Flippase, floppase and scramblase

The cell membrane is composed of cholesterol and phospholipids arranged in a lipid bilayer (outer and inner monolayer).

There is a asymmetric phospholipid distribution in the bilayer. Three families of proteins are responsible for the translocation of phospholipids between the two monolayers (1):

• Flippases move phospholipids from the outer to the inner monolayer.
• Floppases do the opposite operation.
• Scramblases move phospholipids in both directions.

ATP10A and ATP11A

Flippase ATP10A flips phosphatidylcholine at the plasmamembrane. This activity drives membrane curvature (2).

Flippase ATP11A has flippase activity toward phosphatidylserine and phosphatidylethanolamine (3).

The gene ATP10A has changed DNA methylation pattern in peripheral blood mononuclear cells (PBMC) from ME patients (4, 5, 6).

The gene ATP11A has changed DNA methylation pattern in PBMC from ME patients (4, 5).

PLSCR1 and PLSCR3

Phospholipid scramblase 1 (PLSCR1) is also known as erythrocyte phospholipid scramblase.

Use link to see figure (7):
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5992676/figure/F7/

PLSCR1 aggravates anaphylactic reactions by increasing FcεRI-dependent mast cell degranulation. (8).

PLSCR3 may be involved in translocation of cardiolipin from the inner to the outer mitochondrial membrane (1).

PLSCR1 gene expression in whole blood was related to ME/CFS in adolescents (9, 10).

The gene PLSCR3 was hypomethylated in PBMC from ME patients (6). And PLSCR3 was differntially methylated in PBMC from ME patient subtypes (5).

CRIM1 and PLSCRs

CRIM1 interacts with PLSCRs (11):

CRIM1: Cysteine rich transmembrane BMP regulator 1 (chordin-like); May play a role in CNS development by interacting with growth factors implicated in motor neuron differentiation and survival. May play a role in capillary formation and maintenance during angiogenesis. Modulates BMP activity by affecting its processing and delivery to the cell surface (11).

PLSCR1: Phospholipid scramblase 1; May mediate accelerated ATP-independent bidirectional transbilayer migration of phospholipids upon binding calcium ions that results in a loss of phospholipid asymmetry in the plasma membrane. May play a central role in the initiation of fibrin clot formation, in the activation of mast cells and in the recognition of apoptotic and injured cells by the reticuloendothelial system (11).

Phospholipid scramblase 2; May mediate accelerated ATP-independent bidirectional transbilayer migration of phospholipids upon binding calcium ions that results in a loss of phospholipid asymmetry in the plasma membrane. May play a central role in the initiation of fibrin clot formation, in the activation of mast cells and in the recognition of apoptotic and injured cells by the reticuloendothelial system (11).

PLSCR3: Phospholipid scramblase 3; May mediate accelerated ATP-independent bidirectional transbilayer migration of phospholipids upon binding calcium ions that results in a loss of phospholipid asymmetry in the plasma membrane. May play a central role in the initiation of fibrin clot formation, in the activation of mast cells and in the recognition of apoptotic and injured cells by the reticuloendothelial system. Seems to play a role in apoptosis, through translocation of cardiolipin from the inner to the outer mitochondrial membrane (11).

The gene CRIM1 has changed DNA methylation pattern in PBMC from ME patients (4, 5, 6), and in CD4+ T-cells from ME patients (12).

New research:

Phospholipid scramblase 1 interacts with influenza A virus NP, impairing its nuclear import and thereby suppressing virus replication https://www.ncbi.nlm.nih.gov/pubmed/29352288

References

1. Wikipedia: Phospholipid scramblase
2. PMID: 29599178
3. PMID: 26567335
4. de Vega et al: Epigenetic modifications and glucocorticoid sensitivity in ME/CFS. BMC Medical Genomics, 2017, 10, 11 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5324230/
5. de Vega et al: Integration of DNA methylation & health scores identifies subtypes in ME/CFS. Epigenomics 2018, 10, 5 https://www.futuremedicine.com/doi/full/10.2217/epi-2017-015
6. Trivedi et al: Identification of ME/CFS - associated DNA methylation patterns.
   Plos One 2018, 13, 7 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0201066
7. Huisjes et al: Sqeezing for life - Properties of Red Blood Cell Deformability. Front Physiol. 2018 Jun 1;9:656. doi: 10.3389/fphys.2018.00656. eCollection 2018. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5992676/
8. PMID: 28282470 https://www.ncbi.nlm.nih.gov/pubmed/?term=28282470
9. 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.  https://www.ncbi.nlm.nih.gov/pubmed/28494812
10. Nguyen et al: Associations between clinical symptoms, plasma norepinephrine and deregulated immune gene networks in subgroups of adolescent with CFS. Brain, Behavior and immunity.
11.  https://www.genecards.org/  CRIM1
12. Brenu et al: Methylation profile of CD4+ T cells in CFS/ME. J. Clin Cell Immunol 5, 228https://www.omicsonline.org/open-access/methylation-profile-of-cd-t-cells-in-chronic-fatigue-syndromemyalgic-encephalomyelitis-2155-9899.1000228.php?aid=27598

Bile acid transporter SLCO3A1 and ME

Bile acid transporters maintain bile acid homeostasis.

Solute Carrier Organic Anion Transporter Family Member 3A1 (SLCO3A1) Is a Bile Acid Efflux Transporter in Cholestasis (1).

SLCO3A1 is up-regulated as an adaptive response to cholestasis (1).

Genome-wide association analysis identified a single nucleotide polymorphism (SNP) in SLCO3A1 in ME patients (2).

Epigenetic analysis identified that the gene SLCO3A1 (5'UTR) was hypomethylated in peripheral blood mononuclear cells (PBMC) from ME patients. (3).

Metabolomic analysis on plasma from ME patients identified lower levels of (4):

• glycocholate
• glycochenodeoxycholate
• glycolithocholate
• lithocholate
• sulfoglycolithocholate
• taurine

How is SLCO3A1 involved in ME?

Interestingly, bile acids activated receptors regulate innate immunity (5).

References

1) Pan et al. Solute Carrier Organic Anion Transporter Family Member 3A1 Is a Bile Acid Efflux Transporter in Cholestasis. Gastroenterology. 2018 Nov;155(5):1578-1592.e16. doi: 10.1053/j.gastro.2018.07.031. Epub 2018 Jul 29. https://www.ncbi.nlm.nih.gov/pubmed/30063921

2) Schlauch et al: Genome-wide association analysis identifies genetic variations in subjects with ME/CFS. 2016.doi.10.1038/tp.2015.208

3) Trivedi et al: Identification of ME/CFS - associated DNA methylation patterns.
Plos One 2018, 13, 7 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0201066

4) Germain et al: Metabolic profiling of a ME/CFS discovery cohort reveals disturbances in fatty acid and lipid metabolism. Mol. BioSyst. 2017, 13, 371 https://pubs.rsc.org/en/Content/ArticleLanding/2017/MB/C6MB00600K#!divAbstract

5) Fiorucci et al. Bile Acids Activated Receptors Regulate Innate Immunity. Front Immunol. 2018 Aug 13;9:1853. doi: 10.3389/fimmu.2018.01853. eCollection 2018.
https://www.ncbi.nlm.nih.gov/pubmed/30150987

Lipid Transfer Proteins in ME

Lipid metabolism is dysregulated in ME patients (1, 2, 3).

Genes encoding lipid transfer proteins (LTPs) are epigentic changed in peripheral blood mononuclear cells (PBMC) from ME patients (4, 5, 6, 7).

Protein levels of LTPs are changed in the spinal fluid from ME patients (8).

Lipid Transfer Proteins

Within the eukaryotic cell, more than 1000 species of lipids define a series of membranes essential for cell function. Tightly controlled systems of lipid transport underlie the proper spatiotemporal distribution of membrane lipids, the coordination of spatially separated lipidmetabolic pathways, and lipid signaling mediated by soluble proteins that may be localized some distance away from membranes. Alongside the well-established vesicular transport of lipids, non-vesicular transport mediated by a group of proteins referred to as lipid-transfer proteins(LTPs) is emerging as a key mechanism of lipid transport in a broad range of biological processes. More than a hundred LTPs exist in humans and these can be divided into at least ten protein families. LTPs are widely distributed in tissues, organelles and membrane contact sites (MCSs), as well as in the extracellular space. They all possess a soluble and globular domain that encapsulates a lipid monomer and they specifically bind and transport a wide range of lipids (9).

Fig. 5. Lipid-transfer proteins have multiple modes of action (Figure from Chiappariono et al. ref 9)
a, LTPs can transfer lipids between cellular membranes and act as transporters. b, Some LTPs (chaperones) present lipids to an acceptor protein (e.g. enzymes, LTPs, transmembrane (TM) transporters or transcription factors). c, The LTD can be engaged in intramolecular interactions with other domains (illustrated here in purple) or proteins (not illustrated). Binding to the lipid cargo acts as a trigger that induces conformational changes and leads to the activation of signaling. This mechanism is sometimes coupled to the mechanisms described in a and b. LTPs have pleiotropic functions and can modulate lipid homeostasis, signaling and the structural organization of membranes.

Fig. 4. Domain organizations of human lipid-transfer proteins. The members of the ten families of LTPs are displayed.  (Figure from Chiapparino et al. ref 9).

PITPNA, PITPNC1 and PITPNM2 in ME

The genes encoding the phosphatidylinositol transfer proteins PITPNA, PITPNC1 and PITPNM2 were hypomethylated in PBMC from ME patients in Trivedi's study (7). PITPNM2 was hypomethylated in the genic regions: 1stExon, TSS200, TSS1500 and 3'UTR; and also showed changed DNA methylation pattern in 3 other studies (4, 5, 6).

GM2A in ME

A number of LTPs can transfer lipids to downstream enzymes. GM2 ganglioside activator (GM2A) is a lysomal LTP that works as a cofactor for the glycosphingolipid-degrading enzyme beta-hexosaminidase A (HEXA). GM2A is also involved in presentation of antigenic lipids by CD1 to T cells.

The GM2A gene promoter was hypomethylated in ME patients (table S7 in ref 7).

GM2A precursor, number of unique peptides identified in cerebrospinal fluid (table S1 in ref 8):

1) Controls: 12

2) ME patients: 32

3) Post  treatment  Lyme patients:32

HEXA chain precursor, number of unique peptides identified in cerebrospinal fluid (table S1 in ref 8):

1) Controls: 16

2) ME patients: 30

3) Post  treatment  Lyme patients:28

PLTP in ME

The gene encoding phospholipid transfer protein (PLTP) was hypomethylated (TSS1500) in PBMC from ME patients (7).

PLTP (TSS1500) was differentially methylated in PBMC from ME patients subtypes (6).

PLTP precursor, number of unique peptides identified in cerebrospinal fluid (table S1 in ref 8):

1) Controls: 16

2) ME patients: 31

3) Post  treatment  Lyme patients: 26

STARD13 and ME

The gene encoding StAR related lipid transfer domain containing 13 (STARD13) was hypermethylated in genic region 3'UTR and hypomethylated in TSS200 in PBMC from ME patients (7).

STARD13 was differentially methylated in PBMC from ME patients subtypes (6).

This was some of the LTPs involved in ME.

References

1) Naviaux RK, Naviaux JC, Li K, Bright AT, Alaynick WA, Wang L, Baxter A, Nathan N et al (2016) Metabolic features of chronic fatigue syndrome. Proc Natl Acad Sci U S A 113:E5472–E5480. https://doi.org/10.1073/pnas.1607571113 

2) Germain et al: Metabolic profiling of a ME/CFS discovery cohort reveals disturbances in fatty acid and lipid metabolism. Mol. BioSyst. 2017, 13, 371 https://pubs.rsc.org/en/Content/ArticleLanding/2017/MB/C6MB00600K#!divAbstract

3) Nagy-Szakal et al: Insights into ME/CFS phenotypes through comprehensive metabolomics. Nat. Sci. Rep, 2018, 8. https://www.nature.com/articles/s41598-018-28477-9

4) de Vega et al: DNA methylation Modifications associated with CFS. PlosOne, 2014, 9, 8. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0104757 

5) de Vega et al: Epigenetic modifications and glucocorticoid sensitivity in ME/CFS. BMC Medical Genomics, 2017, 10, 11 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5324230/

6) de Vega et al: Integration of DNA methylation & health scores identifies subtypes in ME/CFS. Epigenomics 2018, 10, 5 https://www.futuremedicine.com/doi/full/10.2217/epi-2017-015

7) Trivedi et al: Identification of ME/CFS - associated DNA methylation patterns.
Plos One 2018, 13, 7 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0201066

8) Schutzer et al: Distinct Cerebrospinal Fluid Proteomes Differentiate Post- Treatment Lyme Disease from Chronic Fatigue Syndrome. PLOS One February 2011, volume 6, Issue  https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0017287

9) Chiapparino et al: The orchestra of lipid-transfer proteins at the crossroads between metabolism and signaling. Prog Lipid Res. 2016 Jan;61:30-9. doi: 10.1016/j.plipres.2015.10.004 https://www.ncbi.nlm.nih.gov/pubmed/26658141

Red blood cell deformability, metabolism and extracellular vesicles in ME/CFS

Red blood cell deformability

Red blood cells (RBCs; erythrocytes) are typically biconcave in shape, transport hemoglobin-bound oxygen and are reversibly deformable facilitating trafficking through capillaries. Decreased deformability of RBCs adversely affects tissue oxygenation (1).

RBC deformability is reduced in some ME/CFS patients (2).

Metabolism and red blood cell membrane

The cell membranes in red blood cells are made up of proteins, fats, and carbohydrates. This means that abnormalities in the cell membrane can be a good way to spot disordered metabolism of these nutrients. Issues with producing too much of a certain metabolite, or not being able to break down a nutrient can cause abnormalities in the cell membrane, which lead to irregular shapes of RBCs (2).

Erythrocyte omega-3 index (5.75%) and n-3 PUFA levels are low in individuals with CFS/ME (3).

Extracellular vesicles in sepsis decrease RBC deformability

A growing body of evidence suggests that extracellular vesicles (EVs) play a role in cell-to-cell communication, and are involved in both physiological and pathological processes (4).

A study on mice showed a significant decrease in RBC deformability following sepsis. Extracellular vesicles isolated from the plasma of mice with sepsis significantly decreased deformability of RBCs ex vivo (1).

Extracellular vesicles in blood from ME patients have been analyzed: The amount of EV-enriched fraction was significantly higher in CFS/ME subjects than in healthy controls (HCs) (p = 0.007) and that EVs were significantly smaller in CFS/ME patients (p = 0.014). Circulating EVs could be an emerging tool for biomedical research in CFS/ME. These findings provide preliminary evidence that blood-derived EVs may distinguish CFS/ME patients from HCs (4).

I suggest a pilot study:

ME/CFS vesicles put together with red blood cells from healthy controls. Can microvesicles from ME/CFS patients decrease deformability of RBCs from healthy controls in vitro?

References

1) Subramini et al. Effect of plasma-derived extracellular vesicles on erythrocyte deformability in polymicrobial sepsis. Int Immunopharmacol. 2018 Oct 16;65:244-247. doi: 10.1016/j.intimp.2018.10.011. https://www.ncbi.nlm.nih.gov/pubmed/?term=30340103

2) Erythrocyte Deformability As a Potential Biomarker for Chronic Fatigue Syndrome. Amit K Saha, Brendan R Schmidt, Julie Wilhelmy, Vy Nguyen, Justin Do, Vineeth C Suja, Mohsen Nemat-Gorgani, Anand K Ramasubramanian and Ronald W Davis

Blood 2018 132:4874; doi: https://doi.org/10.1182/blood-2018-99-117260 http://www.bloodjournal.org/content/132/Suppl_1/4874

OMF-funded research: red blood cell deformability in ME/CFS
https://www.omf.ngo/2018/03/21/omf-funded-research-red-blood-cell-deformability-in-me-cfs/

RBC shape, RBC deformability
https://www.omf.ngo/2018/04/04/rbc-shape-rbc-deformability/

3) Castro-Marrero et al: Low omega-3 index and polyunsaturated fatty acid status in patients with chronic fatigue syndrome/myalgic encephalomyelitis.
Prostaglandins, Leukotrienes and Essential Fatty Acids
Volume 139, December 2018, Pages 20-24
https://www.sciencedirect.com/science/article/pii/S095232781830053X

4) Castro-Marrero et al:
Circulating extracellular vesicles as potential biomarkers in chronic fatigue syndrome/myalgic encephalomyelitis: an exploratory pilot study. J Extracell Vesicles. 2018 Mar 22;7(1):1453730. doi: 10.1080/20013078.2018.1453730. eCollection 2018. https://www.ncbi.nlm.nih.gov/pubmed/29696075

NPY, AgRP, POMC and NUCB2 in ME

Hypothalamic Pro-opiomelanocortin (POMC) and Neuropeptide Y/Agouti-Related Peptide (NPY/AgRP) neurons are critical nodes of a circuit within the brain that sense key metabolic cues as well as regulate metabolism. Importantly, these neurons retain an innate ability to rapidly reorganize synaptic inputs and electrophysiological properties in response to metabolic state (1).

Exercise (single bout and/or chronic training) increases insulin sensitivity leading to improved insulin stimulated glucose uptake in muscle and reduced basal hepatic glucose production . Within the arcuate nucleus, the melanocortin system is an interface between signals of metabolic state and neural pathways governing energy balance and glucose metabolism. In particular, the orexigenic neuropeptide Y/Agoutirelated peptide (NPY/AgRP) neurons are activated in response to food deprivation, while the anorexigenic proopiomelanocortin (POMC)- expressing cells are inhibited . In addition to contributing to energy balance, the activity of arcuate NPY/AgRP and POMC neurons also have profound effects on glucose metabolism. These changes in cellular activity have been attributed to both native channel properties as well as (re)organization of synaptic connectivity (1 and references herein).

New research shows: Cellular and synaptic reorganization of arcuate NPY/AgRP and POMC neurons after exercise (1).

Nesfatin-1 is an 82–amino acid polypeptide derived from the precursor protein nucleobindin 2 (NUCB2), whose processing also yields nesfatin-2 and -3, two peptides with so far unknown functions (2).

Nesfatin-1 is involved in several processes including modulation of gastrointestinal functions, energy metabolism, glucose and lipid metabolism, thermogenesis, mediation of anxiety and depression, as well as cardiovascular and reproductive functions (2).

Use the link to se figure with NUCB2 and the hypothalamus (3): 

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3402310/figure/F1/

As you can se in the figure, the hypothalamus is a key brain area for maintaining glucose and energy homeostasis via the ability of hypothalamic neurons to sense, integrate, and respond to numerous metabolic signals.

Mitochondrial function has emerged as an important component in the regulation of hypothalamic neurons controlling glucose and energy homeostasis. Although the underlying mechanisms are not fully understood, emerging evidence indicates that mitochondrial dysfunction in hypothalamic neurons may contribute to the development of various metabolic diseases (4).

NPY, AgRP, POMC and NUCB2 in ME

NPY precursor, number of unique peptides identified in cerebrospinal fluid (table S1 in ref 5):

1) Controls: 4

2) ME patients: 7

3) Post  treatment  Lyme patients: 6

The plasma level of neuropeptide Y is elevated in ME patiens (6).

POMC, number of unique peptides identified in cerebrospinal fluid (table S1 in ref 5):

1) Controls: 1

2) ME patients: 2 

3) Post  treatment Lyme patients: 1

Some ME patients have single nucleotide plymorphism (SNP) in POMC (7).

The gene POMC (TSS1500, 5'UTR) is hypomethylated in peripheral blood mononuclear cells  (PBMC) from ME patients (8).

NUCB1 precursor, number of unique peptides identified in cerebrospinal fluid (table S1 in ref 5):

1) Controls: 29

2) ME patients: 43

3) Post  treatment Lyme patients: 51

NUCB2 precursor, number of unique peptides identified in cerebrospinal fluid (table S1 in ref 5):

1) Controls: 9

2) ME patients: 8

3) Post  treatment Lyme patients: 13

The gene NUCB2 (5'UTR) is hypomethylated in PBMC from ME patients (8).

The gene NUCB2 (5'UTR) is differentially methylated in PBMC from ME patient subtyes (9).

References

1) He et al: Cellular and synaptic reorganization of arcuate NPY/AgRP and POMC neurons after exercise. Mol Metab. 2018 Sep 12. pii: S2212-8778(18)30870-6. doi: 10.1016/j.molmet.2018.08.011 https://www.ncbi.nlm.nih.gov/pubmed/30292523

2) Schalla and Stengel: Current Understanding of the Role of Nesfatin-1. J Endocr Soc. 2018 Oct 1; 2(10): 1188–1206. Published online 2018 Sep 10. doi: [10.1210/js.2018-00246]
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6169466/

3) Figure from:  Diabetes. 2012 Aug; 61(8): 1920–1922.
and https://www.ncbi.nlm.nih.gov/pubmed/22826310

4) Jin and Diano: Mitochondrial Dynamics and Hypothalamic Regulation of Metabolism. Endocrinology, Volume 159, Issue 10, 1 October 2018, Pages 3596–3604,https://doi.org/10.1210/en.2018-00667 https://academic.oup.com/endo/article-abstract/159/10/3596/5091402?redirectedFrom=fulltext

5) Schutzer et al: Distinct Cerebrospinal Fluid Proteomes Differentiate Post- Treatment Lyme Disease from Chronic Fatigue Syndrome. PLOS One February 2011, volume 6, Issue  https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0017287

6) Fletcher et al: Plasma neuropeptide Y: a biomarker for symptom severity in chronic fatigue syndrome. Behav Brain Funct. 2010 Dec 29;6:76. doi: 10.1186/1744-9081-6-76 https://www.ncbi.nlm.nih.gov/pubmed/21190576

7) Smith et al: Polymorphisms in genes regulating the HPA axis associated with empirically delineated classes of unexplained chronic fatigue. PHARMACOGENOMICSVOL. 7, NO. 3COLLABORATIVE STUDY: CHRONIC FATIGUE SYNDROME – RESEARCH REPORT
https://www.futuremedicine.com/doi/10.2217/14622416.7.3.387

8) Trivedi et al: Identification of ME/CFS - associated DNA methylation patterns.
Plos One 2018, 13, 7 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0201066

9) de Vega et al: Integration of DNA methylation & health scores identifies subtypes in ME/CFS. Epigenomics 2018, 10, 5 https://www.futuremedicine.com/doi/full/10.2217/epi-2017-015

TECR (trans-2-enoyl-CoA reductase), VLCFAs and sphingolipids in ME

Very long-chain fatty acids (VLCFAs) are fatty acids (FAs) with a chain-length of ≥22 carbons. Mammals have a variety of VLCFAs differing in chain-length and the number of double bonds. Each VLCFA exhibits certain functions, for example in skin barrier formation, liver homeostasis, myelin maintenance, spermatogenesis, retinal function and anti-inflammation. These functions are elicited not by free VLCFAsthemselves, but through their influences as components of membrane lipids (sphingolipids and glycerophospholipids) or precursors of inflammation-resolving lipid mediators. VLCFAs are synthesized by endoplasmic reticulum membrane-embedded enzymes through a four-step cycle. The most important enzymes determining the tissue distribution of VLCFAs are FA elongases, which catalyze the first, rate-limiting step of the FA elongation cycle. Mammals have seven elongases (ELOVL1-7), each exhibiting a characteristic substrate specificity. Several inherited disorders are caused by mutations in genes involved in VLCFA synthesis or degradation (1).

FAs are elongated by endoplasmic reticulum (ER) membrane-embedded enzymes following their conversion to acyl-CoAs. FA elongation occurs by cycling through a four-step process: condensation, reduction, dehydration and reduction (1).

Fig. 2. from ref 2: Mammalian FA elongation cycle. The FA elongation cycle and enzymes involved in each step are illustrated. In each cycle, acyl-CoA incorporates two carbon units from malonyl-CoA.

In the last reduction step, trans-2-enoyl-CoA is converted to acyl-CoA, which is longer than the original acyl-CoA by two carbons. The trans-2-enoyl-CoA reductase responsible for this reaction is TER (also known as TECR), and the reaction requires NADPH as a cofactor (Moon and Horton, 2003 from ref 2).

TER is involved in both the production of VLCFAs used in the fatty acid moiety of sphingolipids as well as in the degradation of the sphingosine moiety of sphingolipids via S1P (3).

An impaired TER function affects VLCFA synthesis and thereby alters the cellular sphingolipid profile. Maintenance of a proper VLCFA level may be important for neural function (4).

The levels of sphingolipids and glycerolipids in plasma from ME patients are dysregulated (5).

The gene TECR (body) is hypermethylated in peripheral blood mononuclear cells (PBMC) from ME patients. This DNA methylation  is related to quality of life in the ME patients (table S7 in ref 6).

TECR is differentially methylated in PBMC from ME patients subtypes (table S3 in ref 7).

The gene TECR is hypomethylated in PBMC from ME patients (table S4 in ref 8).

TECR is located on chromosome 19 together with mir 639 (9):

Chromosome 19 - NC_000019.10

mir 639 is hypomethylated in CD4+ T cells from ME patients (10).

References

1) Akio Kihara: Very long-chain fatty acids: elongation, physiology and related disorders The Journal of Biochemistry, Volume 152, Issue 5, 1 November 2012, Pages 387–395,https://doi.org/10.1093/jb/mvs105
https://academic.oup.com/jb/article/152/5/387/2182729

2) Sassa and Kihara: Metabolism of Very Long-Chain Fatty Acids: Genes and Pathophysiology. Biomol Ther (Seoul). 2014 Mar; 22(2): 83–92.
doi: [10.4062/biomolther.2014.017]

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3975470/

3) Wakashima et al: Dual functions of the trans-2-enoyl-CoA reductase TER in the sphingosine 1-phosphate metabolic pathway and in fatty acid elongation. J Biol Chem. 2014 Sep 5;289(36):24736-48. doi: 10.1074/jbc.M114.571869. Epub 2014 Jul 21.
https://www.ncbi.nlm.nih.gov/pubmed/25049234

4) Abe et al: Mutation for nonsyndromic mental retardation in the trans-2-enoyl-CoA reductase TER gene involved in fatty acid elongation impairs the enzyme activity and stability, leading to change in sphingolipid profile. J Biol Chem. 2013 Dec 20;288(51):36741-9. doi: 10.1074/jbc.M113.493221. Epub 2013 Nov 12.

https://www.ncbi.nlm.nih.gov/pubmed/24220030

5) Naviaux RK, Naviaux JC, Li K, Bright AT, Alaynick WA, Wang L, Baxter A, Nathan N et al (2016) Metabolic features of chronic fatigue syndrome. Proc Natl Acad Sci U S A 113:E5472–E5480. https://doi.org/10.1073/pnas.1607571113

6) de Vega et al: Epigenetic modifications and glucocorticoid sensitivity in ME/CFS. BMC Medical Genomics, 2017, 10, 11 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5324230/

7) de Vega et al: Integration of DNA methylation & health scores identifies subtypes in ME/CFS. Epigenomics 2018, 10, 5 https://www.futuremedicine.com/doi/full/10.2217/epi-2017-015

8) Trivedi et al: Identification of ME/CFS - associated DNA methylation patterns.
Plos One 2018, 13, 7 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0201066

9) Gene mir 639:https://www.ncbi.nlm.nih.gov/gene/693224

10) Brenu et al: Methylation profile of CD4+ T cells in CFS/ME. J. Clin Cell Immunol 5, 228 https://www.omicsonline.org/open-access/methylation-profile-of-cd-t-cells-in-chronic-fatigue-syndromemyalgic-encephalomyelitis-2155-9899.1000228.php?aid=27598

The role of endoplasmic reticulum-mitochondria contact sites

The contact sites that the endoplasmic reticulum (ER) forms with mitochondria, called mitochondria-associated membranes (MAMs), are a hot topic in biological research, and both their molecular determinants and their numerous roles in several signaling pathways are is continuously evolving (1).

MAMs are now considered as structural platform for an optimal bioenergetics response allowing cellular adaptations to environmental changes. Indeed, the transfer of Ca2+from ER to mitochondria is crucial for the control of mitochondria energy metabolism, since mitochondrial Ca2+ levels control the activity of Krebs cycle’s deshydrogenases and impact ATP synthesis (Fig. ​(Fig.2).2 from ref 1).

Fig. 2 from ref 1:  Key components and functions of MAMs involved in the control of glucose homeostasis. ER-mitochondria contact sites shelter several components that impact glucose homeostasis either indirectly by regulating mitochondria biology, UPR signaling and autophagy and immune signalling, or more directly by controlling insulin signaling.

Metabolic regulations are tightly coupled with inflammation and immune responses and exacerbated inflammatory responses have been linked to metabolic diseases. ER-mitochondria contact sites were recently found to be an important actor of the cellular anti-viral response (Fig. 2).

During the inflammatory response, NLRP3 and other inflammasome members move to the MAM to coordinate the appropriate response. Calcium sensing receptor (CASR) activates the NLRP3 inflammasome through phospholipase C, which catalyzes IP3 production and thereby induces the release of Ca2 +from the ER (2). TRPM2 is also involved in NLRP3 activation (3).

The distance between the ER and (outer mitochondrial membrane (OMM) is a critical factor in the efficient transfer of Ca2 +. Aside from the spacing between the two organelles, the contact volume is another important parameter in the regulation of Ca2 + signaling. (2) FHIT overexpression enhances the number of these ER–mitochondria hot spots, favoring mitochondrial Ca2 +accumulation and triggering Ca2 +-dependent apoptosis ( [53] in ref 2).

GIMAP5 is a key regulator of hematopoietic integrity and lymphocyte homeostasis. GIMAP5 has a role in maintaining peripheral tolerance and T cell homeostasis in the gut (4). GIMAP5 alsp functions at the MAM (1).

Phosphatidylserine (PS) is synthesized in ER by the exchange of serine for the choline or ethanolamine head-groups of phosphatidylcholines (PC) or phosphatidylethanolamines (PE) by PS synthase-1 and PS synthase−2, which are enriched at MAMs (ref 24 in ref 1). Then, newly-made PS is transferred into mitochondria through MAMs, where it is decarboxylated to PE via PS decarboxylase in mitochondrial inner membrane (ref 25 in ref 1). PS transfer at MAM interface is mediated by oxysterol-binding proteins-related protein 5 (ORP5) and ORP8, which were also localized at MAMs (ref 26 in ref 1).

The above mentioned proteins (CASR, FHIT, GIMAP5, NLRP3, PML, ORP5, ORP8, TRPM2) are encoded by genes which show up with changed DNA methylation pattern in PBMC from ME patients in either one or several studies (5, 6, 7, 8).

References: 

1) Rieusset:  The role of endoplasmic reticulum-mitochondria contact sites in the control of glucose homeostasis: an update. Cell Death Dis. 2018 Mar; 9(3): 388.   https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5844895/

2) Marchi et al: The endoplasmic reticulum–mitochondria connection: One touch, multiple functions. Biochimica et Biophysica Acta (BBA) - Bioenergetics
Volume 1837, Issue 4, April 2014, Pages 461-469

https://www.sciencedirect.com/science/article/pii/S0005272813001850?via%3Dihub

3) Zhong et al: TRPM2 links oxidative stress to NLRP3 inflammasome activation Nat Commun. 2013;4:1611. doi: 10.1038/ncomms2608. https://www.ncbi.nlm.nih.gov/pubmed/23511475

4) GIMAP5: https://www.ncbi.nlm.nih.gov/gene/246774

5) de Vega et al: DNA methylation Modifications associated with CFS. PlosOne, 2014, 9, 8

6) de Vega et al: Epigenetic modifications and glucocorticoid sensitivity in ME/CFS. BMC Medical Genomics, 2017, 10, 11 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5324230/

7) de Vega et al: Integration of DNA methylation & health scores identifies subtypes in ME/CFS. Epigenomics 2018, 10, 5 https://www.futuremedicine.com/doi/full/10.2217/epi-2017-015

8) Trivedi et al: Identification of ME/CFS - associated DNA methylation patterns.
Plos One 2018, 13, 7 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0201066

PACS2 and ME

Endoplasmic reticulum (ER) and mitochondria are tubular organelles with a characteristic “network structure” that facilitates the formation of inter-organellar connections. As a result, mitochondria-associated ER membranes (MAMs), a subdomain of the ER that is tightly linked to and communicates with mitochondria, serve multiple physiological functions including lipid synthesis and exchange, calcium signaling, bioenergetics, and apoptosis. Importantly, emerging evidence suggests that the abnormality and dysfunction of MAMs have been involved in various neurodegenerative disorders including Alzheimer’s disease, amyotrophic lateral sclerosis, and Parkinson’s disease (1).

Figure 1: Global view of the architecture/choreography of ER–mitochondria contacts. As depicted, a part of ER tubule and mitochondria form quasi-synaptic structure. Several pairs of integral membrane proteins located on mitochondria and ER important for MERC formation and physical tethering of the organelles were identified, including Mfn1/2 tether, Fis1-Bap31 tether, VAPB-PTPIP51 tether and IP3R-grp75-VDAC1 tripartite complex. The latter is essential for the efficient Ca2+ transfer from the ER to mitochondria. MAM: mitochondria associated ER membrane, OMM = outer mitochondrial membrane, IMM: inner mitochondrial membrane, Mx = matrix, ETC: electron transport chain, TAC: tricarboxylic acid cycle  Endoplasmic reticulum-mitochondria tethering in neurodegenerative diseases Transl Neurodegener. 2017;6:21. (ref 1).

Figure 1 shows phosphorin acidic cluster sorting protein 2 (PACS2). PACS2 modulates the Fis1-Bap31 tether (1).

PACS2 is a multifunctionel protein involved in (2): 

• membrane trafficking
• MAM-localized ca2+ signaling
• switching between anabolic and catabolic roles of the MAM
• p53-p21-dependent cell cycle arrest
• apoptosis
• lipid metabolism
• regulating recycling of the metalloproteinase ADAM17
• subcellular distribution of calnexin

PACS2 functions as a metabolic switch that integrates traffic and interorganellar communication with nuclear gene expression in response to anabolic or catabolic cues (2).

Viruses can hijack the PACS2 pathway (2).

The gene PACS2 (TSS1500) is differentially methylated in PBMC from ME patients subtypes (3).

References 

1) LIU and Zhu: Endoplasmic reticulum-mitochondria tethering in neurodegenerative diseases.

Transl Neurodegener. 2017; 6: 21.

Published online 2017 Aug 23. doi:  10.1186/s40035-017-0092-6

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5567882

2) Thomas et al. Caught in the act - protein adaptation and the expanding roles of the PACS proteins in tissue homeostasis and disease.J Cell Sci. 2017 Jun 1;130(11):1865-1876. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5482974/

3)  de Vega et al: Integration of DNA methylation & health scores identifies subtypes in ME/CFS. Epigenomics 2018, 10, 5 https://www.futuremedicine.com/doi/full/10.2217/epi-2017-015

MGRN1 and ME

Mahogunin ring finger 1 (MGRN1) is a cytosolic ubiquitin ligase.

MGRN1 expression increases when cells are exposed to a variety of stressors.

Mice lacking MGRN1 have reduced level of many mitochondrial proteins. They have mitochondrial dysfunction and develop neurodegeneration.

MGRN1 is involved in:

• mitochondrial fusion
• mitochondrial trafficking via regulation of microtubules
• regulation af ER-associated protein degradation and ER-mitochondria junctions via interaction with the ligase GP78

(Ref1-5)

Four studies have shown the gene MGRN1 is differentially methylated in PBMC from ME patients compared to controls (6, 7, 8, 9). The DNA methylation pattern is related to quality of life in the ME patients (7) and is related to ME patient subtypes (8).

References:

1) Mitochondrial dysfunction precedes neurodegeneration in mahogunin (Mgrn1) mutant mice.
Sun K, Johnson BS, Gunn TM.
Neurobiol Aging. 2007 Dec;28(12):1840-52. Epub 2007 Aug 27.
PMID: 17720281

2) Calmodulin regulates MGRN1-GP78 interaction mediated ubiquitin proteasomal degradation system.
Mukherjee R, Bhattacharya A, Sau A, Basu S, Chakrabarti S, Chakrabarti O.
FASEB J. 2018 Sep 19:fj201701413RRR. doi: 10.1096/fj.201701413RRR. [Epub ahead of print]
PMID: 30230921

3) Ubiquitin-mediated regulation of the E3 ligase GP78 by MGRN1 in trans affects mitochondrial homeostasis.
Mukherjee R, Chakrabarti O.
J Cell Sci. 2016 Feb 15;129(4):757-73. doi: 10.1242/jcs.176537. Epub 2016 Jan 7.
PMID: 26743086

4) Regulation of Mitofusin1 by Mahogunin Ring Finger-1 and the proteasome modulates mitochondrial fusion.
Mukherjee R, Chakrabarti O.
Biochim Biophys Acta. 2016 Dec;1863(12):3065-3083. doi: 10.1016/j.bbamcr.2016.09.022. Epub 2016 Oct 4.
PMID: 27713096

5).MGRN1-mediated ubiquitination of α-tubulin regulates microtubule dynamics and intracellular transport.Mukherjee R, Majumder P, Chakrabarti O.
Traffic. 2017 Dec;18(12):791-807. doi: 10.1111/tra.12527. Epub 2017 Oct 4.PMID: 28902452

6) de Vega et al: DNA methylation Modifications associated with CFS. PlosOne, 2014, 9, 8

7) de Vega et al: Epigenetic modifications and glucocorticoid sensitivity in ME/CFS. BMC Medical Genomics, 2017, 10, 11 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5324230/

8) de Vega et al: Integration of DNA methylation & health scores identifies subtypes in ME/CFS. Epigenomics 2018, 10, 5 https://www.futuremedicine.com/doi/full/10.2217/epi-2017-015

9) Trivedi et al: Identification of ME/CFS - associated DNA methylation patterns.
Plos One 2018, 13, 7 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0201066

H2AFY and ME

H2AFY (also known as macroH2A1) is a histone H2A variant. It replaces conventional H2A histones in a subset of nucleosomes.

This gene encodes two splice isoforms, H2AFY1.1 and H2AFY1.2 (also known as mH2A1.1 and mH2A1.2). mH2A1.1 and mH2A1.2 are produced by mutually exclusive use of exons 6b and 6a.  The isoforms have distinct regulatory properties.

H2AFY, ZFR and interferon signaling

ZFR (zinc finger RNA binding protein)  coordinates crosstalk between RNA decay and transcription in innate immunity.

ZFR protein is required for H2AFY expression. ZFR regulates alternative splicing and decay of H2AFY mRNA.

ZFR controls interferon signaling by preventing aberrant splicing and nonsense-mediated decay of histone variant macroH2A1/H2AFY mRNAs (1).

Figure from reference 1: Model for ZFR-mediated regulation of IFNβ. ZFR is required for productive splicing of mH2A1. In the absence of ZFR, mH2A1 pre-mRNA is mis-spliced and resulting transcript is degraded by NMD. In the presence of ZFR, mH2A1 protein is expressed and directly represses the IFNB1 promoter (1).

MacroH2A1.1 regulates mitochondrial respiration

MacroH2A1.1 contains a macrodomain capable of binding NAD+-derived metabolites.

MacroH2A1.1 is rapidly induced during myogenic differentiation through a switch in alternative splicing, and  myotubes that lack macroH2A1.1 have a defect in mitochondrial respiratory capacity (2).

H2AFY and B-cells

The H2AFY1.1 isoform is important for B cell development. Reduction in this isoform may contribute to abnormal hematopoiesis (3).

H2AFY in ME

DNA methylation pattern in the gene H2AFY in peripheral blood mononuclear cells (PBMC) from ME patients:

de Vega 2017(table S7 in ref 4): TSS200, TSS1500 and body are hypermethylated

de Vega 2018 (table S3 in ref 5): Five different probes (rank 96, 229, 277, 711 and 965) show the gene is differentially methylated in ME patients subtypes

Trivedi 2018 (table S6 in ref 6): The gene promoter is hypomethylated

Trivedi 2018 (table S4 in ref 6): Thirteen different probes show that TSS1500 and 3'UTR are hypomethylated

Why is H2AFY hypermethylated in de Vega's study and hypomethylated in Trivedi's study?

H2AFY isoform 2 content in cerebrospinal fluid (7):
1) Controls: no value
2) ME patients: 3
3) Post treatment Lyme patients: 5

What does H2AFY do in ME?

References: 

1) Hauque et al. ZFR coordinates crosstalk between RNA decay and transcription in innate immunity. Nature Communicationsvolume 9, Article number: 1145 (2018)

https://www.nature.com/articles/s41467-018-03326-5
Figure: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5861047/figure/Fig7/

2)  Marjanovic et al. MacroH2A1.1 regulates mitochondrial respiration by limiting nuclear NAD+ consumption. Nature Structural & Molecular Biology,  volume 24, pages902–910 (2017)
https://www.nature.com/articles/nsmb.3481

3) Sanghyun Kim, Monique Chavez, Cara Shirai and Matt Walter. Abstract 5108: The role of H2afy in normal and malignant hematopoiesis.  DOI: 10.1158/1538-7445.AM2018-5108 Published July 2018 http://cancerres.aacrjournals.org/content/78/13_Supplement/5108.short

4) de Vega et al: Epigenetic modifications and glucocorticoid sensitivity in ME/CFS. BMC Medical Genomics, 2017, 10, 11 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5324230/

5) de Vega et al: Integration of DNA methylation & health scores identifies subtypes in ME/CFS. Epigenomics 2018, 10, 5 https://www.futuremedicine.com/doi/full/10.2217/epi-2017-015

6) Trivedi et al: Identification of ME/CFS - associated DNA methylation patterns.

 Plos One 2018, 13, 7   https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0201066

7) Schutzer et al: Distinct Cerebrospinal Fluid Proteomes Differentiate Post- Treatment Lyme Disease from Chronic Fatigue Syndrome. PLOS One February 2011, volume 6, Issue  https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0017287

CLYBL, itaconate and B12 - involved in ME?

The gene citrate lyase subunit beta-like (CLYBL) is a mitochondrial enzyme (1).

Figure 1. A Novel Pathway Linked to Vitamin B12 Metabolism. 

The metabolic role of CLYBL is linked to B12 metabolism and the immunomodulatory metabolite, itaconate (1).

CLYBL in ME

The gene CLYBL (body) is hypermethylated in peripheral blood mononuclear cells (PBMC) from ME patients (table S1 in ref 2).

Some ME patients have single nucleotide polymorphism  (SNP) in the gene CLYBL (3). 

CLYBL, itaconate and B12

CLYBL participates in a relatively unexplored human C5 metabolic pathway.

CLYBL is required for maintaining mitochondrial B12 function.

Immunoresponsive gene 1 (IRG1) is expressed exclusively in activated macrophages. IRG1 produce itaconate through decarboxylation of cis-aconitate, a TCA-cycle intermediate.

In vitro test showed that itaconate added to human B-lymphocytes were converted to itaconyl-CoA inside the cells and dramatically lowered B12.

High concentrations of macrophage-derived itaconate might have autocrine and paracrine effects and poison B12 in nearby tissues, raising the possibility for a localized vitamin deficiency in the setting of inflammation (4). 

The B12 regulation may have important implications for other metabolic pathways and pathophysiological contexts. Serine, glycine and one-carbon (SGOC) metabolism, which requires B12 to couple the methionine and folate cycles, is important for nucleotide biosynthesis, redox homeostasis and methylation reactions (1, 4).

SGOC metabolism in ME

Naviaux et al have described  dysregulated SGOC metabolism in ME patients (ref 5 - do take a look at figure S6 in the article supplementary).

B12 in ME

Some ME patients respond to B12/folic acid support (6).

Further reading about STING and itaconate: 

Is STING involved in ME? http://followmeindenmark.blogspot.com/2018/10/is-sting-involved-in-me.html

References: 

1) A Missing Link to Vitamin B12 Metabolism.

• Michael J. A. Reid, Jihye Paik, Jason W. Locasale
• Published 2017 in Cell
• DOI:10.1016/j.cell.2017.10.030

https://www.semanticscholar.org/paper/A-Missing-Link-to-Vitamin-B12-Metabolism.-Reid-Paik/aec86264a4fb0a28865ef026ace7d772b25f1114/figure/0

2) de Vega et al: Epigenetic modifications and glucocorticoid sensitivity in ME/CFS. BMC Medical Genomics, 2017, 10, 11 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5324230/

3) Smith et al: Convergent genomic studies identify association of GRIK2 and NPAS2 with chronic fatigue syndrome. Neuropsychobiology. 2011;64(4):183-94. doi: 10.1159/000326692. Epub 2011 Sep 9.
 https://www.ncbi.nlm.nih.gov/pubmed/21912186 

4) Shen et al: The Human Knockout Gene CLYBL Connects Itaconate to Vitamin B12. Cell, 171, 771-782, 2017
https://www.sciencedirect.com/science/article/pii/S0092867417311820

5) Naviaux RK, Naviaux JC, Li K, Bright AT, Alaynick WA, Wang L, Baxter A, Nathan N et al (2016) Metabolic features of chronic fatigue syndrome. Proc Natl Acad Sci U S A 113:E5472–E5480.   https://doi.org/10.1073/pnas.1607571113 

6) Response to Vitamin B12 and Folic Acid in Myalgic Encephalomyelitis and Fibromyalgia
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0124648

Is STING involved in ME?

NEW RESEARCH

Nitro-fatty acids are formed in response to virus infection and are potent inhibitors of STING palmitoylation and signaling

Abstract:The adaptor molecule stimulator of IFN genes (STING) is central to production of type I IFNs in response to infection with DNA viruses and to presence of host DNA in the cytosol. Excessive release of type I IFNs through STING-dependent mechanisms has emerged as a central driver of several interferonopathies, including systemic lupus erythematosus (SLE), Aicardi–Goutières syndrome (AGS), and stimulator of IFN genes-associated vasculopathy with onset in infancy (SAVI). The involvement of STING in these diseases points to an unmet need for the development of agents that inhibit STING signaling. Here, we report that endogenously formed nitro-fatty acids can covalently modify STING by nitro-alkylation. These nitro-alkylations inhibit STING palmitoylation, STING signaling, and subsequently, the release of type I IFN in both human and murine cells. Furthermore, treatment with nitro-fatty acids was sufficient to inhibit production of type I IFN in fibroblasts derived from SAVI patients with a gain-of-function mutation in STING. In conclusion, we have identified nitro-fatty acids as endogenously formed inhibitors of STING signaling and propose for these lipids to be considered in the treatment of STING-dependent inflammatory disease (1).

The gene TMEM173 encodes STING.

TMEM173 is hypermethylated (genic location: body, p-value = 4,53E-05, FDR =  0,000816) in peripheral blood mononuclear cells (PBMC) from ME patients compared to controls (2).

TMEM173 is differentially methylated (genic location: 3'UTR, p-value = 7,25E-05, FDR = 0,000184) in PBMC from ME patient subtypes (3).

This DNA methylation pattern is related to degree of disease and quality of life in the ME patients (2, 3).

Is STING (TMEM173) involved in the pathomechanism in ME patient subtypes?

ME patents are metabolic reprogrammed (4, 5, 6, 7). Is a downregulated Nrf2 involved in a STING-pathomechanism in ME? Read about Nrf2 and STING in:


Nrf2 negatively regulates STING indicating a link between antiviral sensing and metabolic reprogramming
Abstract:
The transcription factor Nrf2 is a critical regulator of inflammatory responses. If and how Nrf2 also affects cytosolic nucleic acid sensing is currently unknown. Here we identify Nrf2 as an important negative regulator of STING and suggest a link between metabolic reprogramming and antiviral cytosolic DNA sensing in human cells. Here, Nrf2 activation decreases STING expression and responsiveness to STING agonists while increasing susceptibility to infection with DNA viruses. Mechanistically, Nrf2 regulates STING expression by decreasing STING mRNA stability. Repression of STING by Nrf2 occurs in metabolically reprogrammed cells following TLR4/7 engagement, and is inducible by a cell-permeable derivative of the TCA-cycle-derived metabolite itaconate (4-octyl-itaconate, 4-OI). Additionally, engagement of this pathway by 4-OI or the Nrf2 inducer sulforaphane is sufficient to repress STING expression and type I IFN production in cells from patients with STING-dependent interferonopathies. We propose Nrf2 inducers as a future treatment option in STING-dependent inflammatory diseases (8).

Om STING: 
Fedtstof kan stoppe immunforsvar, der løber løbsk
https://ing.dk/artikel/fedtstof-kan-stoppe-immunforsvar-loeber-loebsk-214342


References:

1) Anne Louise Hansen et al: Nitro-fatty acids are formed in response to virus infection and are potent inhibitors of STING palmitoylation and signaling
PNAS published ahead of print July 30, 2018 https://doi.org/10.1073/pnas.1806239115

2) de Vega et al: Epigenetic modifications and glucocorticoid sensitivity in ME/CFS. BMC Medical Genomics, 2017, 10, 11 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5324230/

3) de Vega et al: Integration of DNA methylation & health scores identifies subtypes in ME/CFS. Epigenomics 2018, 10, 5 https://www.futuremedicine.com/doi/full/10.2217/epi-2017-015

4)  Naviaux et al: Metabolic features of CFS. www.pnas.org/cgi/doi/10.1073/pnas.1607571113

5) Germain et al: Metabolic profiling of a ME/CFS discovery cohort reveals disturbances in fatty acid and lipid metabolism. Mol. BioSyst. 2017, 13, 371.

6) Nagy-Szakal et al: Insights into ME/CFS phenotypes through comprehensive metabolomics. Nat Sci Rep 2018, 8.

7) Reuter and Evans: Long-chain acylcarnitine deficiency in patients with CFS. Potential involvement of altered carnitine palmitoyltransferase-I-activity. J. Int. Med. 2011, 270.

8)  David Olangnier et al: Nrf2 negatively regulates STING indicating a link between antiviral sensing and metabolic reprogramming
Nature Communicationsvolume 9, Article number: 3506 (2018)
https://www.nature.com/articles/s41467-018-05861-7

RPS6KB1, EIF4G1 and CD79A in ME/CFS

RPS6KB1 (5'UTR) is the most hypermethylated gene in peripheral blood mononuclear cells (PBMC) from ME patients with a mean beta-difference: 0,353 compared to controls (table S4 in ref 1).

EIF4G1 (body) is the second most hypermethylated gene in PBMC from ME patients (table 2, page 5 in ref 2). EIF4G1 mRNA expression is upregulated in PBMC from ME patients (figure 1 in ref 3).

CD79A is the gene with lowest expression in whole blood from adolescent CFS patients (table S3 in ref 4).

These three gene products interact (5):

Gene Cards STRING Interaction network RPS6KB1 (5)

RPS6KB1: Ribosomal protein S6 kinase, 70kDa, polypeptide 1; Serine/threonine-protein kinase that acts downstream of mTOR signaling in response to growth factors and nutrients to promote cell proliferation, cell growth and cell cycle progression. Regulates protein synthesis through phosphorylation of EIF4B, RPS6 and EEF2K, and contributes to cell survival by repressing the pro-apoptotic function of BAD. Under conditions of nutrient depletion, the inactive form associates with the EIF3 translation initiation complex.

EIF4G1: Eukaryotic translation initiation factor 4 gamma, 1; Component of the protein complex eIF4F, which is involved in the recognition of the mRNA cap, ATP-dependent unwinding of 5’-terminal secondary structure and recruitment of mRNA to the ribosome.

CD79A: CD79a molecule, immunoglobulin-associated alpha; Required in cooperation with CD79B for initiation of the signal transduction cascade activated by binding of antigen to the B-cell antigen receptor complex (BCR) which leads to internalization of the complex, trafficking to late endosomes and antigen presentation. Also required for BCR surface expression and for efficient differentiation of pro- and pre-B-cells. Stimulates SYK autophosphorylation and activation. Binds to BLNK, bringing BLNK into proximity with SYK and allowing SYK to phosphorylate BLNK.


SYK and BLNK are also in the RPS6KB1 network (5):

Gene Cards STRING Interaction network CMTM8 (5)


Use the link below to see how the B cell Receptor (BCR) functions with CD79A, SYK and BLNK(6):
https://media.springernature.com/m685/nature-assets/nrd/journal/v12/n3/images/nrd3937-f1.jpg


References:

1) Trivedi et al: Identification of ME/CFS - associated DNA methylation patterns.

 Plos One 2018, 13, 7   https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0201066

2) de Vega et al: Epigenetic modifications and glucocorticoid sensitivity in ME/CFS. BMC Medical Genomics, 2017, 10, 11 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5324230/

3) Kerr et al:  Assessment of a 44 Gene Classifier for the Evaluation of Chronic Fatigue Syndrome from Peripheral Blood Mononuclear Cell Gene Expression . Plos One 2011 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0016872

4)  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.  https://www.ncbi.nlm.nih.gov/pubmed/28494812

5) Gene Cards    https://www.genecards.org/

Gene Cards RPS6KB1

Gene Cards CMTM8

6 )Young and Staudt: Targeting pathological B cell receptor signalling in lymphoid malignancies. Nature Reviews Drug Discovery volume12, pages229–243 (2013)
https://www.nature.com/articles/nrd3937