Widespread seasonal gene expression reveals annual differences in human immunity and physiology

Abstract

Seasonal variations are rarely considered a contributing component to human tissue function or health, although many diseases and physiological process display annual periodicities. Here we find more than 4,000 protein-coding mRNAs in white blood cells and adipose tissue to have seasonal expression profiles, with inverted patterns observed between Europe and Oceania. We also find the cellular composition of blood to vary by season, and these changes, which differ between the United Kingdom and The Gambia, could explain the gene expression periodicity. With regards to tissue function, the immune system has a profound pro-inflammatory transcriptomic profile during European winter, with increased levels of soluble IL-6 receptor and C-reactive protein, risk biomarkers for cardiovascular, psychiatric and autoimmune diseases that have peak incidences in winter. Circannual rhythms thus require further exploration as contributors to various aspects of human physiology and disease.

Figure 1. Seasonal mRNA expression in the peripheral human immune system.

Relative expression profiles of seasonal genes (fitted values of the cosinor model). (a) ARNTL expression was increased in the summer months of June, July and August (ANOVA, , P=1.04 × 10⁻²³), compared with the winter months of November through February (1.5097-fold difference between February and August (n=109 individuals). Similarly, the nuclear vitamin D receptor (VDR) shows peak expression in June through August (ANOVA, , P = 1.62 × 10⁻⁰⁶). The housekeeping genes, B2M and GAPDH, did not have seasonal expression profiles. (b) Seasonal ARNTL expression in PBMCs independent of the circadian phase. Similar seasonal ARNTL expression profiles were observed regardless of whether blood samples were collected during morning (BABYDIET, n=109 individuals) or afternoon clinic visits (T1D cohort, n=236 individuals). (c) In the BABYDIET data set, nine known components of the circadian clock had seasonal expression profiles in the peripheral immune system, as did certain hormone, leukotriene and prostaglandin receptors. (d) The receptors for the anti-inflammatory glucocorticoids (NR3C1) and the pro-inflammatory prostaglandins (PTGDR, PTGIR and PTGER4) and leukotrienes (CYSLTR1) had opposing seasonal expression profiles.

Figure 2. Widespread seasonal mRNA expression in the human immune system.

Relative expression profiles of seasonal genes (fitted values of the cosinor model). (a) A total of 5,136 genes (∼23% of the protein-coding genome) were identified as having seasonal variation in expression (genome-wide significance, P≤1.52 × 10⁻⁰⁶) in the BABYDIET PBMC data set. (b) Five thousand randomly selected genes not identified as seasonal are shown as a comparison. (c) Two anti-phasic patterns of gene expression were observed among seasonal genes. We defined the majority of seasonal genes as being either winter- (green) or summer-expressed (blue). In BABYDIET, 2,311 genes were increased in expression in the summer and 2,826 were increased in the winter. One of the seasonal probes did not fall into our definition of summer and winter, shown as a red line.

Figure 3. Seasonal gene expression in geographically distinct cohorts.

(a) Seasonality was also observed in PBMCs collected from T1D patients in the United Kingdom (n=236 individuals). A total of 1,697 genes were seasonal in this data set. (b) The previously defined summer and winter genes from the BABYDIET data set maintained their seasonal expression patterns in the T1D samples. (c) PBMCs from asthmatic patients collected from different countries also showed seasonal gene expression. In the United Kingdom/Ireland (n=26 asthmatic individuals; 85 PBMC samples), 791 genes were seasonal, while 1,257 and 409 genes were seasonal in Australia (n=26 individuals; 85 samples) and United States (n=37 individuals; 123 samples), respectively. (d) Summer and winter BABYDIET genes maintained their seasonal expression patterns in the asthmatic PBMC samples, with their patterns inverted in Australia.

Figure 4. Seasonal changes in the cellular composition of human peripheral blood.

(a) Expression levels of 13 genes that have been used to identify different blood cell types among total PBMCs were strongly correlated (positively and negatively) with seasonal genes identified in the BABYDIET data set. In comparison, non-seasonal genes were less correlated with these marker genes, although exceptions exist: CTLA-4 expression also correlations with non-seasonal genes. (b) Indeed, by analysing full blood count data obtained from 7,343 healthy adult donors enroled in the Cambridge BioResource, we found the cellular composition, and other haematological parameters of blood to vary by season. HCT was the only response that did not show seasonal variation. (c) Distinct seasonal variation in cell counts was observed in a cohort of 4,200 healthy adults and children from The Gambia. EOS, eosinophils; LYM, lymphocytes, NEU, neutrophils, PLT, platelets; RBC, red blood cells; WBC, total white blood cells; BAS, basophils; HGB, haemoglobin; MCH, mean corpuscular haemoglobin; MCV, mean corpuscular volume; MON, monocytes; HCT, haematocrit.

Figure 5. Inflammatory responses predominate the immune system in Europe.

(a) Co-regulated seasonal gene modules were generated to analyse differences in immune function by season: eight winter modules and three summer modules were generated. (b) Two modules of seasonally co-regulated genes from the BABYDIET data set are shown as examples. A module consisting of genes involved in B-cell receptor signalling, (including CR2, BLNK, BTK, FCGR2B, CD72, CD79B) was more highly expressed in the winter, as was a module associated with metabolic processes. In contrast, a RNA-processing module (containing RANBP2, EIF3J, RAE1, NUP54, DDX20, STRAP, NUPL1, PAIP1) was more highly expressed in the summer. (c) IL6R mRNA expression was increased in the winter, in BABYDIET samples (ANOVA, , P=9.33 × 10⁻¹²), as was observed for the circulating level of sIL-6R protein in the serum of BABYDIET/DIAB children (ANOVA, , P=2.74 × 10⁻¹¹). (d) The circulating levels of C-reactive protein displayed seasonal variation in a cohort of 3,412 donors diagnosed as hypertensive but not conventionally dyslipidemic. ASCOT enrolled participants in Ireland, Denmark, Finland, Iceland, Norway, Sweden and the UK (two measurements per donor), with increased levels present during winter HSCRP - high sensitivity C-reactive protein.

Figure 6. Seasonal gene expression in subcutaneous adipose tissue.

In a collection of 856 female adult donors from the United Kingdom, 4,027 genes were found to be seasonal in adipose tissue. As observed in PBMCs, two distinct anti-phasic profiles were present.