{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T00:04:57Z","timestamp":1790208297204,"version":"4.1.0"},"reference-count":35,"publisher":"MDPI AG","issue":"17","license":[{"start":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T00:00:00Z","timestamp":1788134400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Mol. Sci.","IJMS"],"abstract":"<jats:p>Neoadjuvant chemotherapy (NAC) is the standard of care for locally advanced breast cancer, yet the molecular predictors of pathological response remain incompletely defined, particularly regarding microRNA (miRNA) dynamics. We investigated paired pre- and post-NAC miRNA expression profiles in relation to molecular subtype, residual cancer burden (RCB), and clinical timing parameters. Seven patients with invasive breast cancer (Luminal A n = 3, Luminal B n = 1, TNBC n = 2, HER2+ n = 1) who received NAC (AC-T or TCHP) were included in this pilot study. Small-RNA sequencing (NovaSeq X Plus, CeGaT GmbH, project S17293) was performed on 14 FFPE specimens (7 pre-NAC core needle biopsies, 7 post-NAC surgical specimens). Differential expression analysis used the paired Wilcoxon signed-rank test with Benjamini\u2013Hochberg correction. Spearman correlations assessed associations between miRNA expression, RCB score, and clinical timing intervals. Candidate miRNAs were subsequently annotated using experimentally validated miRNA\u2013target interactions. After filtering (\u2265 three counts in \u2265 three samples), 759 miRNAs were analysed. No miRNA reached strict significance (padj &lt; 0.05, |log2FC| &gt; 1.0) after multiple testing correction, consistent with the limited statistical power (n = 7). Under exploratory criteria (p &lt; 0.10, |log2FC| &gt; 0.5), 156 candidate miRNAs were identified: 70 upregulated and 86 downregulated post-NAC. Leading candidates included hsa-miR-139-3p (+2.60), hsa-miR-139-5p (+2.36), and hsa-miR-1323 (+1.55) as upregulated, and hsa-miR-429 (\u22122.53), hsa-miR-141-3p (\u22121.79), and hsa-miR-1277-5p (\u22121.25) as downregulated post-NAC. The single patient achieving the lowest residual disease burden (P3, Luminal B, RCB-I, score 1.32) displayed a distinct pre-treatment miRNA profile, separating from all other pre-NAC specimens on principal component analysis and characterised by higher baseline hsa-miR-139-3p\/-5p and lower baseline hsa-miR-429 and hsa-miR-141-3p expression, suggesting that baseline miRNA expression patterns may contribute to differential chemotherapy response. RCB score showed a non-significant positive trend with post-NAC Ki-67 (\u03c1 = +0.71, p = 0.07). This pilot study identifies NAC-modulated candidate miRNAs in breast cancer and establishes a paired FFPE-based small-RNA-sequencing workflow applicable in routine clinical settings. The distinct pre-treatment profile of the single best responder generates the testable hypothesis that baseline expression of tumour suppressor miRNAs of the miR-139 family, together with low miR-200-family expression, may track chemosensitivity. As no candidate reached statistical significance after multiple testing correction and none has been validated in an independent cohort or by an orthogonal method, all findings are exploratory and hypothesis-generating. The results support larger prospective validation studies examining miRNA signatures as predictive biomarkers of NAC response across breast cancer molecular subtypes.<\/jats:p>","DOI":"10.3390\/ijms27177799","type":"journal-article","created":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T09:48:36Z","timestamp":1788256116000},"page":"7799","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["MicroRNA Expression Profiles Before and After Neoadjuvant Chemotherapy in Breast Cancer: Correlations with Molecular Subtypes, Pathological Response, and Clinical Timing\u2014A Pilot Translational Study"],"prefix":"10.3390","volume":"27","author":[{"given":"Isabela Anda","family":"Komporaly","sequence":"first","affiliation":[{"name":"Department of Oncology, \u201cCarol Davila\u201d University of Medicine and Pharmacy, 020021 Bucharest, Romania"},{"name":"Memorial B\u0103neasa Hospital, 013812 Bucharest, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3589-799X","authenticated-orcid":false,"given":"Adelina Silvana","family":"Gheorghe","sequence":"additional","affiliation":[{"name":"Department of Medical Oncology I, \u201cProf. Dr. Alexandru Trestioreanu\u201d Institute of Oncology, 022328 Bucharest, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elena Adriana","family":"Iov\u0103nescu","sequence":"additional","affiliation":[{"name":"Department of Oncology, \u201cCarol Davila\u201d University of Medicine and Pharmacy, 020021 Bucharest, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bogdan","family":"Georgescu","sequence":"additional","affiliation":[{"name":"Department of Oncology, \u201cCarol Davila\u201d University of Medicine and Pharmacy, 020021 Bucharest, Romania"},{"name":"Neolife Hospital, 077190 Bucharest, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dana Lucia","family":"St\u0103nculeanu","sequence":"additional","affiliation":[{"name":"Department of Oncology, \u201cCarol Davila\u201d University of Medicine and Pharmacy, 020021 Bucharest, Romania"},{"name":"Department of Medical Oncology I, \u201cProf. Dr. Alexandru Trestioreanu\u201d Institute of Oncology, 022328 Bucharest, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,31]]},"reference":[{"key":"ref_1","first-page":"209","article-title":"Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries","volume":"71","author":"Sung","year":"2021","journal-title":"CA Cancer J. Clin."},{"key":"ref_2","first-page":"229","article-title":"Global Cancer Statistics 2022: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries","volume":"74","author":"Bray","year":"2024","journal-title":"CA Cancer J. Clin."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1016\/S0140-6736(13)62422-8","article-title":"Pathological Complete Response and Long-Term Clinical Benefit in Breast Cancer: The CTNeoBC Pooled Analysis","volume":"384","author":"Cortazar","year":"2014","journal-title":"Lancet"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"810","DOI":"10.1056\/NEJMoa1910549","article-title":"Pembrolizumab for Early Triple-Negative Breast Cancer (KEYNOTE-522)","volume":"382","author":"Schmid","year":"2020","journal-title":"N. Engl. J. Med."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.1200\/JCO.2015.63.1010","article-title":"Long-Term Prognostic Risk After Neoadjuvant Chemotherapy Associated with Residual Cancer Burden and Breast Cancer Subtype","volume":"35","author":"Symmans","year":"2017","journal-title":"J. Clin. Oncol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"791","DOI":"10.1016\/S1470-2045(16)00163-7","article-title":"5-Year Analysis of Neoadjuvant Pertuzumab and Trastuzumab in HER2-Positive Breast Cancer (NeoSphere)","volume":"17","author":"Gianni","year":"2016","journal-title":"Lancet Oncol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1056\/NEJMoa1814017","article-title":"Trastuzumab Emtansine for Residual Invasive HER2-Positive Breast Cancer (KATHERINE)","volume":"380","author":"Huang","year":"2019","journal-title":"N. Engl. J. Med."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1016\/j.cell.2009.01.002","article-title":"MicroRNAs: Target Recognition and Regulatory Functions","volume":"136","author":"Bartel","year":"2009","journal-title":"Cell"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Komporaly, I.A., Gheorghe, A.S., Kajanto, L.A., Iov\u0103nescu, E.A., Georgescu, B., Mih\u0103il\u0103, R.I., Radu, A.M., Zob, D.L., Mihai, M.M., and Georgescu, M.T. (2025). miRNA and Its Implications in the Treatment Resistance in Breast Cancer\u2014Narrative Review of What Do We Know So Far. Non-Coding RNA, 11.","DOI":"10.3390\/ncrna11060078"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"809","DOI":"10.1038\/nmeth.3014","article-title":"Evaluation of Quantitative miRNA Expression Platforms in the microRNA Quality Control (miRQC) Study","volume":"11","author":"Mestdagh","year":"2014","journal-title":"Nat. Methods"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1609753","DOI":"10.3389\/pore.2021.1609753","article-title":"Identification of miRNA Signature in Breast Cancer to Predict Neoadjuvant Chemotherapy Response","volume":"27","author":"Xing","year":"2021","journal-title":"Pathol. Oncol. Res."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"596","DOI":"10.20517\/cdr.2023.19","article-title":"Resistance of Breast Cancer Cells to Paclitaxel Is Associated with Low Expressions of miRNA-186 and miRNA-7","volume":"6","author":"Apollonova","year":"2023","journal-title":"Cancer Drug Resist."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1216","DOI":"10.1016\/j.annonc.2021.06.023","article-title":"Customizing Local and Systemic Therapies for Women with Early Breast Cancer: St. Gallen International Consensus Guidelines 2021","volume":"32","author":"Burstein","year":"2021","journal-title":"Ann. Oncol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"702","DOI":"10.1016\/j.bbrc.2015.08.053","article-title":"MiR-139-5p Inhibits the Biological Function of Breast Cancer Cells by Targeting Notch1 and Mediates Chemosensitivity to Docetaxel","volume":"465","author":"Zhang","year":"2015","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1186\/1476-4598-13-124","article-title":"MicroRNA-139-5p Exerts Tumor Suppressor Function by Targeting NOTCH1 in Colorectal Cancer","volume":"13","author":"Zhang","year":"2014","journal-title":"Mol. Cancer"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"322","DOI":"10.1053\/j.gastro.2010.10.006","article-title":"The MicroRNA miR-139 Suppresses Metastasis and Progression of Hepatocellular Carcinoma by Down-Regulating Rho-Kinase 2","volume":"140","author":"Wong","year":"2011","journal-title":"Gastroenterology"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1767","DOI":"10.1261\/rna.042143.113","article-title":"miR-139-5p Is a Regulator of Metastatic Pathways in Breast Cancer","volume":"19","author":"Krishnan","year":"2013","journal-title":"RNA"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"894","DOI":"10.1101\/gad.1640608","article-title":"The miR-200 Family Determines the Epithelial Phenotype of Cancer Cells by Targeting the E-Cadherin Repressors ZEB1 and ZEB2","volume":"22","author":"Park","year":"2008","journal-title":"Genes Dev."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1038\/ncb1722","article-title":"The miR-200 Family and miR-205 Regulate Epithelial to Mesenchymal Transition by Targeting ZEB1 and SIP1","volume":"10","author":"Gregory","year":"2008","journal-title":"Nat. Cell Biol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"7846","DOI":"10.1158\/0008-5472.CAN-08-1942","article-title":"A Double-Negative Feedback Loop between ZEB1-SIP1 and the microRNA-200 Family Regulates Epithelial\u2013Mesenchymal Transition","volume":"68","author":"Bracken","year":"2008","journal-title":"Cancer Res."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1038\/nrn3475","article-title":"Power Failure: Why Small Sample Size Undermines the Reliability of Neuroscience","volume":"14","author":"Button","year":"2013","journal-title":"Nat. Rev. Neurosci."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1038\/sj.bjc.6602678","article-title":"Reporting Recommendations for Tumour Marker Prognostic Studies (REMARK)","volume":"93","author":"McShane","year":"2005","journal-title":"Br. J. Cancer"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Tejero, R., Navarro, A., Campayo, M., Vi\u00f1olas, N., Marrades, R.M., Cordeiro, A., Ru\u00edz-Mart\u00ednez, M., Santasusagna, S., Molins, L., and Ramirez, J. (2014). miR-141 and miR-200c as Markers of Overall Survival in Early-Stage Non-Small-Cell Lung Cancer Adenocarcinoma. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0101899"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"531","DOI":"10.3892\/ijo.2014.2759","article-title":"miR-429 Inhibits Migration and Invasion of Breast Cancer Cells In Vitro","volume":"46","author":"Ye","year":"2015","journal-title":"Int. J. Oncol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"2278","DOI":"10.1002\/1878-0261.12561","article-title":"miRNA Expression Changes during the Course of Neoadjuvant Bevacizumab and Chemotherapy Treatment in Breast Cancer","volume":"13","author":"Lindholm","year":"2019","journal-title":"Mol. Oncol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1007\/s10549-022-06642-z","article-title":"miRNAs as Therapeutic Predictors and Prognostic Biomarkers of Neoadjuvant Chemotherapy in Breast Cancer: A Systematic Review and Meta-Analysis","volume":"194","author":"Zhang","year":"2022","journal-title":"Breast Cancer Res. Treat."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Meng, W., McElroy, J.P., Volinia, S., Palatini, J., Warner, S., Ayers, L.W., Palanichamy, K., Chakravarti, A., and Lautenschlaeger, T. (2013). Comparison of MicroRNA Deep Sequencing of Matched Formalin-Fixed Paraffin-Embedded and Fresh Frozen Cancer Tissues. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0064393"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Kakimoto, Y., Tanaka, M., Kamiguchi, H., Ochiai, E., and Osawa, M. (2016). MicroRNA Stability in FFPE Tissue Samples: Dependence on GC Content. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0163125"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"18275","DOI":"10.1038\/s41598-024-69285-8","article-title":"Systematic Review and Feasibility Study on Pre-Analytical Factors and Genomic Analyses on Archival Formalin-Fixed Paraffin-Embedded Breast Cancer Tissue","volume":"14","author":"Salgkamis","year":"2024","journal-title":"Sci. Rep."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Tiberio, P., Gaudio, M., Belloni, S., Pindilli, S., Benvenuti, C., Jacobs, F., Saltalamacchia, G., Zambelli, A., Santoro, A., and De Sanctis, R. (2023). Unlocking the Potential of Circulating miRNAs in the Breast Cancer Neoadjuvant Setting: A Systematic Review and Meta-Analysis. Cancers, 15.","DOI":"10.3390\/cancers15133424"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Benvenuti, C., Tiberio, P., Gaudio, M., Jacobs, F., Saltalamacchia, G., Pindilli, S., Zambelli, A., Santoro, A., and De Sanctis, R. (2023). Potential Role of Circulating miRNAs for Breast Cancer Management in the Neoadjuvant Setting: A Road to Pave. Cancers, 15.","DOI":"10.3390\/cancers15051410"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1373\/clinchem.2008.112797","article-title":"The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments","volume":"55","author":"Bustin","year":"2009","journal-title":"Clin. Chem."},{"key":"ref_33","first-page":"e109160","article-title":"Predictors of Pathological Complete Response and Patient-Reported Outcomes During Neoadjuvant Chemotherapy in Early Breast Cancer: A Single-Center Retrospective Cohort Study","volume":"18","author":"Komporaly","year":"2026","journal-title":"Cureus"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"lqab068","DOI":"10.1093\/nargab\/lqab068","article-title":"miRge3.0: A Comprehensive microRNA and tRF Sequencing Analysis Pipeline","volume":"3","author":"Patil","year":"2021","journal-title":"NAR Genom. Bioinform."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"D68","DOI":"10.1093\/nar\/gkt1181","article-title":"miRBase: Annotating High-Confidence microRNAs Using Deep Sequencing Data","volume":"42","author":"Kozomara","year":"2014","journal-title":"Nucleic Acids Res."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/17\/7799\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T04:29:35Z","timestamp":1788841775000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/17\/7799"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,31]]},"references-count":35,"journal-issue":{"issue":"17","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["ijms27177799"],"URL":"https:\/\/doi.org\/10.3390\/ijms27177799","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,31]]}}}