tirsdag den 6. november 2018

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): 

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


onsdag den 31. oktober 2018

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_000019.10Genomic Context describing neighboring genes

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]

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

mandag den 29. oktober 2018

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).

An external file that holds a picture, illustration, etc.
Object name is 41419_2018_416_Fig2_HTML.jpg
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

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

søndag den 28. oktober 2018

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.
. 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

onsdag den 24. oktober 2018

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

torsdag den 18. oktober 2018

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)

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.

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

fredag den 12. oktober 2018

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.
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.  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



onsdag den 3. oktober 2018

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

        søndag den 30. september 2018

        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

        lørdag den 1. september 2018

        HOX-genes and MIR10A in ME

        The genes HOXB3, HOXB4, HOXB5, HOXB-AS3 (LOC404266) and MIR10A are located together on chromosome 17.

        MIR10A is hypermethylated, HOXB5 and LOC404266 are hypomethylated in CD4+ T-cells from ME patients (1).

        The HOXB4 gene promoter is hypomethylated in peripheral blood mononuclear cells (PBMC) from ME patients (table S7 in ref 2).

        HOXB3 (5'UTR), HOXB4 (1stExon, 5'UTR), LOC404266, HOXB5 (5'UTR), LOC404266 (TSS200, TSS1500) and MIR10A (1stExon, TSS1500) are hypomethylated in PBMC from ME patients (table S4 in ref 2).

        HOXB3 (5'UTR), HOXB4 (body), HOXB5 (3'UTR), LOC404266 (TSS200, TSS1500, body) and MIR10A (TSS1500) are hypermethylated in PBMC from ME patients (table S7 in ref 3).

        HOXB3, HOXB4, LOC404266 and MIR10A are differentially methylated in ME subtypes (table S3 in ref 4).

        Why are HOX-genes hypomethylated in Trivedi's study and hypermethylated in de Vega's study?

        DNA methyltransferase DNMT3A and DNMT3B are responsible for de novo methylation, while DNMT1 is responsible for maintaining methylation signatures.

        DNMT3A (TSS1500) is hypomethylated in the Trivedi study (table S4 in ref 2).

        DNMT3A (body) and DNMT3B (5'UTR) are hypermethylated in the de Vega (2017) study (table S7 in ref 3).

        DNMT3A (body) and DNMT3B (5'UTR) are differentially methylated in ME subtypes (table S3 in ref 4).

        References:
        1. Brenu et al: Methylation profile of CD4+ T cells in CFS/ME. J. Clin Cell Immunol 5, 228  
        2. 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
        3. 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/
        4. 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-2017-0150

        lørdag den 25. august 2018

        FAM13A, fatty acid oxidation and ME

        Lipid metabolism is dysregulated in ME patients (1, 2, 3, 4).

        Family with sequence similarity 13 number A (FAM13A) regulates fatty acid oxidation (FAO) (5).

        The gene FAM13A is hypomethylated (TSS200 and TSS1500) in peripheral blood mononuclear cells (PBMC) from ME patients (table S4 in ref 6).

        The gene FAM13A is hypermethylated (1stExon/5'UTR), CPT1A is hypermethylated (5'UTR) and CPT1B is hypermethylated (TSS200/5'UTR) in PBMC from ME patients. This DNA methylation pattern is related to quality of life in the ME patients (table S7 in ref 7).

        In whole blood from adolescent CFS patients FAM13A gene expression is elevated (table S3 in ref 8).

        Use the link to see the figure:
        Figure. FAM13A regulates the CPT1A–FAO pathway in chronic obstructive pulmonary disease (COPD).  (Ref. 5)

        FAM13A regulates the CPT1A–FAO pathway in chronic obstructive pulmonary disease (COPD). FAM13 locus has been shown to be associated with increased expression of FAM13A and higher risk for COPD. FAM13 in association with SIRT1 induces the expression of CPT1A, a key enzyme that regulates fatty acid oxidation (FAO) in the mitochondria. Up-regulation of CPT1A promotes FAO and high production of ROS, leading to lung epithelial cell death; this is an important pathogenic mechanism that might lead to COPD. CAT, carnitine translocase; CoA, coenzyme A; CPT1A, carnitine palmitoyltransferase 1; CPT2, carnitine palmitoyltransferase 2; FACS, fatty acyl-CoA synthase; FADH2, flavin adenin dinucleotide; FAM13A, family with sequence similarity 13 member A; NADH, nicotinamide adenine dinucleotide reduced; ROS, reactive oxygen species; SIRT1, sirtuin 1; TCA, tricarboxylic acid cycle.  (Ref. 5)


        Is FAM13A and CPT1A/CPT1B involved in the ME/CFS pathomechanism?

        References
        1. Naviaux et al: Metabolic features of CFS. www.pnas.org/cgi/doi/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.
        3. Nagy-Szakal et al: Insights into ME/CFS phenotypes through comprehensive metabolomics. Nat Sci Rep 2018, 8.
        4. Reuter and Evans: Long-chain acylcarnitine deficiency in patients with CFS. Potential involvement of altered carnitine palmitoyltransferase-I-activity. J. Int. Med. 2011, 270.
        5. Hawkins et al. FAM13A, A Fatty Acid Oxidation Switch in Mitochondria. Friend or Foe in Chronic Obstructive Pulmonary Disease Pathogenesis?  Am J Respir Cell Mol Biol. 2017 Jun; 56(6): 689–691.doi: 10.1165/rcmb.2017-0080ED  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5516298/
        6. Trivedi et al: Identification of ME/CFS - associated DNA methylation patterns. Plos One 2018, 13, 7.
        7. de Vega et al: Epigenetic modifications and glucocorticoid sensitivity in ME/CFS. BMC Medical Genomics, 2017, 10, 11.
        8. 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

        søndag den 19. august 2018

        ACSL3, GPD2 og PDHX i ME

        Forskere har anvendt en ny forbedret teknologi til at undersøge epigenetiske ændringer i blodceller fra ME patienter. Resultatet blev valideret på ME patienter fra både USA og Spanien (1).

        De supplerende tabeller i artiklen rummer værdifulde informationer. Jeg vil nævne tre eksempler (ACSL3, GPD2 og PDHX) fra Tabel 7.

        Tabel S7 er en liste over 144 hypomethylerede gen promotorer. Promotoren er det område på DNA'et, hvorfra transkriptionen af et gen starter. Ændret DNA methylering af promotoren har stor betydning for genekspressionen. Man kan formode, at de 144 hypomethylerede gener er "på overarbejde", og at dette er relateret til ME sygdomsmekanismen. Vi ved ikke hvordan. Måske er de på overarbejde for at kompensere for noget, der er gået galt i cellens metabolisme?

        ACSL3
        Acyl-CoA synthetase long-chain family member 3 (ACSL3) aktiverer langkædede fedtsyrer til både syntese af cellulære lipider og til nedbrydning via beta-oxidation. ACSL3 er nødvendig for at bygge fedtsyrer ind i phosphatidylcholine.

        ACSL3 interagerer med proteiner kodet af generne: CPT1A, CPT1B, PNPLA2 og MGLL. Disse proteiner har en central rolle i lipidmetabolismen. Et tidligere epigenetisk studie har vist, at disse gener er påvirkede hos ME patienter (2).

        GPD2
        Glycerol-3-phosphate dehydrogenase 2 (GPD2) er et mitokondrie enzym, som er komponent i den respiratoriske kæde og i glycerophosphate-shuttlen. Det er et nøgleenzym i skæringspunktet mellem glykolyse, oxidativ fosforylering og fedtsyrer metabolismen (3).

        PDHX
        Pyruvate dehydrogenase complex component X (PDHX) er en delkomponent i PDH-komplekset. Hvis der opstår fejl i dette gen, eller PDHX-proteinet udsættes for et autoimmunt angreb bliver man alvorlig syg. Læs om genet: https://www.ncbi.nlm.nih.gov/gene/8050

        Spørgsmålet er hvorfor er dette gen epigenetisk ændret hos ME patienter? Et nedreguleret PDH-kompleks er allerede sat i centrum af ME sygdoms-mekanismen (4),

        Referencer:
        1. Trivedi et al: Identification of ME/CFS - associated DNA methylation patterns. Plos One 2018, 13, 7 http://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
        3. Mracek et al: The function and the role of the mitochondrial glycerol-3-phosphate dehydrogenase in mammalian tissue. Biochimica et Biophysica Acta 1827, 2013, 401-410.
        4. Fluge et al: Metabolic profiling indicates impaired pyruvate dehydrogenase function in myalgic encephalopathy / chronic fatigue syndrome. JCI Insight. 2016; 1(21):e89376. Doi 10.1172/jci.insight.89276

        mandag den 13. august 2018

        Functions of DNA methylation

        Functions of DNA methylation
        Abstract (ref 1):
        DNA methylation is frequently described as a 'silencing' epigenetic mark, and indeed this function of 5-methylcytosine was originally proposed in the 1970s. Now, thanks to improved genome-scale mapping of methylation, we can evaluate DNA methylation in different genomic contexts: transcriptional start sites with or without CpG islands, in gene bodies, at regulatory elements and at repeat sequences. The emerging picture is that the function of DNA methylation seems to vary with context, and the relationship between DNA methylation and transcription is more nuanced than we realized at first. Improving our understanding of the functions of DNA methylation is necessary for interpreting changes in this mark that are observed in diseases such as cancer.


        The effects of variations in CpG methylation on coding genes depend on the location
        Quote (from ref 2, page 10):
        The effects of variations in CpG methylation on coding genes depend on the location of the
        differential methylation in relation to the gene of interest. There are two genic regions where the
        relationship between CpG methylation and gene expression are generally well understood.
        Increased CpG methylation in the TSS of genes tends to lead to a decrease in transcription either
        due to the prevention of transcription factors from recognizing and binding to the promoter region for the initiation of transcription, or due to the recruitment of other methyl-binding
        proteins and co-repressors [19, 56, 57]. On the other hand, increased CpG methylation in the
        gene body is positively correlated with transcription [58]. Although the exact reasons are
        unclear, gene body methylation is believed to be important for silencing repetitive elements,
        retrotransposons, and regulating alternative splicing events [52]. (references are in ref 2)


        References:
        1) Peter A. Jones: Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Revet Genet, 2012, 13, 7.


        2) de Vega: 
        DNA Methylation Modifications Associated with Glucocorticoid Sensitivity and Clinical Subtypes of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)

        søndag den 12. august 2018

        Mitokondrieproteiner i ME

        Vi forstår endnu ikke mitokondriernes rolle i ME sygdoms-mekanismen. Mitokondrieproteiner dukker sporadisk op i ME forskningen. Lad os se om disse mitokondrie påvirkninger danner et samlet billede, som kan lede os på sporet af hvad der foregår i ME sygdomsmekanismen.

        I studiet af DNA methyleringer på CD4+ - T celler fra ME patienter, er to gener, OXA1L og FTSJ2, henholdsvis hypo- og hypermethyleret. Generne koder proteiner, der anvendes af mitokondrierne (1).

        En tommelfingerregel er, at hypomethylering af et gen er forbundet med øget transkription, og hypermethylering er en nedregulering af genet. Virkeligheden er mere kompliceret, idet methyleringens placering er afgørende for påvirkningen af genet. Som udgangspunkt må vi nøjes med at sige, at generne er epigenetisk ændrede hos ME patienter i forhold til raske kontrolpersoner.

        OXA1L
        I mitokondriernes membraner bygges de respiratoriske komplekser OXPHOS, der søger for, at cellen kan danne energimolekylerne ATP. Del-komponenter til OXPHOS komplekserne kodes af DNA fra cellekernen og fra mitokondriernes eget DNA. Når del-komponenterne er produceret, skal de bygges ind i mitokondriemembranerne og blive til OXPHOS komplekser. OXA1L har en vigtig rolle i OXPHOS byggeprocessen (2).

        OXA1L interagerer også med mitokondrie ribosomerne, dvs proteinet er knyttet til translationen. Den tilknytning er relateret til den respiratoriske funktion.

        Af genecards.org STRING interaction network kan man se de nærmeste proteiner, som OXA1L interagerer med. Nogle af disse OXA1L-samarbejdspartnere dukker også op i ME forskningen:

        MRPL23, er mitochondrial ribosomal protein L23, og har øget genekspression hos ME patienter i tre studier (3, 4, 5).

        ATP5G2, en ATP synthase knyttet til de respiratoriske komplekser. Genet er hypermethyleret (TSS1500) i et studie (6), og hypomethyleret (1stExon) i et andet studie af ME patienter (7).

        ATP6V0C, en del komponent i v-ATPasen. Genet er hypermethyleret (body) og flere andre v-ATPase delkomponenter er fundet epigenetisk ændrede hos ME patienter (6).

        FTSJ2 = MRM2
        FTSJ2 hedder også mitochondrial rRNA methyltransferase 2, MRM2. Proteinet arbejder sammen med MRM3 om dannelse af en mitokondrie-ribosom del-komponent. Hvis man inaktiverer MRM2 og MRM3 i celler forminskes den respiratoriske kapacitet, som en konsekvens af formindsket mitokondrie-translation (8).

        Defekt MRM2 vil resultere i MELAS- syndrom lignende symptomer. MELAS = mitochondrial encephalopathy, lactic acidosis and stroke-like episodes (9).

        MRM2 interagerer med proteinet thyroid adenoma associated (THADA). THADA regulerer balancen mellem energi opbevaring og varme produktion. THADA arbejder sammen med et protein, der hedder SERCA. SERCA regulerer Ca2+ ligevægten i cellen (10).

        Genet THADA er hypermethyleret (body) hos ME patienter i et studie (6), og hypomethyleret (3'UTR) i et andet studie (7).

        MRRF
        I to af studierne hvor ME patienterne havde øget genekspression af MRPL23, så man også øget genekspression af mitochondrial ribosome recycling, MRRF (4, 5).

        Mitokondrie-ribosomerne genbruges til kontinuerlig OXPHOS-produktion. I et forsøg med raske celler så man, at kunstig nedreulering af MRRF medførte:

        • nedsat niveau af samlede OXPHOS-komplekser
        • nedsat respiration
        Det interessante var, at der var en forsinkelse på flere dage, førend den manglende proteinsyntese manifesterede sig (11).

        Spørgsmål er om denne OXPHOS-levering-forsinkelse kan sættes i relation til ME patienters post-exertional-malaise (PEM), som bekendt er et ME-diagnosekriterie. Arbejder ME-celler på højtryk for at levere OXPHOS, og i givet fald - hvorfor?

        GFM1
        G elongation factor mitochondrial 1 (GFM1) er en mitokondrial translations faktor. Hvis GFM1 bliver nedreguleret resulterer det i OXPHOS mangel, og symptomerne er encephalopathy og multi-system sygdom (12).

        Genet GFM1 er hypermethyleret (body) hos ME patienter, og dette er relateret til patienternes livskvalitet (6).

        Jeg har ikke fundet alle relevante DNA methyleringer. Dette var blot et lille eksempel på hvad ME forskningen rummer af ikke udnyttet viden.

        Referencer:
        1. Brenu et al: Methylation profile of CD4+ T cells in CFS/ME. J. Clin Cell Immunol 5, 228
        2. Stoldt et al: The inner-mitochondrial distribution of OXA1 depends on the growth conditions and on the availability of substrates. MBOC, 2012, 23.
        3. Kaushik et al: Gene expression in PBMC from patients with CFS. J Clin Pathol, 2005, 58
        4. Kerr et al: Gene expression subtypes in patients with CFS/ME. JID, 2008, 197.
        5. Frampton et al: Assessment of a 44 gene classifier for the evaluation of CFS from PBMC gene expression. Plos one, 2011, 6, 3.
        6. de Vega et al: Epigenetic modifications and glucocorticoid sensitivity in ME/CFS. BMC Medical Genomics, 2017, 10, 11.
        7. Trivedi et al: Identification of ME/CFS - associated DNA methylation patterns. Plos One 2018, 13, 7.
        8. Rorbach et al: MRM2 and MRM3 are involved in biogenesis of the large subunit of the mitochondrial ribosome. Mol Biol Cell, 2014, 25, 17.
        9. Garone et al: Defective MRM2 causes MELAS-like clinical syndrome. Hum Mol Genet, 2017, 26, 21.
        10. Moraru et al: THADA regulates the organismal balance between energy storage and heat production. Dev Cell, 2017, 41, 1.
        11. Rorbach et al: The human mitochondrial ribosome recycling factor is essential for cell viability. Nucleic Acids Research, 2008, 36, 18.
        12. Simon et al: Activation of a cryptic slice site in the mitochondrial elongation factor GFM1 causes combined OXPHOS deficiency.  Mitochondrion 2017, 34.



        lørdag den 11. august 2018

        SPI1 and ME

        SPI1 (=PU.1) is a transcription factor involved in hematopoiesis. SPI1 regulates B-cell development, but is also important for maturation of macrophages, T cell progenitors and T helper 9 cells.

        SPI1 can either activate or repress the transcription of genes. This is mediated by the ability of SPI1 to build different complexes with a number of different protein partners (1).

        In leukemia SPI1 can be either an oncogene or a tumor suppressor. SPI1 overexpression can trigger cellular senescence, and may be a safeguard against leukemia (12).

        EP300 is a transcriptional co-activator, which interacts with SPI1. Epstein-Barr Virus nuclear antigen leader protein (EBNALP) coactivates EP300 and hereby dysregulates SPI1. An EP300 inhibitor can abolish EBNALP coactivation and may have the potential to control EBV-associated diseases (3).

        SPI1 is a putative upstream regulator in adolescent CFS patients (table S4 in ref 4).

        The gene SPI1 is hypermethylated (body, 5'UTR, 1stExon) in Me patients in one study (5), and hypomethylated (TSS200) in another study (6).

        SPI1 interacts with several proteins where the genes are epigenetic changed. Fx, FLT3, CREBBP, E2F3, ELANE, HOXA10, GFI1, TFDP1 and IRF4 (5)

        SPI1 also interacts with KAT2B (= EP300 / CBP associated factor). The gene promoter of KAT2B is hypomethylated in ME patients (6).

        EP300 and CREBBP interacts with CITED2 (= CBP / p300 - interacting transactivator). CITED2 geneekspression is upregulated in ME patients (7, 8).

        References:

        1. Riel and Rosenbauer: Epigenetic control of hematopoiesis. Biol Chem 2014, 395, 11.
        2. Delestré et al: Senescence is a Spi1-induces anti-proliferative mechanism in primary hematopoietic cells. Haematologica 2017, 102, 11.
        3. Wang et al: Epstein-Barr Virus Nuclear Antigen Leader Protein Coactivates EP300. J Virol, 2018, 92, 9.
        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.
        5. de Vega et al: Epigenetic modifications and glucocorticoid sensitivity in ME/CFS. BMC Medical Genomics, 2017, 10, 11.
        6. Trivedi et al: Identification of ME/CFS - associated DNA methylation patterns. Plos One 2018, 13, 7.
        7. Kerr et al: Gene expression subtypes in patients with CFS/ME. JID, 2008, 197.
        8. Frampton et al: Assessment of a 44 gene classifier for the evaluation of CFS from PBMC gene expression. Plos one, 2011, 6, 3.

        mandag den 30. juli 2018

        HOXA9 and ME

        Histones act as spools around which DNA winds.

        H3 and H4 histones have long tails. The tail can be modified in different ways, that lead to activation or repression of transcription of genes. Fx, trimethylation of H3 lysine 4 (H3K4me3) will acrivate transcription, and trimethylation of H3 lysine 27 (H3K27me3) will repress genes.

        COMPASS (complex of proteins associated with Set1) - like complexes activate transcription. They perform the histone modification H3K4me3.

        Polycomb complexes repress genes. The polycomb repressive complex 2 perform the histone modification H3K27me3.

        Several subunits of COMPASS are shared with the super elongation complex (SEC).

        The balance between COMPASS/SEC mediated transcription and polycomb mediated repression of transcription, regulate many genes - particularly HOX gens.

        MLL is a H3K4 methyltransferase and is part of SEC/COMPASS - like complexes. MLLT1 is a SEC subunit. ASXL1 is a member of the polycomb group.

        MLL and ASXL1 interact with HOXA9, which is involved in hematopoiesis.

        HOXA9 interacts with MEIS1, PBX2 and TRIP6.

        HOXA9 regulates FLT3, MYB and LMO2.

        HOXA9 is a putative upstream regulator in adolescent CFS-patients (table S4 in ref 1).

        Epigenetic changed genes in ME patients:

        • MLL, hypermethylated 3'UTR
        • MLLT1, hypermethylated body, q
        • ASXL1, hypomethylated body, q
        • HOXA9, hypermethylated body, q, s
        • MEIS1, hypermethylated body, q, s
        • PBX2, hypermethylated body, hypomethylated TSS1500, q, s
        • TRIP6, hypermethylated body, TSS1500, q,
        • FLT3, hypermethylated body, q
        • MYB,  hypermethylated body, q, s
        • LMO2, hypermethylated 5'UTR, TSS1500, 1st Exon, q, s
        q = the methylation is related to quality of life in ME patients (2).
        s = the gene is differentially methylated in subtypes of ME patients (3).


        String interaction network - HOXA9 from www.genecards.org

        This is just the tip of the iceberg. Several COMPASS/SEC, polycomb proteins and HOX genes are involved in the ME pathomechanism. And they relate to the dysregulated metabolism.

        References:
        1. 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
        2. de Vega et al: Epigenetic modifications and glucocorticoid sensitivity in ME/CFS. BMC Medical Genomics, 2017, 10, 11
        3. de Vega et al: Integration of DNA methylation & health scores identifies subtypes in ME/CFS. Epigenomics 2018, 10, 5

        torsdag den 26. juli 2018

        Nucleoporins in ME

        The nuclear pore complex (NPC) mediates nuclear transport of RNA. Nucleoporins are the main components of the NPC. Certain nucleoporins have additional function in chromatin organization and transcription regulation.

        NUP98 and NUP96
        The gene NUP98 encodes nucleoporin Nup98 and Nup96. They are expressed from one mRNA. Following translation, autoprotelytic cleavage separates the two proteins. Alternatively, Nup98 can be spliced as a short mRNA that does not encode Nup96 (1).

        Interferon-induced gene promoters containing Nup98 accumulate poised RNA Pol II along with dimethylated histone H3K4 (1).

        NUP98 recruits the Wdr82-Set1A/COMPASS complex to promoters to regulate H3K4 trimethylation in hematopoietic progenitor cells (2).

        Nup98 associates with Trx/MLL and NSL Histone-modifying complexes and regulates Hox Gene expression (3).

        Mice with low levels of Nup96 have impared interferon mediated induction of MHCI and II and altered T- and B-cell function (4).

        NUP98 and HOXA1 are involved in the ME pathomechanism in severely ill ME patients (5).

        Depletion of FOXK1 attenuates virus-inducible interferon-stimulated response element (ISRE) reporter expression. Drosophila FOXK interact with Nup98 to regulate antiviral gene expression (6).

        FOXK1 is hypermethylated in ME patients in two studies (7, 8). The hypermethylation (3'UTR and body) is related to quality of life in ME patients (table S7 in ref 8).

        FOXK1(body) is differentially methylated in ME subtypes (no 673 in table S3 in ref 9).

        References

        1. Franks et Hetzer: The role of Nup98 in transcription regulation in healty and diseased cells. Trends Cell Biol. 2013, 23, 3
        2. Franks et al: Nup98 recruits the Wdr82-Set1a/COMPASS complex to promoters to regulate H3K4 trimethylation in hematopoietic progenitor cells. Genes Dev. 2017, 15, 31
        3. Pascual-Garcia et al: Nucleporin Nup98 associates with Trx/MLL and NSL histone-modifying complexes and regulates HOX gene expression. Cell Rep. 2014, 9
        4. Favia et al: The nucleoporin Nup96 is required for proper expression of interferon-regulated proteins and functions. Immunity 2006, 24
        5. Pihur et al: Metaanalysis of CFS through integration of clinical, gene expression, SNP and proteomic data. Bioinformation 2011, 6, 3
        6. Panda et al: The transcription factor FOXK participates with Nup98 to regulate antiviral gene expression. MBio, 2015, 7, 2
        7. de Vega et al: DNA methylation Modifications associated with CFS. PlosOne, 2014, 9, 8
        8. de Vega et al: Epigenetic modifications and glucocorticoid sensitivity in ME/CFS. BMC Medical Genomics, 2017, 10, 11
        9. de Vega et al: Integration of DNA methylation & health scores identifies subtypes in ME/CFS. Epigenomics 2018, 10, 5

        tirsdag den 24. juli 2018

        mRNA export in ME

        DNA is transcribed into pre-mRNAs.

        mRNAs are packaged into pre-messenger ribonucleoproteins (pre-mRNPs).

        Pre-mRNPs are spliced into mature mRNPs.

        mRNPs are exported out of the nucleus through the nuclear pore complex (NPC).

        SUN1 (=UNC84) is a nuclear envelope protein.

        SYNE proteins (nesprins) are part of a network that connects the nuclear envelope to the cytoskeleton.

        NXF1 is an export factor.

        NUP153 is one of several nucleoporins.

        SUN1 recruits NFX1-containing mRNPs onto the nuclear envelope and hands them over to NUP153 (1).


        An external file that holds a picture, illustration, etc.
Object name is gkv1058fig7.jpg


        Figure from: Li and Noegel: Inner nuclear envelope protein SUN1 plays a prominent role in mammalian mRNA export. Nucleic Acids Research 2015, 43, 20, 9874-9888 (1).

        The gene SUN1 is hypomethylated in CD4+  T cells (2), and in peripheral blood mononuclear cells (PBMC) from ME patients in two studies (3, 4).

        The hypomethylation is related to quality of life in ME patients (table S7 in ref 4).

        SYNE1 and SYNE2 are hypermethylated in ME patients (3, 4). The SYNE2 hypermethylation (body and TSS1500) is related to quality of life in ME patients (table S7 in ref 4).

        SYNE2 is differentially methylated in ME subtypes (no 73 and no 1732 in table S3 in ref 5).

        NXF1 is hypermethylated (TSS1500) in ME patients and the methylation is related to quality of life (table S7 in ref 4).

        NXF1 gene expression is up-regulated (adjustet p-value = 0,0682) in whole blood from adolescent CFS patients (6).

        References:

        1. Li and Noegel: Inner nuclear envelope protein SUN1 plays a prominent role in mammalian mRNA export. Nucleic Acids Research 2015, 43, 20, 9874-9888 (1)
        2. Brenu et al: Methylation Profile of CD4+  T cells in CFS/ME. J. Clin Cell Immunol 2014, 5, 3.
        3. de Vega et al: DNA methylation Modifications associated with CFS. PlosOne, 2014, 9, 8
        4. de Vega et al: Epigenetic modifications and glucocorticoid sensitivity in ME/CFS. BMC Medical Genomics, 2017, 10, 11
        5. de Vega et al: Integration of DNA methylation & health scores identifies subtypes in ME/CFS. Epigenomics 2018, 10, 5.
        6. Nguyen et al: Whole blood gene expression in adolescent CFS: an exploratory cross-sectional study suggesting altered B cell differentiation and survival. J Trans Med, 2017, 15, 102.