New Paper from Australia – British Journal of Nutrition
similar to the US two years ago
Schlagwort-Archive: vitamin-D
Science is the holding of multiple hypothesis
From the famous Chamberlin paper written in 1890 and reprinted 1965
HiPP, HiPP, kein hurra
Eine Pressemitteilung des Bundesverbandes aller Verbraucherzentralen weist auf ein Urteil des Landgerichts München I hin:
Erfolg gegen irreführende Werbung bei Nahrung für Kleinkinder: Das Landgericht München I hat einer Klage des Verbraucherzentrale Bundesverbands (vzbv) gegen die Hipp GmbH & Co. Vertrieb KG Recht gegeben. Demnach sind mehrdeutige Werbeaussagen zum angeblichen Vitamin D- und Calciumbedarf von Kindern bei Milchersatzprodukten untersagt. „Verbraucherinnen und Verbraucher müssen bei Lebensmitteln für Kleinkinder darauf vertrauen können, dass die Unternehmen besonders verantwortungsbewusst handeln. Dazu gehören klare und deutliche Informationen über Vitamine und Nährstoffe“, sagt Susanne Einsiedler, Rechtsreferentin beim vzbv. „Eltern sollten nicht den Eindruck bekommen, dass bestimmte Produkte nötig sind, damit ihr Kind ausreichend versorgt wird. Kinder über einem Jahr brauchen in der Regel keine speziellen Lebensmittel“.
Auch wenn das Urteil noch nicht rechtskräftig ist, gehe ich noch einen Schritt weiter, es braucht überhaupt keinen Vitamin D Zusatz in der Säuglingsmilch, auch nicht in der Anfangsmilch, es wird längst zuviel direkt supplementiert.
Der Vitamin D Hype schadet mehr, als dass er nützt. Orales Vitamin D kann zu späteren Allergien führen, auch wenn Fachgesellschaften die Vitamin D Supplementierung aus Tradition weiterhin unkritisch sehen.
Es ist ja ein lustiger Experte, dieser Dr. med Jürgen Hower, den HiPP da auf der Webseite in einem “Interview” präsentiert neben der hauseigenen Wissenschaftlerin. Seine wissenschaftliche Leistung in der Endokrinologie besteht darin, bei Kindern in seiner Gemeinschaftspraxis Vitamin D Spiegel bestimmt zu haben. Ansonsten vermarktet er mit Vitamin D gepanschte Schokolade als “Dr. Chococo”.
Nichts Neues also unter der Sonne – ich erinnere mich an Aktenberge im Bundesarchiv Berlin, in denen sich einschlägige Geschäftemacher schon vor 80 Jahren einen jahrelangen Streit mit den Behörden lieferten.
Is the Loomis Hypothesis wrong?
I remember an old vitamin D book – I believe it was Feldman’s Vitamin D – that argues that if we are going down the Transsahara Route (Algier-Lagos) human skin color gets always darker towards Tamanrasset due to increased solar power- also known known as the Loomis hypothesis (Science 1967).
So , let’s have a look at three maps. Solar power first.
Second, skin tones – the Tamanrasset observation is correct but the overall picture does not match the Loomis hypothesis.
Neither does the new vitamin D map published last week in the Lancet.
Maps are still patchy but let me already believe that 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.
We are in line #1…
Another nice paper on a genetic interaction is Vimaleswaran et al.
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, is preventable by avoiding CMF (cow milk formula) supplementation for at least the first few days of life. Although examined only indirectly in this study, vitamin D supplementation seems to be involved in the sensitization process.
Note to self – this is now study no 5 of vitamin D related clinical trials on allergy
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.
4. Rosendahl J, Pelkonen AS, Helve O, et al. . High-Dose Vitamin D Supplementation Does Not Prevent Allergic Sensitization of Infants. J Pediatr. 2019 Jun;209:139-145.e1. doi: 10.1016/j.jpeds.2019.02.021
5. Urashima M, Mezawa H, Okuyama M, et al. Primary Prevention of Cow’s Milk Sensitization and Food Allergy by Avoiding Supplementation With Cow’s Milk Formula at Birth. JAMA Pediatr. 2019;173(12):1137-1145. doi:10.1001/jamapediatrics.2019.3544
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.
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?
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, insofern 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.
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.
“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.
Nachtrag 25.6.2020
Am Sachstand ändert sich nichts wenn die Argumente jetzt wiederholt werden.
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: The end of the vitamin D deficiency debate? 8 facts weiterlesen
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.