Supplementary Data 3. List of Antigens Found Immunogenic in Breast Cancer Between DCIS and IBC Sera

Supplementary data 3. List of antigens found immunogenic in breast cancer between DCIS and IBC sera

Gene symbol Swissprot Id Medians DCIS* [range] Medians IBC* [range] P Fold-change Biological process Molecular function References**

κ Q06330 1.9 [0.0 - 28.9] 7.5 [0.0 - 40.4] 0.0178 4.0 Notch signaling pathway, transcription Sequence-specific DNA binding transcription factor activity RBP-J (1) ECHDC1 Q9NTX5 3.3 [1.8 - 7.3] 8.6 [5.3 - 18.7] 0.0001 2.5 Metabolic process Catalytic activity (2) PSRC1 Q6PGN9 2.0 [0.0 - 6.8] 4.1 [0.0 - 9.9] 0.0256 2.1 Cell division, negative regulation of cell growth Microtubule binding (3-4) CTTN Q96H99 3.2 [0.9 - 23.1] 6.3 [1.6 - 45.7] 0.0045 2.0 Unknown Unknown (5-7) WDR5 P61964 6.5 [1.7 - 16.7] 3.6 [0.9 - 9.7] 0.0003 0.5 Histone H3 acetylation, histone H3-K4 methylation Protein binding - C1orf131 Q8NDD1 3.1 [1.5 - 14.7] 1.6 [0.0 - 28.8] 0.0021 0.5 Unknown Unknown - RBM34 P42696 4.5 [1.6 - 11.1] 2.3 [0.9 - 10.1] 0.0002 0.5 Unknown RNA binding - LARP4 Q71RC2 3.2 [1.8 - 5.8] 1.5 [0.2 - 14.3] 0.0001 0.5 Unknown Unknown - H1F0 P07305 3.1 [1.0 - 16.1] 1.5 [0.4 - 6.1] 0.0006 0.5 DNA fragmentation, nucleosome assembly DNA binding (8) ZNF747 Q9BV97 2.9 [0.1 - 5.6] 1.3 [0.0 - 3.29] 0.0002 0.5 Regulation of transcription, DNA-dependent Nucleic acid binding - TTLL7 Q6ZT98 3.3 [0.9 - 7.8] 1.1 [0.2 - 5.8] 0.0001 0.3 Cell differentiation Tubulin-tyrosine ligase activity - C3orf37 Q96FZ2 2.3 [0.4 - 13.2] 0.7 [0.0 - 14.0] 0.0049 0.3 Unknown Unknown - GTPBP1 O00178 3.0 [0.4 - 8.3] 0.9 [0.0 - 3.9] 0.0001 0.3 Immune response, signal transduction GTP binding, GTPase activity - HMGB2 P26583 3.3 [1.0 - 21.8] 0.8 [0.0 - 14.8] 0.0005 0.2 DNA topological change DNA topological change, transcription activator activity (9-10) HP1BP3 Q5SSJ5 3.0 [0.7 - 7.3] 0.6 [0.0 - 3.1] 0.0001 0.2 Nucleosome assembly DNA binding - YTHDF2 Q9Y5A9 3.9 [1.8 - 11.1] 0.7 [0.0 - 6.8] 0.0001 0.2 Humoral immune response Unknown (11) RNPC3 Q96LT9 4.3 [1.2 - 10.1] 0.6 [0.0 - 4.2] 0.0001 0.1 mRNA processing RNA and protein binding - DIDO1 Q9BTC0 1.8 [0.2 - 3.9] 0.2 [0.0 - 7.1] 0.0001 0.1 Apoptosis, transcription Metal ion binding (12) CIRBP Q14011 3.5 [0.3 - 9.9] 0.4 [0.0 - 3.0] 0.0001 0.1 mRNA stabilization, positive regulation of translation mRNA 3'-UTR binding, protein binding (13-16) HMGN1 P05114 1.6 [0.4 - 5.0] 0.1 [0.0 - 32.0] 0.0001 0.1 Regulation of transcription elongation, DNA-dependent RNA polymerase II transcription factor activity (17-18)

* Median of local Z-Score; ** References of protein associations with cancer. Supplementary references:

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2. Menachem TD, Laitman Y, Kaufman B, Friedman E. The RNF146 and ECHDC1 genes as candidates for inherited breast and ovarian cancer in Jewish Ashkenazi women. Fam Cancer. 2009;8:399-402.

3. Hsieh PC, Chang JC, Sun WT, Hsieh SC, Wang MC, Wang FF. p53 downstream target DDA3 is a novel microtubule-associated protein that interacts with end-binding protein EB3 and activates beta-catenin pathway. Oncogene. 2007;26:4928-40.

4. Hsieh WJ, Hsieh SC, Chen CC, Wang FF. Human DDA3 is an oncoprotein down-regulated by p53 and DNA damage. Biochem Biophys Res Commun. 2008;369:567-72.

5. Dedes KJ, Lopez-Garcia MA, Geyer FC, Lambros MB, Savage K, Vatcheva R, et al. Cortactin gene amplification and expression in breast cancer: a chromogenic in situ hybridisation and immunohistochemical study. Breast Cancer Res Treat. 2010;124:653-66.

6. Hirakawa H, Shibata K, Nakayama T. Localization of cortactin is associated with colorectal cancer development. International journal of oncology. 2009;35:1271-6.

7. Buday L, Downward J. Roles of cortactin in tumor pathogenesis. Biochim Biophys Acta. 2007;1775:263-73.

8. Gabrilovich DI, Cheng P, Fan Y, Yu B, Nikitina E, Sirotkin A, et al. H1(0) histone and differentiation of dendritic cells. A molecular target for tumor- derived factors. J Leukoc Biol. 2002;72:285-96.

9. Kwon JH, Kim J, Park JY, Hong SM, Park CW, Hong SJ, et al. Overexpression of high-mobility group box 2 is associated with tumor aggressiveness and prognosis of hepatocellular carcinoma. Clin Cancer Res. 2010;16:5511-21.

10. Sharma A, Ray R, Rajeswari MR. Overexpression of high mobility group (HMG) B1 and B2 proteins directly correlates with the progression of squamous cell carcinoma in skin. Cancer investigation. 2008;26:843-51.

11. Nguyen TT, Ma LN, Slovak ML, Bangs CD, Cherry AM, Arber DA. Identification of novel Runx1 (AML1) translocation partner genes SH3D19, YTHDf2, and ZNF687 in acute myeloid leukemia. Genes, chromosomes & cancer. 2006;45:918-32.

12. Futterer A, Campanero MR, Leonardo E, Criado LM, Flores JM, Hernandez JM, et al. Dido gene expression alterations are implicated in the induction of hematological myeloid neoplasms. J Clin Invest. 2005;115:2351-62. 13. Nishiyama H, Itoh K, Kaneko Y, Kishishita M, Yoshida O, Fujita J. A glycine-rich RNA-binding protein mediating cold-inducible suppression of mammalian cell growth. J Cell Biol. 1997;137:899-908.

14. Artero-Castro A, Callejas FB, Castellvi J, Kondoh H, Carnero A, Fernandez-Marcos PJ, et al. Cold-inducible RNA-binding protein bypasses replicative senescence in primary cells through extracellular signal-regulated kinase 1 and 2 activation. Mol Cell Biol. 2009;29:1855-68.

15. Guo X, Wu Y, Hartley RS. Cold-inducible RNA-binding protein contributes to human antigen R and cyclin E1 deregulation in breast cancer. Mol Carcinog. 2010;49:130-40.

16. Li XM, Delaunay F, Dulong S, Claustrat B, Zampera S, Fujii Y, et al. Cancer inhibition through circadian reprogramming of tumor transcriptome with meal timing. Cancer Res. 2010;70:3351-60.

17. Kim YC, Gerlitz G, Furusawa T, Catez F, Nussenzweig A, Oh KS, et al. Activation of ATM depends on chromatin interactions occuring before induction of DNA damage. Nat Cell Biol. 2009;11:92-6.

18. Zou Y, Jiang X, Wang Y. Identification of novel in vivo phosphorylation sites in high mobility group N1 protein from the MCF-7 human breast cancer cells. Biochemistry. 2004;43:6322-9.