Tag Archives: vitamin-D

What is wrong with the 2011 NEJM paper?

16.10.2019 admin

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. The PARSIFAL participants in this study included Steiner schools — anthroposophic medicine mostly avoids vitamin D (another 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 may miss helminth eggs although being highly 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? And 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. Does that really mean that farm are irrelevant?

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

Vitamins

The end of the vitamin D deficiency debate? 8 facts

9.01.2017 admin

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 →

Allergy, Genetics

SMAD3, Vitamin D and asthma

22.12.2016 admin

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).

Allergy

You get what you pay for

29.01.2016 admin

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?

Allergy, Vitamins

A step forward in allergy research

25.08.2015 admin

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.

Allergy, Genetics, Vitamins

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

9.06.2015 admin

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.

Vitamins

No wonder pill

16.04.2015 admin

“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?

Allergy, Vitamins

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

5.02.2015 admin

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.

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

Vitamins

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

20.05.2014 admin

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.

Genetics, Joke, Vitamins

Cycling is good for you (and vitamin D is an activity marker)

14.04.2014 admin

Vitamin D level is an activity or lifestyle marker, although this has been largely neglected in the medical literature, maybe except Gannage 2000, Hyppönen 2007, Sohl 2013 and Choi 213. A new paper by de Rui in PLoS now shows that

serum 25OHD levels were significantly higher in individuals who engaged in outdoor pastimes … compared to those who did not. In particular, subjects regularly practicing gardening or cycling had higher serum 25OHD levels than those who did not, whereas 25OHD levels differed little between subjects who did or did not undertake indoor activities.

While these are good news for older cyclists Continue reading Cycling is good for you (and vitamin D is an activity marker) →

Allergy, Vitamins

Take care of your last sentence

3.04.2014 admin

I have been told long ago to take care of the last sentence in a paper, avoiding any unjustified conclusion or any unwarranted speculation. Let’s start with a fully justified last sentence in the new volume of “International Nutrition: Achieving Millennium Goals and Beyond”

It says that Continue reading Take care of your last sentence →

Philosophy, Vitamins

Reference values should be based on reference populations and not on politics

3.12.2013 admin

For a long time this has been a general rule. Just take the mean and substract two standard deviations and you get some useful reference values. Or whatever algorithm you like. This changed considerably where commercial or any other personal interests come into play. The cholesterin discussion settled only by studies showing that people with a history of cardiovascular disease may derive benefit from statins irrespective of their cholesterol levels.
I see some analogy in the vitamin D field. There is a German dermatologist who believes that 60% of all Germans are vitamin D deficient (the comments following the interview highlight this as an epiphany “totale Erleuchtung”). And a more recent paper showed that “89.9%” of all healthy newborns being insufficient. Really looks like a mix-up of some basic concepts in clinical medicine, yea, yea.

Allergy, Vitamins

The first proven risk factor for allergy

10.09.2013 admin

After more than a century of research, the first successful clinical trial of an allergy risk factor has been performed. It looks like the authors even did not anticipate such an effect (known as triple blind design). But read what the Pubmed article about the Norizoe et al. paper says

To elucidate whether maternal vitamin D supplementation during lactation improves infantile eczema and other subsequent allergic disorders, a randomized, double-blind, placebo-controlled trial was performed.
Mothers (n=164) of infants with facial eczema at one-month checkup were randomly assigned to receive vitamin D3 supplements (n=82; 800 IU/day) or placebo (n=82) for 6 weeks from May 2009 to January 2011. The primary outcome was infantile eczema quantified by Scoring Atopic Dermatitis (SCORAD) index at the three-month checkup, and the secondary outcomes were atopic dermatitis, food allergy, and wheeze diagnosed by doctors up to 2 years of age.
There was no significant difference in SCORAD at 3-month checkup between two comparative groups. Doctor-diagnosed food allergy was significantly more common up to age 2 years in vitamin D group (10/39: 25.7%) than in placebo group (3/40: 7.5%; RR=3.42, 95%CI=1.02 to 11.77, P=0.030). Moreover, at least one secondary outcome was also significantly more common in vitamin D group (17/39: 43.6%) than in placebo group (7/40: 17.5%; RR=2.49, 95%CI=1.16 to 5.34, P=0.012).
These results suggest that vitamin D supplementation may not decrease the severity of infantile eczema at three months of age, but may rather increase the risk of later food allergy up to two years of age. Because a large number of subjects was lost to follow-up, further study is needed to confirm the findings.

Of course, there may be some weakness in the study design, a large loss to follow-up and the way how food allergy was diagnosed will be critized. I think, however, that this is a major breakthrough that raises the hope that we will finally understand how allergy develops.

Addendum Dec 23th, 2013

I should have added “true” risk factor, as there are positive trials on probiotics and atopic dermatitis. The meta-analysis by Lee immediately lead to a rebuttal

Their review fails to meet published standards for the quality of systematic reviews on several criteria, and this has led to inappropriate conclusions. […] These defects in methodologic rigor have led to an exaggeration of the clinical benefits of probiotics for eczema prevention.

The Cochrane Summaries are also negativ