Tag Archives: vitamin-D

Is the Loomis Hypothesis wrong?

I remember an old vitamin D book – I believe it was Feldman’s Vitamin D – that going down the Transsahara Route (Algier-Lagos) human skin color gets always darker towards Tamanrasset due to increased solar power (also known as Loomis Hypothese).

Let’s look at three maps now.

1. Solar power. Source: https://upload.wikimedia.org/wikipedia/commons/1/1e/Global_Map_of_Global_Horizontal_Radiation.png

The above map does not match the skin tones.

2. Skin tone. Source https://science.sciencemag.org/content/358/6365/867.full For full details see the original paper

Neither does a new vitamin D map published last week in the Lancet

3. Vitamin D map. Source: https://linkinghub.elsevier.com/retrieve/pii/S2214109X19304577 For full details see the original paper

Although the maps are still patchy, I think the Loomis hypothesis is wrong.

VDR variants are associated with asthma

It is always nice to see an own study 15 years later appearing in a meta-analysis. A new paper in the Annals of Allergy, Asthma and Immunology now shows the results of 17 case–control studies.

Pooled odds ratio (OR) and 95% confidence interval of individual studies and pooled data for the association between TaqI polymorphism and asthma risk in overall populations and B for tt vs. TTof the TaqI variant.

We are in line #1…

Primary prevention of cow’s milk sensitization and food allergy by avoiding supplementation

A new study by Urashima et al. shows that sensitization to cow’s milk and food allergy, including CMA and anaphylaxis, are primarily preventable by avoiding CMF supplementation for at least the first 3 days of life. Although examined only indirectly, vitamin D supplements could be involved in the sensitization process.

Note to self – this is study no 4 of vitamin D related RCTs
1. De Montis G, Gendrel D, Chemillier-Truong M, Dupont C. Sensitisation to peanut and vitamin D oily preparations. The Lancet 1993;341(8857):1411.6.
2. Norizoe C, Akiyama N, Segawa T, Tachimoto H, Mezawa H, Ida H, Urashima M. Increased food allergy with vitamin D: A randomized, double-blind, placebo-controlled trial. Pediatr Int 2014; 56:6-12.7.
3. Rueter K, Jones AP, Siafarikas A, Lim EM, Bear N, Noakes PS, et al. Direct infant UV light exposure is associated with eczema and immune development. J Allergy Clin Immunol 2018; in press, doi: 10.1016/j.jaci.2018.08.037.

BTW The Urashima study is accompanied by a valuable editorial of George du Toit and Kari Nadeau

There is currently a lack of consensus among national allergy societies .. Although the EAACI3 and American Academy of Allergy, Asthma and Immunology (AAAI) currently recommend the use of hypoallergenic formulas in infants at high risk of allergy, the Australian Society of Clinical Immunology and Allergy does not. The EAACI and the AAAI are likely to reconsider their guidelines because results of more re- cent studies have been contradictory. …
Guidelines in the United States and United Kingdom recommend routine vitamin D supplementation in all breastfed infants, whereas guidelines in Australia recommend supplementation only in breastfed infants at high risk of vitamin D insufficiency.

I think I will emigrate to Australia.

 

Medizin ist keine Wissenschaft sondern eine Kunst

Fragil ist das wissenschaftliche Fundament in der Medizin ja schon immer auch wenn es die hauptsächliche Abgrenzung zur Quacksalberei ist.
Aber auch wenn man sich manche Fragen der Schulmedizin genauer anschaut, wie zum Beispiel letzte Woche die Empfehlung zu Säuglingsnahrungen oder heute ein Artikel zu Verschreibungen auf Säuglingsstationen, dann ist das weder Wissenschaft noch Kunst sondern bestenfalls industriegeleiteter Aktionismus.
Mesek et al. untersuchten dabei in 21  europäischen Ländern die Verschreibungspraxis auf 89 Stationen. Versorgungsforschung ist ja noch am nähesten an der Realität.

Vitamine sind die am häufigsten verschriebene Pharmaka, wobei unklar ist, warum in machen Regionen 74% und in andern nur 5% Vitamine verschreiben. Wenn es generall notwendig wäre, warum dann nicht 100%? Und wenn es nicht notwendig ist, warum dann nicht 0%?

What is wrong with the 2011 NEJM paper?

N Engl J Med 2011;364:701-9 is another paper with 1000+ citations  that had a lasting impression on some but not all people.

First, I can’t remember of any study with such an enormous selection bias  where >94% of individuals have been lost.

Second, we should not forget that farm is not protective per se – farmers may just avoid a known allergy risk factor.  PARSIFAL participants in this study included Steiner schools — anthroposophic medicine mostly avoids vitamin D (ref). This is of course a major issue for any cross-sectional study that doesn’t take into account the temporality of events.

Third, in PARSIFAL dust from children’s mattresses were collected by vacuuming — it is not very likely that many helminthic eggs were transported  from stable to bedroom. In GABRIELA, only airborne dust samples  were collected which again may miss helminth eggs although being certainly present in stable dust.

Fourth, more  microbial exposure and more fungal taxa on farms are a trivial finding.

The inverse associations of the diversity scores with asthma were not confounded by status with respect to living on a farm because adjustment did not change the respective point estimates for asthma (Table 2), although the associations became nonsignificant.

Small sample size, borderline p-values even after a long fishing expedition?

What do these strange “probability” plots  really show – the probability of asthma or the probability to live on a farm?

N Engl J Med 2011;364:701-9 Figure 3 Does it refute any general effect of diversity?

The plots are misleading if adjustment for farm living does not change the parameter estimates for bacterial/fungal diversity.

Sixth – even many years later, the main findings of this study have not been independently replicated. There is not any single study that shows listeriosis (Listeria) or diphtheria (Corynebacterium)  to be protective.

Es gibt keine Menschenrassen

Es gibt keine Menschenrassen, von Rassen spricht man nur noch im Zusammenhang mit der Tierzucht, wo bestimmte Gruppeneigenschaften gezüchtet werden.

Trotzdem habe ich Probleme mit der Jenaer Erklärung (zitiert nach hpd.de)

Aus genetischer Sicht gebe es im Genom des Menschen “keinen einzigen fixierten Unterschied, der zum Beispiel Afrikaner von Nicht-Afrikanern trennt. Es gibt – um es explizit zu sagen – somit nicht nur kein einziges Gen, welches ‘rassische’ Unterschiede begründet, sondern noch nicht mal ein einziges Basenpaar”. Äußere Merkmale, an denen Rassisten ihre Abwertung von bestimmten Menschengruppen festmachen, seien oberflächliche und biologisch leicht wandelbare Anpassungen an geographische Gegebenheiten. Bis vor 8000 Jahren seien die Menschen in Europa noch “stark pigmentiert” gewesen. Erst durch die Einwanderung von Menschen mit hellerer Hautfarbe aus Anatolien und dem damit einsetzenden Beginn der Landwirtschaft habe sich dies geändert, da es sich bei einer stark pflanzenbasierten Kost im dunklen Winter Europas als evolutionärer Vorteil erwies, hellere Haut zu haben und damit genügend Vitamin D produzieren zu können.
“Die helle Hautfarbe der Menschen im nördlichen Europa ist jünger als 5000 Jahre”, hält die Jenaer Erklärung fest. “Die Verknüpfung von Merkmalen wie der Hautfarbe mit Eigenschaften oder gar angeblich genetisch fixierten Persönlichkeitsmerkmalen und Verhaltensweisen, wie sie in der Blütezeit des anthropologischen Rassismus verwendet wurden, ist inzwischen eindeutig widerlegt. Diese Argumentation heute noch als angeblich wissenschaftlich zu verwenden, ist falsch und niederträchtig. Es gibt auch keinen wissenschaftlich nachgewiesenen Zusammenhang zwischen Intelligenz und geographischer Herkunft, aber einen deutlichen mit sozialer Herkunft.”

Die Erklärung hat natürlich recht, als dass der Rassebegriff nur noch von Rassisten verwendet wird.

Es gibt aber durchaus fixierte phänotypische und genetische Unterschiede in geographischen Regionen – also einzelnen Volksgruppen oder Populationen.

M9 ist nach gängiger Forschung der “out of Africa” Marker, siehe Wikipedia

Die Erklärung sagt schliesslich auch, dass Europäer näher verwandt sind mit Ostafrikanern, als Ostafrikaner mit Südafrikanern. Wie sollte eine solche Aussage möglich sein, wenn man keine Marker dafür hätte?

Für Abstammungstheorien wird oft die Kombination von SNP Marker verwandt. Mit Hilfe der “principal component analysis” wurde zum Beispiel der ursprüngliche afrikanische Stammbaum  im letzten Jahr revidiert.

Quelle und Details auf https://academic.oup.com/hmg/article/27/R2/R209/4993963

“Helle Hautfarbe / bessere Vitamin D Konversion” auch bekannt als Loomis Hypothese  als Triebfeder der Evolution ist strittig. Ohne die Literatur zur Pigmentierung der Haut zu rekapitulieren – der Zweck der Pigmentierung ist eher Schutz der Basalzellschicht vor UV Strahlung als eine Limitierung der Vitamin D Produktion. Vitamin D Konversion ist auch ganz ohne starke Pigmentierung selbst limitierend. Sie setzt allenfalls früher, nämlich ca 20 Minuten nach Bestrahlung statt nach 40 Minuten ein.

Nach aktuellem Kenntnisstand stimmt auch nicht, dass dunkle Hautfarbe die ursprüngliche Hautfarbe von H. sapiens in Afrika ist und Europäer mit heller Hautfarbe Mutanten sind (auch wenn es die SZ erneut verbreitet). Helle und dunkle Hautfarbe sind wohl eher die Extreme einer ansonsten mittleren Helligkeit. Der letzte Stand steht dabei  in dem Science 2017 Paper von Sarah Tishkoff.

Examining ethnically diverse African genomes, we identify variants in or near SLC24A5, MFSD12, DDB1, TMEM138, OCA2, and HERC2 that are significantly associated with skin pigmentation. … Functional analyses indicate that MFSD12 encodes a lysosomal protein that affects melanogenesis in zebrafish and mice, and that mutations in melanocyte-specific regulatory regions near DDB1/TMEM138 correlate with expression of ultraviolet response genes under selection in Eurasians.

In dieser Liste steht jedenfalls kein einziges Vitamin D – Gen, so dass die Jenaer Erklärung auch hier nicht dem Wissenstand entspricht.

The end of the vitamin D deficiency debate? 8 facts

Most recently, a NEJM paper “Vitamin D Deficiency — Is There Really a Pandemic?” by Manson, Brannon, Rosen, and Taylor explains the big misunderstandings that let some authors conclude that whole populations are being vitamin D deficient. Just to recall, the IOM recommended in 2010 serum concentrations of vitamin D (i.e., 25-hydroxyvitamin D [25(OH)D]) above 20 ng per milliliter (or 50 nmol per liter) as appropriate level and supplementation with 600 to 800 IU per day as Recommended Dietary Allowance (RDA). And here are the 8 facts: Continue reading The end of the vitamin D deficiency debate? 8 facts

SMAD3, Vitamin D and asthma

A new JACI paper claims

in three independent birth cohorts (N=60, N=30, N=28) DNA methylation at the SMAD3 promoter was selectively increased in asthmatic children of asthmatic mothers and was associated with risk of childhood asthma.

and argues

although associations between SMAD3 variants rs17228058, rs744910, rs17294280 and asthma have been reported in GWAS, asthma-related SMAD3 methylation differences were unlikely to be influenced by SMAD3 genotype

while I am not convinced as it is common wisdom that

If a SNP interferes with or alters a TF binding site, it could potentially affect both DNA methylation and gene expression independently.

So this possibility needs to be excluded before drawing any conclusions. BTW, SMAD3 is a well know vitamin D target…

1,25-dihydroxyvitamin D3–bound [1,25(OH)2D3-bound] vitamin D receptor (VDR) specifically inhibits TGF-β–SMAD signal transduction through direct interaction with SMAD3.

while so far only IL2 methylation was linked to asthma  (another super Vitamin D target).

You get what you pay for

Finally, the Copenhagen and Boston clinical trials of vitamin D supplementation in pregnancy have been published in JAMA today. There is no protection against asthma or wheezing when comparing  4400 IU or 2800 IU vitamin D vs 400 IU vitamin D.
From basic pharmacology and immunology, this is an expected result: the only interesting point would have been to compare vitamin vs placebo. Even the editorial missed the most important point – what happens to the newborn immune system when being supplemented with vitamin D?

A step forward in allergy research

The most recent paper of my Australian collaborators is a relevant step forward: Polymorphisms affecting vitamin D-binding protein modify the relationship between serum vitamin D (25[OH]D3) and food allergy. Basically they show an

… association between serum 25-hydroxyvitamin D3 (25[OH]D3) levels and food allergy at age 1 year (338 challenge-proven food-allergic and 269 control participants) and age 2 years (55 participants with persistent and 50 participants with resolved food allergy)… Analyses were stratified by genotype at rs7041 as a proxy marker of DBP levels… Low serum 25(OH)D3 level (<50 nM/L) at age 1 years was associated with food allergy, particularly among infants with the GG genotype (odds ratio [OR], 6.0; 95% CI, 0.9-38.9) … Maternal antenatal vitamin D supplementation was associated with less food allergy, particularly in infants with the GT/TT genotype (OR, 0.10; 95% CI, 0.03-0.41)… This increases the biological plausibility of a role for vitamin D in the development of food allergy.

Maybe it would be helpful to have also “real” DBP levels for estimating bioavailability (and even data of supplement use) but already the reported results are another strong argument for the vitamin D – allergy axis. This is also largely in line with what I predicted back in 2012

Both vitamin D insufficiency and vitamin D supplementation have been linked to allergy and asthma. This apparent paradox is explained by epigenetic programming in pregnancy by low vitamin D levels and the excessive high supplementation in the newborn period.

Maybe I should have emphasized that genetic variants in the vitamin D pathway are also important for biological effects.

5% of methylated sites escape reprogramming – a new allergy research direction

New Scientist Health has a short report how parents’ lives could change children’s DNA.

Azim Surani at Cambridge University and colleagues have demonstrated that some genes in the developing fetus escape the cleaning mechanism. Surani’s team analysed methylation patterns in a type of fetal cell that later forms a fetus’s own sperm or eggs. We would expect these cells to have been wiped clean when the fetus’s epigenome was reset at the early embryo stage. “However, about 2 to 5 per cent of methylation across the genome escaped this reprogramming,” says Surani.

The current wave of interest stems from three new papers: “The Transcriptome and DNA Methylome Landscapes of Human Primordial Germ Cells” by Guo demonstrates

The transcriptome of human primordial germ cells from the migrating stage to the gonadal stage reveals that both pluripotency genes and germline-specific genes are simultaneously expressed within the same individual cells. The global erasure of DNA methylation creates a super-hypomethylated germline genome.

So at week 10 after gestation, all analyzed 233  primordial germ cells lost their parental methylation marks except of 6% of the male and 8% of the female genome (which is a bit larger) . Unfortunately I did not find a list of genes there that have their parental methylation status transmitted.

Tang from a British consortium “A Unique Gene Regulatory Network Resets the Human Germline Epigenome for Development” writes

A unique transcriptome drives extensive epigenome resetting in human primordial germ cells for establishment of totipotency. Some loci associated with metabolic and neurological disorders exhibit resistance to reprogramming and are candidates for transgenerational epigenetic inheritance.

Here evolutionarily young and potentially hazardous retroelements, like SVA, remain methylated ( the number of embryos  being examined is not given). Evolutionarily young and potentially hazardous retroelements, like SVA, remain methylated. When testing for resistant loci, they found that H3K9me3 marked escaping ; resistant regions were also enriched for KAP1 (alias TRIM28) binding sites of ESCs. But still no gene list there.

Sofia Gkountela “DNA Demethylation Dynamics in the Human Prenatal Germline” from the US

performed whole-genome bisulfite sequencing (WGBS) and RNA-sequencing (RNA-seq) of human prenatal germline cells from 53 to 137 days of development. We discovered that the transcriptome and methylome of human germ-line is distinct from both human PSCs and the inner cell mass (ICM) of human blastocysts … Gene expression do not correlate with global changes in DNA methylation.

In this paper finally there is the gene list, I was looking for — basically not demethylated, parentally inherited genes. Persistent methylated regions (also termed DMR, differential methylated regions) in advanced germline cells (AGCs) were seen in 500+ genes as given in table S4:

AADACL2-AS1, ABCA7, ABCC5, ABHD12, ABR, AC093375.1, ACSL4, ACSM1, ACVR1C, ACYP1, ADAMTSL3, ADARB2, ADK, AGBL4, AGK, AGPS, AIG1, AKAP9, AKR1B15, ALPK2, ANK1, ANKHD1, ANKHD1-EIF4EBP3, ANKRD11, ANKRD12, ANKRD19P, ANKRD20A9P, ANKRD24, ANKRD26, ANKRD26P1, ANKRD30BL, ANKRD31, AP2A2, AP3D1, AP4E1, ARAP2, ARHGAP26, ARHGAP39, ARHGAP44, ARHGEF18, ARHGEF4, ARHGEF7, ARID3A, ARL13B, ASB3, ASH1L, ASTN2, ASZ1, ATAD3A, ATF1, ATP11A, ATP13A1, ATP2C1, ATP8A2, ATP9B, AUH, AVEN, BAGE, BAGE2, BAGE3, BAGE4, BAGE5, BASP1P1, BAZ1A, BBS9, BCAS3, BCO2, BCYRN1, BEND3, BEND7, BRE, BRSK2, C14orf159, C15orf37, C1GALT1, C1orf159, C20orf196, C22orf34, C2orf61, C3orf67, C3orf67-AS1, C7orf50, C7orf60, C9orf3, CACNA1B, CACNG4, CALN1, CAMK1D, CARF, CARS2, CC2D2A, CCBL2, CCDC101, CCDC130, CCDC148, CCDC149, CCDC57, CCDC88C, CCDC97, CCNY, CCSER1, CD163, CD2AP, CD46, CDH12, CDH4, CDKAL1, CELF2, CEP70, CERK, CERS4, CFH, CHD2, CHD6, CHODL, CHRM5, CHRNA10, CHRNA4, CLEC16A, CLIC5, CLIC6, CNOT2, CNTN6, CNTNAP2, COG2, COL15A1, COL18A1, COL24A1, COL6A4P2, COLEC11, CORO2B, CPVL, CRTC3, CSMD1, CSMD2, CSNK1D, CTB-7E3.1, CTDP1, CTIF, CTNNA2, CTNNA3, CUBN, CXCR2, CXorf49, CXorf49B, CYCS, CYP3A5, DAPK2, DCDC2C, DDA1, DENND1A, DENND5A, DGUOK-AS1, DIP2C, DLG1, DLK1, DNAH6, DNAH8, DNAJC1, DNER, DOC2GP, DOCK1, DOCK7, DPP10, DSTN, DTNB, DYX1C1, DYX1C1-CCPG1, EBF3, ECHDC2, EDIL3, EEPD1, EFCAB10, EFCAB4B, EFTUD1, EHBP1, EIF2B3, ELMO1, EP400NL, EPHA6, EPPK1, ERC1, ERCC8, ERICH1-AS1, ERP44, ETFA, EVC2, EXD3, EXOC2, EYS, F11-AS1, FAAH, FAM172A, FAM174A, FAM207A, FAM209A, FAM86FP, FANCC, FBN3, FBXO39, FGD4, FGF14, FHIT, FIG4, FLJ30403, FNBP4, FOXN3, FREM3, FZR1, GABRA2, GAS6, GBP2, GCNT7, GDA, GGCX, GLCCI1, GLRA1, GLRA2, GMDS, GNAI1, GOLIM4, GPR75-ASB3, GRIK2, GRM7, GTF3C6, GTPBP10, GUSBP1, H6PD, HCCAT3, HCN4, HDAC4, HECTD4, HEG1, HPGD, HRNR, HS6ST3, HTR7, IFNAR1, IGF2BP3, IGSF11, IGSF22, IGSF9B, IL1RAPL2, IL31RA, IMMP2L, IMPG2, INF2, INTS1, INVS, IPO7, IQCF3, IQCG, IRAK1BP1, ISOC2, ISPD, ITFG1, ITGB1BP2, ITGBL1, JAM3, JAZF1, JMJD1C, KALRN, KATNBL1, KDM3B, KDM4C, KIAA0825, KIAA1328, KIF4A, KIF5B, KLHL20, KLHL3, LANCL3, LDB2, LDLRAD3, LHCGR, LINC00239, LINC00408, LINC00469, LINC00670, LINC00871, LINC00922, LINC01193, LINC01194, LINGO2, LMF1, LOC100128505, LOC100133669, LOC100188947, LOC100289333, LOC101927069, LOC101927280, LOC101927286, LOC101929064, LOC101929387, LOC102723742, LOC145837, LOC283683, LOC285768, LOC286083, LOC442132, LPA, LPPR1, LRP1B, LRRC4C, LTBP1, LUZP2, MAD1L1, MAGT1, MAML3, MAOA, MAP3K15, MAP4K5, MAPK10, MAPK8, MAPK8IP3, MAST2, MCTP1, MCU, MEF2A, MEI4, MELK, METTL15, METTL9, MFHAS1, MIR1273H, MIR518B, MIR518F, MIR520B, MIR548H2, MIR548O2, MIR6130, MIR6744, MOB3B, MOCOS, MTG1, MTMR7, MUC2, MUC5B, MUM1L1, MYO10, MYO5A, MYO9A, MYT1, MYT1L, NAA20, NAALADL2, NAT1, NAV2, NBPF10, NBPF20, NCALD, NCOA2, NEBL, NFATC3, NIFK-AS1, NIPA1, NKAIN2, NKAIN3, NLRP4, NME7, NOC4L, NONO, NPHP4, NQO2, NRXN3, NSUN6, NTSR1, NUBPL, NXN, OGG1, OR8S1, OSBP2, OSBPL6, OSMR, PACS2, PARK2, PARL, PAWR, PCBP3, PCDH19, PCDH9, PCNT, PCNXL2, PCSK6, PDAP1, PDE11A, PDE4D, PGAM1P5, PGAM5, PHKB, PHRF1, PIK3C2A, PIK3CA, PIP5K1B, PKD2L1, PKHD1, PKIB, PLCD1, PLCH1, PLEC, PLOD2, POLR1A, POMK, PPARA, PPARGC1B, PPP2R5C, PRH1, PRH1-PRR4, PRICKLE1, PRKAR1B, PRKCZ, PROSER2, PROSER2-AS1, PRR26, PRUNE2, PTCD3, PTDSS2, PTGFRN, PTPN21, PTPRD, PTPRN2, PYGB, RAB28, RAB3D, RAB3GAP2, RAB3IP, RABGAP1L, RAPGEF6, RBFOX1, RC3H2, RFX7, RGS6, RGS7, RNF115, RNH1, RNU6-52P, RNU6-81P, RPH3AL, RPIA, RPL35A, RPS6KC1, RSPH1, RYR1, S100Z, SCAPER, SCCPDH, SCEL, SCFD2, SCHLAP1, SCMH1, SDHAP3, SDK1, SEC14L1, SEC24D, SEL1L, SEMA3C, SERPINB3, SESN2, SESTD1, SETD1A, SETDB1, SHANK2, SHC2, SIL1, SIN3B, SLC12A3, SLC22A15, SLC24A2, SLC38A10, SLC44A5, SLC6A1, SLC8A1-AS1, SNORD115-1, SNORD115-2, SNTB2, SNTG2, SNX29, SORCS2, SOX5, SPATA5, SPIDR, SPIRE1, SPTB, SPTBN2, SPTLC3, SRD5A1, SRRM4, ST20, ST20-MTHFS, ST6GAL1, STARD9, STIM1, STK31, STK38, STON1-GTF2A1L, STXBP5-AS1, SUPT3H, SYN3, TAF1L, TAS2R19, TENM2, TENM3, THRB, THSD7B, TIMM23B, TJP2, TLK1, TMCC1, TMED1, TMEM132D, TMEM218, TMEM66, TMTC2, TNRC6B, TPST1, TPTE, TRAPPC9, TRIO, TRPC4AP, TRPM2, TRRAP, TSNARE1, TSPAN15, TSPEAR, TSSC1, TTC28, TTC40, TULP4, TYRO3P, TYSND1, TYW1B, UGGT2, UHRF1, ULK4, UNC5D, UNC79, UNC93A, USP13, USP15, USP34, USP50, VGLL4, VPRBP, VPS53, WDPCP, WDR1, WDR19, WDR36, WDR60, WWOX, XAF1, ZBTB20, ZCWPW2, ZFPM2, ZFYVE9, ZKSCAN5, ZMAT1, ZMYM4, ZNF135, ZNF14, ZNF317, ZNF32, ZNF32-AS1, ZNF32-AS2, ZNF32-AS3, ZNF335, ZNF341, ZNF350, ZNF382, ZNF415, ZNF556, ZNF595, ZNF664-FAM101A, ZNF670, ZNF670-ZNF695, ZNF7, ZNF717, ZNF718, ZNF767P, ZNF808, ZNF845, ZNRF1, ZSWIM5

(I dropped two genes as they are only date-formatted numbers in the supplied Excel sheet).

The interesting question for me is if there is an interaction with genes identified earlier in asthma and allergy research. According to the GWAS catalog there are 190 associated genes that match only 9 on the list above: AS1, CLEC16A, CTNNA3, EDIL3, PDE4D, PGAM1P5, SDK1, WDR36. Nothing exciting, in particular no HLA association. WDR36 is the only gene, we published some years ago. I find also only one match (COL15A1) of the 73 low methylation IgE loci published earlier.

Possibly, any of these persistent methylated genes can even stand on its own feet with just one silenced / activated gene  being responsible for the pathology in a pedigree. I cannot identify so many signals in the list above, maybe some IL1 related stuff (IL1RAPL2, IL31RA, IRAK1BP1). CD46 at least is a good candidate as it is known that enhanced CD46-induced regulatory T cells will suppress allergic inflammation after allergen specific immunotherapy.

Unexpectedly, there are also no vitamin D related genes, no VDR, no cytochrome P450 enzymes. Nevertheless I recognize a whole bunch of calcium related genes:  STIM1 (transmembrane protein that mediates Ca2+ influx),  ATP11A + ATP2C1 (ATP dependent Ca2+ transporter), TRPM2 ( another Ca2+ channel), TRPC4AP + RYR1 (sarcoplasmic reticulum calcium channels) and NCALD (a cytosolic calcium transporter).

So would be definitely interesting to test the methylation status of these genes along with vitamin D levels in allergic parents and their kids.

No wonder pill

“In the case of religion, we put our faith in gods. And in nutrition, we have vitamins,” writes journalist Catherine Price in Vitamania, in which she traces vitamin crazes from the 1920s to the present.

Harvard Magazine reports about a new cancer vitamin D study. It includes more than 1,000 patients with metastatic colorectal cancer but going into the details it is a phase 3 clinical trial of chemotherapy and NOT a clinical trial of vitamin D. Vitamin D serum levels are used for posthoc stratification only although we know that these kind of studies are always misleading.  At least HM quotes VITAL research Manson with

Clinical enthusiasm for supplemental vitamin D has outpaced available evidence on its effectiveness

I wish the VDAART chairs at  Brigham and Women’s Hospital would have a similar realistic assessment. Their results are overdue with June 2014 ending of data collection for the primary outcome. Is it just the simple fact that vitamin D is not a wonder pill?

A jubilee – today we have 1000 papers on allergy and vitamin D

It is a long time period from our first paper in July 1999 in Allergy, but more than 15 years later there is now a huge list of papers.

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When looking for potential paradigm shift in research, however, vitamin D is still largely ignored.

    • Professional organizations that give legitimacy to the paradigm: NONE
    • Dynamic leaders who introduce and purport the paradigm: FEW
    • Journals and editors who write about the system of thought: FEW
    • Government agencies who give credence to the paradigm: NONE
    • Educators who propagate the paradigm’s ideas by teaching it to students: NONE
    • Conferences conducted that are devoted to discussing ideas central to the paradigm: YES
    • Media coverage: MINOR
    • Lay groups, or groups based around the concerns of lay persons, that embrace the beliefs central to the paradigm: FEW
    • Sources of funding to further research on the paradigm: NONE

 

A large inter-individual variation for the efficiency of vitamin D3 supplementation

I believe this already since my first step into the vitamin D field but only now a review shows that

The integration of all these genome-wide data facilitates the identification of the most important VDR binding sites and associated primary 1,25(OH)2D3 target genes. Expression changes of these key genes can serve as biomarkers for the actions of vitamin D3 and its metabolites in different tissues and cell types of human individuals. Analysis of primary tissues obtained from vitamin D3 intervention studies using such markers indicated a large inter-individual variation for the efficiency of vitamin D3 supplementation.

It is a continuous medical malpractice to supplement newborn children with vitamin D without taking into account variation of the inter-individual response, body weight, or any co-medication.