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Current Topics in Medicinal Chemistry

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ISSN (Print): 1568-0266
ISSN (Online): 1873-4294

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Review Article

An Overview Regarding Pharmacogenomics and Biomarkers Discovery: Focus on Breast Cancer

Author(s): Thalita Basso Scandolara, Bruno Ricardo Barreto Pires, Beatriz Vacario, Isis Salviano Soares de Amorim, Priscyanne Barreto Siqueira, Juliana Mara Serpeloni, André Luiz Mencalha, Cibele Rodrigues Bonvicino and Carolina Panis*

Volume 22, Issue 20, 2022

Published on: 27 August, 2022

Page: [1654 - 1673] Pages: 20

DOI: 10.2174/1568026622666220801115040

Price: $65

Abstract

Breast cancer represents a health concern worldwide for being the leading cause of cancer- related women's death. The main challenge for breast cancer treatment involves its heterogeneous nature with distinct clinical outcomes. It is clinically categorized into five subtypes: luminal A; luminal B, HER2-positive, luminal-HER, and triple-negative. Despite the significant advances in the past decades, critical issues involving the development of efficient target-specific therapies and overcoming treatment resistance still need to be better addressed. OMICs-based strategies have marked a revolution in cancer biology comprehension in the past two decades. It is a consensus that Next-Generation Sequencing (NGS) is the primary source of this revolution and the development of relevant consortia translating pharmacogenomics into clinical practice. Still, new approaches, such as CRISPR editing and epigenomic sequencing are essential for target and biomarker discoveries. Here, we discuss genomics and epigenomics techniques, how they have been applied in clinical management and to improve therapeutic strategies in breast cancer, as well as the pharmacogenomics translation into the current and upcoming clinical routine.

Keywords: Breast cancer, Pharmacogenomics, Omics, Epigenomics, Drug development, Drug discovery.

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[1]
Sung, H.; Ferlay, J.; Siegel, R.L.; Laversanne, M.; Soerjomataram, I.; Jemal, A.; Bray, F. 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.
[http://dx.doi.org/10.3322/caac.21660] [PMID: 33538338]
[2]
Siegel, R.L.; Miller, K.D.; Fuchs, H.E.; Jemal, A. Cancer statistics, 2022. CA Cancer J. Clin., 2022, 72(1), 7-33.
[http://dx.doi.org/10.3322/caac.21708] [PMID: 35020204]
[3]
Sørlie, T.; Perou, C.M.; Tibshirani, R.; Aas, T.; Geisler, S.; Johnsen, H.; Hastie, T.; Eisen, M.B.; van de Rijn, M.; Jeffrey, S.S.; Thorsen, T.; Quist, H.; Matese, J.C.; Brown, P.O.; Botstein, D.; Lønning, P.E.; Børresen-Dale, A.L. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc. Natl. Acad. Sci. USA, 2001, 98(19), 10869-10874.
[http://dx.doi.org/10.1073/pnas.191367098] [PMID: 11553815]
[4]
Voduc, K.D.; Cheang, M.C.U.; Tyldesley, S.; Gelmon, K.; Nielsen, T.O.; Kennecke, H. Breast cancer subtypes and the risk of local and regional relapse. J. Clin. Oncol., 2010, 28(10), 1684-1691.
[http://dx.doi.org/10.1200/JCO.2009.24.9284] [PMID: 20194857]
[5]
Kern, R.; Correa, S.C.; Scandolara, T.B.; Carla da Silva, J.; Pires, B.R.; Panis, C. Current advances in the diagnosis and personalized treatment of breast cancer: Lessons from tumor biology. Per. Med., 2020, 17(5), 399-420.
[http://dx.doi.org/10.2217/pme-2020-0070] [PMID: 32804054]
[6]
Jones, R.L.; Constantinidou, A.; Reis-Filho, J.S. Molecular classification of breast cancer. Surg. Pathol. Clin., 2012, 5(3), 701-717.
[http://dx.doi.org/10.1016/j.path.2012.06.008] [PMID: 26838285]
[7]
Ingle, J.N. Pharmacogenomics of endocrine therapy in breast cancer. J. Hum. Genet., 2013, 58(6), 306-312.
[http://dx.doi.org/10.1038/jhg.2013.35] [PMID: 23635953]
[8]
Tong, C.W.S.; Wu, M.; Cho, W.C.S.; To, K.K.W. Recent advances in the treatment of breast cancer. Front. Oncol., 2018, 8, 227.
[http://dx.doi.org/10.3389/fonc.2018.00227] [PMID: 29963498]
[9]
Buzdar, A.U. Role of biologic therapy and chemotherapy in hormone receptor- and HER2-positive breast cancer. Ann. Oncol., 2009, 20(6), 993-999.
[http://dx.doi.org/10.1093/annonc/mdn739] [PMID: 19150946]
[10]
Baselga, J.; Dent, S.F.; Cortés, J.; Im, Y.H.; Diéras, V.; Harbeck, N.; Krop, I.E.; Verma, S.; Wilson, T.R.; Jin, H.; Wang, L.; Schimmoller, F.; Hsu, J.Y.; He, J.; DeLaurentiis, M.; Drullinsky, P.; Jacot, W. Phase III study of taselisib (GDC-0032) + fulvestrant (FULV) v FULV in patients (pts) with estrogen receptor (ER)-positive, PIK3CA -mutant (MUT), locally advanced or metastatic breast cancer (MBC): Primary analysis from SANDPIPER. J. Clin. Oncol., 2018, 36(18), LBA1006.
[http://dx.doi.org/10.1200/JCO.2018.36.18_suppl.LBA1006]
[11]
André, F.; Ciruelos, E.; Rubovszky, G.; Campone, M.; Loibl, S.; Rugo, H.S.; Iwata, H.; Conte, P.; Mayer, I.A.; Kaufman, B.; Yamashita, T.; Lu, Y.S.; Inoue, K.; Takahashi, M.; Pápai, Z.; Longin, A.S.; Mills, D.; Wilke, C.; Hirawat, S.; Juric, D. Alpelisib for PIK3CA-mutated, hormone receptor-positive advanced breast cancer. N. Engl. J. Med., 2019, 380(20), 1929-1940.
[http://dx.doi.org/10.1056/NEJMoa1813904] [PMID: 31091374]
[12]
Belachew, E.B.; Sewasew, D.T. Corrigendum: Molecular mechanisms of endocrine resistance in estrogen-receptor-positive breast cancer. Front. Endocrinol. (Lausanne), 2021, 12, 689705.
[http://dx.doi.org/10.3389/fendo.2021.689705] [PMID: 34046016]
[13]
García-Becerra, R.; Santos, N.; Díaz, L.; Camacho, J. Mechanisms of resistance to endocrine therapy in breast cancer: Focus on signaling pathways, miRNAs and genetically based resistance. Int. J. Mol. Sci., 2012, 14(1), 108-145.
[http://dx.doi.org/10.3390/ijms14010108] [PMID: 23344024]
[14]
Fribbens, C.; O’Leary, B.; Kilburn, L.; Hrebien, S.; Garcia-Murillas, I.; Beaney, M.; Cristofanilli, M.; Andre, F.; Loi, S.; Loibl, S.; Jiang, J.; Bartlett, C.H.; Koehler, M.; Dowsett, M.; Bliss, J.M.; Johnston, S.R.; Turner, N.C. Plasma ESR1 mutations and the treatment of estrogen receptor-positive advanced breast cancer. J. Clin. Oncol., 2016, 34(25), 2961-2968.
[http://dx.doi.org/10.1200/JCO.2016.67.3061] [PMID: 27269946]
[15]
Nik-Zainal, S.; Davies, H.; Staaf, J.; Ramakrishna, M.; Glodzik, D.; Zou, X.; Martincorena, I.; Alexandrov, L.B.; Martin, S.; Wedge, D.C.; Van Loo, P.; Ju, Y.S.; Smid, M.; Brinkman, A.B.; Morganella, S.; Aure, M.R.; Lingjærde, O.C.; Langerød, A.; Ringnér, M.; Ahn, S.M.; Boyault, S.; Brock, J.E.; Broeks, A.; Butler, A.; Desmedt, C.; Dirix, L.; Dronov, S.; Fatima, A.; Foekens, J.A.; Gerstung, M.; Hooijer, G.K.; Jang, S.J.; Jones, D.R.; Kim, H.Y.; King, T.A.; Krishnamurthy, S.; Lee, H.J.; Lee, J.Y.; Li, Y.; McLaren, S.; Menzies, A.; Mustonen, V.; O’Meara, S.; Pauporté, I.; Pivot, X.; Purdie, C.A.; Raine, K.; Ramakrishnan, K.; Rodríguez-González, F.G.; Romieu, G.; Sieuwerts, A.M.; Simpson, P.T.; Shepherd, R.; Stebbings, L.; Stefansson, O.A.; Teague, J.; Tommasi, S.; Treilleux, I.; Van den Eynden, G.G.; Vermeulen, P.; Vincent-Salomon, A.; Yates, L.; Caldas, C.; van’t Veer, L.; Tutt, A.; Knappskog, S.; Tan, B.K.; Jonkers, J.; Borg, Å.; Ueno, N.T.; Sotiriou, C.; Viari, A.; Futreal, P.A.; Campbell, P.J.; Span, P.N.; Van Laere, S.; Lakhani, S.R.; Eyfjord, J.E.; Thompson, A.M.; Birney, E.; Stunnenberg, H.G.; van de Vijver, M.J.; Martens, J.W.; Børresen-Dale, A.L.; Richardson, A.L.; Kong, G.; Thomas, G.; Stratton, M.R. Landscape of somatic mutations in 560 breast cancer whole-genome sequences. Nature, 2016, 534(7605), 47-54.
[http://dx.doi.org/10.1038/nature17676] [PMID: 27135926]
[16]
Turke, A.B.; Song, Y.; Costa, C.; Cook, R.; Arteaga, C.L.; Asara, J.M.; Engelman, J.A. MEK inhibition leads to PI3K/AKT activation by relieving a negative feedback on ERBB receptors. Cancer Res., 2012, 72(13), 3228-3237.
[http://dx.doi.org/10.1158/0008-5472.CAN-11-3747] [PMID: 22552284]
[17]
Ahmed, S.; Sami, A.; Xiang, J. HER2-directed therapy: Current treatment options for HER2-positive breast cancer. Breast Cancer, 2015, 22(2), 101-116.
[http://dx.doi.org/10.1007/s12282-015-0587-x] [PMID: 25634227]
[18]
Genuino, A.J.; Chaikledkaew, U.; The, D.O.; Reungwetwattana, T.; Thakkinstian, A. Adjuvant trastuzumab regimen for HER2-positive early-stage breast cancer: A systematic review and meta-analysis. Expert Rev. Clin. Pharmacol., 2019, 12(8), 815-824.
[http://dx.doi.org/10.1080/17512433.2019.1637252] [PMID: 31287333]
[19]
Gajria, D.; Chandarlapaty, S. HER2-amplified breast cancer: Mechanisms of trastuzumab resistance and novel targeted therapies. Expert Rev. Anticancer Ther., 2011, 11(2), 263-275.
[http://dx.doi.org/10.1586/era.10.226] [PMID: 21342044]
[20]
Jeibouei, S.; Akbari, M.E.; Kalbasi, A.; Aref, A.R.; Ajoudanian, M.; Rezvani, A.; Zali, H. Personalized medicine in breast cancer: Pharmacogenomics approaches. Pharm. Genomics Pers. Med., 2019, 12, 59-73.
[http://dx.doi.org/10.2147/PGPM.S167886] [PMID: 31213877]
[21]
Iqbal, N.; Iqbal, N. Human epidermal growth factor receptor 2 (HER2) in cancers: Overexpression and therapeutic implications. Mol. Biol. Int., 2014, 2014, 852748.
[http://dx.doi.org/10.1155/2014/852748] [PMID: 25276427]
[22]
Mehraj, U.; Mushtaq, U.; Mir, M.A.; Saleem, A.; Macha, M.A.; Lone, M.N.; Hamid, A.; Zargar, M.A.; Ahmad, S.M.; Wani, N.A. Chemokines in triple-negative breast cancer heterogeneity: New challenges for clinical implications. Semin. Cancer Biol., 2022, S1044-579X(22), 00064-5.
[http://dx.doi.org/10.1016/j.semcancer.2022.03.008] [PMID: 35278636]
[23]
Yin, L.; Duan, J.J.; Bian, X.W.; Yu, S.C. Triple-negative breast cancer molecular subtyping and treatment progress. Breast Cancer Res., 2020, 22(1), 61.
[http://dx.doi.org/10.1186/s13058-020-01296-5] [PMID: 32517735]
[24]
van der Groep, P.; van der Wall, E.; van Diest, P.J. Pathology of hereditary breast cancer. Cell Oncol. (Dordr.), 2011, 34(2), 71-88.
[http://dx.doi.org/10.1007/s13402-011-0010-3] [PMID: 21336636]
[25]
Nedeljković, M.; Damjanović, A. Mechanisms of chemotherapy resistance in triple-negative breast cancer-how we can rise to the challenge. Cells, 2019, 8(9), 957.
[http://dx.doi.org/10.3390/cells8090957] [PMID: 31443516]
[26]
Wu, Q.; Siddharth, S.; Sharma, D. Triple negative breast cancer: A mountain yet to be scaled despite the triumphs. Cancers (Basel), 2021, 13(15), 3697.
[http://dx.doi.org/10.3390/cancers13153697] [PMID: 34359598]
[27]
Bianchini, G.; De Angelis, C.; Licata, L.; Gianni, L. Treatment landscape of triple-negative breast cancer - expanded options, evolving needs. Nat. Rev. Clin. Oncol., 2022, 19(2), 91-113.
[http://dx.doi.org/10.1038/s41571-021-00565-2] [PMID: 34754128]
[28]
Hahnen, E.; Lederer, B.; Hauke, J.; Loibl, S.; Kröber, S.; Schneeweiss, A.; Denkert, C.; Fasching, P.A.; Blohmer, J.U.; Jackisch, C.; Paepke, S.; Gerber, B.; Kümmel, S.; Schem, C.; Neidhardt, G.; Huober, J.; Rhiem, K.; Costa, S.; Altmüller, J.; Hanusch, C.; Thiele, H.; Müller, V.; Nürnberg, P.; Karn, T.; Nekljudova, V.; Untch, M.; von Minckwitz, G.; Schmutzler, R.K. Germline mutation status, pathological complete response, and disease-free survival in triple-negative breast cancer: Secondary analysis of the geparsixto randomized clinical trial. JAMA Oncol., 2017, 3(10), 1378-1385.
[http://dx.doi.org/10.1001/jamaoncol.2017.1007] [PMID: 28715532]
[29]
Audeh, M.W. Novel treatment strategies in triple-negative breast cancer: Specific role of poly(adenosine diphosphate-ribose) polymerase inhibition. Pharm. Genomics Pers. Med., 2014, 7(Oct), 307-316.
[http://dx.doi.org/10.2147/PGPM.S39765] [PMID: 25342917]
[30]
Roden, D.M.; McLeod, H.L.; Relling, M.V.; Williams, M.S.; Mensah, G.A.; Peterson, J.F. Pharmacogenomics. Lancet, 2019, 394(10197), 521-532.
[31]
Relling, M.V.; Evans, W.E. Pharmacogenomics in the clinic. Nature, 2015, 526(7573), 343-350.
[http://dx.doi.org/10.1038/nature15817] [PMID: 26469045]
[32]
Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature, 2012, 490(7418), 61-70.
[http://dx.doi.org/10.1038/nature11412] [PMID: 23000897]
[33]
Evans, W.E.; Relling, M.V. Moving towards individualized medicine with pharmacogenomics. Nature, 2004, 429(6990), 464-468.
[http://dx.doi.org/10.1038/nature02626] [PMID: 15164072]
[34]
Syvänen, A.C. Accessing genetic variation: Genotyping single nucleotide polymorphisms. Nat. Rev. Genet., 2001, 2(12), 930-942.
[http://dx.doi.org/10.1038/35103535] [PMID: 11733746]
[35]
Ciccolini, J.; Fanciullino, R.; Serdjebi, C.; Milano, G. Pharmacogenetics and breast cancer management: Current status and perspectives. Expert Opin. Drug Metab. Toxicol., 2015, 11(5), 719-729.
[http://dx.doi.org/10.1517/17425255.2015.1008447] [PMID: 25690018]
[36]
Weinshilboum, R.; Wang, L. Pharmacogenomics: Bench to bedside. Nat. Rev. Drug Discov., 2004, 3(9), 739-748.
[http://dx.doi.org/10.1038/nrd1497] [PMID: 15340384]
[37]
Hasin, Y.; Seldin, M.; Lusis, A. Multi-omics approaches to disease. Genome Biol., 2017, 18(1), 83.
[http://dx.doi.org/10.1186/s13059-017-1215-1] [PMID: 28476144]
[38]
Schaid, D.J.; Chen, W.; Larson, N.B. From genome-wide associations to candidate causal variants by statistical fine-mapping. Nat. Rev. Genet., 2018, 19(8), 491-504.
[http://dx.doi.org/10.1038/s41576-018-0016-z] [PMID: 29844615]
[39]
Xu, C.F.; Lewis, K.F.; Yeo, A.J.; McCarthy, L.C.; Maguire, M.F.; Anwar, Z.; Danoff, T.M.; Roses, A.D.; Purvis, I.J. Identification of a pharmacogenetic effect by linkage disequilibrium mapping. Pharmacogenomics J., 2004, 4(6), 374-378.
[http://dx.doi.org/10.1038/sj.tpj.6500268] [PMID: 15303110]
[40]
Grady, B.J.; Ritchie, M.D. Statistical optimization of pharmacogenomics association studies: Key considerations from study design to analysis. Curr. Pharmacogenomics Person. Med., 2011, 9(1), 41-66.
[http://dx.doi.org/10.2174/187569211794728805] [PMID: 21887206]
[41]
Limdi, N.A.; Veenstra, D.L. Expectations, validity, and reality in pharmacogenetics. J. Clin. Epidemiol., 2010, 63(9), 960-969.
[http://dx.doi.org/10.1016/j.jclinepi.2009.09.006] [PMID: 19995676]
[42]
Takeuchi, F.; McGinnis, R.; Bourgeois, S.; Barnes, C.; Eriksson, N.; Soranzo, N.; Whittaker, P.; Ranganath, V.; Kumanduri, V.; McLaren, W.; Holm, L.; Lindh, J.; Rane, A.; Wadelius, M.; Deloukas, P. A genome-wide association study confirms VKORC1, CYP2C9, and CYP4F2 as principal genetic determinants of warfarin dose. PLoS Genet., 2009, 5(3), e1000433.
[http://dx.doi.org/10.1371/journal.pgen.1000433] [PMID: 19300499]
[43]
Buniello, A.; MacArthur, J.A.L.; Cerezo, M.; Harris, L.W.; Hayhurst, J.; Malangone, C.; McMahon, A.; Morales, J.; Mountjoy, E.; Sollis, E.; Suveges, D.; Vrousgou, O.; Whetzel, P.L.; Amode, R.; Guillen, J.A.; Riat, H.S.; Trevanion, S.J.; Hall, P.; Junkins, H.; Flicek, P.; Burdett, T.; Hindorff, L.A.; Cunningham, F.; Parkinson, H. The NHGRI-EBI GWAS catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Res., 2019, 47(D1), D1005-D1012.
[http://dx.doi.org/10.1093/nar/gky1120] [PMID: 30445434]
[44]
Choi, J.; Tantisira, K.G.; Duan, Q.L. Whole genome sequencing identifies high-impact variants in well-known pharmacogenomic genes. Pharmacogenomics J., 2019, 19(2), 127-135.
[http://dx.doi.org/10.1038/s41397-018-0048-y] [PMID: 30214008]
[45]
Reisberg, S.; Krebs, K.; Lepamets, M.; Kals, M.; Mägi, R.; Metsalu, K.; Lauschke, V.M.; Vilo, J.; Milani, L. Translating genotype data of 44,000 biobank participants into clinical pharmacogenetic recommendations: Challenges and solutions. Genet. Med., 2019, 21(6), 1345-1354.
[http://dx.doi.org/10.1038/s41436-018-0337-5] [PMID: 30327539]
[46]
Tafazoli, A.; Guchelaar, H.J.; Miltyk, W.; Kretowski, A.J.; Swen, J.J. Applying next-generation sequencing platforms for pharmacogenomic testing in clinical practice. Front. Pharmacol., 2021, 12(Aug), 693453.
[http://dx.doi.org/10.3389/fphar.2021.693453] [PMID: 34512329]
[47]
Chen, Y.X.; Rong, Y.; Jiang, F.; Chen, J.B.; Duan, Y.Y.; Dong, S.S.; Zhu, D.L.; Chen, H.; Yang, T.L.; Dai, Z.; Guo, Y. An integrative multi-omics network-based approach identifies key regulators for breast cancer. Comput. Struct. Biotechnol. J., 2020, 18, 2826-2835.
[http://dx.doi.org/10.1016/j.csbj.2020.10.001] [PMID: 33133424]
[48]
Barrett, J.H. Genome-wide association studies of therapeutic response: Addressing the complexities. Pharmacogenomics, 2019, 20(4), 213-216.
[http://dx.doi.org/10.2217/pgs-2018-0204] [PMID: 30767725]
[49]
McInnes, G.; Yee, S.W.; Pershad, Y.; Altman, R.B. Genomewide association studies in pharmacogenomics. Clin. Pharmacol. Ther., 2021, 110(3), 637-648.
[http://dx.doi.org/10.1002/cpt.2349] [PMID: 34185318]
[50]
Arbitrio, M.; Di Martino, M.T.; Scionti, F.; Barbieri, V.; Pensabene, L.; Tagliaferri, P. Pharmacogenomic profiling of ADME gene variants: Current challenges and validation perspectives. High Throughput, 2018, 7(4), 40.
[http://dx.doi.org/10.3390/ht7040040] [PMID: 30567415]
[51]
Norppa, H. Genetic susceptibility, biomarker respones, and cancer. Mutat. Res., 2003, 544(2-3), 339-348.
[http://dx.doi.org/10.1016/j.mrrev.2003.09.006] [PMID: 14644336]
[52]
Al-Mahayri, Z.N.; Patrinos, G.P.; Ali, B.R. Toxicity and pharmacogenomic biomarkers in breast cancer chemotherapy. Front. Pharmacol., 2020, 11, 445.
[http://dx.doi.org/10.3389/fphar.2020.00445] [PMID: 32351390]
[53]
Sacco, K.; Grech, G. Actionable pharmacogenetic markers for prediction and prognosis in breast cancer. EPMA J., 2015, 6(1), 15.
[http://dx.doi.org/10.1186/s13167-015-0037-z] [PMID: 26203310]
[54]
Westbrook, K.; Stearns, V. Pharmacogenomics of breast cancer therapy: An update. Pharmacol. Ther., 2013, 139(1), 1-11.
[http://dx.doi.org/10.1016/j.pharmthera.2013.03.001] [PMID: 23500718]
[55]
Lauschke, V.M.; Zhou, Y.; Ingelman-Sundberg, M. Novel genetic and epigenetic factors of importance for inter-individual differences in drug disposition, response and toxicity. Pharmacol. Ther., 2019, 197, 122-152.
[http://dx.doi.org/10.1016/j.pharmthera.2019.01.002] [PMID: 30677473]
[56]
Wakil, S.M.; Nguyen, C.; Muiya, N.P.; Andres, E.; Lykowska-Tarnowska, A.; Baz, B.; Tahir, A.I.; Meyer, B.F.; Morahan, G.; Dzimiri, N. The affymetrix DMET plus platform reveals unique distribution of ADME-related variants in ethnic Arabs. Dis. Markers, 2015, 2015, 542543.
[http://dx.doi.org/10.1155/2015/542543] [PMID: 25802476]
[57]
Peeters, R.P.; van Toor, H.; Klootwijk, W.; de Rijke, Y.B.; Kuiper, G.G.J.M.; Uitterlinden, A.G.; Visser, T.J. Polymorphisms in thyroid hormone pathway genes are associated with plasma TSH and iodothyronine levels in healthy subjects. J. Clin. Endocrinol. Metab., 2003, 88(6), 2880-2888.
[http://dx.doi.org/10.1210/jc.2002-021592] [PMID: 12788902]
[58]
Roden, D.M.; Wilke, R.A.; Kroemer, H.K.; Stein, C.M. Pharmacogenomics: The genetics of variable drug responses. Circulation, 2011, 123(15), 1661-1670.
[http://dx.doi.org/10.1161/CIRCULATIONAHA.109.914820] [PMID: 21502584]
[59]
Mroz, P.; Michel, S.; Allen, J.D.; Meyer, T.; McGonagle, E.J.; Carpentier, R.; Vecchia, A.; Schlichte, A.; Bishop, J.R.; Dunnenberger, H.M.; Yohe, S.; Thyagarajan, B.; Jacobson, P.A.; Johnson, S.G. Development and implementation of in-house pharmacogenomic testing program at a major academic health system. Front. Genet., 2021, 12(Oct), 712602.
[http://dx.doi.org/10.3389/fgene.2021.712602] [PMID: 34745204]
[60]
FDA. Table of pharmacogenomic biomarkers in drug labeling., Available from: https://www.fda.gov/drugs/science-and-research-drugs/table-pharmacogenomic-biomarkers-drug-labeling
[61]
Forbes, S.A.; Beare, D.; Boutselakis, H.; Bamford, S.; Bindal, N.; Tate, J.; Cole, C.G.; Ward, S.; Dawson, E.; Ponting, L.; Stefancsik, R.; Harsha, B.; Kok, C.Y.; Jia, M.; Jubb, H.; Sondka, Z.; Thompson, S.; De, T.; Campbell, P.J. COSMIC: Somatic cancer genetics at high-resolution. Nucleic Acids Res., 2017, 45(D1), D777-D783.
[http://dx.doi.org/10.1093/nar/gkw1121] [PMID: 27899578]
[62]
Pasternak, A.L.; Ward, K.M.; Luzum, J.A.; Ellingrod, V.L.; Hertz, D.L. Germline genetic variants with implications for disease risk and therapeutic outcomes. Physiol. Genomics, 2017, 49(10), 567-581.
[http://dx.doi.org/10.1152/physiolgenomics.00035.2017] [PMID: 28887371]
[63]
Yang, Y.; Botton, M.R.; Scott, E.R.; Scott, S.A. Sequencing the CYP2D6 gene: From variant allele discovery to clinical pharmacogenetic testing. Pharmacogenomics, 2017, 18(7), 673-685.
[http://dx.doi.org/10.2217/pgs-2017-0033] [PMID: 28470112]
[64]
Chan, C.W.H.; Li, C.; Xiao, E.J.; Li, M.; Phiri, P.G.M.; Yan, T.; Chan, J.Y.W. Association between genetic polymorphisms in cytochrome P450 enzymes and survivals in women with breast cancer receiving adjuvant endocrine therapy: A systematic review and meta-analysis. Expert Rev. Mol. Med., 2022, 24, e1.
[http://dx.doi.org/10.1017/erm.2021.28] [PMID: 34991754]
[65]
Jayaraman, S.; Reid, J.M.; Hawse, J.R.; Goetz, M.P. Endoxifen, an estrogen receptor targeted therapy: From bench to bedside. Endocrinology, 2021, 162(12), bqab191.
[http://dx.doi.org/10.1210/endocr/bqab191] [PMID: 34480554]
[66]
Cronin-Fenton, D.P.; Damkier, P.; Lash, T.L. Metabolism and transport of tamoxifen in relation to its effectiveness: New perspectives on an ongoing controversy. Future Oncol., 2014, 10(1), 107-122.
[http://dx.doi.org/10.2217/fon.13.168] [PMID: 24328412]
[67]
Gaedigk, A.; Ingelman-Sundberg, M.; Miller, N.A.; Leeder, J.S.; Whirl-Carrillo, M.; Klein, T.E. The Pharmacogene Variation (PharmVar) consortium: Incorporation of the human cytochrome P450 (CYP) allele nomenclature database. Clin. Pharmacol. Ther., 2018, 103(3), 399-401.
[http://dx.doi.org/10.1002/cpt.910] [PMID: 29134625]
[68]
Mulder, T.A.M.; de With, M.; Del Re, M.; Danesi, R.; Mathijssen, R.H.J.; van Schaik, R.H.N. Clinical CYP2D6 genotyping to personalize adjuvant tamoxifen treatment in ER-positive breast cancer patients: Current status of a controversy. Cancers (Basel), 2021, 13(4), 771.
[http://dx.doi.org/10.3390/cancers13040771] [PMID: 33673305]
[69]
Relling, M.V.; Klein, T.E. CPIC: Clinical pharmacogenetics implementation consortium of the pharmacogenomics research network. Clin. Pharmacol. Ther., 2011, 89(3), 464-467.
[http://dx.doi.org/10.1038/clpt.2010.279] [PMID: 21270786]
[70]
Caudle, K.E.; Klein, T.E.; Hoffman, J.M.; Muller, D.J.; Whirl-Carrillo, M.; Gong, L.; McDonagh, E.M.; Sangkuhl, K.; Thorn, C.F.; Schwab, M.; Agundez, J.A.; Freimuth, R.R.; Huser, V.; Lee, M.T.; Iwuchukwu, O.F.; Crews, K.R.; Scott, S.A.; Wadelius, M.; Swen, J.J.; Tyndale, R.F.; Stein, C.M.; Roden, D.; Relling, M.V.; Williams, M.S.; Johnson, S.G. Incorporation of pharmacogenomics into routine clinical practice: The Clinical Pharmacogenetics Implementation Consortium (CPIC) guideline development process. Curr. Drug Metab., 2014, 15(2), 209-217.
[http://dx.doi.org/10.2174/1389200215666140130124910] [PMID: 24479687]
[71]
Sperber, N.R.; Dong, O.M.; Roberts, M.C.; Dexter, P.; Elsey, A.R.; Ginsburg, G.S.; Horowitz, C.R.; Johnson, J.A.; Levy, K.D.; Ong, H.; Peterson, J.F.; Pollin, T.I.; Rakhra-Burris, T.; Ramos, M.A.; Skaar, T.; Orlando, L.A. Strategies to integrate genomic medicine into clinical care: Evidence from the IGNITE network. J. Pers. Med., 2021, 11(7), 647.
[http://dx.doi.org/10.3390/jpm11070647] [PMID: 34357114]
[72]
Whirl-Carrillo, M.; McDonagh, E.M.; Hebert, J.M.; Gong, L.; Sangkuhl, K.; Thorn, C.F.; Altman, R.B.; Klein, T.E. Pharmacogenomics knowledge for personalized medicine. Clin. Pharmacol. Ther., 2012, 92(4), 414-417.
[http://dx.doi.org/10.1038/clpt.2012.96] [PMID: 22992668]
[73]
Weitzel, K.W.; Alexander, M.; Bernhardt, B.A.; Calman, N.; Carey, D.J.; Cavallari, L.H.; Field, J.R.; Hauser, D.; Junkins, H.A.; Levin, P.A.; Levy, K.; Madden, E.B.; Manolio, T.A.; Odgis, J.; Orlando, L.A.; Pyeritz, R.; Wu, R.R.; Shuldiner, A.R.; Bottinger, E.P.; Denny, J.C.; Dexter, P.R.; Flockhart, D.A.; Horowitz, C.R.; Johnson, J.A.; Kimmel, S.E.; Levy, M.A.; Pollin, T.I.; Ginsburg, G.S. The IGNITE network: A model for genomic medicine implementation and research. BMC Med. Genomics, 2016, 9(1), 1.
[http://dx.doi.org/10.1186/s12920-015-0162-5] [PMID: 26729011]
[74]
Zamami, Y.; Hamano, H.; Niimura, T.; Aizawa, F.; Yagi, K.; Goda, M.; Izawa-Ishizawa, Y.; Ishizawa, K. Drug-repositioning approaches based on medical and life science databases. Front. Pharmacol., 2021, 12, 752174.
[http://dx.doi.org/10.3389/fphar.2021.752174] [PMID: 34790124]
[75]
Kouzarides, T. Chromatin modifications and their function. Cell, 2007, 128(4), 693-705.
[http://dx.doi.org/10.1016/j.cell.2007.02.005] [PMID: 17320507]
[76]
Bernstein, B.E.; Meissner, A.; Lander, E.S. The mammalian epigenome. Cell, 2007, 128(4), 669-681.
[http://dx.doi.org/10.1016/j.cell.2007.01.033] [PMID: 17320505]
[77]
Jiang, C.; Pugh, B.F. Nucleosome positioning and gene regulation: Advances through genomics. Nat. Rev. Genet., 2009, 10(3), 161-172.
[http://dx.doi.org/10.1038/nrg2522] [PMID: 19204718]
[78]
Robertson, K.D. DNA methylation and chromatin - unraveling the tangled web. Oncogene, 2002, 21(35), 5361-5379.
[http://dx.doi.org/10.1038/sj.onc.1205609] [PMID: 12154399]
[79]
Ehrlich, M. DNA methylation in cancer: Too much, but also too little. Oncogene, 2002, 21(35), 5400-5413.
[http://dx.doi.org/10.1038/sj.onc.1205651] [PMID: 12154403]
[80]
Lim, W.J.; Kim, K.H.; Kim, J.Y.; Jeong, S.; Kim, N. Identification of DNA-Methylated CpG islands associated with gene silencing in the adult body tissues of the ogye chicken using RNA-seq and reduced representation bisulfite sequencing. Front. Genet., 2019, 10, 346.
[http://dx.doi.org/10.3389/fgene.2019.00346] [PMID: 31040866]
[81]
Saghafinia, S.; Mina, M.; Riggi, N.; Hanahan, D.; Ciriello, G. Pan-cancer landscape of aberrant DNA methylation across human tumors. Cell Rep., 2018, 25(4), 1066-1080.e8.
[http://dx.doi.org/10.1016/j.celrep.2018.09.082] [PMID: 30355485]
[82]
Wang, Y.; Leung, F.C.C. An evaluation of new criteria for CpG islands in the human genome as gene markers. Bioinformatics, 2004, 20(7), 1170-1177.
[http://dx.doi.org/10.1093/bioinformatics/bth059] [PMID: 14764558]
[83]
Takai, D.; Jones, P.A. Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc. Natl. Acad. Sci. USA, 2002, 99(6), 3740-3745.
[http://dx.doi.org/10.1073/pnas.052410099] [PMID: 11891299]
[84]
Santini, V.; Kantarjian, H.M.; Issa, J.P. Changes in DNA methylation in neoplasia: Pathophysiology and therapeutic implications. Ann. Intern. Med., 2001, 134(7), 573-586.
[http://dx.doi.org/10.7326/0003-4819-134-7-200104030-00011] [PMID: 11281740]
[85]
Zhang, S.; Wang, Y.; Gu, Y.; Zhu, J.; Ci, C.; Guo, Z.; Chen, C.; Wei, Y.; Lv, W.; Liu, H.; Zhang, D.; Zhang, Y. Specific breast cancer prognosis-subtype distinctions based on DNA methylation patterns. Mol. Oncol., 2018, 12(7), 1047-1060.
[http://dx.doi.org/10.1002/1878-0261.12309] [PMID: 29675884]
[86]
Li, S.; Tollefsbol, T.O. DNA methylation methods: Global DNA methylation and methylomic analyses. Methods, 2021, 187, 28-43.
[http://dx.doi.org/10.1016/j.ymeth.2020.10.002] [PMID: 33039572]
[87]
Frommer, M.; McDonald, L.E.; Millar, D.S.; Collis, C.M.; Watt, F.; Grigg, G.W.; Molloy, P.L.; Paul, C.L. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc. Natl. Acad. Sci. USA, 1992, 89(5), 1827-1831.
[http://dx.doi.org/10.1073/pnas.89.5.1827] [PMID: 1542678]
[88]
Li, Q.; Hermanson, P.J.; Springer, N.M. Detection of DNA methylation by whole-genome bisulfite sequencing. In: Methods in Molecular Biology. Maize; Lagrimini, L., Ed.; Humana Press: New York, 2018; pp. 185-196.
[http://dx.doi.org/10.1007/978-1-4939-7315-6_11]
[89]
Bassil, C.F.; Huang, Z.; Murphy, S.K. Bisulfite pyrosequencing. Methods Mol. Biol., 2013, 1049, 95-107.
[http://dx.doi.org/10.1007/978-1-62703-547-7_9]
[90]
Bradbury, J. Human epigenome project--up and running. PLoS Biol., 2003, 1(3), E82.
[http://dx.doi.org/10.1371/journal.pbio.0000082] [PMID: 14691553]
[91]
Meissner, A.; Gnirke, A.; Bell, G.W.; Ramsahoye, B.; Lander, E.S.; Jaenisch, R. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res., 2005, 33(18), 5868-5877.
[http://dx.doi.org/10.1093/nar/gki901] [PMID: 16224102]
[92]
Lister, R.; Pelizzola, M.; Dowen, R.H.; Hawkins, R.D.; Hon, G.; Tonti-Filippini, J.; Nery, J.R.; Lee, L.; Ye, Z.; Ngo, Q.M.; Edsall, L.; Antosiewicz-Bourget, J.; Stewart, R.; Ruotti, V.; Millar, A.H.; Thomson, J.A.; Ren, B.; Ecker, J.R. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature, 2009, 462(7271), 315-322.
[http://dx.doi.org/10.1038/nature08514] [PMID: 19829295]
[93]
Chen, Z.; He, X. Application of third-generation sequencing in cancer research. Med. Rev., 2021, 1(2), 150-171.
[http://dx.doi.org/10.1515/mr-2021-0013]
[94]
Stirzaker, C.; Zotenko, E.; Song, J.Z.; Qu, W.; Nair, S.S.; Locke, W.J.; Stone, A.; Armstong, N.J.; Robinson, M.D.; Dobrovic, A.; Avery-Kiejda, K.A.; Peters, K.M.; French, J.D.; Stein, S.; Korbie, D.J.; Trau, M.; Forbes, J.F.; Scott, R.J.; Brown, M.A.; Francis, G.D.; Clark, S.J. Methylome sequencing in triple-negative breast cancer reveals distinct methylation clusters with prognostic value. Nat. Commun., 2015, 6(1), 5899.
[http://dx.doi.org/10.1038/ncomms6899] [PMID: 25641231]
[95]
Subramaniam, M.M.; Chan, J.Y.; Soong, R.; Ito, K.; Ito, Y.; Yeoh, K.G.; Salto-Tellez, M.; Putti, T.C. RUNX3 inactivation by frequent promoter hypermethylation and protein mislocalization constitute an early event in breast cancer progression. Breast Cancer Res. Treat., 2009, 113(1), 113-121.
[http://dx.doi.org/10.1007/s10549-008-9917-4] [PMID: 18256927]
[96]
Qian, X.; Ruan, L. APC gene promoter aberrant methylation in serum as a biomarker for breast cancer diagnosis: A meta-analysis. Thorac. Cancer, 2018, 9(2), 284-290.
[http://dx.doi.org/10.1111/1759-7714.12580] [PMID: 29297603]
[97]
Martínez-Galán, J.; Torres-Torres, B.; Núñez, M.I.; López-Peñalver, J.; Del Moral, R.; Ruiz De Almodóvar, J.M.; Menjón, S.; Concha, A.; Chamorro, C.; Ríos, S.; Delgado, J.R. ESR1 gene promoter region methylation in free circulating DNA and its correlation with estrogen receptor protein expression in tumor tissue in breast cancer patients. BMC Cancer, 2014, 14(1), 59.
[http://dx.doi.org/10.1186/1471-2407-14-59] [PMID: 24495356]
[98]
Martínez-Galán, J.; Torres, B.; Del Moral, R.; Muñoz-Gámez, J.A.; Martín-Oliva, D.; Villalobos, M.; Núñez, M.I.; Luna, J.D.; Oliver, F.J.; Ruiz de Almodóvar, J.M. Quantitative detection of methylated ESR1 and 14-3-3-σ gene promoters in serum as candidate biomarkers for diagnosis of breast cancer and evaluation of treatment efficacy. Cancer Biol. Ther., 2008, 7(6), 958-965.
[http://dx.doi.org/10.4161/cbt.7.6.5966] [PMID: 18379196]
[99]
Wang, X.; Jia, J.; Gu, X.; Zhao, W.W.; Chen, C.; Wu, W.; Wang, J.; Xu, M. Screening of breast cancer methylation biomarkers based on the TCGA database. Int. J. Gen. Med., 2021, 14, 9833-9839.
[http://dx.doi.org/10.2147/IJGM.S322857] [PMID: 34938104]
[100]
Chen, T.; Dent, S.Y.R. Chromatin modifiers and remodellers: Regulators of cellular differentiation. Nat. Rev. Genet., 2014, 15(2), 93-106.
[http://dx.doi.org/10.1038/nrg3607] [PMID: 24366184]
[101]
Berger, S.L. The complex language of chromatin regulation during transcription. Nature, 2007, 447(7143), 407-412.
[http://dx.doi.org/10.1038/nature05915] [PMID: 17522673]
[102]
Bannister, A.J.; Kouzarides, T. Regulation of chromatin by histone modifications. Cell Res., 2011, 21(3), 381-395.
[http://dx.doi.org/10.1038/cr.2011.22] [PMID: 21321607]
[103]
Audia, J.E.; Campbell, R.M. Histone modifications and cancer. Cold Spring Harb. Perspect. Biol., 2016, 8(4), a019521.
[http://dx.doi.org/10.1101/cshperspect.a019521] [PMID: 27037415]
[104]
Grosselin, K.; Durand, A.; Marsolier, J.; Poitou, A.; Marangoni, E.; Nemati, F.; Dahmani, A.; Lameiras, S.; Reyal, F.; Frenoy, O.; Pousse, Y.; Reichen, M.; Woolfe, A.; Brenan, C.; Griffiths, A.D.; Vallot, C.; Gérard, A. High-throughput single-cell ChIP-seq identifies heterogeneity of chromatin states in breast cancer. Nat. Genet., 2019, 51(6), 1060-1066.
[http://dx.doi.org/10.1038/s41588-019-0424-9] [PMID: 31152164]
[105]
Di Cerbo, V.; Schneider, R. Cancers with wrong HATs: The impact of acetylation. Brief. Funct. Genom., 2013, 12(3), 231-243.
[http://dx.doi.org/10.1093/bfgp/els065] [PMID: 23325510]
[106]
Zhao, Z.; Shilatifard, A. Epigenetic modifications of histones in cancer. Genome Biol., 2019, 20(1), 245.
[http://dx.doi.org/10.1186/s13059-019-1870-5] [PMID: 31747960]
[107]
Samec, M.; Liskova, A.; Koklesova, L.; Mestanova, V.; Franekova, M.; Kassayova, M.; Bojkova, B.; Uramova, S.; Zubor, P.; Janikova, K.; Danko, J.; Samuel, S.M.; Büsselberg, D.; Kubatka, P. Fluctuations of histone chemical modifications in breast, prostate, and colorectal cancer: An implication of phytochemicals as defenders of chromatin equilibrium. Biomolecules, 2019, 9(12), 829.
[http://dx.doi.org/10.3390/biom9120829] [PMID: 31817446]
[108]
Tang, Z.; Ding, S.; Huang, H.; Luo, P.; Qing, B.; Zhang, S.; Tang, R. HDAC1 triggers the proliferation and migration of breast cancer cells via upregulation of interleukin-8. Biol. Chem., 2017, 398(12), 1347-1356.
[http://dx.doi.org/10.1515/hsz-2017-0155] [PMID: 28779562]
[109]
Kamarulzaman, N.S.; Dewadas, H.D.; Leow, C.Y.; Yaacob, N.S.; Mokhtar, N.F. The role of REST and HDAC2 in epigenetic dysregulation of Nav1.5 and nNav1.5 expression in breast cancer. Cancer Cell Int., 2017, 17(1), 74.
[http://dx.doi.org/10.1186/s12935-017-0442-6] [PMID: 28785170]
[110]
Zhao, L.; Pang, A.; Li, Y. Function of GCN5 in the TGF-β1-induced epithelial-to-mesenchymal transition in breast cancer. Oncol. Lett., 2018, 16(3), 3955-3963.
[http://dx.doi.org/10.3892/ol.2018.9134] [PMID: 30128014]
[111]
Wang, L.T.; Liu, K.Y.; Jeng, W.Y.; Chiang, C.M.; Chai, C.Y.; Chiou, S.S.; Huang, M.S.; Yokoyama, K.K.; Wang, S.N.; Huang, S.K.; Hsu, S.H. PCAF-mediated acetylation of ISX recruits BRD4 to promote epithelial-mesenchymal transition. EMBO Rep., 2020, 21(2), e48795.
[http://dx.doi.org/10.15252/embr.201948795] [PMID: 31908141]
[112]
Wu, Q.; Odwin-Dacosta, S.; Cao, S.; Yager, J.D.; Tang, W.Y. Estrogen down regulates COMT transcription via promoter DNA methylation in human breast cancer cells. Toxicol. Appl. Pharmacol., 2019, 367, 12-22.
[http://dx.doi.org/10.1016/j.taap.2019.01.016] [PMID: 30684530]
[113]
Huang, H.; Lin, S.; Garcia, B.A.; Zhao, Y. Quantitative proteomic analysis of histone modifications. Chem. Rev., 2015, 115(6), 2376-2418.
[http://dx.doi.org/10.1021/cr500491u] [PMID: 25688442]
[114]
Völker-Albert, M.C.; Schmidt, A.; Forne, I.; Imhof, A. Analysis of histone modifications by mass spectrometry. Curr. Protoc. Protein Sci., 2018, 92(1), e54.
[http://dx.doi.org/10.1002/cpps.54] [PMID: 30040183]
[115]
Lu, C.; Coradin, M.; Porter, E.G.; Garcia, B.A. Accelerating the field of epigenetic histone modification through mass spectrometry-based approaches. Mol. Cell. Proteomics, 2021, 20, 100006.
[http://dx.doi.org/10.1074/mcp.R120.002257] [PMID: 33203747]
[116]
Zhuang, J.; Huo, Q.; Yang, F.; Xie, N. Perspectives on the role of histone modification in breast cancer progression and the advanced technological tools to study epigenetic determinants of metastasis. Front. Genet., 2020, 11, 603552.
[http://dx.doi.org/10.3389/fgene.2020.603552] [PMID: 33193750]
[117]
Faserl, K.; Sarg, B.; Lindner, H.H. Application of CE-MS for the analysis of histones and histone modifications. Methods, 2020, 184, 125-134.
[http://dx.doi.org/10.1016/j.ymeth.2020.01.017] [PMID: 32014606]
[118]
Noberini, R.; Uggetti, A.; Pruneri, G.; Minucci, S.; Bonaldi, T. Pathology tissue-quantitative mass spectrometry analysis to profile histone post-translational modification patterns in patient samples. Mol. Cell. Proteom., 2016, 15(3), 866-877.
[http://dx.doi.org/10.1074/mcp.M115.054510] [PMID: 26463340]
[119]
Nakato, R.; Sakata, T. Methods for ChIP-seq analysis: A practical workflow and advanced applications. Methods, 2021, 187, 44-53.
[http://dx.doi.org/10.1016/j.ymeth.2020.03.005] [PMID: 32240773]
[120]
Lee, B.H.; Rhie, S.K. Molecular and computational approaches to map regulatory elements in 3D chromatin structure. Epigen. Chromatin, 2021, 14(1), 14.
[http://dx.doi.org/10.1186/s13072-021-00390-y] [PMID: 33741028]
[121]
Lo, P.K.; Sukumar, S. Epigenomics and breast cancer. Pharmacogenomics, 2008, 9(12), 1879-1902.
[http://dx.doi.org/10.2217/14622416.9.12.1879] [PMID: 19072646]
[122]
Messier, T.L.; Gordon, J.A.R.; Boyd, J.R.; Tye, C.E.; Browne, G.; Stein, J.L.; Lian, J.B.; Stein, G.S. Histone H3 lysine 4 acetylation and methylation dynamics define breast cancer subtypes. Oncotarget, 2016, 7(5), 5094-5109.
[http://dx.doi.org/10.18632/oncotarget.6922] [PMID: 26783963]
[123]
Xi, Y.; Shi, J.; Li, W.; Tanaka, K.; Allton, K.L.; Richardson, D.; Li, J.; Franco, H.L.; Nagari, A.; Malladi, V.S.; Coletta, L.D.; Simper, M.S.; Keyomarsi, K.; Shen, J.; Bedford, M.T.; Shi, X.; Barton, M.C.; Kraus, W.L.; Li, W.; Dent, S.Y.R. Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes. BMC Genom., 2018, 19(1), 150.
[http://dx.doi.org/10.1186/s12864-018-4533-0] [PMID: 29458327]
[124]
Brind’Amour, J.; Liu, S.; Hudson, M.; Chen, C.; Karimi, M.M.; Lorincz, M.C. An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations. Nat. Commun., 2015, 6(1), 6033.
[http://dx.doi.org/10.1038/ncomms7033] [PMID: 25607992]
[125]
Zhang, B.; Zheng, H.; Huang, B.; Li, W.; Xiang, Y.; Peng, X.; Ming, J.; Wu, X.; Zhang, Y.; Xu, Q.; Liu, W.; Kou, X.; Zhao, Y.; He, W.; Li, C.; Chen, B.; Li, Y.; Wang, Q.; Ma, J.; Yin, Q.; Kee, K.; Meng, A.; Gao, S.; Xu, F.; Na, J.; Xie, W. Allelic reprogramming of the histone modification H3K4me3 in early mammalian development. Nature, 2016, 537(7621), 553-557.
[http://dx.doi.org/10.1038/nature19361] [PMID: 27626382]
[126]
Zhu, B.; Hsieh, Y.P.; Murphy, T.W.; Zhang, Q.; Naler, L.B.; Lu, C. MOWChIP-seq for low-input and multiplexed profiling of genome-wide histone modifications. Nat. Protoc., 2019, 14(12), 3366-3394.
[http://dx.doi.org/10.1038/s41596-019-0223-x] [PMID: 31666743]
[127]
Rotem, A.; Ram, O.; Shoresh, N.; Sperling, R.A.; Goren, A.; Weitz, D.A.; Bernstein, B.E. Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state. Nat. Biotechnol., 2015, 33(11), 1165-1172.
[http://dx.doi.org/10.1038/nbt.3383] [PMID: 26458175]
[128]
Harada, A.; Maehara, K.; Handa, T.; Arimura, Y.; Nogami, J.; Hayashi-Takanaka, Y.; Shirahige, K.; Kurumizaka, H.; Kimura, H.; Ohkawa, Y. A chromatin integration labelling method enables epigenomic profiling with lower input. Nat. Cell Biol., 2019, 21(2), 287-296.
[http://dx.doi.org/10.1038/s41556-018-0248-3] [PMID: 30532068]
[129]
Skene, P.J.; Henikoff, S. An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. eLife, 2017, 6, 6.
[http://dx.doi.org/10.7554/eLife.21856] [PMID: 28079019]
[130]
Ku, W.L.; Nakamura, K.; Gao, W.; Cui, K.; Hu, G.; Tang, Q.; Ni, B.; Zhao, K. Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification. Nat. Methods, 2019, 16(4), 323-325.
[http://dx.doi.org/10.1038/s41592-019-0361-7] [PMID: 30923384]
[131]
Ma, S.; Zhang, Y. Profiling chromatin regulatory landscape: Insights into the development of ChIP-seq and ATAC-seq. Mol. Biomed., 2020, 1(1), 9.
[http://dx.doi.org/10.1186/s43556-020-00009-w]
[132]
Dinger, M.E.; Pang, K.C.; Mercer, T.R.; Mattick, J.S. Differentiating protein-coding and noncoding RNA: Challenges and ambiguities. PLOS Comput. Biol., 2008, 4(11), e1000176.
[http://dx.doi.org/10.1371/journal.pcbi.1000176] [PMID: 19043537]
[133]
Winkle, M.; El-Daly, S.M.; Fabbri, M.; Calin, G.A. Noncoding RNA therapeutics - challenges and potential solutions. Nat. Rev. Drug Discov., 2021, 20(8), 629-651.
[http://dx.doi.org/10.1038/s41573-021-00219-z] [PMID: 34145432]
[134]
Bartel, D.P. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell, 2004, 116(2), 281-297.
[http://dx.doi.org/10.1016/S0092-8674(04)00045-5] [PMID: 14744438]
[135]
Friedman, R.C.; Farh, K.K.H.; Burge, C.B.; Bartel, D.P. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res., 2009, 19(1), 92-105.
[http://dx.doi.org/10.1101/gr.082701.108] [PMID: 18955434]
[136]
Morlando, M.; Fatica, A. Alteration of epigenetic regulation by long noncoding RNAs in cancer. Int. J. Mol. Sci., 2018, 19(2), 570.
[http://dx.doi.org/10.3390/ijms19020570] [PMID: 29443889]
[137]
Abolghasemi, M.; Tehrani, S.S.; Yousefi, T.; Karimian, A.; Mahmoodpoor, A.; Ghamari, A.; Jadidi-Niaragh, F.; Yousefi, M.; Kafil, H.S.; Bastami, M.; Edalati, M.; Eyvazi, S.; Naghizadeh, M.; Targhazeh, N.; Yousefi, B.; Safa, A.; Majidinia, M.; Rameshknia, V. MicroRNAs in breast cancer: Roles, functions, and mechanism of actions. J. Cell. Physiol., 2020, 235(6), 5008-5029.
[http://dx.doi.org/10.1002/jcp.29396] [PMID: 31724738]
[138]
Loh, H.Y.; Norman, B.P.; Lai, K.S.; Rahman, N.M.A.N.A.; Alitheen, N.B.M.; Osman, M.A. The regulatory role of MicroRNAs in breast cancer. Int. J. Mol. Sci., 2019, 20(19), 4940.
[http://dx.doi.org/10.3390/ijms20194940] [PMID: 31590453]
[139]
Amelio, I.; Bernassola, F.; Candi, E. Emerging roles of long non-coding RNAs in breast cancer biology and management. Semin. Cancer Biol., 2021, 72, 36-45.
[http://dx.doi.org/10.1016/j.semcancer.2020.06.019] [PMID: 32619506]
[140]
Gupta, R.A.; Shah, N.; Wang, K.C.; Kim, J.; Horlings, H.M.; Wong, D.J.; Tsai, M.C.; Hung, T.; Argani, P.; Rinn, J.L.; Wang, Y.; Brzoska, P.; Kong, B.; Li, R.; West, R.B.; van de Vijver, M.J.; Sukumar, S.; Chang, H.Y. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature, 2010, 464(7291), 1071-1076.
[http://dx.doi.org/10.1038/nature08975] [PMID: 20393566]
[141]
Sørensen, K.P.; Thomassen, M.; Tan, Q.; Bak, M.; Cold, S.; Burton, M.; Larsen, M.J.; Kruse, T.A. Long non-coding RNA HOTAIR is an independent prognostic marker of metastasis in estrogen receptor-positive primary breast cancer. Breast Cancer Res. Treat., 2013, 142(3), 529-536.
[http://dx.doi.org/10.1007/s10549-013-2776-7] [PMID: 24258260]
[142]
Zhang, S.; Zhang, J.; An, Y.; Zeng, X.; Qin, Z.; Zhao, Y.; Xu, H.; Liu, B. Multi-omics approaches identify SF3B3 and SIRT3 as candidate autophagic regulators and druggable targets in invasive breast carcinoma. Acta Pharm. Sin. B, 2021, 11(5), 1227-1245.
[http://dx.doi.org/10.1016/j.apsb.2020.12.013] [PMID: 34094830]
[143]
Kashi, K.; Henderson, L.; Bonetti, A.; Carninci, P. Discovery and functional analysis of lncRNAs: Methodologies to investigate an uncharacterized transcriptome. Biochim. Biophys. Acta, 2016, 1859(1), 3-15.
[PMID: 27522016]
[144]
Moody, L.; He, H.; Pan, Y.X.; Chen, H. Methods and novel technology for microRNA quantification in colorectal cancer screening. Clin. Epigenetics, 2017, 9(1), 119.
[http://dx.doi.org/10.1186/s13148-017-0420-9] [PMID: 29090038]
[145]
Turner, A.W.; Wong, D.; Khan, M.D.; Dreisbach, C.N.; Palmore, M.; Miller, C.L. Multi-omics approaches to study long non-coding RNA function in atherosclerosis. Front. Cardiovasc. Med., 2019, 6, 9.
[http://dx.doi.org/10.3389/fcvm.2019.00009] [PMID: 30838214]
[146]
Siddika, T.; Heinemann, I.U. Bringing MicroRNAs to light: Methods for MicroRNA quantification and visualization in live cells. Front. Bioeng. Biotechnol., 2021, 8, 619583.
[http://dx.doi.org/10.3389/fbioe.2020.619583] [PMID: 33537295]
[147]
Pantaleão, L.C.; Ozanne, S.E. Small RNA sequencing: A technique for miRNA profiling. In: Investigations of Early Nutrition Effects on Long-Term Health Methods in Molecular Biology; Guest, P.C., Ed.; Humana Press: New York, 2018; pp. 321-330.
[http://dx.doi.org/10.1007/978-1-4939-7614-0_21]
[148]
Murugesan, M.; Premkumar, K. Integrative miRNA-mRNA functional analysis identifies miR-182 as a potential prognostic biomarker in breast cancer. Mol. Omics, 2021, 17(4), 533-543.
[http://dx.doi.org/10.1039/D0MO00160K] [PMID: 33884382]
[149]
Denkiewicz, M.; Saha, I.; Rakshit, S.; Sarkar, J.P.; Plewczynski, D. Identification of breast cancer subtype specific MicroRNAs using survival analysis to find their role in transcriptomic regulation. Front. Genet., 2019, 10, 10.
[http://dx.doi.org/10.3389/fgene.2019.01047]
[150]
Hannafon, B.N.; Cai, A.; Calloway, C.L.; Xu, Y.F.; Zhang, R.; Fung, K.M.; Ding, W.Q. miR-23b and miR-27b are oncogenic microRNAs in breast cancer: Evidence from a CRISPR/Cas9 deletion study. BMC Cancer, 2019, 19(1), 642.
[http://dx.doi.org/10.1186/s12885-019-5839-2] [PMID: 31253120]
[151]
Liu, Y.; Cao, Z.; Wang, Y.; Guo, Y.; Xu, P.; Yuan, P.; Liu, Z.; He, Y.; Wei, W. Genome-wide screening for functional long noncoding RNAs in human cells by Cas9 targeting of splice sites. Nat. Biotechnol., 2018, 36(12), 1203-1210.
[http://dx.doi.org/10.1038/nbt.4283] [PMID: 30395134]
[152]
Esposito, R.; Bosch, N.; Lanzós, A.; Polidori, T.; Pulido-Quetglas, C.; Johnson, R. Hacking the cancer genome: Profiling therapeutically actionable long non-coding RNAs using CRISPR-Cas9 screening. Cancer Cell, 2019, 35(4), 545-557.
[http://dx.doi.org/10.1016/j.ccell.2019.01.019] [PMID: 30827888]
[153]
Barton, M.; Santucci-Pereira, J.; Vaccaro, O.G.; Nguyen, T.; Su, Y.; Russo, J. BC200 overexpression contributes to luminal and triple negative breast cancer pathogenesis. BMC Cancer, 2019, 19(1), 994.
[http://dx.doi.org/10.1186/s12885-019-6179-y] [PMID: 31646972]
[154]
Jin, X.; Xu, X.E.; Jiang, Y.Z.; Liu, Y.R.; Sun, W.; Guo, Y.J.; Ren, Y.X.; Zuo, W.J.; Hu, X.; Huang, S.L.; Shen, H.J.; Lan, F.; He, Y.F.; Hu, G.H.; Di, G.H.; He, X.H.; Li, D.Q.; Liu, S.; Yu, K.D.; Shao, Z.M. The endogenous retrovirus-derived long noncoding RNA TROJAN promotes triple-negative breast cancer progression via ZMYND8 degradation. Sci. Adv., 2019, 5(3), eaat9820.
[http://dx.doi.org/10.1126/sciadv.aat9820] [PMID: 30854423]
[155]
Miranda Furtado, C.L.; Dos Santos Luciano, M.C.; Silva Santos, R.D.; Furtado, G.P.; Moraes, M.O.; Pessoa, C. Epidrugs: Targeting epigenetic marks in cancer treatment. Epigenetics, 2019, 14(12), 1164-1176.
[http://dx.doi.org/10.1080/15592294.2019.1640546] [PMID: 31282279]
[156]
Evens, A.M.; Balasubramanian, S.; Vose, J.M.; Harb, W.; Gordon, L.I.; Langdon, R.; Sprague, J.; Sirisawad, M.; Mani, C.; Yue, J.; Luan, Y.; Horton, S.; Graef, T.; Bartlett, N.L. A phase I/II multicenter, open-label study of the oral histone deacetylase inhibitor abexinostat in relapsed/refractory lymphoma. Clin. Cancer Res., 2016, 22(5), 1059-1066.
[http://dx.doi.org/10.1158/1078-0432.CCR-15-0624] [PMID: 26482040]
[157]
Jiang, Z.; Li, W.; Hu, X.; Zhang, Q.; Sun, T.; Cui, S.; Wang, S.; Ouyang, Q.; Yin, Y.; Geng, C.; Tong, Z.; Cheng, Y.; Pan, Y.; Sun, Y.; Wang, H.; Ouyang, T.; Gu, K.; Feng, J.; Wang, X.; Wang, S.; Liu, T.; Gao, J.; Cristofanilli, M.; Ning, Z.; Lu, X. Tucidinostat plus exemestane for postmenopausal patients with advanced, hormone receptor-positive breast cancer (ACE): A randomised, double-blind, placebo-controlled, phase 3 trial. Lancet Oncol., 2019, 20(6), 806-815.
[http://dx.doi.org/10.1016/S1470-2045(19)30164-0] [PMID: 31036468]
[158]
Chung, W.; Kelly, A.D.; Kropf, P.; Fung, H.; Jelinek, J.; Su, X.Y.; Roboz, G.J.; Kantarjian, H.M.; Azab, M.; Issa, J.J. Genomic and epigenomic predictors of response to guadecitabine in relapsed/refractory acute myelogenous leukemia. Clin. Epigenetics, 2019, 11(1), 106.
[http://dx.doi.org/10.1186/s13148-019-0704-3] [PMID: 31331399]
[159]
Connolly, R.M.; Li, H.; Jankowitz, R.C.; Zhang, Z.; Rudek, M.A.; Jeter, S.C.; Slater, S.A.; Powers, P.; Wolff, A.C.; Fetting, J.H.; Brufsky, A.; Piekarz, R.; Ahuja, N.; Laird, P.W.; Shen, H.; Weisenberger, D.J.; Cope, L.; Herman, J.G.; Somlo, G.; Garcia, A.A.; Jones, P.A.; Baylin, S.B.; Davidson, N.E.; Zahnow, C.A.; Stearns, V. Combination epigenetic therapy in advanced breast cancer with 5-azacitidine and entinostat: A phase II National Cancer Institute/stand up to cancer study. Clin. Cancer Res., 2017, 23(11), 2691-2701.
[http://dx.doi.org/10.1158/1078-0432.CCR-16-1729] [PMID: 27979916]
[160]
Arce, C.; Pérez-Plasencia, C.; González-Fierro, A.; de la Cruz-Hernández, E.; Revilla-Vázquez, A.; Chávez-Blanco, A.; Trejo-Becerril, C.; Pérez-Cárdenas, E.; Taja-Chayeb, L.; Bargallo, E.; Villarreal, P.; Ramírez, T.; Vela, T.; Candelaria, M.; Camargo, M.F.; Robles, E.; Dueñas-González, A. A proof-of-principle study of epigenetic therapy added to neoadjuvant doxorubicin cyclophosphamide for locally advanced breast cancer. PLoS One, 2006, 1(1), e98.
[http://dx.doi.org/10.1371/journal.pone.0000098] [PMID: 17183730]
[161]
Witta, S.E.; Jotte, R.M.; Konduri, K.; Neubauer, M.A.; Spira, A.I.; Ruxer, R.L.; Varella-Garcia, M.; Bunn, P.A., Jr; Hirsch, F.R. Randomized phase II trial of erlotinib with and without entinostat in patients with advanced non-small-cell lung cancer who progressed on prior chemotherapy. J. Clin. Oncol., 2012, 30(18), 2248-2255.
[http://dx.doi.org/10.1200/JCO.2011.38.9411] [PMID: 22508830]
[162]
Yardley, D.A.; Ismail-Khan, R.R.; Melichar, B.; Lichinitser, M.; Munster, P.N.; Klein, P.M.; Cruickshank, S.; Miller, K.D.; Lee, M.J.; Trepel, J.B. Randomized phase II, double-blind, placebo-controlled study of exemestane with or without entinostat in postmenopausal women with locally recurrent or metastatic estrogen receptor-positive breast cancer progressing on treatment with a nonsteroidal aromatase inhibitor. J. Clin. Oncol., 2013, 31(17), 2128-2135.
[http://dx.doi.org/10.1200/JCO.2012.43.7251] [PMID: 23650416]
[163]
Idrissou, M.; Sanchez, A.; Penault-Llorca, F.; Bignon, Y.J.; Bernard-Gallon, D. Epi-drugs as triple-negative breast cancer treatment. Epigenomics, 2020, 12(8), 725-742.
[http://dx.doi.org/10.2217/epi-2019-0312] [PMID: 32396394]
[164]
Kumari, A.; Bhawal, S.; Kapila, S.; Yadav, H.; Kapila, R. Health-promoting role of dietary bioactive compounds through epigenetic modulations: A novel prophylactic and therapeutic approach. Crit. Rev. Food Sci. Nutr., 2022, 62(3), 619-639.
[http://dx.doi.org/10.1080/10408398.2020.1825286] [PMID: 33081489]
[165]
Ávila-Gálvez, M.Á.; González-Sarrías, A.; Martínez-Díaz, F.; Abellán, B.; Martínez-Torrano, A.J.; Fernández-López, A.J.; Giménez-Bastida, J.A.; Espín, J.C. Disposition of dietary polyphenols in breast cancer patients’ tumors, and their associated anticancer activity: The particular case of curcumin. Mol. Nutr. Food Res., 2021, 65(12), e2100163.
[http://dx.doi.org/10.1002/mnfr.202100163] [PMID: 33939887]
[166]
Zhang, W.; Guan, X.; Tang, J. The long non-coding RNA landscape in triple-negative breast cancer. Cell Prolif., 2021, 54(2), e12966.
[http://dx.doi.org/10.1111/cpr.12966] [PMID: 33314471]
[167]
Qiao, K.; Ning, S.; Wan, L.; Wu, H.; Wang, Q.; Zhang, X.; Xu, S.; Pang, D. LINC00673 is activated by YY1 and promotes the proliferation of breast cancer cells via the miR-515-5p/MARK4/Hippo signaling pathway. J. Exp. Clin. Cancer Res., 2019, 38(1), 418.
[http://dx.doi.org/10.1186/s13046-019-1421-7] [PMID: 31623640]
[168]
Hu, Q.; Ye, Y.; Chan, L.C.; Li, Y.; Liang, K.; Lin, A.; Egranov, S.D.; Zhang, Y.; Xia, W.; Gong, J.; Pan, Y.; Chatterjee, S.S.; Yao, J.; Evans, K.W.; Nguyen, T.K.; Park, P.K.; Liu, J.; Coarfa, C.; Donepudi, S.R.; Putluri, V.; Putluri, N.; Sreekumar, A.; Ambati, C.R.; Hawke, D.H.; Marks, J.R.; Gunaratne, P.H.; Caudle, A.S.; Sahin, A.A.; Hortobagyi, G.N.; Meric-Bernstam, F.; Chen, L.; Yu, D.; Hung, M.C.; Curran, M.A.; Han, L.; Lin, C.; Yang, L. Oncogenic lncRNA downregulates cancer cell antigen presentation and intrinsic tumor suppression. Nat. Immunol., 2019, 20(7), 835-851.
[http://dx.doi.org/10.1038/s41590-019-0400-7] [PMID: 31160797]
[169]
Vaidya, A.M.; Sun, Z.; Ayat, N.; Schilb, A.; Liu, X.; Jiang, H.; Sun, D.; Scheidt, J.; Qian, V.; He, S.; Gilmore, H.; Schiemann, W.P.; Lu, Z.R. Systemic delivery of tumor-targeting siRNA nanoparticles against an oncogenic LncRNA facilitates effective triple-negative breast cancer therapy. Bioconjug. Chem., 2019, 30(3), 907-919.
[http://dx.doi.org/10.1021/acs.bioconjchem.9b00028] [PMID: 30739442]
[170]
Jadaliha, M.; Zong, X.; Malakar, P.; Ray, T.; Singh, D.K.; Freier, S.M.; Jensen, T.; Prasanth, S.G.; Karni, R.; Ray, P.S.; Prasanth, K.V. Functional and prognostic significance of long non-coding RNA MALAT1 as a metastasis driver in ER negative lymph node negative breast cancer. Oncotarget, 2016, 7(26), 40418-40436.
[http://dx.doi.org/10.18632/oncotarget.9622] [PMID: 27250026]
[171]
Xia, Y.; Xiao, X.; Deng, X.; Zhang, F.; Zhang, X.; Hu, Q.; Sheng, W. Targeting long non-coding RNA ASBEL with oligonucleotide antagonist for breast cancer therapy. Biochem. Biophys. Res. Commun., 2017, 489(4), 386-392.
[http://dx.doi.org/10.1016/j.bbrc.2017.05.136] [PMID: 28552529]
[172]
Azangou-Khyavy, M.; Ghasemi, M.; Khanali, J.; Boroomand-Saboor, M.; Jamalkhah, M.; Soleimani, M.; Kiani, J. CRISPR/Cas: From tumor gene editing to T cell-based immunotherapy of cancer. Front. Immunol., 2020, 11, 2062.
[http://dx.doi.org/10.3389/fimmu.2020.02062] [PMID: 33117331]
[173]
Patel, S.J.; Sanjana, N.E.; Kishton, R.J.; Eidizadeh, A.; Vodnala, S.K.; Cam, M.; Gartner, J.J.; Jia, L.; Steinberg, S.M.; Yamamoto, T.N.; Merchant, A.S.; Mehta, G.U.; Chichura, A.; Shalem, O.; Tran, E.; Eil, R.; Sukumar, M.; Guijarro, E.P.; Day, C.P.; Robbins, P.; Feldman, S.; Merlino, G.; Zhang, F.; Restifo, N.P. Identification of essential genes for cancer immunotherapy. Nature, 2017, 548(7669), 537-542.
[http://dx.doi.org/10.1038/nature23477] [PMID: 28783722]
[174]
Findlay, G.M.; Daza, R.M.; Martin, B.; Zhang, M.D.; Leith, A.P.; Gasperini, M.; Janizek, J.D.; Huang, X.; Starita, L.M.; Shendure, J. Accurate classification of BRCA1 variants with saturation genome editing. Nature, 2018, 562(7726), 217-222.
[http://dx.doi.org/10.1038/s41586-018-0461-z] [PMID: 30209399]
[175]
Liu, Y.; Yin, X.; Zhong, J.; Guan, N.; Luo, Z.; Min, L.; Yao, X.; Bo, X.; Dai, L.; Bai, H. Systematic identification and assessment of therapeutic targets for breast cancer based on genome-wide RNA interference transcriptomes. Genes (Basel), 2017, 8(3), 86.
[http://dx.doi.org/10.3390/genes8030086] [PMID: 28245581]
[176]
Singh, D.D.; Hawkins, R.D.; Lahesmaa, R.; Tripathi, S.K. CRISPR/Cas9 guided genome and epigenome engineering and its therapeutic applications in immune mediated diseases. Semin. Cell Dev. Biol., 2019, 96, 32-43.
[http://dx.doi.org/10.1016/j.semcdb.2019.05.007] [PMID: 31112800]
[177]
Krebs, K.; Milani, L. Translating pharmacogenomics into clinical decisions: Do not let the perfect be the enemy of the good. Hum. Genomics, 2019, 13(1), 39.
[http://dx.doi.org/10.1186/s40246-019-0229-z] [PMID: 31455423]

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