Oxysterols, oxidized derivatives of cholesterol, act in breast cancer (BC) as selective estrogen receptor modulators and affect cholesterol homeostasis, drug transport, nuclear and cell receptors, and other signaling proteins. Using data from three highly overlapping sets of patients (N = 162 in total) with early-stage estrogen-receptor-positive luminal BC-high-coverage targeted DNA sequencing (113 genes), mRNA sequencing, and full micro-RNA (miRNA) transcriptome microarrays-we describe complex oxysterol-related interaction (correlation) networks, with validation in public datasets (n = 538) and 11 databases. The ESR1-CH25H-INSIG1-ABCA9 axis was the most prominent, interconnected through miR-125b-5p, miR-99a-5p, miR-100-5p, miR-143-3p, miR-199b-5p, miR-376a-3p, and miR-376c-3p. Mutations in SC5D, CYP46A1, and its functionally linked gene set were associated with multiple differentially expressed oxysterol-related genes. STARD5 was upregulated in patients with positive lymph node status. High expression of hsa-miR-19b-3p was weakly associated with poor survival. This is the first study of oxysterol-related genes in BC that combines DNA, mRNA, and miRNA multiomics with detailed clinical data. Future studies should provide links between intratumoral oxysterol signaling depicted here, circulating oxysterol levels, and therapy outcomes, enabling eventual clinical exploitation of present findings.

3rd Faculty of Medicine Charles University Prague Czech Republic

Aeskulab k s Prague Czech Republic

Biomedical Center Faculty of Medicine in Pilsen Charles University Pilsen Czech Republic

Comprehensive Cancer Center Novy Jicin Hospital Novy Jicin Czech Republic

Department of Oncology 2nd Faculty of Medicine Charles University and Motol University Hospital Prague Czech Republic

Department of Oncosurgery MEDICON Prague Czech Republic

Department of Pathology 2nd Faculty of Medicine Charles University and Motol University Hospital Prague Czech Republic

Department of Surgery EUC Hospital Zlin and Tomas Bata University in Zlin Czech Republic

Toxicogenomics Unit National Institute of Public Health Prague Czech Republic

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Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, et al. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2021;71(3):209–249. PubMed

Crimini E, Repetto M, Aftimos P, Botticelli A, Marchetti P, Curigliano G. Precision medicine in breast cancer: from clinical trials to clinical practice. Cancer Treat Rev. 2021;98:102223. PubMed

Olivier M, Asmis R, Hawkins GA, Howard TD, Cox LA. The need for multi‐omics biomarker signatures in precision medicine. Int J Mol Sci. 2019;20(19):E4781. PubMed PMC

Schroepfer GJ. Oxysterols: modulators of cholesterol metabolism and other processes. Physiol Rev. 2000;80(1):361–554. PubMed

Brown AJ, Sharpe LJ, Rogers MJ. Oxysterols: from physiological tuners to pharmacological opportunities. Br J Pharmacol. 2021;178(16):3089–3103. PubMed

Umetani M, Domoto H, Gormley AK, Yuhanna IS, Cummins CL, Javitt NB, et al. 27‐hydroxycholesterol is an endogenous SERM that inhibits the cardiovascular effects of estrogen. Nat Med. 2007;13(10):1185–1192. PubMed

Kloudova A, Guengerich FP, Soucek P. The role of oxysterols in human cancer. Trends Endocrinol Metab. 2017;28(7):485–496. PubMed PMC

Kloudova‐Spalenkova A, Holy P, Soucek P. Oxysterols in cancer management: from therapy to biomarkers. Br J Pharmacol. 2021;178(16):3235–3247. PubMed

Catalanotto C, Cogoni C, Zardo G. MicroRNA in control of gene expression: an overview of nuclear functions. Int J Mol Sci. 2016;17(10):1712. PubMed PMC

Loh H‐Y, Norman BP, Lai K‐S, Rahman NMANA, Alitheen NBM, Osman MA. The regulatory role of MicroRNAs in breast cancer. Int J Mol Sci. 2019;20(19):4940. PubMed PMC

Kandettu A, Radhakrishnan R, Chakrabarty S, Sriharikrishnaa S, Kabekkodu SP. The emerging role of miRNA clusters in breast cancer progression. Biochim Biophys Acta Rev Cancer. 2020;1874(2):188413. PubMed

DiMarco DM, Fernandez ML. The regulation of reverse cholesterol transport and cellular cholesterol homeostasis by microRNAs. Biology (Basel). 2015;4(3):494–511. PubMed PMC

Rotllan N, Fernández‐Hernando C. MicroRNA regulation of cholesterol metabolism. Cholesterol. 2012;2012:847849. PubMed PMC

Mutemberezi V, Guillemot‐Legris O, Muccioli GG. Oxysterols: from cholesterol metabolites to key mediators. Prog Lipid Res. 2016;64:152–169. PubMed

Holý P, Hlaváč V, Ostašov P, Brynychová V, Koževnikovová R, Trnková M, et al. Germline and somatic genetic variability of oxysterol‐related genes in breast cancer patients with early disease of the luminal subtype. Biochimie. 2022;199:158–169. PubMed

Holy P, Kloudova A, Soucek P. Importance of genetic background of oxysterol signaling in cancer. Biochimie. 2018;153:109–138. PubMed

Kloudova A, Brynychova V, Vaclavikova R, Vrana D, Gatek J, Mrhalova M, et al. Expression of oxysterol pathway genes in oestrogen‐positive breast carcinomas. Clin Endocrinol (Oxf). 2017;86(6):852–861. PubMed

Tavassoli F, Devilee P. Pathology and genetics of tumours of the breast and female genital organs. Lyon, France: IARC Press; 2003.

Cheang MCU, Chia SK, Voduc D, Gao D, Leung S, Snider J, et al. Ki67 index, HER2 status, and prognosis of patients with luminal B breast cancer. J Natl Cancer Inst. 2009;101(10):736–750. PubMed PMC

Fragomeni SM, Sciallis A, Jeruss JS. Molecular subtypes and local‐regional control of breast cancer. Surg Oncol Clin N Am. 2018;27(1):95–120. PubMed PMC

Coates AS, Winer EP, Goldhirsch A, Gelber RD, Gnant M, Piccart‐Gebhart M, et al. Tailoring therapies–improving the management of early breast cancer: St Gallen international expert consensus on the primary therapy of early breast cancer 2015. Ann Oncol. 2015;26(8):1533–1546. PubMed PMC

Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics. 2007;8(1):118–127. PubMed

Chen C, Grennan K, Badner J, Zhang D, Gershon E, Jin L, et al. Removing batch effects in analysis of expression microarray data: an evaluation of six batch adjustment methods. PLoS One. 2011;6(2):e17238. PubMed PMC

Andrews S. FastQC: a quality control tool for high throughput sequence data. 2010. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, et al. GENCODE 2021. Nucleic Acids Res. 2020;49(D1):D916–D923. 10.1093/nar/gkaa1087 PubMed DOI PMC

Bray NL, Pimentel H, Melsted P, Pachter L. Near‐optimal probabilistic RNA‐seq quantification. Nat Biotechnol. 2016;34(5):525–527. PubMed

Somatic short variant discovery (SNVs + indels). GATK, https://gatk.broadinstitute.org/hc/en‐us/articles/360035894731‐Somatic‐short‐variant‐discovery‐SNVs‐Indels‐. Accessed 22 March 2022.

O'Leary NA, Wright MW, Brister JR, Ciufo S, Haddad D, McVeigh R, et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 2016;44(D1):D733–D745. PubMed PMC

R Core Team . R: a language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing. 2022. Available online at: https://www.R-project.org/

Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139–140. PubMed PMC

Mar JC. The rise of the distributions: why non‐normality is important for understanding the transcriptome and beyond. Biophys Rev. 2019;11(1):89–94. PubMed PMC

Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B Methodol. 1995;57(1):289–300.

Ru Y, Kechris KJ, Tabakoff B, Hoffman P, Radcliffe RA, Bowler R, et al. The multiMiR R package and database: integration of microRNA–target interactions along with their disease and drug associations. Nucleic Acids Res. 2014;42(17):e133. PubMed PMC

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498–2504. 10.1101/gr.1239303 PubMed DOI PMC

Kolde R. pheatmaps: Pretty heatmaps. 2019. Available online at: https://CRAN.R-project.org/package=pheatmap

Rohart F, Gautier B, Singh A, Cao K‐AL. mixOmics: an R package for ‘omics feature selection and multiple data integration. PLoS Comput Biol. 2017;13(11):e1005752. PubMed PMC

Singh A, Shannon CP, Gautier B, Rohart F, Vacher M, Tebbutt SJ, et al. DIABLO: an integrative approach for identifying key molecular drivers from multi‐omics assays. Bioinformatics. 2019;35(17):3055–3062. PubMed PMC

Tweedie S, Braschi B, Gray K, Jones TEM, Seal RL, Yates B, et al. Genenames.Org: the HGNC and VGNC resources in 2021. Nucleic Acids Res. 2021;49(D1):D939–D946. PubMed PMC

Xu T, Su N, Liu L, Zhang J, Wang H, Zhang W, et al. miRBaseConverter: an R/Bioconductor package for converting and retrieving miRNA name, accession, sequence and family information in different versions of miRBase. BMC Bioinformatics. 2018;19(19):514. PubMed PMC

Kabekkodu SP, Shukla V, Varghese VK, D' Souza J, Chakrabarty S, Satyamoorthy K. Clustered miRNAs and their role in biological functions and diseases. Biol Rev Camb Philos Soc. 2018;93(4):1955–1986. PubMed

Brufsky AM, Dickler MN. Estrogen receptor‐positive breast cancer: exploiting signaling pathways implicated in endocrine resistance. Oncologist. 2018;23(5):528–539. PubMed PMC

Cao Q, Liu Z, Xiong Y, Zhong Z, Ye Q. Multiple roles of 25‐hydroxycholesterol in lipid metabolism, antivirus process, inflammatory response, and cell survival. Oxid Med Cell Longev. 2020;2020:8893305. PubMed PMC

Lappano R, Recchia AG, De Francesco EM, Angelone T, Cerra MC, Picard D, et al. The cholesterol metabolite 25‐hydroxycholesterol activates estrogen receptor α‐mediated signaling in cancer cells and in cardiomyocytes. PloS One. 2011;6(1):e16631. PubMed PMC

Ouyang S, Mo Z, Sun S, Yin K, Lv Y. Emerging role of Insig‐1 in lipid metabolism and lipid disorders. Clin Chim Acta. 2020;508:206–212. PubMed

Simigdala N, Gao Q, Pancholi S, Roberg‐Larsen H, Zvelebil M, Ribas R, et al. Cholesterol biosynthesis pathway as a novel mechanism of resistance to estrogen deprivation in estrogen receptor‐positive breast cancer. Breast Cancer Res. 2016;18(1):58. PubMed PMC

Peelman F, Labeur C, Vanloo B, Roosbeek S, Devaud C, Duverger N, et al. Characterization of the ABCA transporter subfamily: identification of prokaryotic and eukaryotic members, phylogeny and topology. J Mol Biol. 2003;325(2):259–274. PubMed

Piehler A, Kaminski WE, Wenzel JJ, Langmann T, Schmitz G. Molecular structure of a novel cholesterol‐responsive a subclass ABC transporter, ABCA9. Biochem Biophys Res Commun. 2002;295(2):408–416. PubMed

Dvorak P, Pesta M, Soucek P. ABC gene expression profiles have clinical importance and possibly form a new hallmark of cancer. Tumour Biol. 2017;39(5):1010428317699800. PubMed

Hlavac V, Brynychova V, Vaclavikova R, Ehrlichova M, Vrana D, Pecha V, et al. The expression profile of ATP‐binding cassette transporter genes in breast carcinoma. Pharmacogenomics. 2013;14(5):515–529. PubMed

Søkilde R, Persson H, Ehinger A, Pirona AC, Fernö M, Hegardt C, et al. Refinement of breast cancer molecular classification by miRNA expression profiles. BMC Genomics. 2019;20(1):503. PubMed PMC

Haakensen VD, Nygaard V, Greger L, Aure MR, Fromm B, Bukholm IRK, et al. Subtype‐specific micro‐RNA expression signatures in breast cancer progression. Int J Cancer. 2016;139(5):1117–1128. PubMed

Wang S, Li L, Yang M, Wang X, Zhang H, Wu N, et al. Identification of three circulating MicroRNAs in plasma as clinical biomarkers for breast cancer detection. J Clin Med. 2023;12(1):322. PubMed PMC

Huo D, Clayton WM, Yoshimatsu TF, Chen J, Olopade OI. Identification of a circulating microRNA signature to distinguish recurrence in breast cancer patients. Oncotarget. 2016;7(34):55231–55248. PubMed PMC

Rodriguez‐Agudo D, Malacrida L, Kakiyama G, Sparrer T, Fortes C, Maceyka M, et al. StarD5: an ER stress protein regulates plasma membrane and intracellular cholesterol homeostasis. J Lipid Res. 2019;60(6):1087–1098. PubMed PMC

Liu Q, Du X, Yu Z, Yao Q, Meng X, Zhang K, et al. STARD5 as a potential clinical target of hepatocellular carcinoma. Med Oncol. 2022;39(10):156. PubMed

Zhao W, Gupta A, Krawczyk J, Gupta S. The miR‐17‐92 cluster: Yin and Yang in human cancers. Cancer Treat Res Commun. 2022;33:100647. PubMed

Olive V, Bennett MJ, Walker JC, Ma C, Jiang I, Cordon‐Cardo C, et al. miR‐19 is a key oncogenic component of mir‐17‐92. Genes Dev. 2009;23(24):2839–2849. PubMed PMC

Li C, Zhang J, Ma Z, Zhang F, Yu W. miR‐19b serves as a prognostic biomarker of breast cancer and promotes tumor progression through PI3K/AKT signaling pathway. Onco Targets Ther. 2018;11:4087–4095. PubMed PMC

Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, et al. Minimum information about a microarray experiment (MIAME)—toward standards for microarray data. Nat Genet. 2001;29(4):365–371. PubMed

Edgar R, Domrachev M, Lash AE. Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002;30(1):207–210. PubMed PMC

Brazma A, Ball C, Bumgarner R, Furlanello C, Miller M, Quackenbush J, et al. MINSEQE: Minimum Information about a high‐throughput Nucleotide SeQuencing Experiment – a proposal for standards in functional genomic data reporting. Zenodo; 2012. 10.5281/zenodo.5706412 DOI