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Kalinkin AI, Sigin VO, Kuznetsova EB, Ignatova EO, Vinogradov II, Vinogradov MI, Vinogradov IY, Zaletaev DV, Nemtsova MV, Kutsev SI, Tanas AS, Strelnikov VV. Epigenomic Profiling Advises Therapeutic Potential of Leukotriene Receptor Inhibitors for a Subset of Triple-Negative Breast Tumors. Int J Mol Sci 2023;24:17343. [PMID: 38139172 PMCID: PMC10743620 DOI: 10.3390/ijms242417343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/04/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open

Abstract

Triple-negative breast cancer (TNBC) is the most aggressive molecular subtype, with a poor survival rate compared to others subtypes. For a long time, chemotherapy was the only systemic treatment for TNBC, and the identification of actionable molecular targets might ultimately improve the prognosis for TNBC patients. We performed a genome-wide analysis of DNA methylation at CpG islands on a collection of one hundred ten breast carcinoma samples and six normal breast tissue samples using reduced representation bisulfite sequencing with the XmaI restriction enzyme (XmaI-RRBS) and identified a subset of TNBC samples with significant hypomethylation at the LTB4R/LTB4R2 genes' CpG islands, including CpG dinucleotides covered with cg12853742 and cg21886367 HumanMethylation 450K microarray probes. Abnormal DNA hypomethylation of this region in TNBC compared to normal samples was confirmed by bisulfite Sanger sequencing. Gene expression generally anticorrelates with promoter methylation, and thus, the promoter hypomethylation detected and confirmed in our study might be revealed as an indirect marker of high LTB4R/LTB4R2 expression using a simple methylation-sensitive PCR test. Analysis of RNA-seq expression and DNA methylation data from the TCGA dataset demonstrates that the expression of the LTB4R and LTB4R2 genes significantly negatively correlates with DNA methylation at both CpG sites cg12853742 (R = -0.4, p = 2.6 × 10-6; R = -0.21, p = 0.015) and cg21886367 (R = -0.45, p = 7.3 × 10-8; R = -0.24, p = 0.005), suggesting the upregulation of these genes in tumors with abnormal hypomethylation of their CpG island. Kaplan-Meier analysis using the TCGA-BRCA gene expression and clinical data revealed poorer overall survival for TNBC patients with an upregulated LTB4R. To this day, only the leukotriene inhibitor LY255283 has been tested on an MCF-7/DOX cell line, which is a luminal A breast cancer molecular subtype. Other studies compare the effects of Montelukast and Zafirlukast (inhibitors of the cysteinyl leukotriene receptor, which is different from LTB4R/LTB4R2) on the MDA-MB-231 (TNBC) cell line, with high methylation and low expression levels of LTB4R. In our study, we assess the therapeutic effects of various drugs (including leukotriene receptor inhibitors) with the DepMap gene effect and drug sensitivity data for TNBC cell lines with hypomethylated and upregulated LTB4R/LTB4R2 genes. LY255283, Minocycline, Silibinin, Piceatannol, Mitiglinide, 1-Azakenpaullone, Carbetocin, and Pim-1-inhibitor-2 can be considered as candidates for the additional treatment of TNBC patients with tumors demonstrating LTB4R/LTB4R2 hypomethylation/upregulation. Finally, our results suggest that the epigenetic status of leukotriene B4 receptors is a novel, potential, predictive, and prognostic biomarker for TNBC. These findings might improve individualized therapy for TNBC patients by introducing new therapeutic adjuncts as anticancer agents.

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Affiliation(s)

Alexey I. Kalinkin Research Centre for Medical Genetics, 115522 Moscow, Russia; (V.O.S.); (E.B.K.); (E.O.I.); (D.V.Z.); (M.V.N.); (S.I.K.); (A.S.T.); (V.V.S.)
Vladimir O. Sigin Research Centre for Medical Genetics, 115522 Moscow, Russia; (V.O.S.); (E.B.K.); (E.O.I.); (D.V.Z.); (M.V.N.); (S.I.K.); (A.S.T.); (V.V.S.)
Ekaterina B. Kuznetsova Research Centre for Medical Genetics, 115522 Moscow, Russia; (V.O.S.); (E.B.K.); (E.O.I.); (D.V.Z.); (M.V.N.); (S.I.K.); (A.S.T.); (V.V.S.) Laboratory of Medical Genetics, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119992 Moscow, Russia
Ekaterina O. Ignatova Research Centre for Medical Genetics, 115522 Moscow, Russia; (V.O.S.); (E.B.K.); (E.O.I.); (D.V.Z.); (M.V.N.); (S.I.K.); (A.S.T.); (V.V.S.) Nikolay Nikolaevich Blokhin National Medical Research Center of Oncology, 115478 Moscow, Russia
Ilya I. Vinogradov Regional Clinical Oncology Dispensary, 390011 Ryazan, Russia; Department of Histology, Pathological Anatomy and Medical Genetics, Ryazan State Medical University, 390026 Ryazan, Russia; (M.I.V.); (I.Y.V.)
Maxim I. Vinogradov Department of Histology, Pathological Anatomy and Medical Genetics, Ryazan State Medical University, 390026 Ryazan, Russia; (M.I.V.); (I.Y.V.)
Igor Y. Vinogradov Department of Histology, Pathological Anatomy and Medical Genetics, Ryazan State Medical University, 390026 Ryazan, Russia; (M.I.V.); (I.Y.V.)
Dmitry V. Zaletaev Research Centre for Medical Genetics, 115522 Moscow, Russia; (V.O.S.); (E.B.K.); (E.O.I.); (D.V.Z.); (M.V.N.); (S.I.K.); (A.S.T.); (V.V.S.)
Marina V. Nemtsova Research Centre for Medical Genetics, 115522 Moscow, Russia; (V.O.S.); (E.B.K.); (E.O.I.); (D.V.Z.); (M.V.N.); (S.I.K.); (A.S.T.); (V.V.S.) Laboratory of Medical Genetics, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119992 Moscow, Russia
Sergey I. Kutsev Research Centre for Medical Genetics, 115522 Moscow, Russia; (V.O.S.); (E.B.K.); (E.O.I.); (D.V.Z.); (M.V.N.); (S.I.K.); (A.S.T.); (V.V.S.)
Alexander S. Tanas Research Centre for Medical Genetics, 115522 Moscow, Russia; (V.O.S.); (E.B.K.); (E.O.I.); (D.V.Z.); (M.V.N.); (S.I.K.); (A.S.T.); (V.V.S.)
Vladimir V. Strelnikov Research Centre for Medical Genetics, 115522 Moscow, Russia; (V.O.S.); (E.B.K.); (E.O.I.); (D.V.Z.); (M.V.N.); (S.I.K.); (A.S.T.); (V.V.S.)

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Puhr HC, Puhr R, Kuchling DA, Jahic L, Takats J, Reiter TJ, Paireder M, Jomrich G, Schoppmann SF, Berghoff AS, Preusser M, Ilhan-Mutlu A. Development of an alarm symptom-based risk prediction score for localized oesophagogastric adenocarcinoma (VIOLA score). ESMO Open 2022;7:100519. [PMID: 35759854 PMCID: PMC9434169 DOI: 10.1016/j.esmoop.2022.100519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/19/2022] [Accepted: 05/22/2022] [Indexed: 12/01/2022] Open