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López-Cortés A, Cabrera-Andrade A, Echeverría-Garcés G, Echeverría-Espinoza P, Pineda-Albán M, Elsitdie N, Bueno-Miño J, Cruz-Segundo CM, Dorado J, Pazos A, Gonzáles-Díaz H, Pérez-Castillo Y, Tejera E, Munteanu CR. Unraveling druggable cancer-driving proteins and targeted drugs using artificial intelligence and multi-omics analyses. Sci Rep 2024; 14:19359. [PMID: 39169044 PMCID: PMC11339426 DOI: 10.1038/s41598-024-68565-7] [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: 03/04/2024] [Accepted: 07/25/2024] [Indexed: 08/23/2024] Open
Abstract
The druggable proteome refers to proteins that can bind to small molecules with appropriate chemical affinity, inducing a favorable clinical response. Predicting druggable proteins through screening and in silico modeling is imperative for drug design. To contribute to this field, we developed an accurate predictive classifier for druggable cancer-driving proteins using amino acid composition descriptors of protein sequences and 13 machine learning linear and non-linear classifiers. The optimal classifier was achieved with the support vector machine method, utilizing 200 tri-amino acid composition descriptors. The high performance of the model is evident from an area under the receiver operating characteristics (AUROC) of 0.975 ± 0.003 and an accuracy of 0.929 ± 0.006 (threefold cross-validation). The machine learning prediction model was enhanced with multi-omics approaches, including the target-disease evidence score, the shortest pathways to cancer hallmarks, structure-based ligandability assessment, unfavorable prognostic protein analysis, and the oncogenic variome. Additionally, we performed a drug repurposing analysis to identify drugs with the highest affinity capable of targeting the best predicted proteins. As a result, we identified 79 key druggable cancer-driving proteins with the highest ligandability, and 23 of them demonstrated unfavorable prognostic significance across 16 TCGA PanCancer types: CDKN2A, BCL10, ACVR1, CASP8, JAG1, TSC1, NBN, PREX2, PPP2R1A, DNM2, VAV1, ASXL1, TPR, HRAS, BUB1B, ATG7, MARK3, SETD2, CCNE1, MUTYH, CDKN2C, RB1, and SMARCA4. Moreover, we prioritized 11 clinically relevant drugs targeting these proteins. This strategy effectively predicts and prioritizes biomarkers, therapeutic targets, and drugs for in-depth studies in clinical trials. Scripts are available at https://github.com/muntisa/machine-learning-for-druggable-proteins .
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Affiliation(s)
- Andrés López-Cortés
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador.
| | - Alejandro Cabrera-Andrade
- Grupo de Bio-Quimioinformática, Universidad de Las Américas, Quito, Ecuador
- Escuela de Enfermería, Facultad de Ciencias de la Salud, Universidad de Las Américas, Quito, Ecuador
| | - Gabriela Echeverría-Garcés
- Centro de Referencia Nacional de Genómica, Secuenciación y Bioinformática, Instituto Nacional de Investigación en Salud Pública "Leopoldo Izquieta Pérez", Quito, Ecuador
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Santiago, Chile
| | | | - Micaela Pineda-Albán
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | - Nicole Elsitdie
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | - José Bueno-Miño
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | - Carlos M Cruz-Segundo
- RNASA-IMEDIR, Computer Science Faculty, University of A Coruna, A Coruña, Spain
- Tecnológico de Estudios Superiores de Jocotitlán, Jocotitlán, Mexico
| | - Julian Dorado
- RNASA-IMEDIR, Computer Science Faculty, University of A Coruna, A Coruña, Spain
- Centro de Investigación en Tecnologías de la Información y las Comunicaciones (CITIC), University of A Coruna, A Coruña, Spain
| | - Alejandro Pazos
- RNASA-IMEDIR, Computer Science Faculty, University of A Coruna, A Coruña, Spain
- Centro de Investigación en Tecnologías de la Información y las Comunicaciones (CITIC), University of A Coruna, A Coruña, Spain
- Biomedical Research Institute of A Coruna (INIBIC), University Hospital Complex of A Coruna (CHUAC), A Coruña, Spain
| | - Humberto Gonzáles-Díaz
- Department of Organic Chemistry II, University of the Basque Country UPV/EHU, Biscay, Spain
- IKERBASQUE, Basque Foundation for Science, Biscay, Spain
| | | | - Eduardo Tejera
- Grupo de Bio-Quimioinformática, Universidad de Las Américas, Quito, Ecuador
| | - Cristian R Munteanu
- RNASA-IMEDIR, Computer Science Faculty, University of A Coruna, A Coruña, Spain
- Centro de Investigación en Tecnologías de la Información y las Comunicaciones (CITIC), University of A Coruna, A Coruña, Spain
- Biomedical Research Institute of A Coruna (INIBIC), University Hospital Complex of A Coruna (CHUAC), A Coruña, Spain
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2
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Tomusiak A, Floro A, Tiwari R, Riley R, Matsui H, Andrews N, Kasler HG, Verdin E. Development of an epigenetic clock resistant to changes in immune cell composition. Commun Biol 2024; 7:934. [PMID: 39095531 PMCID: PMC11297166 DOI: 10.1038/s42003-024-06609-4] [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: 09/22/2023] [Accepted: 07/14/2024] [Indexed: 08/04/2024] Open
Abstract
Epigenetic clocks are age predictors that use machine-learning models trained on DNA CpG methylation values to predict chronological or biological age. Increases in predicted epigenetic age relative to chronological age (epigenetic age acceleration) are connected to aging-associated pathologies, and changes in epigenetic age are linked to canonical aging hallmarks. However, epigenetic clocks rely on training data from bulk tissues whose cellular composition changes with age. Here, we found that human naive CD8+ T cells, which decrease in frequency during aging, exhibit an epigenetic age 15-20 years younger than effector memory CD8+ T cells from the same individual. Importantly, homogenous naive T cells isolated from individuals of different ages show a progressive increase in epigenetic age, indicating that current epigenetic clocks measure two independent variables, aging and immune cell composition. To isolate the age-associated cell intrinsic changes, we created an epigenetic clock, the IntrinClock, that did not change among 10 immune cell types tested. IntrinClock shows a robust predicted epigenetic age increase in a model of replicative senescence in vitro and age reversal during OSKM-mediated reprogramming.
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Affiliation(s)
- Alan Tomusiak
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, 94945, CA, USA
- Department of Gerontology, University of Southern California, 3715 McClintock Ave, Los Angeles, 90089, CA, USA
| | - Ariel Floro
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, 94945, CA, USA
- Department of Gerontology, University of Southern California, 3715 McClintock Ave, Los Angeles, 90089, CA, USA
| | - Ritesh Tiwari
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, 94945, CA, USA
| | - Rebeccah Riley
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, 94945, CA, USA
| | - Hiroyuki Matsui
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, 94945, CA, USA
| | - Nicolas Andrews
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, 94945, CA, USA
| | - Herbert G Kasler
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, 94945, CA, USA
| | - Eric Verdin
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, 94945, CA, USA.
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3
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Tevini J, Aminzadeh-Gohari S, Weber DD, Catalano L, Stefan VE, Redl E, Herzog C, Lang R, Widschwendter M, Felder TK, Kofler B. A validated HPLC-MS/MS method for the quantification of systemic mifepristone after subcutaneous application in mice. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024. [PMID: 39045617 DOI: 10.1039/d4ay00546e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Mifepristone (RU486, MIF) is a synthetic steroidal hormone with progesterone and glucocorticoid receptor antagonistic characteristics. MIF is commonly used for pharmalogical abortions, but also for the treatment of endometrial and endocrine disorders. The goal of the study was to establish and validate a targeted HPLC-MS/MS method for the quantification of MIF and one of its active metabolites metapristone (MET) in plasma after subcutaneous implantation of slow-release MIF pellets in female BALB/c mice. Additionally, we aimed to apply the analytical method to tissue of several organs to understand the tissue-specific distribution of both analytes after release into systemic circulation. Sample preparation comprised a simple liquid-liquid extraction with diethylether and required 100 μl of plasma or homogenates of approximately 50 mg of tissue. The presented HPLC-MS/MS method showed high sensitivity with baseline separation of MIF, MET, and the internal standard levonorgestrel within a run time of only 8.0 minutes and comparable limits of quantification for plasma and tissue homogenates ranging from 40 pg ml-1 to 105 pg ml-1 for MIF and MET. The presented study is suitable for murine plasma and tissues and can be easily applied to human samples.
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Affiliation(s)
- Julia Tevini
- Research Program for Receptor Biochemistry and Tumor Metabolism, Department of Pediatrics, University Hospital of the Paracelsus Medical University, Salzburg, Austria.
| | - Sepideh Aminzadeh-Gohari
- Research Program for Receptor Biochemistry and Tumor Metabolism, Department of Pediatrics, University Hospital of the Paracelsus Medical University, Salzburg, Austria.
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, University Innsbruck, Hall in Tirol, Innsbruck, Austria
- Institute for Biomedical Aging Research, University Innsbruck, Innsbruck, Austria
| | - Daniela D Weber
- Research Program for Receptor Biochemistry and Tumor Metabolism, Department of Pediatrics, University Hospital of the Paracelsus Medical University, Salzburg, Austria.
| | - Luca Catalano
- Research Program for Receptor Biochemistry and Tumor Metabolism, Department of Pediatrics, University Hospital of the Paracelsus Medical University, Salzburg, Austria.
| | - Victoria E Stefan
- Research Program for Receptor Biochemistry and Tumor Metabolism, Department of Pediatrics, University Hospital of the Paracelsus Medical University, Salzburg, Austria.
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Elisa Redl
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, University Innsbruck, Hall in Tirol, Innsbruck, Austria
- Institute for Biomedical Aging Research, University Innsbruck, Innsbruck, Austria
| | - Chiara Herzog
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, University Innsbruck, Hall in Tirol, Innsbruck, Austria
- Institute for Biomedical Aging Research, University Innsbruck, Innsbruck, Austria
| | - Roland Lang
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, Salzburg, Austria
| | - Martin Widschwendter
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, University Innsbruck, Hall in Tirol, Innsbruck, Austria
- Institute for Biomedical Aging Research, University Innsbruck, Innsbruck, Austria
- Department of Women's and Children's Health, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
- Department of Women's Cancer, University College London, London, UK
| | - Thomas K Felder
- Department of Laboratory Medicine, Paracelsus Medical University, Salzburg, Austria.
- Institute of Pharmacy, Paracelsus Medical University, Salzburg, Austria
| | - Barbara Kofler
- Research Program for Receptor Biochemistry and Tumor Metabolism, Department of Pediatrics, University Hospital of the Paracelsus Medical University, Salzburg, Austria.
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Utjés D, Boggavarapu NR, Rasul MF, Koberg I, Zulliger A, Ponandai-Srinivasan S, von Grothusen C, Lalitkumar PG, Papaikonomou K, Alkasalias T, Gemzell-Danielsson K. Transcriptomic Profile of Breast Tissue of Premenopausal Women Following Treatment with Progesterone Receptor Modulator: Secondary Outcomes of a Randomized Controlled Trial. Int J Mol Sci 2024; 25:7590. [PMID: 39062832 PMCID: PMC11277027 DOI: 10.3390/ijms25147590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 06/19/2024] [Accepted: 06/22/2024] [Indexed: 07/28/2024] Open
Abstract
Progesterone receptor antagonism is gaining attention due to progesterone's recognized role as a major mitogen in breast tissue. Limited but promising data suggest the potential efficacy of antiprogestins in breast cancer prevention. The present study presents secondary outcomes from a randomized controlled trial and examines changes in breast mRNA expression following mifepristone treatment in healthy premenopausal women. We analyzed 32 paired breast biopsies from 16 women at baseline and after two months of mifepristone treatment. In total, 27 differentially expressed genes were identified, with enriched biological functions related to extracellular matrix remodeling. Notably, the altered gene signature induced by mifepristone in vivo was rather similar to the in vitro signature. Furthermore, this gene expression signature was linked to breast carcinogenesis and notably linked with progesterone receptor expression status in breast cancer, as validated in The Cancer Genome Atlas dataset using the R2 platform. The present study is the first to explore the breast transcriptome following mifepristone treatment in normal breast tissue in vivo, enhancing the understanding of progesterone receptor antagonism and its potential protective effect against breast cancer.
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Affiliation(s)
- Deborah Utjés
- Department of Women’s and Children’s Health, Karolinska Institutet, 171 77 Stockholm, Sweden; (D.U.); (N.R.B.); (M.F.R.); (I.K.); (A.Z.); (S.P.-S.); (C.v.G.); (P.G.L.); (K.P.); (K.G.-D.)
- Department of Gynecology and Reproductive Medicine, Karolinska University Hospital, 141 57 Stockholm, Sweden
| | - Nageswara Rao Boggavarapu
- Department of Women’s and Children’s Health, Karolinska Institutet, 171 77 Stockholm, Sweden; (D.U.); (N.R.B.); (M.F.R.); (I.K.); (A.Z.); (S.P.-S.); (C.v.G.); (P.G.L.); (K.P.); (K.G.-D.)
| | - Mohammed Fatih Rasul
- Department of Women’s and Children’s Health, Karolinska Institutet, 171 77 Stockholm, Sweden; (D.U.); (N.R.B.); (M.F.R.); (I.K.); (A.Z.); (S.P.-S.); (C.v.G.); (P.G.L.); (K.P.); (K.G.-D.)
- Department of Pharmaceutical Basic Science, Faculty of Pharmacy, Tishk International University, Erbil 44001, Iraq
| | - Isabelle Koberg
- Department of Women’s and Children’s Health, Karolinska Institutet, 171 77 Stockholm, Sweden; (D.U.); (N.R.B.); (M.F.R.); (I.K.); (A.Z.); (S.P.-S.); (C.v.G.); (P.G.L.); (K.P.); (K.G.-D.)
| | - Alexander Zulliger
- Department of Women’s and Children’s Health, Karolinska Institutet, 171 77 Stockholm, Sweden; (D.U.); (N.R.B.); (M.F.R.); (I.K.); (A.Z.); (S.P.-S.); (C.v.G.); (P.G.L.); (K.P.); (K.G.-D.)
| | - Sakthivignesh Ponandai-Srinivasan
- Department of Women’s and Children’s Health, Karolinska Institutet, 171 77 Stockholm, Sweden; (D.U.); (N.R.B.); (M.F.R.); (I.K.); (A.Z.); (S.P.-S.); (C.v.G.); (P.G.L.); (K.P.); (K.G.-D.)
| | - Carolina von Grothusen
- Department of Women’s and Children’s Health, Karolinska Institutet, 171 77 Stockholm, Sweden; (D.U.); (N.R.B.); (M.F.R.); (I.K.); (A.Z.); (S.P.-S.); (C.v.G.); (P.G.L.); (K.P.); (K.G.-D.)
| | - Parameswaran Grace Lalitkumar
- Department of Women’s and Children’s Health, Karolinska Institutet, 171 77 Stockholm, Sweden; (D.U.); (N.R.B.); (M.F.R.); (I.K.); (A.Z.); (S.P.-S.); (C.v.G.); (P.G.L.); (K.P.); (K.G.-D.)
| | - Kiriaki Papaikonomou
- Department of Women’s and Children’s Health, Karolinska Institutet, 171 77 Stockholm, Sweden; (D.U.); (N.R.B.); (M.F.R.); (I.K.); (A.Z.); (S.P.-S.); (C.v.G.); (P.G.L.); (K.P.); (K.G.-D.)
- Department of Gynecology and Reproductive Medicine, Karolinska University Hospital, 141 57 Stockholm, Sweden
| | - Twana Alkasalias
- Department of Women’s and Children’s Health, Karolinska Institutet, 171 77 Stockholm, Sweden; (D.U.); (N.R.B.); (M.F.R.); (I.K.); (A.Z.); (S.P.-S.); (C.v.G.); (P.G.L.); (K.P.); (K.G.-D.)
- General Directorate of Scientific Research Center, Salahaddin University-Erbil, Erbil 44001, Iraq
| | - Kristina Gemzell-Danielsson
- Department of Women’s and Children’s Health, Karolinska Institutet, 171 77 Stockholm, Sweden; (D.U.); (N.R.B.); (M.F.R.); (I.K.); (A.Z.); (S.P.-S.); (C.v.G.); (P.G.L.); (K.P.); (K.G.-D.)
- Department of Gynecology and Reproductive Medicine, Karolinska University Hospital, 141 57 Stockholm, Sweden
- WHO Collaborating Centre, Division of Gynecology and Reproduction, Karolinska University Hospital, 171 76 Stockholm, Sweden
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Elia A, Pataccini G, Saldain L, Ambrosio L, Lanari C, Rojas P. Antiprogestins for breast cancer treatment: We are almost ready. J Steroid Biochem Mol Biol 2024; 241:106515. [PMID: 38554981 DOI: 10.1016/j.jsbmb.2024.106515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/05/2024] [Accepted: 03/20/2024] [Indexed: 04/02/2024]
Abstract
The development of antiprogestins was initially a gynecological purpose. However, since mifepristone was developed, its application for breast cancer treatment was immediately proposed. Later, new compounds with lower antiglucocorticoid and antiandrogenic effects were developed to be applied to different pathologies, including breast cancer. We describe herein the studies performed in the breast cancer field with special focus on those reported in recent years, ranging from preclinical biological models to those carried out in patients. We highlight the potential use of antiprogestins in breast cancer prevention in women with BRCA1 mutations, and their use for breast cancer treatment, emphasizing the need to elucidate which patients will respond. In this sense, the PR isoform ratio has emerged as a possible tool to predict antiprogestin responsiveness. The effects of combined treatments of antiprogestins together with other drugs currently used in the clinic, such as tamoxifen, CDK4/CDK6 inhibitors or pembrolizumab in preclinical models is discussed since it is in this scenario that antiprogestins will be probably introduced. Finally, we explain how transcriptomic or proteomic studies, that were carried out in different luminal breast cancer models and in breast cancer samples that responded or were predicted to respond to the antiprogestin therapy, show a decrease in proliferative pathways. Deregulated pathways intrinsic of each model are discussed, as well as how these analyses may contribute to a better understanding of the mechanisms involved.
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Affiliation(s)
- Andrés Elia
- Laboratory of Hormonal Carcinogenesis, Instituto de Biología y Medicina Experimental (IBYME CONICET), Buenos Aires, Argentina
| | - Gabriela Pataccini
- Laboratory of Hormonal Carcinogenesis, Instituto de Biología y Medicina Experimental (IBYME CONICET), Buenos Aires, Argentina
| | - Leo Saldain
- Laboratory of Hormonal Carcinogenesis, Instituto de Biología y Medicina Experimental (IBYME CONICET), Buenos Aires, Argentina
| | - Luisa Ambrosio
- Laboratory of Hormonal Carcinogenesis, Instituto de Biología y Medicina Experimental (IBYME CONICET), Buenos Aires, Argentina
| | - Claudia Lanari
- Laboratory of Hormonal Carcinogenesis, Instituto de Biología y Medicina Experimental (IBYME CONICET), Buenos Aires, Argentina
| | - Paola Rojas
- Laboratory of Hormonal Carcinogenesis, Instituto de Biología y Medicina Experimental (IBYME CONICET), Buenos Aires, Argentina.
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Khan SA. Breast Cancer Risk Reduction: Current Status and Emerging Trends to Increase Efficacy and Reduce Toxicity of Preventive Medication. Surg Oncol Clin N Am 2023; 32:631-646. [PMID: 37714633 DOI: 10.1016/j.soc.2023.05.001] [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] [Indexed: 09/17/2023]
Abstract
The primary prevention of breast cancer is a worthwhile goal for which the efficacy of antiestrogens is well established. However, implementation has been problematic related to low prioritization by providers and the reluctance of high-risk women to experience medication side effects. Emerging solutions include improved risk estimation through the use of polygenic risk scores and the application of radiomics to screening mammograms; and optimization of medication dose to limit toxicity. The identification of agents to prevent estrogen receptor negative or HER2-positive tumors is being pursued, but personalization of medical risk reduction requires the prediction of tumor subtypes.
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Affiliation(s)
- Seema Ahsan Khan
- Department of Surgery, Feinberg School of Medicine of Northwestern University, 303 East Superior Street, Chicago, IL 60614, USA.
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7
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Herzog C, Jones A, Evans I, Zikan M, Cibula D, Harbeck N, Colombo N, Rådestad AF, Gemzell-Danielsson K, Pashayan N, Widschwendter M. DNA methylation at quantitative trait loci (mQTLs) varies with cell type and nonheritable factors and may improve breast cancer risk assessment. NPJ Precis Oncol 2023; 7:99. [PMID: 37758816 PMCID: PMC10533818 DOI: 10.1038/s41698-023-00452-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
To individualise breast cancer (BC) prevention, markers to follow a person's changing environment and health extending beyond static genetic risk scores are required. Here, we analysed cervical and breast DNA methylation (n = 1848) and single nucleotide polymorphisms (n = 1442) and demonstrate that a linear combination of methylation levels at 104 BC-associated methylation quantitative trait loci (mQTL) CpGs, termed the WID™-qtBC index, can identify women with breast cancer in hormone-sensitive tissues (AUC = 0.71 [95% CI: 0.65-0.77] in cervical samples). Women in the highest combined risk group (high polygenic risk score and WID™-qtBC) had a 9.6-fold increased risk for BC [95% CI: 4.7-21] compared to the low-risk group and tended to present at more advanced stages. Importantly, the WID™-qtBC is influenced by non-genetic BC risk factors, including age and body mass index, and can be modified by a preventive pharmacological intervention, indicating an interaction between genome and environment recorded at the level of the epigenome. Our findings indicate that methylation levels at mQTLs in relevant surrogate tissues could enable integration of heritable and non-heritable factors for improved disease risk stratification.
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Affiliation(s)
- Chiara Herzog
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, Milser Str. 10, 6060, Hall in Tirol, Austria
- Research Institute for Biomedical Aging Research, Universität Innsbruck, 6020, Innsbruck, Austria
| | - Allison Jones
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, WC1E 6AU, London, UK
| | - Iona Evans
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, WC1E 6AU, London, UK
| | - Michal Zikan
- Department of Gynecology and Obstetrics, Charles University in Prague, First Faculty of Medicine and Hospital Na Bulovce, Prague, Czech Republic
| | - David Cibula
- Gynaecologic Oncology Center, Department of Obstetrics and Gynecology, First Faculty of Medicine, Charles University in Prague, General University Hospital in Prague, Prague, Czech Republic
| | - Nadia Harbeck
- Breast Center, Department of Obstetrics and Gynecology and CCC Munich, LMU University Hospital, Munich, Germany
| | - Nicoletta Colombo
- Istituto Europeo di Oncologia, Milan, Italy
- University of Milano-Bicocca, Milan, Italy
| | | | | | - Nora Pashayan
- Department of Applied Health Research, University College London, London, UK
| | - Martin Widschwendter
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, Milser Str. 10, 6060, Hall in Tirol, Austria.
- Research Institute for Biomedical Aging Research, Universität Innsbruck, 6020, Innsbruck, Austria.
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, WC1E 6AU, London, UK.
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.
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8
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Moyer CL, Brown PH. Targeting nuclear hormone receptors for the prevention of breast cancer. Front Med (Lausanne) 2023; 10:1200947. [PMID: 37583424 PMCID: PMC10424511 DOI: 10.3389/fmed.2023.1200947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/30/2023] [Indexed: 08/17/2023] Open
Abstract
Advancements in research have led to the steady decline of breast cancer mortality over the past thirty years. However, breast cancer incidence has continued to rise, resulting in an undue burden on healthcare costs and highlighting a great need for more effective breast cancer prevention strategies, including targeted chemo preventative agents. Efforts to understand the etiology of breast cancer have uncovered important roles for nuclear receptors in the development and progression of breast cancer. Targeted therapies to inhibit estrogen receptor (ER) and progesterone receptor (PR) signaling (selective ER modulators, aromatase inhibitors and selective PR modulators) have shown great promise for the treatment and prevention of hormone receptor (HR)-positive breast cancer. However, these drugs do not prevent HR-negative disease. Therefore, recent efforts have focused on novel targeted therapies with the potential to prevent both HR-positive and HR-negative breast cancer. Among these include drugs that target other nuclear receptors, such as retinoic acid receptor (RAR), retinoid X receptor (RXR) and vitamin D receptor (VDR). In this review we provide an overview of recent preclinical and clinical trials targeting members of the nuclear receptor superfamily for the prevention of breast cancer.
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Affiliation(s)
- Cassandra L. Moyer
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Powel H. Brown
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States
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9
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Lee O, Wang M, Hosseini O, Bosland MC, Muzzio M, Helenowski I, Khan SA. Z-Endoxifen prevents aggressive mammary cancers in mice by inhibiting cell proliferation and creating a tumor suppressive microenvironment. Biomed Pharmacother 2023; 162:114607. [PMID: 37001185 DOI: 10.1016/j.biopha.2023.114607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/24/2023] [Accepted: 03/24/2023] [Indexed: 03/31/2023] Open
Abstract
Aggressive estrogen receptor (ER) positive breast cancer is frequently tamoxifen-resistant; alternative endocrine approaches exist for therapy, but not for prevention, particularly in premenopausal women. We examined the efficacy of the selective ER modulator (Z-endoxifen) as monotherapy and in combination with the selective progesterone receptor modulators (onapristone and ulipristal acetate) in the tamoxifen-insensitive C3(1)/SV40TAg mouse mammary tumorigenesis model. Unlike tamoxifen at human equivalent dose (HED) 101 mg/day, endoxifen at HED 24 mg/day significantly increased latency and reduced tumor growth relative to untreated controls. Ulipristal acetate (UPA) at HED 81 mg/day also significantly increased latency however failed to inhibit tumor growth, while onapristone (HED 98 mg/day) had no tumor prevention efficacy in this model. Addition of UPA to endoxifen did not enhance preventive efficacy over endoxifen alone. The expression of genes associated with cell cycle, cell proliferation and extracellular matrix remodeling was similarly repressed by endoxifen and UPA however only endoxifen significantly downregulated prominent genes associated with poor prognosis (Col11a1, Il17b, Pdgfa, Tnfrsf11a). Our results indicate that endoxifen can prevent breast cancers, even when tamoxifen-resistant, through its role in favorable tissue remodeling and immunomodulation.
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Affiliation(s)
- Oukseub Lee
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Minhua Wang
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Omid Hosseini
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Maarten C Bosland
- Department of Pathology, University of Illinois at Chicago, Chicago, IL, USA
| | - Miguel Muzzio
- Analytical Chemistry Division, Illinois Institute of Technology Research Institute, Chicago, IL, USA
| | - Irene Helenowski
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Seema A Khan
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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10
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Prokurotaite E, Condorelli M, Dechene J, Bouziotis J, Lambertini M, Demeestere I. Impact of Breast Cancer and Germline BRCA Pathogenic Variants on Fertility Preservation in Young Women. Life (Basel) 2023; 13:930. [PMID: 37109459 PMCID: PMC10146760 DOI: 10.3390/life13040930] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/24/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND Several studies have suggested that breast cancer (BC) and germline BRCA pathogenic variants (gBRCA PVs) could have a deleterious impact on ovarian reserve. Nevertheless, data are limited and mixed. Our objective was to evaluate the performance of fertility preservation (FP) in terms of the number of collected mature oocytes after ovarian stimulation (OS) in young women carrying a gBRCA PV, associated or not with BC. METHODS We conducted a retrospective monocentric study at HUB-Hôpital Erasme in Brussels. All women aged between 18 and 41 years diagnosed with invasive non-metastatic BC and/or gBRCA PV carriers who underwent OS for FP or preimplantation genetic testing for monogenic disorder (PGT-M) between November 2012 and October 2021 were included. Three groups were compared: BC patients without a gBRCA PV, BC patients with a gBRCA PV, and healthy gBRCA PV carriers. Ovarian reserve was evaluated based on the efficacy of OS and AMH levels. RESULTS A total of 85 patients underwent 100 cycles. The mean age (32.2 ± 3.9 years; p = 0.61) and median AMH level (1.9 [0.2-13] μg/L; p = 0.22) were similar between groups. Correlations between the number of mature oocytes and AMH level (p < 0.001) and between AMH and age (p < 0.001) were observed. No differences in the number of retrieved mature oocytes were observed between groups (p = 0.41), or for other OS parameters. CONCLUSION Neither BC nor a gBRCA PV significantly affects ovarian reserve and FP efficacy in terms of the number of mature oocytes retrieved.
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Affiliation(s)
- Elze Prokurotaite
- Fertility Clinic, Department of Obstetrics and Gynecology, H.U.B—Hôpital Erasme, Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Margherita Condorelli
- Fertility Clinic, Department of Obstetrics and Gynecology, H.U.B—Hôpital Erasme, Université Libre de Bruxelles, 1070 Brussels, Belgium
- Research Laboratory on Human Reproduction, Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Julie Dechene
- Research Laboratory on Human Reproduction, Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Jason Bouziotis
- Department of Biomedical Research, H.U.B—Hôpital Erasme, Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Matteo Lambertini
- Department of Internal Medicine and Medical Specialties (DiMI), School of Medicine, University of Genova, 16132 Genova, Italy
- Department of Medical Oncology, U.O. Clinica di Oncologia Medica, IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy
| | - Isabelle Demeestere
- Fertility Clinic, Department of Obstetrics and Gynecology, H.U.B—Hôpital Erasme, Université Libre de Bruxelles, 1070 Brussels, Belgium
- Research Laboratory on Human Reproduction, Université Libre de Bruxelles, 1070 Brussels, Belgium
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11
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Bartlett TE, Evans I, Jones A, Barrett JE, Haran S, Reisel D, Papaikonomou K, Jones L, Herzog C, Pashayan N, Simões BM, Clarke RB, Evans DG, Ghezelayagh TS, Ponandai-Srinivasan S, Boggavarapu NR, Lalitkumar PG, Howell SJ, Risques RA, Rådestad AF, Dubeau L, Gemzell-Danielsson K, Widschwendter M. Correction: Antiprogestins reduce epigenetic field cancerization in breast tissue of young healthy women. Genome Med 2022; 14:76. [PMID: 35854342 PMCID: PMC9295457 DOI: 10.1186/s13073-022-01086-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Thomas E Bartlett
- Department of Statistical Science, University College London, London, WC1E 7HB, UK
| | - Iona Evans
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Allison Jones
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - James E Barrett
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, Universität Innsbruck, 6060, Hall in Tirol, Austria
- Research Institute for Biomedical Aging Research, Universität Innsbruck, 6020, Innsbruck, Austria
| | - Shaun Haran
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Daniel Reisel
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Kiriaki Papaikonomou
- Department of Women's and Children's Health, Division of Obstet- rics and Gynecology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Louise Jones
- Centre for Tumour Biology Department, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Chiara Herzog
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, Universität Innsbruck, 6060, Hall in Tirol, Austria
- Research Institute for Biomedical Aging Research, Universität Innsbruck, 6020, Innsbruck, Austria
| | - Nora Pashayan
- Department of Applied Health Research, University College London, 1-19 Torrington Place, London, WC1E 7HB, UK
| | - Bruno M Simões
- Breast Biology Group, Manchester Breast Centre, Divi- sion of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK, England
| | - Robert B Clarke
- Breast Biology Group, Manchester Breast Centre, Divi- sion of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK, England
| | - D Gareth Evans
- University of Manchester, St. Mary's Hospital, and University Hospital of South Manchester, Manchester, UK
| | - Talayeh S Ghezelayagh
- Department of Laboratory Medicine and Pathology, University of Washing- ton, Seattle, WA, 98195, USA
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, 98195, USA
| | - Sakthivignesh Ponandai-Srinivasan
- Department of Women's and Children's Health, Division of Obstet- rics and Gynecology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Nageswara R Boggavarapu
- Department of Women's and Children's Health, Division of Obstet- rics and Gynecology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Parameswaran G Lalitkumar
- Department of Women's and Children's Health, Division of Obstet- rics and Gynecology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Sacha J Howell
- Breast Biology Group, Manchester Breast Centre, Divi- sion of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK, England
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK
| | - Rosa Ana Risques
- Department of Laboratory Medicine and Pathology, University of Washing- ton, Seattle, WA, 98195, USA
| | - Angelique Flöter Rådestad
- Department of Women's and Children's Health, Division of Obstet- rics and Gynecology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Louis Dubeau
- Department of Pathology, Keck School of Medicine, USC/Norris Comprehensive Cancer Centre, University of Southern California, Los Angeles, USA
| | - Kristina Gemzell-Danielsson
- Department of Women's and Children's Health, Division of Obstet- rics and Gynecology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Martin Widschwendter
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK.
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, Universität Innsbruck, 6060, Hall in Tirol, Austria.
- Research Institute for Biomedical Aging Research, Universität Innsbruck, 6020, Innsbruck, Austria.
- Department of Women's and Children's Health, Division of Obstet- rics and Gynecology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.
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