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Clinical

GSE53472 is a subseries of the superseries GS53473.

Purpose

The prevalence of immune-mediated diseases such as allergies and autoimmune diseases is on the rise in the developed world. Microbial exposure is known to modulate the risk for these diseases. In order to explore differences in the gene expression patterns induced in utero in infants born in contrasting standards of living and hygiene, we collected umbilical cord blood RNA samples from full-term newborn infants born with normal vaginal delivery in Finland (modern society), Estonia (rapidly developing society) and the Republic of Karelia, Russia (poor economical conditions). Transcriptomic profiles were analyzed using whole genome microarrays including gender, gestational age, birth month and HLA allele genotype as confounding variables in the analysis. The data revealed that the whole blood transcriptome of Finnish and Estonian neonates differ from their Karelian counterparts. Samples from Karelian infants had an increase in transcripts associated with LPS induction and bacterial sepsis observed in 1-year-old infants in earlier studies. The results suggest exposure to toll like receptor (TLR) ligands and a more matured immune response in infants born in Petrozavodsk compared to the Finnish and Estonian infants. These results further support the concept of a conspicuous plasticity in the developing immune system: the environmental factors that play a role in the susceptibility/protection towards immune-mediated diseases begin to shape the neonatal immunity already in utero and direct the maturation of both the adaptive and the innate immune responses in accordance with the surrounding microbial milieu.

Hypothesis

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Experimental Design

These 15 rehybridized samples were only utilized in the batch correction and excluded from any further analysis steps. Umbilical cord blood was drawn into Tempus Blood RNA tubes (Applied Biosystems) from children born at the maternity unit of Jorvi hospital (Espoo, Finland; n=4), maternity units of Tartu and Põlva (Estonia; n=4), or two maternity departments in Petrozavodsk (capital of the Republic of Karelia, Russian Federation; n=7) according to the manufacturer´s protocol and then stored in -70 °C until analyzed.

Experimental Variables

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Controls

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Methods

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Additional Information

[15 rehybridized/batch correction samples]

Microarray
Affymetrix HG-U219 v1
15 Samples Loaded: 15
Human (Homo sapiens)
Neonatal , Whole Blood
Sample Set Spreadsheet
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Samples Preview
Sample ID !Sample Title Gender dr4-dq8 dr3-dq2 country
GSM1294267 Cord_blood_Espoo_13_rehybridized Female - - Finland
GSM1294268 Cord_blood_Espoo_29_rehybridized Female - - Finland
GSM1294269 Cord_blood_Espoo_37_rehybridized Female + + Finland
GSM1294270 Cord_blood_Espoo_44_rehybridized Male + - Finland
GSM1294271 Cord_blood_Petrozavodsk_5_rehybridized Female - - Russia
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Sample ID !Sample Title Gender Dr4-dq8 Dr3-dq2 Country Hla risk category (np=neutral/protective, m=medium, h=high, vh=very high) Hybridization batch Sample month Gestational week Group name
GSM1294267
Cord_blood_Espoo_13_rehybridized
Female
-
-
Finland
NP
1
January
42
Espoo
GSM1294268
Cord_blood_Espoo_29_rehybridized
Female
-
-
Finland
NP
1
February
41
Espoo
GSM1294269
Cord_blood_Espoo_37_rehybridized
Female
+
+
Finland
VH
1
February
39
Espoo
GSM1294270
Cord_blood_Espoo_44_rehybridized
Male
+
-
Finland
H
1
March
41
Espoo
GSM1294271
Cord_blood_Petrozavodsk_5_rehybridized
Female
-
-
Russia
NP
3
February
40
Petrozavodsk
GSM1294272
Cord_blood_Petrozavodsk_9_rehybridized
Female
-
-
Russia
NP
3
March
42
Petrozavodsk
GSM1294273
Cord_blood_Petrozavodsk_15_rehybridized
Female
-
-
Russia
NP
3
March
40
Petrozavodsk
GSM1294274
Cord_blood_Petrozavodsk_19_rehybridized
Male
-
-
Russia
NP
3
March
40
Petrozavodsk
GSM1294275
Cord_blood_Petrozavodsk_20_rehybridized
Male
-
-
Russia
NP
3
March
40
Petrozavodsk
GSM1294276
Cord_blood_Petrozavodsk_32_rehybridized
Male
-
-
Russia
NP
3
April
40
Petrozavodsk
GSM1294277
Cord_blood_Petrozavodsk_40_rehybridized
Male
-
-
Russia
NP
3
May
38
Petrozavodsk
GSM1294278
Cord_blood_Tartu_1_rehybridized
Male
+
+
Estonia
VH
1
January
38
Tartu
GSM1294279
Cord_blood_Tartu_17_rehybridized
Male
-
-
Estonia
NP
1
February
41
Tartu
GSM1294280
Cord_blood_Tartu_20_rehybridized
Female
-
-
Estonia
NP
1
April
40
Tartu
GSM1294281
Cord_blood_Tartu_24_rehybridized
Male
-
+
Estonia
M
1
May
40
Tartu

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