lørdag den 27. maj 2017

BACH2, PRDM1, PRDM2, ELL2 and ME

BACH2, PRDM1, PRDM2 and ELL2 are epigenetic changed in ME patients (1).

  • Bach2 is a transcription factor, essential for B-cells.
  • PRDM1 encodes Blimp-1, the master regulator of plasma cells.
  • PRDM2 act as a transcriptional activator of the heme-oxygenase-1 gene.
  • Transcription elongation factor ELL2 drives Ig secretory specific mRNA production (2,3)
Heme regulates B-cell differentiation, antibody class switch and hemeoxygenase-1 expression in B cells as a ligand of Bach2 (2).

Heme inhibits Bach2.

Bach2 inhibits Blimp-1.

Blimp-1 activates ELL2.

Ig classes are dysregulated in some ME patients (4).

Some ME patients have reduced representation of pathways for heme biosynthesis (5).

References:
  1. Vega et al. DNA methylation Modifications associated with CFS. Plos One, aug 2014, vol 9, Issue 8, e104757
  2. Watanabe-Matsu et al: B-cell differentiation, antibody class switch and hemeoxygenase-1 expression in B cells as a ligand of Bach2. Blood 19.may2011, vol117, No.20.
  3. Minnich et al: Multifunctional role of the transcription factor Blimp-1 in coordinating plasma cell differentiation. Nat Immun 17, 2016
  4. FollowMEinDenmark "Immunological findings" 17.august 2013.
  5. Nagy-Szakal et al: Fecal metagenomic profiles in subgroups of patients with ME/CFS. Microbiome 2017,5,44.

mandag den 24. april 2017

COG3, LPAAT3, ERGIC and ME

What is going on in the endoplasmic reticulum (ER) and the golgi complex in ME patients?

The gene COG3, component of oligomeric golgi complex 3, is hypomethylated in ME patients (1). The COG is required for normal golgi morphology and localization. Defects in the COG complex result in multiple deficiencies in protein glycosylation (2).

Some ME patients have SNP in the gene AGPAT3, also known as LPAAT3, lysophosphatidic acid acyltransferase 3 (3). LPAAT3 regulates golgi complex structure and function (4).

The gene ERGIC1, ER-golgi intermediate compartment 1, is hypermethylated (5). ERGIC1 is a cycling membrane protein which interacts with other members of this protein family to increase their turnover (2).

The ERGIC53 precursor is up-regulated in the cerebrospinal fluid, CFS:9 and normal value:1 (6). ERGIC53 is also known as LMAN1, lectin mannose binding 1. The protein cycles between ER and golgi, functioning as a cargo receptor for glycoprotein transport (2). LPAAT3 affects the recycling of ERGIC53 (4).

Ceramides are downregulated in the plasma from ME patients (7). The spingosine backbone from short chain ceramides is used (recycled) to make long chain ceramides. This process takes place in the golgi complex. The mycotoxin brefeldin A is used in golgi research, because it causes disassembly of the golgi complex. Research has shown that the salvage of the sphingosine backbone of short-chain ceramide to form long-chain ceramide was attenuated by brefeldin A (8).

There are many more ER/golgi genes and proteins, which are changed in ME patients compared to normal controls in references 5 and 6. Are the changes involved in cause or consequence of the ME pathomechanism?

References:

  1. Brenu et al: Methylation profile of CD4+ T cells in CFS/ME. J. Clin Cell Immunol 5, 228
  2. www.ncbi.nlm.nih.gov/gene
  3. Schlauch et al: Genome-wide association analysis identifies genetic variations in subjects with ME/CTS. 2016.doi.10.1038/tp.2015.208
  4. Schmidt and Brown: Lysophosphatic acid acyltransferase 3 regulates golgi complex structure and function. J. Cell Biol. Vol. 186, No2, 2009
  5. Vega et al. DNA methylation Modifications associated with CFS. Plos One, aug 2014, vol 9, Issue 8, e104757
  6. Schutzer et al: Distinct Cerebrospinal Fluid Proteomes Differentiate Post- Treatment Lyme Disease from Chronic Fatigue Syndrome. PLOS One February 2011, volume 6, Issue
  7. Naviaux et al: Metabolic features of CFS. www.pnas.org/cgi/doi/10.1073/pnas.1607571113
  8. Kitatani: The sphingolipid salvage pathway inceramide metabolism and signaling. Cell Signal 2008 Jun 20, 6.



    søndag den 2. april 2017

    Choline, ME og POTS

    Choline ( dansk: kolin) er et næringsstof, som vi indtager gennem kosten. Choline er byggesten for:
    • phosphatidylcholine, som er et lipid i cellemembranen
    • neurotransmitteren acetylcholine
    • betaine, som er methylgruppe-donor og en vigtig osmolyt

    Opdagelse af choline

    Tre typer transportproteiner sørger for optagelse af choline:
    • organic cation transporters
    • high affinity choline transporters, som er tæt associeret med syntese af acetylcholine i neuronerne
    • solute carriers, SLC44A1, SLC44A2 og SLC44A3

    Syntese af phosphatidylcholine

    Choline omdannes til phosphatidylcholine (PC) via tre enzymer i tre trin, som hedder CDP-choline eller Kennedy stivejen:
    • choline omdannes til phospho-choline af choline kinase
    • phospho-choline omdannes til cytidinediphosphocholine (CDP-choline) af phosphocholinecytidyltransferase (PCYT1A)
    • CDP-choline omdannes til PC af cholinephosphotransferase (1)

    ME forskning

    Følgende gener er fundet epigenetisk ændrede hos ME patienter (2,3):
    • PCYT1A, hypomethyleret
    • SLC44A1, hypermethyleret
    • SLC44A2, hypermethyleret
    • SLC44A3, hypermethyleret
    Metaboliterne CDP-choline og choline phosphate(1-) er fundet nedregulerede i plasma fra ME-patienter (4).

    POTS forskning

    Undersøgelse af celler fra en enkelt POTS-patient viste, at patienten havde nedsat mRNA ekspression af SLC44A1 og choline optagelsen var reduceret med 60%. Lipidsammensætning i lipid rafts var ændret, hvilket påvirkede membran-permabilitet og funktion. Samtidig blev der påvist mitokondrie dysfunktion (5).

    Referencer:
    1. Fagone og Jackowski: Phosphatidylcholine and the CDP-Choline Cycle. Biochim Biophys Acto. 2013 March, 1831, 3, 523-532.
    2. Vega et al. DNA methylation Modifications associated with CFS. Plos One, aug 2014, vol 9, Issue 8, e104757
    3. Vega et al: Epigenetic modifications and glucocorticoid sensitivity in ME/CFS. BMC Medical Genomics, 2017, 10, 11
    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
    5. Schenkel et al: Mechanism of choline deficiency and membrane alteration in POTS primary skin fibroblasts. FASEB Journal, April 2015, Vol 29.

    søndag den 12. marts 2017

    Galdesyrer, tarmflora og ME

    Basisviden

    Galdesyrer har antimikrobielle egenskaber og påvirker sammensætningen af tarmfloraen.

    Nedsat niveau af galdesyrer i tarmen favoriserer gramnegative bakterier, som kan producere giftig lipopolysakkarid (LPS). Øget niveau af galdesyrer favoriserer grampositive Firmicutes, hvilket anses for at være gunstigt for helbredet.

    Infektion af Clostridium difficile er svær at behandle. Forskere ser på muligheden for at behandle med Clostridium scindens, som kan omsætte primære galdesyrer til sekundære galdesyrer i tarmen. Den sekundære galdesyre deoxycholic acid har stor antimikrobiel effekt og beskytter mod Clostridium difficile infektion. (1)

    ME Forskning

    ME patienter har reduceret niveau af galdesyrer (se blogindlæg af 19 feb 2017).

    ME patienter har reduceret niveau af Firmicutes i tarmfloraen, og signifikant højt plasmaniveau af LPS (2)

    Det kunne være interessant med et studie, der undersøgte sammenhængen mellem galdesyreniveau og tarmflora hos ME patienter.

    Referencer:
    1. Fiorucci og Distrutti. Trends in Mol. Med. Nov 2015, 21:11
    2. Giloteaux et al. Microbiome, 2016, 4:30

    søndag den 19. februar 2017

    Kolesterol og galdesyrer i ME

    Basisviden

    Kolesterol indgår i cellens membran og påvirker cellesignalering. Kolesterol-molekylet er "byggesten" for en del hormoner, D-vitamin og galdesyrer. Kroppen tilføres kolesterol gennem maden, og resten af det kolesterol man skal bruge dannes i leveren. Ordet kolesterol kommer af det græske chole = galde og stear = fedt.

    Galdesyrer dannes i leveren, som de primære galdesyrer:
    • cholic acid (CA), dansk: kolsyre
    • chenodeoxycholic acid (CDCA), dansk: kenodeoxykolsyre
    De primære galdesyrer omsættes i tarmen af tarmbakterier til sekundære galdesyrer:
    • deoxycholic acid (DCA)
    • lithocholic acid (LCA).
    Galdesalte er natrium og kalium salte af galdesyrer konjugeret (=bundet) med glycine og taurin.

    Galdesyrer søger for, at vi kan opløse og optage det fedt vi spiser, og at vi kan optage de fedtopløselige vitaminer A, D, E og K.

    ME forskning

    Naviaux's undersøgelse af ME patienters metabolisme viste, at de biokemiske stiveje, der sørger for syntese af kolesterol og galdesyrer var dysregulerede. En metabolit i stivejene, lathosterol, var reduceret i blodet hos både mænd og kvinder i Kolesterolniveauet var normalt. Kvinderne havde nedsat niveau af galdesyren CDCA (1).

    Germain's undersøgelse af kvindelige ME patienters metabolisme viste nedregulering af følgende metabollitter (2):
    • glycocholate
    • glycochenodeoxycholate
    • glycolithocholate
    • lithocholate
    • sulfoglycolithocholate
    • taurine
    Vegas's epigenetiske studier af ME patienter afspejler en påvirkning af kolesterol/galdesyrer omsætning, idet følgende gener var epigenetiske ændrede (hypermethylerede) (3):
    • SLC10A1, transportprotein fra familien af natrium/galdesyre cotransportere.
    • OSTalpha, organic solute transporter, ligeledes et transport protein. Det er involveret i det enterohepatiske kredsløb.
    • ABCC1, transportprotein med flere funktioner, bl.a. transport af glukuronider og sulfat konjugater af steroid hormoner og galdesalte.
    • OSBPL10, oxysterol-binding protein familien er intracellulære lipid receptorer, der påvirker lipid ligevægten i cellen.
    • NPC1, Nieman -Pick C1 protein, involveret i kolesterol transport inde i cellen.
    • RAB11FIP1, RAB11 family interacting protein, involveret i kolesteroltransport inde i cellen, samtidig påvirker kolesterol lipidendocytose gennem RAB11.
    • RABGAP1, RAB GTPase activating protein, stikord til RAB GTPaser er noget med lipider, phospholiper og membrantransport gennem endo- og exocytiske stiveje.
    • CYB5R2, er involveret i kolesterol syntese, fedtsyre desaturation og elongation. CYB5R2 findes på kromosom 11, lige ved siden af genet PPFIBP2 (også hypermethyleret hos ME patienter). Det er en beta liprin, der er involveret i axon guidance og dannelse af synapser.
    Det er oplagt, at dysregulerede kolesterol/galdesyrer stiveje kan forklare irritabel tarm, især ved store fedtrige måltider. Men kan dysreguleringerne i ME patienters metabolisme også påvirke de kolesterolholdige lipid rafts i cellemembranerne og herigennem cellesignalering?
    Referencer:

    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. Vega et al. DNA methylation Modifications associated with CFS. Plos One, aug 2014, vol 9, Issue 8, e104757
    Kolesterolviden: Ikonen: Cellular cholesterol trafficking and compartmentalization. Nature Reviews, 9, Feb(2008).
    Basisviden om gener: www.ncbi.nlm.nih.gov/gene

    torsdag den 9. februar 2017

    Phosphoinositides and ME

    Germain et al:

    "Another hypothesis that could be drawn from the pathway analysis concerns the glycerophospholipid metabolism, as we observed five altered metabolites involved in biological membrane composition. Phosphoinositides are phospholipids that play critical roles in the brain and the spinal cord and peripheral nerves, by being involved in cell regulation and membrane dynamics."

    I believe this hypothesis is true and very important.

    Phosphoinositides (PIs) are generated in the PI-cycle. The first step in the PI-cycle is the conversion of diacylglycerol (DAG) to phosphatidic acid (PA) via the enzyme diacylglycerol kinase (DGK).

    The last step is genration of PIP2. PIP2 is involved in cell signaling, fx regulation of TRPs.

    Glycerol-3-phosphate can be converted to lysophosphatidic acid, which can be converted to PA. Lipin (gene: LPIN) can convert PA to DAG.

    Epigenetic changed genes in ME:

    • DGKA (DGK-alpha) hypomethylated (2)
    • DGKQ (DGK-theta) hypermethylated, with a negative foldchange (3)
    • LPIN1 hypermethylated (2)
    References:


      1. Germain et al: Metabolic profiling of a ME/CFS discovery cohort reveals disturbances in fatty acid and lipid metabolism. Mol. BioSyst. 2017, 13, 371
      2. Vega et al. DNA methylation Modifications associated with CFS. Plos One, aug 2014, vol 9, Issue 8, e104757
      3. Brenu et al: Methylation profile of CD4+ T cells in CFS/ME. J. Clin Cell Immunol 5, 228

      GPD2, the glycerophosphate-shuttle and ME

      Glucose/pyruvate and lipid metabolism have been found dysregulated in ME (1, 2, 3)

      Glycero-3-phosphate has been found up-regulated in ME (3).

      The gene GPD2 codes mithochondrial glycerol-3-phosphate dehydrogenase (mGPDH).

      mGPDH oxidizes glycerol-3-phosphate to dihydroxyacetone phosphate.

      mGPDH is a very important enzyme of intermediary metabolism and as a component of glycerophosphate shuttle at the crossroads of glycolysis, oxidative phosphorylation and fatty acid metabolism (4).

      These genes have been found epigenetic changed (hypermethylated) in ME (5):

      • GPD2, glycerol-3-phosphate dehydrogenase 2
      • SLC37A3, solute carrier family 37, glycerol-3-phosphate transporter
      • DAK, dihydroxyacetone kinase 2 homolog
      References:

      1. 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
      2. Naviaux et al: Metabolic features of CFS. www.pnas.org/cgi/doi/10.1073/pnas.1607571113
      3. Germain et al: Metabolic profiling of a ME/CFS discovery cohort reveals disturbances in fatty acid and lipid metabolism. Mol. BioSyst. 2017, 13, 371
      4. 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.
      5. Vega et al. DNA methylation Modifications associated with CFS. Plos One, aug 2014, vol 9, Issue 8, e104757