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

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).


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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.

søndag den 4. marts 2018

GRAMD1A - a tether, which transfers sterols.

de Vega et al showed that the most hypermethylated gene associated with quality of life in ME patients was GRAMD1A. A hypermethylated gene is often associated with supressed transcription (1).

GRAMD1A is a tether protein between the plasma membrane and endoplasmic reticulum (2).



Figure 8 from Marina Besprozvannaya, et al. eLife. 2018;7:e31019 (2)



GRAMD1A transfer sterols (3)

Is GRAMD1A involved in the dysregulated sterol and sphingolipid homeostasis in ME patients?


References:

  1. Vega et al: Epigenetic modifications and glucocorticoid sensitivity in ME/CFS. BMC Medical Genomics, 2017, 10, 11
  2. GRAM domain proteins specialize functionally distinct ER-PM contact sites in human cells.
    Besprozvannaya M, Dickson E, Li H, Ginburg KS, Bers DM, Auwerx J, Nunnari J.
    Elife. 2018 Feb 22;7. pii: e31019. doi: 10.7554/eLife.31019
  3. Horenkamp et al: Molecular basis for sterol transport by START-like lipid transfer domains. EMBO  J. 2018 Feb 21

lørdag den 20. januar 2018

KDM2B, PHYH, P3H2, PLOD3 and ME

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

The following examples are relevant for ME research.

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

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

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

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

References:

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

torsdag den 18. januar 2018

D2HGDH, PHYKPL and ME

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

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

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

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

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

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

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

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

References:

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

søndag den 7. januar 2018

DGKZ and ME

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

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

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

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

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

References:

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

lørdag den 6. januar 2018

ATP6V0E2, PRF1, GNLY and ME

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

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

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

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

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

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

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

References:

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

tirsdag den 2. januar 2018

ACVR1, activiner og ME

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

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

Forhøjede niveauer af activin A og B kan påvises ved inflammatorisk respons. Hos ME patienter har man fundet:
  • normalt niveau af activin A
  • forhøjet niveau af activin B
  • lavere niveau af det activin-bindende protein follistatin (FST)
  • forhøjet ratio af activin A/FST
  • forhøjet ratio af activin B/FST
  • forhøjet ratio af activin B/activin A
Proteinet STAR transporterer kolesterol fra den ydre til den indre mitokondrie membran. Herved kan kolesterol omdannes til pregnenolone, som anvendes til videre steroid produktion.

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

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

Referencer:

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