KDM2B, PHYH, P3H2, PLOD3 and ME

Alpha-ketoglutarate dependent dioxygenases are also called 2-oxoglutarate oxygenases. They are a large family of enzymes with most diverse functions (1).

The following examples are relevant for ME research.

KDM2B
KDM2B (lysine demethylase 2B) is one of the 2OG-oxygenases described in ref 1. The gene KDM2B is hypermethylated in ME patients (2). And KDM2B is hypomethylated in CD4⁺  T cells from ME patients (3). KDM2B is able to regulate histone 3 methylation. KDM2B expression is also known to regulate ribosome biogenesis, and is a positive regulator of glycolysis. KDM2B is an important mediator of hematopoietic cell development.

PHYH
PHYH (phytanoyl-CoA 2-hydroxylase) is a peroxisomal protein that is involved in the alpha-oxidation of 3-methyl branched fatty acids. The gene is hypermethylated in ME patients (2).

P3H2
P3H2 (prolyl 3-hydroxylase 2, also known as LEPREL1) play a critical role in collagen chain assembly, stability and cross-linking by catalyzing post-translational 3-hydroxylation of proline residues. This is important to basement membranes. Interestingly, P3H2 has a FIS1 mitochondrial fission protein1) domain. P3H2 is hypomethylated in ME patients (2).

PLOD3
PLOD3 (procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3) catalyzes the hydroxylation of lysyl residues in collagen-like peptides. PLOD3 is found in the basement membrane. Reduced levels are associated to disease. Spinal fluid PLOD3 levels in ME patients:9 and normal value:14 (4). Interestingly, PLOD3 is located on chromosome 7 besides FIS1 and CLDN15. CLDN15 is hypermethylated in ME patients and this is associated to quality of life (2).CLDN15 (claudin 15) is an integral membrane pretein and component of tight junction strands. CLDN15 has been associated with irritabel bowel syndrome.

References:

1. Loenarz and Schofield: Expanding chemical biology of 2-oxoglutarate oxygenases. Nat Chem Biol, 2008, 4, 3.
2. Vega et al: Epigenetic modifications and glucocorticoid sensitivity in ME/CFS. BMC Medical Genomics, 2017, 10, 11
3. Brenu et al: Methylation profile of CD4+ T cells in CFS/ME. J. Clin Cell Immunol 5, 228
4. Schutzer et al: Distinct Cerebrospinal Fluid Proteomes Differentiate Post- Treatment Lyme Disease from Chronic Fatigue Syndrome. PLOS One February 2011, volume 6, Issue

         Knowledge about the genes: www.ncbi.nlm.nih.gov/gene

D2HGDH, PHYKPL and ME

The gene D2HGDH is hypomethylated in ME patients, and this is associated with quality of life (1). Hypomethylation can result in upregulation of gene transcription. In agreement with this, gene expression of D2HGDH was upregulated in whole blood from adolescent ME/CFS patients (2).

D2HGDH encodes D-2-hydroxy-glutarate dehydrogenase, which converts D-2-hydroxyglutarate to alpha-ketoglutarate (alpha - KG). Mutations in D2HGDH are present in D-2-hydroxyglutaric aciduria, a rare neurometabolic disorder.

It is possible that 2-hydroxy glutarate is generated in relation to lysine breakdown. PHYKPL, 5-phosphohydroxy-L-lysine phospholyase, gene expression is upregulated in ME/CFS patients (2).

D2HGDH regulates alpha-KG levels and alpha-KG dependent dioxygenase function by modulating isocitrate dehydrogenase 2 (IDH2) (3).

Some of the enzymes that regulate histone and DNA methylation belong to the family of alpha-KG dependent dioxygenases.

Fx, D2HGHD induces demethylation of histone H3K4me3, so it becomes H3K4. This change is relevant to B cell differentiation (3,4)

D2HGDH is one of the genes that when mutant may promote epigenetic changes in B-cell cancer (3).

Furthermore, alpha-KG metabolism and IDH2 expression are part of the metabolic reprogramming-response in pyruvate dehydrogenase deficient cells (5).

References:

1. Vega et al: Epigenetic modifications and glucocorticoid sensitivity in ME/CFS. BMC Medical Genomics, 2017, 10, 11
2. Nguyen et al: Whole blood gene expression in adolescent CFS: an exploratory crosssectional study suggesting altered B cell differentiation and survival. J Transl Med. 2017,15,102.
3. Lin et al: D2HGDH regulates alpha-ketoglutarate levels and dioxygenase function by modulating IDH2. Nat Comm. 16.jul 2015.
4. Barneda-Zahonero et al: Epigenetic regulation of B lymphocyte differentiation, transdifferentiation and reprogramming. Hindawi, 2012, ID564381
5. Rajagopalan et al. Metabolic plasticity maintains proliferation in pyruvate dehydrogenase deficient cells. Cancer & Metabolism (2015) 3:7

DGKZ and ME

ME patients have two hypermeyhylated sites in the gene DGKZ. They are associated with quality of life (1). Hypermethylation can result in suppressed transcription of the gene.

The enzyme diacylglycerol kinase zeta (DGKZ) catalyzes diacylglycerol (DAG) to phosphatidic acid (PA).

DGKZ controls DAG metabolism at the immonological synapse between the T cell and a target cell.

Disruption of DAG metabolism impairs the induction of T cell anergy, which is a process important to maintain peripheral T cell totelance.

DGKZ deficiency is associated with enhanced T cell response (2).

References:

1. Vega et al: Epigenetic modifications and glucocorticoid sensitivity in ME/CFS. BMC Medical Genomics, 2017, 10, 11
2. Gharbi et al: DGKZ controls diacylglycerol metabolism at the immunological synapse. Mol Biol Cell, 2011, 22, 15.

ATP6V0E2, PRF1, GNLY and ME

The T-cell forms an immunological synapse with a target cell. Then vesicles containing perforin and cytotoxic enzymes are released to kill the target cell. Perforin forms small pores in the membrane of the target cell. The cytotoxic vesicles are acidic (pH 5,1 - 5,4), which prevents perforin activation. Activation of perforin requires a neutral pH environment (1).

Hypermethylated genes nr. 2 and nr. 3 associated with quality of life in ME patients are ATP6V0E2 and ATP6V0E2 antisense RNA1 (2).

The gene ATP6V0E2 encodes a component of vacuolar ATPase which mediates acidification of several intracellular compartments and secretory granules/vesicles. The v-ATPase is also called proton pump or H⁺- ATPase.

ATP6V0E2 is an isoform of the V0e subunit. Diverse physiological functions of the v-ATPase in different membranes are established through the utilization of specific subunit isoforms.

The genes PRF1 (perforin 1) and GNLY (granulysin) are hypermethylated and associated with quality of life in ME patients (2).

Granulysin is also present in the cytotoxic vesicles of T-cells. It has antimicrobial activity.

Is the hypermethylated ATP6V0E2 related to a "pH-situation" in the cytotoxic vesicles and/or in the immunological synapse?

References:

1. Kloc et al: The newly found functions of MTOC in immunological response. J Leucocyte Biology, 2014, 95.
2. Vega et al: Epigenetic modifications and glucocorticoid sensitivity in ME/CFS. BMC Medical Genomics, 2017, 10, 11

ACVR1, activiner og ME

Activiner er vækst og differentiations faktorer, der tilhører TGF-beta superfamilien. Activiner signalerer gennem et receptor kompleks bestående af flere forskellige receptorer. Én af disse er activin A receptor type 1 (ACVR1).

Genet for ACVR1 er hypermethyleret to forskellige steder hos ME patienter. ACVR1 optræder derfor både på 11. og 12. pladsen over epigenetiske ændrede gener, der relaterer til ME patienters livskvalitet (1).

Forhøjede niveauer af activin A og B kan påvises ved inflammatorisk respons. Hos ME patienter har man fundet:

• normalt niveau af activin A
• forhøjet niveau af activin B
• lavere niveau af det activin-bindende protein follistatin (FST)
• forhøjet ratio af activin A/FST
• forhøjet ratio af activin B/FST
• forhøjet ratio af activin B/activin A

Proteinet STAR transporterer kolesterol fra den ydre til den indre mitokondrie membran. Herved kan kolesterol omdannes til pregnenolone, som anvendes til videre steroid produktion.

Activin A, B og AB nedregulerer STAR expression og progesterone produktion i granulosa celler i æggestokkene (3).

Kan den generelle STAR ekspression og kolesterolomsætning være påvirket af activin / follistatinaksen hos ME patienter?

Referencer:

1. Vega et al: Epigenetic modifications and glucocorticoid sensitivity in ME/CFS. BMC Medical Genomics, 2017, 10, 11
2. Lidbury et al: Activin B is a novel biomarker for CFS/ME. J. Transl. Med. 2017, 15, 60.
3. Chang et al. PMID26001835