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Dragonetti M, Turco C, Benedetti A, Goeman F, Forcato M, Scalera S, Allegretti M, Esposito G, Fazi F, Blandino G, Donzelli S, Fontemaggi G. The lncRNAMALAT1-WTAP axis: a novel layer of EMT regulation in hypoxic triple-negative breast cancer. Cell Death Discov 2024; 10:276. [PMID: 38862471 PMCID: PMC11166650 DOI: 10.1038/s41420-024-02058-4] [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: 02/22/2024] [Revised: 05/30/2024] [Accepted: 06/04/2024] [Indexed: 06/13/2024] Open
Abstract
Early metastatic disease development is one characteristic that defines triple-negative breast cancer (TNBC) as the most aggressive breast cancer (BC) subtype. Numerous studies have identified long non-coding RNAs (lncRNA) as critical players in regulating tumor progression and metastasis formation. Here, we show that MALAT1, a long non-coding RNA known to promote various features of BC malignancy, such as migration and neo angiogenesis, regulates TNBC cell response to hypoxia. By profiling MALAT1-associated transcripts, we discovered that lncRNA MALAT1 interacts with the mRNA encoding WTAP protein, previously reported as a component of the N6-methyladenosine (m6A) modification writer complex. In hypoxic conditions, MALAT1 positively regulates WTAP protein expression, which influences the response to hypoxia by favoring the transcription of the master regulators HIF1α and HIF1β. Furthermore, WTAP stimulates BC cell migratory ability and the expression of N-Cadherin and Vimentin, hallmarks of epithelial-to-mesenchymal transition (EMT). In conclusion, this study highlights the functional axis comprising MALAT1 and WTAP as a novel prognostic marker of TNBC progression and as a potential target for the development of therapeutic approaches for TNBC treatment.
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Affiliation(s)
- Martina Dragonetti
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - Chiara Turco
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - Anna Benedetti
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - Frauke Goeman
- SAFU Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - Mattia Forcato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Stefano Scalera
- Biostatistics and Bioinformatics Unit, Clinical Trial Center, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Matteo Allegretti
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - Gabriella Esposito
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - Francesco Fazi
- Department of Anatomical, Histological, Forensic & Orthopaedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Via A. Scarpa, 16, 00161, Rome, Italy
| | - Giovanni Blandino
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - Sara Donzelli
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy.
| | - Giulia Fontemaggi
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy.
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Rossi M, Radisky DC. Multiplex Digital Spatial Profiling in Breast Cancer Research: State-of-the-Art Technologies and Applications across the Translational Science Spectrum. Cancers (Basel) 2024; 16:1615. [PMID: 38730568 PMCID: PMC11083340 DOI: 10.3390/cancers16091615] [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: 03/21/2024] [Revised: 04/17/2024] [Accepted: 04/21/2024] [Indexed: 05/13/2024] Open
Abstract
While RNA sequencing and multi-omic approaches have significantly advanced cancer diagnosis and treatment, their limitation in preserving critical spatial information has been a notable drawback. This spatial context is essential for understanding cellular interactions and tissue dynamics. Multiplex digital spatial profiling (MDSP) technologies overcome this limitation by enabling the simultaneous analysis of transcriptome and proteome data within the intact spatial architecture of tissues. In breast cancer research, MDSP has emerged as a promising tool, revealing complex biological questions related to disease evolution, identifying biomarkers, and discovering drug targets. This review highlights the potential of MDSP to revolutionize clinical applications, ranging from risk assessment and diagnostics to prognostics, patient monitoring, and the customization of treatment strategies, including clinical trial guidance. We discuss the major MDSP techniques, their applications in breast cancer research, and their integration in clinical practice, addressing both their potential and current limitations. Emphasizing the strategic use of MDSP in risk stratification for women with benign breast disease, we also highlight its transformative potential in reshaping the landscape of breast cancer research and treatment.
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Affiliation(s)
| | - Derek C. Radisky
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA;
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Patrucco D, Cutrin JC, Longo DL, Botto E, Cong L, Aime S, Delli Castelli D. In Situ Insonation of Alkaline Buffer Containing Liposomes Leads to a Net Improvement of the Therapeutic Outcome in a Triple Negative Breast Cancer Murine Model. Adv Healthc Mater 2023; 12:e2301480. [PMID: 37709294 DOI: 10.1002/adhm.202301480] [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: 06/14/2023] [Revised: 09/12/2023] [Indexed: 09/16/2023]
Abstract
Breast cancer is characterized by an acidic micro-environment. Acidic extracellular pH gives cancer cells an evolutionary advantage, hence, neutralization of the extracellular pH has been considered as a potential therapeutic strategy. To address the issue of systemic pH alteration, an approach based on the targeted delivery of the buffering solution to the tumor region is investigated. The method relies on the use of low frequency ultrasound and sono-sensitive liposomes loaded with buffers at alkaline pH (LipHUS). After the i.v. injection of LipHUS, the application of ultrasound (US) at the sites of the pathology induces a local increase of pH that results highly effective in i) inhibiting primary tumor growth, ii) reducing tumor recurrence after surgery, and iii) suppressing metastases' formation. The experiments are carried out on a triple negative breast cancer mouse model. The results obtained demonstrate that localized and triggered release of bicarbonate or PBS buffer from sonosensitive liposomes represents an efficient therapeutic tool for treating triple-negative breast cancer. This approach holds promise for potential clinical translation.
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Affiliation(s)
- Deyssy Patrucco
- Department of Molecular Biotechnology and Health Science, University of Turin, Via Nizza 52, Turin, 10126, Italy
| | - Juan Carlos Cutrin
- Department of Molecular Biotechnology and Health Science, University of Turin, Via Nizza 52, Turin, 10126, Italy
| | - Dario Livio Longo
- Istituto di Biostrutture e Bioimmagini (IBB), Consiglio Nazionale delle Ricerche (CNR), Via Tommaso De Amicis, 95, Naples, 80145, Italy
| | - Elena Botto
- Istituto di Biostrutture e Bioimmagini (IBB), Consiglio Nazionale delle Ricerche (CNR), Via Tommaso De Amicis, 95, Naples, 80145, Italy
| | - Li Cong
- Key Laboratory of Smart Drug Delivery, Ministry of Education, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Silvio Aime
- IRCCS SDN, SYNLAB, Via Gianturco 113, Naples, 80143, Italy
| | - Daniela Delli Castelli
- Department of Molecular Biotechnology and Health Science, University of Turin, Via Nizza 52, Turin, 10126, Italy
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Wang G, Yao Y, Huang H, Zhou J, Ni C. Multiomics technologies for comprehensive tumor microenvironment analysis in triple-negative breast cancer under neoadjuvant chemotherapy. Front Oncol 2023; 13:1131259. [PMID: 37284197 PMCID: PMC10239824 DOI: 10.3389/fonc.2023.1131259] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 05/08/2023] [Indexed: 06/08/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is one of the most aggressive breast cancer subtypes and is characterized by abundant infiltrating immune cells within the microenvironment. As standard care, chemotherapy remains the fundamental neoadjuvant treatment in TNBC, and there is increasing evidence that supplementation with immune checkpoint inhibitors may potentiate the therapeutic efficiency of neoadjuvant chemotherapy (NAC). However, 20-60% of TNBC patients still have residual tumor burden after NAC and require additional chemotherapy; therefore, it is critical to understand the dynamic change in the tumor microenvironment (TME) during treatment to help improve the rate of complete pathological response and long-term prognosis. Traditional methods, including immunohistochemistry, bulk tumor sequencing, and flow cytometry, have been applied to elucidate the TME of breast cancer, but the low resolution and throughput may overlook key information. With the development of diverse high-throughput technologies, recent reports have provided new insights into TME alterations during NAC in four fields, including tissue imaging, cytometry, next-generation sequencing, and spatial omics. In this review, we discuss the traditional methods and the latest advances in high-throughput techniques to decipher the TME of TNBC and the prospect of translating these techniques to clinical practice.
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Affiliation(s)
- Gang Wang
- Department of Surgical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
| | - Yao Yao
- Department of Breast Surgery, Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Huanhuan Huang
- Department of Breast Surgery, Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Jun Zhou
- Department of Breast Surgery, Affiliated Hangzhou First People’s Hospital, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chao Ni
- Department of Breast Surgery, Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, China
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Park S, Yi G. Development of Gene Expression-Based Random Forest Model for Predicting Neoadjuvant Chemotherapy Response in Triple-Negative Breast Cancer. Cancers (Basel) 2022; 14:cancers14040881. [PMID: 35205629 PMCID: PMC8870575 DOI: 10.3390/cancers14040881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/28/2022] [Accepted: 02/02/2022] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Only 20–50% of patients with triple negative breast cancer achieve a pathological complete response from neoadjuvant chemotherapy, a strong indicator of patient survival. Therefore, there is an urgent need for a reliable predictive model of the patient’s pathological complete response prior to actual treatment. The purpose of this study was to develop such a model based on random forest recursive feature elimination and to benchmark the performance of the proposed model against existing predictive models. Our study suggests that an 86-gene-based random forest model associated to DNA repair and cell cycle mechanisms can provide reliable predictions of neoadjuvant chemotherapy response in patients with triple negative breast cancer. Abstract Neoadjuvant chemotherapy (NAC) response is an important indicator of patient survival in triple negative breast cancer (TNBC), but predicting chemosensitivity remains a challenge in clinical practice. We developed an 86-gene-based random forest (RF) classifier capable of predicting neoadjuvant chemotherapy response (pathological Complete Response (pCR) or Residual Disease (RD)) in TNBC patients. The performance of pCR classification of the proposed model was evaluated by Receiver Operating Characteristic (ROC) curve and Precision Recall (PR) curve. The AUROC and AUPRC of the proposed model on the test set were 0.891 and 0.829, respectively. At a predefined specificity (>90%), the proposed model shows a superior sensitivity compared to the best performing reported NAC response prediction model (69.2% vs. 36.9%). Moreover, the predicted pCR status by the model well explains the distance recurrence free survival (DRFS) of TNBC patients. In addition, the pCR probabilities of the proposed model using the expression profiles of the CCLE TNBC cell lines show a high Spearman rank correlation with cyclophosphamide sensitivity in the TNBC cell lines (SRCC =0.697, p-value =0.031). Associations between the 86 genes and DNA repair/cell cycle mechanisms were provided through function enrichment analysis. Our study suggests that the random forest-based prediction model provides a reliable prediction of the clinical response to neoadjuvant chemotherapy and may explain chemosensitivity in TNBC.
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Čelešnik H, Potočnik U. Peripheral Blood Transcriptome in Breast Cancer Patients as a Source of Less Invasive Immune Biomarkers for Personalized Medicine, and Implications for Triple Negative Breast Cancer. Cancers (Basel) 2022; 14:591. [PMID: 35158858 PMCID: PMC8833511 DOI: 10.3390/cancers14030591] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 01/14/2022] [Accepted: 01/19/2022] [Indexed: 12/21/2022] Open
Abstract
Transcriptome studies of peripheral blood cells can advance our understanding of the systemic immune response to the presence of cancer and the mechanisms underlying cancer onset and progression. This enables the identification of novel minimally invasive immune biomarkers for early cancer detection and personalized cancer management and may bring forward new immunotherapy options. Recent blood gene expression analyses in breast cancer (BC) identified distinct patient subtypes that differed in the immune reaction to cancer and were distinct from the clinical BC subtypes, which are categorized based on expression of specific receptors on tumor cells. Introducing new BC subtypes based on peripheral blood gene expression profiles may be appropriate, since it may assist in BC prognosis, the identification of patients likely to benefit from immunotherapy, and treatment efficacy monitoring. Triple-negative breast cancer (TNBC) is an aggressive, heterogeneous, and difficult-to-treat disease, and identification of novel biomarkers for this BC is crucial for clinical decision-making. A few studies have reported TNBC-enriched blood transcriptional signatures, mostly related to strong inflammation and augmentation of altered immune signaling, that can differentiate TNBC from other classical BC subtypes and facilitate diagnosis. Future research is geared toward transitioning from expression signatures in unfractionated blood cells to those in immune cell subpopulations.
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Affiliation(s)
- Helena Čelešnik
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova Ulica 17, 2000 Maribor, Slovenia;
- Center for Human Genetics & Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia
| | - Uroš Potočnik
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova Ulica 17, 2000 Maribor, Slovenia;
- Center for Human Genetics & Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia
- Department for Science and Research, University Medical Centre Maribor, Ljubljanska Ulica 5, 2000 Maribor, Slovenia
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