcytosine, a carbocyclic nucleoside targeted at CTP synthetase . Biochemical Pharmacology . 41 . 12 . 1821–1829 . June 1991 . 1710119 . 7111160 . 10.1016/0006-2952(91)90120-t .
  29. Liang JH, Wang C, Yiu SP, Zhao B, Guo R, Gewurz BE . Epstein-Barr Virus Induced Cytidine Metabolism Roles in Transformed B-Cell Growth and Survival . mBio . 12 . 4 . e0153021 . August 2021 . 34281398 . 8406234 . 10.1128/mBio.01530-21 .
  30. Rao Y, Wang TY, Qin C, Espinosa B, Liu Q, Ekanayake A, Zhao J, Savas AC, Zhang S, Zarinfar M, Liu Y, Zhu W, Graham NA, Jiang T, Zhang C, Feng P . Targeting CTP Synthetase 1 to Restore Interferon Induction and Impede Nucleotide Synthesis in SARS-CoV-2 Infection . bioRxiv . 2021.02.05.429959 . February 2021 . 33564769 . 7872357 . 10.1101/2021.02.05.429959 .