A gene network regulated by the transcription factor VGLL3 as a promoter of sex-biased autoimmune diseases

Abstract

Autoimmune diseases affect 7.5% of the US population, and they are among the leading causes of death and disability. A notable feature of many autoimmune diseases is their greater prevalence in females than in males, but the underlying mechanisms of this have remained unclear. Through the use of high-resolution global transcriptome analyses, we demonstrated a female-biased molecular signature associated with susceptibility to autoimmune disease and linked this to extensive sex-dependent co-expression networks. This signature was independent of biological age and sex-hormone regulation and was regulated by the transcription factor VGLL3, which also had a strong female-biased expression. On a genome-wide level, VGLL3-regulated genes had a strong association with multiple autoimmune diseases, including lupus, scleroderma and Sjögren's syndrome, and had a prominent transcriptomic overlap with inflammatory processes in cutaneous lupus. These results identified a VGLL3-regulated network as a previously unknown inflammatory pathway that promotes female-biased autoimmunity. They demonstrate the importance of studying immunological processes in females and males separately and suggest new avenues for therapeutic development.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: Identification of sex-biased genes from human skin biopsies.
Figure 2: Female-biased genes encode products associated with autoimmune processes.
Figure 3: Expression of female-biased genes encoding products related to immunity is dependent on SLE disease states but not on sex-hormone levels.
Figure 4: VGLL3 regulates genes associated with autoimmune diseases.
Figure 5: VGLL3 targets encode products involved in multiple autoimmune conditions.
Figure 6: VGLL3 regulation of genes altered in SS.

Accession codes

Primary accessions

Gene Expression Omnibus

References

  1. 1

    American Autoimmune Related Diseases Association. The cost burden of autoimmune disease: the latest front in the war on healthcare spending. (American Autoimmune Related Diseases Association, Eastpointe, Michigan, USA, 2011).

  2. 2

    Fish, E.N. The X-files in immunity: sex-based differences predispose immune responses. Nat. Rev. Immunol. 8, 737–744 (2008).

    Article  CAS  PubMed  Google Scholar 

  3. 3

    Whitacre, C.C. Sex differences in autoimmune disease. Nat. Immunol. 2, 777–780 (2001).

    Article  CAS  PubMed  Google Scholar 

  4. 4

    Klein, S.L. The effects of hormones on sex differences in infection: from genes to behavior. Neurosci. Biobehav. Rev. 24, 627–638 (2000).

    Article  CAS  PubMed  Google Scholar 

  5. 5

    Holroyd, C.R. & Edwards, C.J. The effects of hormone replacement therapy on autoimmune disease: rheumatoid arthritis and systemic lupus erythematosus. Climacteric 12, 378–386 (2009).

    Article  CAS  PubMed  Google Scholar 

  6. 6

    Seligman, V.A., Lum, R.F., Olson, J.L., Li, H. & Criswell, L.A. Demographic differences in the development of lupus nephritis: a retrospective analysis. Am. J. Med. 112, 726–729 (2002).

    Article  PubMed  Google Scholar 

  7. 7

    Mackay, I.R. Science, medicine and the future: tolerance and autoimmunity. Br. Med. J. 321, 93–96 (2000).

    Article  CAS  Google Scholar 

  8. 8

    Sánchez-Guerrero, J. et al. Menopause hormonal therapy in women with systemic lupus erythematosus. Arthritis Rheum. 56, 3070–3079 (2007).

    Article  CAS  PubMed  Google Scholar 

  9. 9

    Mok, C.C. et al. Safety of hormonal replacement therapy in postmenopausal patients with systemic lupus erythematosus. Scand. J. Rheumatol. 27, 342–346 (1998).

    Article  CAS  PubMed  Google Scholar 

  10. 10

    Nestle, F.O., Di Meglio, P., Qin, J.Z. & Nickoloff, B.J. Skin immune sentinels in health and disease. Nat. Rev. Immunol. 9, 679–691 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. 11

    Cervera, R. et al. Systemic lupus erythematosus: clinical and immunologic patterns of disease expression in a cohort of 1,000 patients. Medicine (Baltimore) 72, 113–124 (1993).

    Article  CAS  Google Scholar 

  12. 12

    Cooper, G.S. & Stroehla, B.C. The epidemiology of autoimmune diseases. Autoimmun. Rev. 2, 119–125 (2003).

    Article  PubMed  Google Scholar 

  13. 13

    Vincent, F.B., Morand, E.F., Schneider, P. & Mackay, F. The BAFF (APRIL) system in SLE pathogenesis. Nat. Rev. Rheumatol. 10, 365–373 (2014).

    Article  CAS  PubMed  Google Scholar 

  14. 14

    Harley, J.B. et al. Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci. Nat. Genet. 40, 204–210 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. 15

    Grundberg, E. et al. Mapping cis- and trans-regulatory effects across multiple tissues in twins. Nat. Genet. 44, 1084–1089 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. 16

    Maeda, T., Chapman, D.L. & Stewart, A.F. Mammalian vestigial-like 2, a cofactor of TEF-1 and MEF2 transcription factors that promotes skeletal muscle differentiation. J. Biol. Chem. 277, 48889–48898 (2002).

    Article  CAS  PubMed  Google Scholar 

  17. 17

    Barson, N.J. et al. Sex-dependent dominance at a single locus maintains variation in age at maturity in salmon. Nature 528, 405–408 (2015).

    Article  CAS  PubMed  Google Scholar 

  18. 18

    Ram, M., Sherer, Y. & Shoenfeld, Y. Matrix metalloproteinase 9 and autoimmune diseases. J. Clin. Immunol. 26, 299–307 (2006).

    Article  CAS  PubMed  Google Scholar 

  19. 19

    Yang, W. et al. Genome-wide association study in Asian populations identifies variants in ETS1 and WDFY4 associated with systemic lupus erythematosus. PLoS Genet. 6, e1000841 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. 20

    Lee, L.F. et al. IL-7 promotes TH1 development and serum IL-7 predicts clinical response to interferon-β in multiple sclerosis. Sci. Transl. Med. 3, 93ra68 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  21. 21

    Pickens, S.R. et al. Characterization of interleukin-7 and interleukin-7 receptor in the pathogenesis of rheumatoid arthritis. Arthritis Rheum. 63, 2884–2893 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. 22

    Bikker, A. et al. Increased expression of interleukin-7 in labial salivary glands of patients with primary Sjögren's syndrome correlates with increased inflammation. Arthritis Rheum. 62, 969–977 (2010).

    Article  CAS  PubMed  Google Scholar 

  23. 23

    Wuthrich, R.P., Jevnikar, A.M., Takei, F., Glimcher, L.H. & Kelley, V.E. Intercellular adhesion molecule–1 (ICAM-1) expression is upregulated in autoimmune murine lupus nephritis. Am. J. Pathol. 136, 441–450 (1990).

    CAS  PubMed  PubMed Central  Google Scholar 

  24. 24

    Bö, L. et al. Distribution of immunoglobulin superfamily members ICAM-1, ICAM-2, ICAM-3 and the β2-integrin LFA-1 in multiple sclerosis lesions. J. Neuropathol. Exp. Neurol. 55, 1060–1072 (1996).

    Article  PubMed  Google Scholar 

  25. 25

    Anderson, M.E. & Siahaan, T.J. Targeting ICAM-1–LFA-1 interaction for controlling autoimmune diseases: designing peptide and small-molecule inhibitors. Peptides 24, 487–501 (2003).

    Article  CAS  PubMed  Google Scholar 

  26. 26

    Baechler, E.C. et al. Interferon-inducible gene expression signature in peripheral blood cells of patients with severe lupus. Proc. Natl. Acad. Sci. USA 100, 2610–2615 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. 27

    Obermoser, G. & Pascual, V. The interferon-α signature of systemic lupus erythematosus. Lupus 19, 1012–1019 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. 28

    Banchereau, J. & Pascual, V. Type I interferon in systemic lupus erythematosus and other autoimmune diseases. Immunity 25, 383–392 (2006).

    Article  CAS  Google Scholar 

  29. 29

    Ohl, K. & Tenbrock, K. Inflammatory cytokines in systemic lupus erythematosus. J. Biomed. Biotechnol. 2011, 432595 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. 30

    Gudjonsson, J.E. & Elder, J.T. Psoriasis: epidemiology. Clin. Dermatol. 25, 535–546 (2007).

    Article  PubMed  Google Scholar 

  31. 31

    Leitenberger, J.J. et al. Distinct autoimmune syndromes in morphea: a review of 245 adult and pediatric cases. Arch. Dermatol. 145, 545–550 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  32. 32

    Mayes, M.D. et al. Prevalence, incidence, survival and disease characteristics of systemic sclerosis in a large US population. Arthritis Rheum. 48, 2246–2255 (2003).

    Article  PubMed  Google Scholar 

  33. 33

    Milano, A. et al. Molecular subsets in the gene expression signatures of scleroderma skin. PLoS One 3, e2696 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. 34

    Patel, R. & Shahane, A. The epidemiology of Sjögren's syndrome. Clin. Epidemiol. 6, 247–255 (2014).

    PubMed  PubMed Central  Google Scholar 

  35. 35

    Horvath, S. et al. Systems analysis of primary Sjögren's syndrome pathogenesis in salivary glands identifies shared pathways in human and a mouse model. Arthritis Res. Ther. 14, R238 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. 36

    Hillen, M.R. et al. High soluble-IL-7 receptor expression in Sjögren's syndrome identifies patients with increased immunopathology and dryness. Ann. Rheum. Dis. 75, 1735–1736 (2016).

    Article  CAS  PubMed  Google Scholar 

  37. 37

    Bikker, A. et al. IL-7-activated T cells and monocytes drive B cell activation in patients with primary Sjogren's syndrome. Ann. Rheum. Dis. 70, A63 (2011).

    Article  Google Scholar 

  38. 38

    Jin, J.O., Kawai, T., Cha, S. & Yu, Q. Interleukin-7 enhances the TH1 response to promote the development of Sjögren's-syndrome-like autoimmune exocrinopathy in mice. Arthritis Rheum. 65, 2132–2142 (2013).

    Article  CAS  PubMed  Google Scholar 

  39. 39

    Yao, Y., Liu, Z., Jallal, B., Shen, N. & Rönnblom, L. Type I interferons in Sjögren's syndrome. Autoimmun. Rev. 12, 558–566 (2013).

    Article  CAS  PubMed  Google Scholar 

  40. 40

    Jin, J.O., Shinohara, Y. & Yu, Q. Innate immune signaling induces interleukin-7 production from salivary gland cells and accelerates the development of primary Sjögren's syndrome in a mouse model. PLoS One 8, e77605 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. 41

    Kim, A.M., Tingen, C.M. & Woodruff, T.K. Sex bias in trials and treatment must end. Nature 465, 688–689 (2010).

    Article  CAS  PubMed  Google Scholar 

  42. 42

    Woodruff, T.K. Sex, equity and science. Proc. Natl. Acad. Sci. USA 111, 5063–5064 (2014).

    Article  CAS  PubMed  Google Scholar 

  43. 43

    Kachgal, S., Mace, K.A. & Boudreau, N.J. The dual roles of homeobox genes in vascularization and wound healing. Cell Adh. Migr. 6, 457–470 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  44. 44

    Ben-Chetrit, E., Bergmann, S. & Sood, R. Mechanism of the anti-inflammatory effect of colchicine in rheumatic diseases: a possible new outlook through microarray analysis. Rheumatology 45, 274–282 (2006).

    Article  CAS  PubMed  Google Scholar 

  45. 45

    Umazume, T. et al. Lacrimal gland inflammation de-regulates extracellular matrix remodeling and alters molecular signature of epithelial stem/progenitor cells. Invest. Ophthalmol. Vis. Sci. 56, 8392–8402 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. 46

    Kalin, T.V. et al. Pulmonary mastocytosis and enhanced lung inflammation in mice heterozygous null for the Foxf1 gene. Am. J. Resp. Cell Mol. 39, 390–399 (2008).

    Article  CAS  Google Scholar 

  47. 47

    Shang, Y., Karmen, A. & Xiaoyu, H. Transcription repressor Hes1 is a selective regulator of TLR-induced CXCL1 expression and neutrophil responses. J. Immunol. 192, 62–69 (2014).

    Google Scholar 

  48. 48

    Steinbrecher, A. et al. Targeting dipeptidyl peptidase IV (CD26) suppresses autoimmune encephalomyelitis and upregulates TGF-β1 secretion in vivo. J. Immunol. 166, 2041–2048 (2001).

    Article  CAS  PubMed  Google Scholar 

  49. 49

    Rovere, P. et al. The long pentraxin PTX3 binds to apoptotic cells and regulates their clearance by antigen-presenting dendritic cells. Blood 96, 4300–4306 (2000).

    Article  CAS  PubMed  Google Scholar 

  50. 50

    Hall, P.A. & Russell, S.E. The pathobiology of the septin gene family. J. Pathol. 204, 489–505 (2004).

    Article  CAS  PubMed  Google Scholar 

  51. 51

    Tsoi, L.C. et al. Analysis of long noncoding RNAs highlights tissue-specific expression patterns and epigenetic profiles in normal and psoriatic skin. Genome Biol. 16, 24 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. 52

    Welter, D. et al. The NHGRI GWAS Catalog, a curated resource of SNP–trait associations. Nucleic Acids Res. 42, D1001–D1006 (2014).

    Article  CAS  PubMed  Google Scholar 

  53. 53

    Carson, C.G. Risk factors for developing atopic dermatitis. Dan. Med. J. 60, B4687 (2013).

    PubMed  Google Scholar 

  54. 54

    Scrivener, Y., Grosshans, E. & Cribier, B. Variations of basal cell carcinomas according to gender, age, location and histopathological subtype. Br. J. Dermatol. 147, 41–47 (2002).

    Article  CAS  PubMed  Google Scholar 

  55. 55

    Elder, J.T. et al. Retinoic acid receptor gene expression in human skin. J. Invest. Dermatol. 96, 425–433 (1991).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank A.A. Dlugosz for critical discussions and reading of the manuscript; S. Stoll, Y. Xu, T. Quan, Y. Li, L. Wolterink and L. Reingold for technical help; and A. Libs for help with biopsy samples and files. Supported by the US National Institutes of Health (K08-AR060802 and R01-AR069071to J.E.G.; and R03-AR066337 and K08-AR063668 to J.M.K.), an A. Alfred Taubman Medical Research Institute Kenneth and Frances Eisenberg Emerging Scholar Award (J.E.G.), the Doris Duke Charitable Foundation (2013106 to J.E.G.) and a Pfizer Aspire Award (J.E.G.).

Author information

Affiliations

Authors

Contributions

Y.L., J.E.G., J.T.E., J.M.K. and J.J.V. designed the study and wrote the manuscript; Y.L., X.X., M.A.B., P.W.H., P.E.S., M.K.S., R.P.N. and C.C.B. collected and analyzed data; and L.C.T. and W.R.S. analyzed data. All authors reviewed and commented on the manuscript.

Corresponding author

Correspondence to Johann E Gudjonsson.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 X-inactivation in human skin.

a, pie chart of the percentage of genes that underwent and escaped X inactivation in female human skins. b-d, examples of the expression of escapees with Y orthologues in females and males. e-g, examples of the expression of escapees without Y orthologues in females and males. Mean+stdev, * P<0.05. Student’s t-test.

Supplementary Figure 2 Sex differences in expression correlation.

a, genome-wide gender-differences in expression correlation for female-biased genes. b, correlation between gene-gene spearman correlations estimated from RNA-seq samples (columns) versus those estimated from microarray data (rows). *, significant correlation.

Supplementary Figure 3 Female-biased genes and autoimmune diseases.

a, top functions enriched in female-biased genes. b, SLE/Systemic sclerosis and the atopic dermatitis loci are enriched with female-bias genes. c, the null distribution for the expected overlap for random loci, with red lines illustrating the observed overlap results from the SLE/SS (top) and AD (bottom), respectively. d, qRT-PCR analyses of female-biased immune genes in T cells extracted from blood of healthy humans (n=9 each sex). F, female. M, male. Mean ± s.e.m, * P<0.05. Student’s t-test. e-i, scatter plot of gene expression levels from RNA-Seq of human skin biopsies versus age at biopsy for ITGAM, C3, CFB, DOCK2, and FCER1G.

Supplementary Figure 4 Knockdown of female-biased transcription factors.

a-e, qRT-PCR analyses of VGLL3, UTX, ZFX, FEZ, FHL upon their knockdown by RNAi (n=3). f, qRT-PCR analyses of UTX and ZFX upon VGLL3 knockdown (n=3). Mean ± s.e.m, * P<0.05. Student’s t-test.

Supplementary Figure 5 eQTL and functional enrichment analyses of VGLL3-regulated genes.

a, cis-eQTL signal at chr3:87902673 (p=4e-05) around VGLL3. b, significant eQTL results for chr3:87902673 against different expression traits. c, Top pathways regulated by VGLL3.

Supplementary Figure 6 VGLL3 targets in autoimmune diseases.

a, log2(FC) of autoimmune disease genes upon VGLL3 RNAi. b, density plot of log2(FC) levels upon VGLL3 knockdown for plaque psoriasis (PP) and non-PP genes. c, density plot of log2(FC) levels upon VGLL3 knockdown for SCLE and PP genes. d, density plot of log2(FC) levels upon Fez knockdown for SCLE and non-SCLE genes. e, density plot of log2(FC) levels upon Fyn knockdown for SCLE and non-SCLE genes. b-e, Wilcoxon-Matt-Whitney test. f, gene expression levels in female (F) and male (M) SCLE patients by RNA-Seq. Mean+s.e.m. g, associations of VGLL3 targets with various autoimmune conditions, with (*) indicating the observed mean of VGLL3 target gene expression and box indicating 1st and 3rd percentile for the null distribution for the mean signed log10 P-value (2000 simulations). h, expression of VGLL3 targets and non-targets in Sjögren’s syndrome, showing higher percentage of Vgll3 targets that have increased expression in disease (red boxed region) compared to non-targets (grey boxed region). Mann-Whitney U test.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–6 (PDF 981 kb)

Supplementary Table 1

Lists of gender biased genes (XLSX 50 kb)

Supplementary Table 2

Details for TF screening for regulation of gender biased genes. (XLSX 35 kb)

Supplementary Table 3

VGLL3-regulated genes in keratinocytes (XLSX 58 kb)

Supplementary Table 4

Overlap between VGLL3-regulated genes and lupus-upregulated genes (XLSX 57 kb)

Supplementary Table 5

Lists of SCLE- and psoriasis-altered genes (XLSX 72 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Liang, Y., Tsoi, L., Xing, X. et al. A gene network regulated by the transcription factor VGLL3 as a promoter of sex-biased autoimmune diseases. Nat Immunol 18, 152–160 (2017). https://doi.org/10.1038/ni.3643

Download citation

Further reading