IDH1

Isocitrate dehydrogenase 1 (NADP+), soluble is an enzyme that in humans is encoded by the IDH1 gene on chromosome 2. Isocitrate dehydrogenases catalyze the oxidative decarboxylation of isocitrate to 2-oxoglutarate. These enzymes belong to two distinct subclasses, one of which uses NAD⁺ as the electron acceptor and the other NADP⁺. Five isocitrate dehydrogenases have been reported: three NAD⁺-dependent isocitrate dehydrogenases, which localize to the mitochondrial matrix, and two NADP⁺-dependent isocitrate dehydrogenases, one of which is mitochondrial and the other predominantly cytosolic. Each NADP⁺-dependent isozyme is a homodimer. The protein encoded by this gene is the NADP⁺-dependent isocitrate dehydrogenase found in the cytoplasm and peroxisomes. It contains the PTS-1 peroxisomal targeting signal sequence. The presence of this enzyme in peroxisomes suggests roles in the regeneration of NADPH for intraperoxisomal reductions, such as the conversion of 2,4-dienoyl-CoAs to 3-enoyl-CoAs, as well as in peroxisomal reactions that consume 2-oxoglutarate, namely the alpha-hydroxylation of phytanic acid. The cytoplasmic enzyme serves a significant role in cytoplasmic NADPH production. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Sep 2013][5]

IDH1
Available structures PDB Ortholog search: PDBe RCSB List of PDB id codes 1T09, 1T0L, 3INM, 3MAP, 3MAR, 3MAS, 4I3K, 4I3L, 4KZO, 4L03, 4L04, 4L06, 4UMX, 4UMY, 4XRX, 5DE1, 4XS3, 5K10, 5K11
Identifiers
Aliases	IDH1, HEL-216, HEL-S-26, IDCD, IDH, IDP, IDPC, PICD, isocitrate dehydrogenase (NADP(+)) 1, cytosolic, isocitrate dehydrogenase (NADP(+)) 1
External IDs	OMIM: 147700 MGI: 96413 HomoloGene: 21195 GeneCards: IDH1
Gene location (Human) Chr. Chromosome 2 (human)[1] Band 2q34 Start 208,236,227 bp[1] End 208,266,074 bp[1]
Gene location (Mouse) Chr. Chromosome 1 (mouse)[2] Band 1 C2|1 32.91 cM Start 65,158,616 bp[2] End 65,186,500 bp[2]
Gene ontology Molecular function • magnesium ion binding • protein homodimerization activity • oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor • receptor binding • isocitrate dehydrogenase (NADP+) activity • oxidoreductase activity • NAD binding • isocitrate dehydrogenase activity • NADP binding • metal ion binding • (R)-2-hydroxyglutarate dehydrogenase activity • cadherin binding • identical protein binding Cellular component • peroxisome • cytosol • extracellular exosome • peroxisomal matrix • cytoplasm • mitochondrion • extracellular region • secretory granule lumen • tertiary granule lumen • ficolin-1-rich granule lumen Biological process • female gonad development • NADPH regeneration • response to oxidative stress • response to organic cyclic compound • response to steroid hormone • 2-oxoglutarate metabolic process • regulation of phospholipid catabolic process • isocitrate metabolic process • glyoxylate cycle • tricarboxylic acid cycle • regulation of phospholipid biosynthetic process • glutathione metabolic process • oxidation-reduction process • neutrophil degranulation • protein targeting to peroxisome • NADP metabolic process Sources:Amigo / QuickGO
Orthologs
Species	Human	Mouse
Entrez	3417	15926
Ensembl	ENSG00000138413	ENSMUSG00000025950
UniProt	O75874	O88844
RefSeq (mRNA)	NM_005896 NM_001282386 NM_001282387	NM_001111320 NM_010497
RefSeq (protein)	NP_001269315 NP_001269316 NP_005887	NP_001104790 NP_034627
Location (UCSC)	Chr 2: 208.24 – 208.27 Mb	Chr 1: 65.16 – 65.19 Mb
PubMed search	[3]	[4]
Wikidata
View/Edit Human View/Edit Mouse

Structure

IDH1 is one of three isocitrate dehydrogenase isozymes, the other two being IDH2 and IDH3, and encoded by one of five isocitrate dehydrogenase genes, which are IDH1, IDH2, IDH3A, IDH3B, and IDH3G.[6]

IDH1 forms an asymmetric homodimer in the cytoplasm and carries out its function through two hydrophilic active sites formed by both protein subunits.[7][8][9][10][11] Each subunit or monomer is composed of three domains: a large domain (residues 1–103 and 286–414), a small domain (residues 104–136 and 186–285), and a clasp domain (residues 137 to 185). The large domain contains a Rossmann fold, while the small domain forms an α/β sandwich structure, and the clasp domain folds as two stacked double-stranded anti-parallel β-sheets. A β-sheet joins the large and small domains and is flanked by two clefts on opposite sides. The deep cleft, also known as the active site, is formed by the large and small domains of one subunit and a small domain of the other subunit. This active site includes the NADP-binding site and the isocitrate-metal ion-binding site. The shallow cleft, also referred to as the back cleft, is formed by both domains of one subunit and participates in the conformational changes of homodimeric IDH1. Finally, the clasp domains of both subunits intertwine to form a double layer of four-stranded anti-parallel β-sheets linking together the two subunits and the two active sites.[11]

Furthermore, conformational changes to the subunits and a conserved structure at the active site affect the activity of the enzyme. In its open, inactive form, the active site structure forms a loop while one subunit adopts an asymmetric open conformation and the other adopts a quasi-open conformation.[9][11] This conformation enables isocitrate to bind the active site, inducing a closed conformation that also activates IDH1.[9] In its closed, inactive form, the active site structure becomes an α-helix that can chelate metal ions. An intermediate, semi-open form features this active site structure as a partially unraveled α-helix.[11]

There is also a type 1 peroxisomal targeting sequence at its C-terminal that targets the protein to the peroxisome.[11]

Function

As an isocitrate dehydrogenase, IDH1 catalyzes the reversible oxidative decarboxylation of isocitrate to yield α-ketoglutarate (α-KG) as part of the TCA cycle in glucose metabolism.[6][7][8][10][11] This step also allows for the concomitant reduction of nicotinamide adenine dinucleotide phosphate (NADP+) to reduced nicotinamide adenine dinucleotide phosphate (NADPH).[7][8][10] Since NADPH and α-KG function in cellular detoxification processes in response to oxidative stress, IDH1 also indirectly participates in mitigating oxidative damage.[6][7][11][12] In addition, IDH1 is key to β-oxidation of unsaturated fatty acids in the peroxisomes of liver cells.[11] IDH1 also participates in the regulation of glucose-induced insulin secretion.[6] Notably, IDH1 is the primary producer of NADPH in most tissues, especially in brain.[7] Within cells, IDH1 has been observed to localize to the cytoplasm, peroxisome, and endoplasmic reticulum.[10][12]

Under hypoxic conditions, IDH1 catalyzes the reverse reaction of α-KG to isocitrate, which contributes to citrate production via glutaminolysis.[6][7] Isocitrate can also be converted into acetyl-CoA for lipid metabolism.[6]

Mutation

IDH1 mutations are heterozygous, typically involving an amino acid substitution in the active site of the enzyme in codon 132.[13][14] The mutation results in a loss of normal enzymatic function and the abnormal production of 2-hydroxyglutarate (2-HG).[13] It has been considered to take place due to a change in the binding site of the enzyme.[15] 2-HG has been found to inhibit enzymatic function of many alpha-ketoglutarate dependent dioxygenases, including histone and DNA demethylases, causing widespread changes in histone and DNA methylation and potentially promoting tumorigenesis.[14][16]

Clinical Significance

Mutations in this gene have been shown to cause metaphyseal chondromatosis with aciduria.[17]

Mutations in IDH1 are also implicated in cancer. Originally, mutations in IDH1 were detected in an integrated genomic analysis of human glioblastoma multiforme.[18] Since then it has become clear that mutations in IDH1 and its homologue IDH2 are among the most frequent mutations in diffuse gliomas, including diffuse astrocytoma, anaplastic astrocytoma, oligodendroglioma, anaplastic oligodendroglioma, oligoastrocytoma, anaplastic oligoastrocytoma, and secondary glioblastoma.[19] Mutations in IDH1 are often the first hit in the development of diffuse gliomas, suggesting IDH1 mutations as key events in the formation of these brain tumors.[20][21][22] Glioblastomas with a wild-type IDH1 gene have a median overall survival of only 1 year, whereas IDH1-mutated glioblastoma patients have a median overall survival of over 2 years.[23] Tumors of various tissue types with IDH1/2 mutations show improved responses to radiation and chemotherapy.[24][25] The best-studied mutation in IDH1 is R132H, which has been show to act as a tumor suppressor.[26]

In addition to being mutated in diffuse gliomas, IDH1 has also been shown to harbor mutations in human acute myeloid leukemia.[27][28]

The IDH1 mutation is considered a driver alteration and occurs early during tumorigenesis, in specific in glioma and glioblastoma multiforme, its possible use as a new tumour-specific antigen to induce antitumor immunity for the cancer treatment has recently been prompted.[29] A tumour vaccine can stimulate the body’s immune system, upon exposure to a tumour-specific peptide antigen, by activation or amplification of a humoral and cytotoxic immune response targeted at the specific cancer cells.

The study of Schumacher et al. has been shown that this attractive target (the mutation in the isocitrate dehydrogenase 1) from an immunological perspective represents a potential tumour-specific neoantigen with high uniformity and penetrance and could be exploited by immunotherapy through vaccination. Accordingly, some patients with IDH1-mutated gliomas demonstrated spontaneous peripheral CD4+ T-cell responses against the mutated IDH1 region with generation B-cell producing antibodies. Vaccination of MHC-humanized transgenic mice with mutant IDH1 peptide induced an IFN-γ CD4+ T-helper 1 cell response, indicating an endogenous processing through MHC class II, and production of antibodies targeting mutant IDH1. Tumour vaccination, both prophylactic and therapeutic, resulted in growth suppression of transplanted IDH1-expressing sarcomas in MHC-humanized mice. This in vivo data shows a specific and potent immunologic response in both transplanted and existing tumours.[29]

As a drug target

Mutated and normal forms of IDH1 had been studied for drug inhibition both in silico and in vitro,[30][31][32][33] and some drugs are being developed (e.g. Ivosidenib). Ivosidenib was approved by the FDA in July 2018 for relapsed or refractory acute myeloid leukemia (AML) with an IDH1 mutation.[34]

References

1. GRCh38: Ensembl release 89: ENSG00000138413 - Ensembl, May 2017
2. GRCm38: Ensembl release 89: ENSMUSG00000025950 - Ensembl, May 2017
3. "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
4. "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
5. "Entrez Gene: Isocitrate dehydrogenase 1 (NADP+), soluble". Retrieved 2011-12-30.
6. Dimitrov L, Hong CS, Yang C, Zhuang Z, Heiss JD (2015). "New developments in the pathogenesis and therapeutic targeting of the IDH1 mutation in glioma". International Journal of Medical Sciences. 12 (3): 201–13. doi:10.7150/ijms.11047. PMC 4323358. PMID 25678837.
7. Molenaar RJ, Radivoyevitch T, Maciejewski JP, van Noorden CJ, Bleeker FE (December 2014). "The driver and passenger effects of isocitrate dehydrogenase 1 and 2 mutations in oncogenesis and survival prolongation". Biochimica et Biophysica Acta (BBA) - Reviews on Cancer. 1846 (2): 326–41. doi:10.1016/j.bbcan.2014.05.004. PMID 24880135.
8. Kim HJ, Fei X, Cho SC, Choi BY, Ahn HC, Lee K, et al. (December 2015). "Discovery of α-mangostin as a novel competitive inhibitor against mutant isocitrate dehydrogenase-1". Bioorganic & Medicinal Chemistry Letters. 25 (23): 5625–31. doi:10.1016/j.bmcl.2015.10.034. PMID 26508549.
9. Zhao S, Guan KL (December 2010). "IDH1 mutant structures reveal a mechanism of dominant inhibition". Cell Research. 20 (12): 1279–81. doi:10.1038/cr.2010.160. PMID 21079649. S2CID 41199424.
10. Guo C, Pirozzi CJ, Lopez GY, Yan H (December 2011). "Isocitrate dehydrogenase mutations in gliomas: mechanisms, biomarkers and therapeutic target". Current Opinion in Neurology. 24 (6): 648–52. doi:10.1097/WCO.0b013e32834cd415. PMC 3640434. PMID 22002076.
11. Xu X, Zhao J, Xu Z, Peng B, Huang Q, Arnold E, Ding J (August 2004). "Structures of human cytosolic NADP-dependent isocitrate dehydrogenase reveal a novel self-regulatory mechanism of activity". The Journal of Biological Chemistry. 279 (32): 33946–57. doi:10.1074/jbc.M404298200. PMID 15173171. S2CID 7513167.
12. Fu Y, Huang R, Du J, Yang R, An N, Liang A (June 2010). "Glioma-derived mutations in IDH: from mechanism to potential therapy". Biochemical and Biophysical Research Communications. 397 (2): 127–30. doi:10.1016/j.bbrc.2010.05.115. PMID 20510884.
13. Turkalp Z, Karamchandani J, Das S (October 2014). "IDH mutation in glioma: new insights and promises for the future". JAMA Neurology. 71 (10): 1319–25. doi:10.1001/jamaneurol.2014.1205. PMID 25155243.
14. Liu X, Ling ZQ (October 2015). "Role of isocitrate dehydrogenase 1/2 (IDH 1/2) gene mutations in human tumors". Histology and Histopathology. 30 (10): 1155–60. doi:10.14670/HH-11-643. PMID 26147657.
15. Bascur, Juan P.; Alegria-Arcos, Melissa; Araya-Duran, Ingrid; Juritz, Ezequiel I.; Gonzalez-Nilo, Fernando D.; Almonacid, Daniel E. (2018-10-20). "IDH1 and IDH2 mutants identified in cancer lose inhibition by isocitrate because of a change in their binding sites". bioRxiv: 425025. doi:10.1101/425025. S2CID 91257424.
16. Wang YP, Lei QY (May 2018). "Metabolic recoding of epigenetics in cancer". Cancer Communications. 38 (1): 25. doi:10.1186/s40880-018-0302-3. PMC 5993135. PMID 29784032.
17. Vissers LE, Fano V, Martinelli D, Campos-Xavier B, Barbuti D, Cho TJ, et al. (November 2011). "Whole-exome sequencing detects somatic mutations of IDH1 in metaphyseal chondromatosis with D-2-hydroxyglutaric aciduria (MC-HGA)". American Journal of Medical Genetics. Part A. 155A (11): 2609–16. doi:10.1002/ajmg.a.34325. PMID 22025298. S2CID 33345097.
18. Parsons DW, Jones S, Zhang X, Lin JC, Leary RJ, Angenendt P, et al. (September 2008). "An integrated genomic analysis of human glioblastoma multiforme". Science. 321 (5897): 1807–12. Bibcode:2008Sci...321.1807P. doi:10.1126/science.1164382. PMC 2820389. PMID 18772396.
19. Yan H, Parsons DW, Jin G, McLendon R, Rasheed BA, Yuan W, et al. (February 2009). "IDH1 and IDH2 mutations in gliomas". The New England Journal of Medicine. 360 (8): 765–73. doi:10.1056/NEJMoa0808710. PMC 2820383. PMID 19228619.
20. Watanabe T, Nobusawa S, Kleihues P, Ohgaki H (April 2009). "IDH1 mutations are early events in the development of astrocytomas and oligodendrogliomas". The American Journal of Pathology. 174 (4): 1149–53. doi:10.2353/ajpath.2009.080958. PMC 2671348. PMID 19246647.
21. Bleeker FE, Molenaar RJ, Leenstra S (May 2012). "Recent advances in the molecular understanding of glioblastoma". Journal of Neuro-Oncology. 108 (1): 11–27. doi:10.1007/s11060-011-0793-0. PMC 3337398. PMID 22270850.
22. Bai H, Harmancı AS, Erson-Omay EZ, Li J, Coşkun S, Simon M, et al. (January 2016). "Integrated genomic characterization of IDH1-mutant glioma malignant progression". Nature Genetics. 48 (1): 59–66. doi:10.1038/ng.3457. PMC 4829945. PMID 26618343.
23. Molenaar RJ, Verbaan D, Lamba S, Zanon C, Jeuken JW, Boots-Sprenger SH, et al. (September 2014). "The combination of IDH1 mutations and MGMT methylation status predicts survival in glioblastoma better than either IDH1 or MGMT alone". Neuro-Oncology. 16 (9): 1263–73. doi:10.1093/neuonc/nou005. PMC 4136888. PMID 24510240.
24. Molenaar RJ, Maciejewski JP, Wilmink JW, van Noorden CJ (April 2018). "Wild-type and mutated IDH1/2 enzymes and therapy responses". Oncogene. 37 (15): 1949–1960. doi:10.1038/s41388-017-0077-z. PMC 5895605. PMID 29367755.
25. Miyata S, Tominaga K, Sakashita E, Urabe M, Onuki Y, Gomi A, et al. (July 2019). "R132H Clinical Glioma Samples Reveals Suppression of β-oxidation Due to Carnitine Deficiency". Scientific Reports. 9 (1): 9787. doi:10.1038/s41598-019-46217-5. PMC 6611790. PMID 31278288.
26. Núñez FJ, Mendez FM, Kadiyala P, Alghamri MS, Savelieff MG, Garcia-Fabiani MB, et al. (February 2019). "IDH1-R132H acts as a tumor suppressor in glioma via epigenetic up-regulation of the DNA damage response". Science Translational Medicine. 11 (479): eaaq1427. doi:10.1126/scitranslmed.aaq1427. PMC 6400220. PMID 30760578.
27. Mardis ER, Ding L, Dooling DJ, Larson DE, McLellan MD, Chen K, et al. (September 2009). "Recurring mutations found by sequencing an acute myeloid leukemia genome". The New England Journal of Medicine. 361 (11): 1058–66. doi:10.1056/NEJMoa0903840. PMC 3201812. PMID 19657110.
28. Shih AH, Abdel-Wahab O, Patel JP, Levine RL (September 2012). "The role of mutations in epigenetic regulators in myeloid malignancies". Nature Reviews. Cancer. 12 (9): 599–612. doi:10.1038/nrc3343. PMID 22898539. S2CID 20214444.
29. Schumacher T, Bunse L, Pusch S, Sahm F, Wiestler B, Quandt J, et al. (August 2014). "A vaccine targeting mutant IDH1 induces antitumour immunity". Nature. 512 (7514): 324–7. Bibcode:2014Natur.512..324S. doi:10.1038/nature13387. PMID 25043048. S2CID 4468160.
30. Juritz EI, Bascur JP, Almonacid DE, González-Nilo FD (June 2018). "wt-R132H in Cancer: An In-Silico Approach". Molecular Diagnosis & Therapy. 22 (3): 369–380. doi:10.1007/s40291-018-0331-2. PMID 29651790. S2CID 4798363.
31. Jakob CG, Upadhyay AK, Donner PL, Nicholl E, Addo SN, Qiu W, et al. (August 2018). "Novel Modes of Inhibition of Wild-Type Isocitrate Dehydrogenase 1 (IDH1): Direct Covalent Modification of His315". Journal of Medicinal Chemistry. 61 (15): 6647–6657. doi:10.1021/acs.jmedchem.8b00305. OSTI 1471640. PMID 30004704.
32. Xie X, Baird D, Bowen K, Capka V, Chen J, Chenail G, et al. (March 2017). "Allosteric Mutant IDH1 Inhibitors Reveal Mechanisms for IDH1 Mutant and Isoform Selectivity". Structure. 25 (3): 506–513. doi:10.1016/j.str.2016.12.017. PMID 28132785.
33. Jones S, Ahmet J, Ayton K, Ball M, Cockerill M, Fairweather E, et al. (December 2016). "Discovery and Optimization of Allosteric Inhibitors of Mutant Isocitrate Dehydrogenase 1 (R132H IDH1) Displaying Activity in Human Acute Myeloid Leukemia Cells". Journal of Medicinal Chemistry. 59 (24): 11120–11137. doi:10.1021/acs.jmedchem.6b01320. PMID 28002956.
34. Commissioner, Office of the. "Press Announcements - FDA approves first targeted treatment for patients with relapsed or refractory acute myeloid leukemia who have a certain genetic mutation". www.fda.gov. Retrieved 2019-01-11.

Further reading

• Geisbrecht BV, Gould SJ (October 1999). "The human PICD gene encodes a cytoplasmic and peroxisomal NADP(+)-dependent isocitrate dehydrogenase". The Journal of Biological Chemistry. 274 (43): 30527–33. doi:10.1074/jbc.274.43.30527. PMID 10521434. S2CID 42785832.
• Shechter I, Dai P, Huo L, Guan G (November 2003). "IDH1 gene transcription is sterol regulated and activated by SREBP-1a and SREBP-2 in human hepatoma HepG2 cells: evidence that IDH1 may regulate lipogenesis in hepatic cells". Journal of Lipid Research. 44 (11): 2169–80. doi:10.1194/jlr.M300285-JLR200. PMID 12923220.
• Xu X, Zhao J, Xu Z, Peng B, Huang Q, Arnold E, Ding J (August 2004). "Structures of human cytosolic NADP-dependent isocitrate dehydrogenase reveal a novel self-regulatory mechanism of activity". The Journal of Biological Chemistry. 279 (32): 33946–57. doi:10.1074/jbc.M404298200. PMID 15173171. S2CID 7513167.
• Memon AA, Chang JW, Oh BR, Yoo YJ (2005). "Identification of differentially expressed proteins during human urinary bladder cancer progression". Cancer Detection and Prevention. 29 (3): 249–55. doi:10.1016/j.cdp.2005.01.002. PMID 15936593.
• Guo D, Han J, Adam BL, Colburn NH, Wang MH, Dong Z, et al. (December 2005). "Proteomic analysis of SUMO4 substrates in HEK293 cells under serum starvation-induced stress". Biochemical and Biophysical Research Communications. 337 (4): 1308–18. doi:10.1016/j.bbrc.2005.09.191. PMID 16236267.
• Kullberg M, Nilsson MA, Arnason U, Harley EH, Janke A (August 2006). "Housekeeping genes for phylogenetic analysis of eutherian relationships". Molecular Biology and Evolution. 23 (8): 1493–503. doi:10.1093/molbev/msl027. PMID 16751257.
• Wanders RJ, Waterham HR (2006). "Biochemistry of mammalian peroxisomes revisited". Annual Review of Biochemistry. 75: 295–332. doi:10.1146/annurev.biochem.74.082803.133329. PMID 16756494.
• Balss J, Meyer J, Mueller W, Korshunov A, Hartmann C, von Deimling A (December 2008). "Analysis of the IDH1 codon 132 mutation in brain tumors". Acta Neuropathologica. 116 (6): 597–602. doi:10.1007/s00401-008-0455-2. PMID 18985363. S2CID 9530236.
• Bleeker FE, Lamba S, Leenstra S, Troost D, Hulsebos T, Vandertop WP, et al. (January 2009). "IDH1 mutations at residue p.R132 (IDH1(R132)) occur frequently in high-grade gliomas but not in other solid tumors". Human Mutation. 30 (1): 7–11. doi:10.1002/humu.20937. PMID 19117336. S2CID 7742965.

This article incorporates text from the United States National Library of Medicine, which is in the public domain.