1
|
Garrone O, La Porta CAM. Artificial Intelligence for Precision Oncology of Triple-Negative Breast Cancer: Learning from Melanoma. Cancers (Basel) 2024; 16:692. [PMID: 38398083 PMCID: PMC10887240 DOI: 10.3390/cancers16040692] [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: 11/09/2023] [Revised: 01/18/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Thanks to new technologies using artificial intelligence (AI) and machine learning, it is possible to use large amounts of data to try to extract information that can be used for personalized medicine. The great challenge of the future is, on the one hand, to acquire masses of biological data that nowadays are still limited and, on the other hand, to develop innovative strategies to extract information that can then be used for the development of predictive models. From this perspective, we discuss these aspects in the context of triple-negative breast cancer, a tumor where a specific treatment is still lacking and new therapies, such as immunotherapy, are under investigation. Since immunotherapy is already in use for other tumors such as melanoma, we discuss the strengths and weaknesses identified in the use of immunotherapy with melanoma to try to find more successful strategies. It is precisely in this context that AI and predictive tools can be extremely valuable. Therefore, the discoveries and advancements in immunotherapy for melanoma provide a foundation for developing effective immunotherapies for triple-negative breast cancer. Shared principles, such as immune system activation, checkpoint inhibitors, and personalized treatment, can be applied to TNBC to improve patient outcomes and offer new hope for those with aggressive, hard-to-treat breast cancer.
Collapse
Affiliation(s)
- Ornella Garrone
- Medical Oncology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy;
| | - Caterina A. M. La Porta
- Department of Environmental Science and Policy, University of Milan, 20133 Milan, Italy
- Center for Complexity and Biosystems, University of Milan, 20133 Milan, Italy
| |
Collapse
|
2
|
Heilala M, Lehtonen A, Arasalo O, Peura A, Pokki J, Ikkala O, Nonappa, Klefström J, Munne PM. Fibrin Stiffness Regulates Phenotypic Plasticity of Metastatic Breast Cancer Cells. Adv Healthc Mater 2023; 12:e2301137. [PMID: 37671812 DOI: 10.1002/adhm.202301137] [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: 04/11/2023] [Revised: 08/18/2023] [Indexed: 09/07/2023]
Abstract
The extracellular matrix (ECM)-regulated phenotypic plasticity is crucial for metastatic progression of triple negative breast cancer (TNBC). While ECM faithful cell-based models are available for in situ and invasive tumors, such as cell aggregate cultures in reconstituted basement membrane and in collagenous gels, there are no ECM faithful models for metastatic circulating tumor cells (CTCs). Such models are essential to represent the stage of metastasis where clinical relevance and therapeutic opportunities are significant. Here, CTC-like DU4475 TNBC cells are cultured in mechanically tunable 3D fibrin hydrogels. This is motivated, as in circulation fibrin aids CTC survival by forming a protective coating reducing shear stress and immune cell-mediated cytotoxicity and promotes several stages of late metastatic processes at the interface between circulation and tissue. This work shows that fibrin hydrogels support DU4475 cell growth, resulting in spheroid formation. Furthermore, increasing fibrin stiffness from 57 to 175 Pa leads to highly motile, actin and tubulin containing cellular protrusions, which are associated with specific cell morphology and gene expression patterns that markedly differ from basement membrane or suspension cultures. Thus, mechanically tunable fibrin gels reveal specific matrix-based regulation of TNBC cell phenotype and offer scaffolds for CTC-like cells with better mechano-biological properties than liquid.
Collapse
Affiliation(s)
- Maria Heilala
- Department of Applied Physics, Aalto University, P.O. Box 15100, Aalto, Espoo, FI-00076, Finland
| | - Arttu Lehtonen
- Department of Electrical Engineering and Automation, Aalto University, P.O. Box 12200, Aalto, Espoo, FI-00076, Finland
| | - Ossi Arasalo
- Department of Electrical Engineering and Automation, Aalto University, P.O. Box 12200, Aalto, Espoo, FI-00076, Finland
| | - Aino Peura
- Finnish Cancer Institute and FICAN South, Helsinki University Hospital & Cancer Cell Circuitry Laboratory, Translational Cancer Medicine, Medical Faculty, University of Helsinki, P.O. Box 63 (Haartmaninkatu 8), Helsinki, 00014, Finland
| | - Juho Pokki
- Department of Electrical Engineering and Automation, Aalto University, P.O. Box 12200, Aalto, Espoo, FI-00076, Finland
| | - Olli Ikkala
- Department of Applied Physics, Aalto University, P.O. Box 15100, Aalto, Espoo, FI-00076, Finland
| | - Nonappa
- Faculty of Engineering and Natural Sciences, Tampere University, P.O. Box 541, Tampere, FI-33720, Finland
| | - Juha Klefström
- Finnish Cancer Institute and FICAN South, Helsinki University Hospital & Cancer Cell Circuitry Laboratory, Translational Cancer Medicine, Medical Faculty, University of Helsinki, P.O. Box 63 (Haartmaninkatu 8), Helsinki, 00014, Finland
| | - Pauliina M Munne
- Finnish Cancer Institute and FICAN South, Helsinki University Hospital & Cancer Cell Circuitry Laboratory, Translational Cancer Medicine, Medical Faculty, University of Helsinki, P.O. Box 63 (Haartmaninkatu 8), Helsinki, 00014, Finland
| |
Collapse
|
3
|
Zapperi S, La Porta CAM. The Response of Triple-Negative Breast Cancer to Neoadjuvant Chemotherapy and the Epithelial–Mesenchymal Transition. Int J Mol Sci 2023; 24:ijms24076422. [PMID: 37047393 PMCID: PMC10094549 DOI: 10.3390/ijms24076422] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/25/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
It would be highly desirable to find prognostic and predictive markers for triple-negative breast cancer (TNBC), a strongly heterogeneous and invasive breast cancer subtype often characterized by a high recurrence rate and a poor outcome. Here, we investigated the prognostic and predictive capabilities of ARIADNE, a recently developed transcriptomic test focusing on the epithelial–mesenchymal transition. We first compared the stratification of TNBC patients obtained by ARIADNE with that based on other common pathological indicators, such as grade, stage and nodal status, and found that ARIADNE was more effective than the other methods in dividing patients into groups with different disease-free survival statistics. Next, we considered the response to neoadjuvant chemotherapy and found that the classification provided by ARIADNE led to statistically significant differences in the rates of pathological complete response within the groups.
Collapse
|
4
|
La Porta CAM, Zapperi S. Artificial intelligence in breast cancer diagnostics. Cell Rep Med 2022; 3:100851. [PMID: 36543102 PMCID: PMC9798018 DOI: 10.1016/j.xcrm.2022.100851] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 12/24/2022]
Abstract
Since breast cancer deaths are mainly due to metastasis, predicting the risk that a primary tumor will develop metastasis after a first diagnosis is a central issue that could be addressed by artificial intelligence. To overcome the problem posed by limited availability of standardized datasets, algorithms should include biological insight.
Collapse
Affiliation(s)
- Caterina AM. La Porta
- Department of Environmental Science and Policy, Center for Complexity & Biosystems, University of Milan, via Celoria 10, 20133 Milan, Italy,CNR - Consiglio Nazionale delle Ricerche, Istituto di Biofisica, via Celoria 10, 20133 Milan, Italy,Corresponding author
| | - Stefano Zapperi
- Department of Physics, Center for Complexity & Biosystems, University of Milan, via Celoria 16, 20133 Milan, Italy,CNR - Consiglio Nazionale delle Ricerche, Istituto di Chimica della Materia Condensata e di Tecnologie per l'Energia, Via R. Cozzi 53, 20125 Milano, Italy
| |
Collapse
|
5
|
Nierengarten MB. Molecular insights into triple-negative breast cancer metastasis: Epithelial- mesenchymal transition: There is a need to better understand the molecular drivers behind triple-negative breast cancer to help curb the incidence of metastasis: There is a need to better understand the molecular drivers behind triple-negative breast cancer to help curb the incidence of metastasis. Cancer 2022; 128:4174. [PMID: 36445103 DOI: 10.1002/cncr.34546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/09/2022] [Accepted: 10/24/2022] [Indexed: 12/03/2022]
|
6
|
Lionetti MC, Fumagalli MR, La Porta CAM. Nuclear Biophysical Changes during Human Melanoma Plasticity. Cells Tissues Organs 2022; 213:120-132. [PMID: 36509081 DOI: 10.1159/000528601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022] Open
Abstract
Tumor plasticity is an emerging property of tumor cells which allows them to change their phenotype in dependence on the environment. The epithelial-mesenchymal transition plays a crucial role in helping cells acquire a more aggressive phenotype when they are in the mesenchymal state. Herein, we investigated the biophysical changes occurring during phenotypic switching in human melanoma cells, considering the blebbiness of the nuclei, their stiffness, and the involvement of polycombs with lamins. We show that the formation of cellular heterogeneity involves many crucial nuclear changes including the interaction between different types of polycombs with lamins and chromosome accessibility. Altogether, our results shed new light on the molecular mechanisms involved in the formation of a heterogeneous cell population during phenotypic switching. In particular, our results show that phenotypic switching in melanoma involves chromatin remodeling changing the transcriptional activity of cells and consequently their phenotype.
Collapse
Affiliation(s)
- Maria Chiara Lionetti
- Department of Environmental Science and Policy, Center for Complexity and Biosystems, University of Milan, Milan, Italy
| | - Maria Rita Fumagalli
- Department of Environmental Science and Policy, Center for Complexity and Biosystems, University of Milan, Milan, Italy
- CNR - Consiglio Nazionale delle Ricerche, Biophysics Institute, Genoa, Italy
| | - Caterina A M La Porta
- Department of Environmental Science and Policy, Center for Complexity and Biosystems, University of Milan, Milan, Italy
- CNR - Consiglio Nazionale delle Ricerche, Biophysics Institute, Genoa, Italy
| |
Collapse
|
7
|
Fatima M, Abourehab MAS, Aggarwal G, Jain GK, Sahebkar A, Kesharwani P. Advancement of cell-penetrating peptides in combating triple-negative breast cancer. Drug Discov Today 2022; 27:103353. [PMID: 36099963 DOI: 10.1016/j.drudis.2022.103353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/23/2022] [Accepted: 09/06/2022] [Indexed: 11/03/2022]
Abstract
Extensive research efforts have been made and are still ongoing in the search for an ideal anti-cancer therapy. Almost all chemotherapeutics require a carrier or vehicle, a drug delivery system that can transport the drug specifically to the targeted cancer cells, sparing normal cells. Cell-penetrating peptides (CPPs) provide an effective and efficient pathway for the intra-cellular transportation of various bioactive molecules in several biomedical therapies. They are now well-recognized as facilitators of intracellular cargo delivery and have excellent potential for targeted anti-cancer therapy. In this review, we explain CPPs, recent progress in the development of new CPPs, and their utilization to transport cargoes such as imaging agents, chemotherapeutics, and short-interfering RNAs (siRNA) into tumor cells, contributing to the advancement of novel tumor-specific delivery systems.
Collapse
Affiliation(s)
- Mahak Fatima
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi 110 062, India
| | - Mohammed A S Abourehab
- Department of Pharmaceutics, College of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia; Department of Pharmaceutics and Industrial Pharmacy, College of Pharmacy, Minia University, Minia 61519, Egypt
| | - Geeta Aggarwal
- Department of Pharmaceutics, Delhi Pharmaceutical Sciences and Research University, New Delhi 110 017, India
| | - Gaurav K Jain
- Department of Pharmaceutics, Delhi Pharmaceutical Sciences and Research University, New Delhi 110 017, India
| | - Amirhossein Sahebkar
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Prashant Kesharwani
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi 110 062, India.
| |
Collapse
|
8
|
Classification of triple negative breast cancer by epithelial mesenchymal transition and the tumor immune microenvironment. Sci Rep 2022; 12:9651. [PMID: 35688895 PMCID: PMC9187759 DOI: 10.1038/s41598-022-13428-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/09/2022] [Indexed: 11/22/2022] Open
Abstract
Triple-negative breast cancer (TNBC) accounts for about 15–20% of all breast cancers and differs from other invasive breast cancer types because it grows and spreads rapidly, it has limited treatment options and typically worse prognosis. Since TNBC does not express estrogen or progesterone receptors and little or no human epidermal growth factor receptor (HER2) proteins are present, hormone therapy and drugs targeting HER2 are not helpful, leaving chemotherapy only as the main systemic treatment option. In this context, it would be important to find molecular signatures able to stratify patients into high and low risk groups. This would allow oncologists to suggest the best therapeutic strategy in a personalized way, avoiding unnecessary toxicity and reducing the high costs of treatment. Here we compare two independent patient stratification strategies for TNBC based on gene expression data: The first is focusing on the epithelial mesenchymal transition (EMT) and the second on the tumor immune microenvironment. Our results show that the two stratification strategies are not directly related, suggesting that the aggressiveness of the tumor can be due to a multitude of unrelated factors. In particular, the EMT stratification is able to identify a high-risk population with high immune markers that is, however, not properly classified by the tumor immune microenvironment based strategy.
Collapse
|
9
|
Hirway SU, Weinberg SH. A review of computational modeling, machine learning and image analysis in cancer metastasis dynamics. COMPUTATIONAL AND SYSTEMS ONCOLOGY 2022. [DOI: 10.1002/cso2.1044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Shreyas U. Hirway
- Department of Biomedical Engineering The Ohio State University Columbus Ohio USA
| | - Seth H. Weinberg
- Department of Biomedical Engineering The Ohio State University Columbus Ohio USA
| |
Collapse
|
10
|
Bocci F, Zhou P, Nie Q. Single-Cell RNA-Seq Analysis Reveals the Acquisition of Cancer Stem Cell Traits and Increase of Cell-Cell Signaling during EMT Progression. Cancers (Basel) 2021; 13:5726. [PMID: 34830900 PMCID: PMC8616061 DOI: 10.3390/cancers13225726] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/06/2021] [Accepted: 11/14/2021] [Indexed: 01/31/2023] Open
Abstract
Intermediate cell states (ICSs) during the epithelial-mesenchymal transition (EMT) are emerging as a driving force of cancer invasion and metastasis. ICSs typically exhibit hybrid epithelial/mesenchymal characteristics as well as cancer stem cell (CSC) traits including proliferation and drug resistance. Here, we analyze several single-cell RNA-seq (scRNA-seq) datasets to investigate the relation between several axes of cancer progression including EMT, CSC traits, and cell-cell signaling. To accomplish this task, we integrate computational methods for clustering and trajectory inference with analysis of EMT gene signatures, CSC markers, and cell-cell signaling pathways, and highlight conserved and specific processes across the datasets. Our analysis reveals that "standard" measures of pluripotency often used in developmental contexts do not necessarily correlate with EMT progression and expression of CSC-related markers. Conversely, an EMT circuit energy that quantifies the co-expression of epithelial and mesenchymal genes consistently increases along EMT trajectories across different cancer types and anatomical locations. Moreover, despite the high context specificity of signal transduction across different cell types, cells undergoing EMT always increased their potential to send and receive signals from other cells.
Collapse
Affiliation(s)
- Federico Bocci
- Department of Mathematics, University of California, Irvine, CA 92697, USA; (F.B.); (P.Z.)
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, CA 92697, USA
| | - Peijie Zhou
- Department of Mathematics, University of California, Irvine, CA 92697, USA; (F.B.); (P.Z.)
| | - Qing Nie
- Department of Mathematics, University of California, Irvine, CA 92697, USA; (F.B.); (P.Z.)
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, CA 92697, USA
| |
Collapse
|
11
|
Alfaro-García JP, Granados-Alzate MC, Vicente-Manzanares M, Gallego-Gómez JC. An Integrated View of Virus-Triggered Cellular Plasticity Using Boolean Networks. Cells 2021; 10:cells10112863. [PMID: 34831086 PMCID: PMC8616224 DOI: 10.3390/cells10112863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/18/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022] Open
Abstract
Virus-related mortality and morbidity are due to cell/tissue damage caused by replicative pressure and resource exhaustion, e.g., HBV or HIV; exaggerated immune responses, e.g., SARS-CoV-2; and cancer, e.g., EBV or HPV. In this context, oncogenic and other types of viruses drive genetic and epigenetic changes that expand the tumorigenic program, including modifications to the ability of cancer cells to migrate. The best-characterized group of changes is collectively known as the epithelial–mesenchymal transition, or EMT. This is a complex phenomenon classically described using biochemistry, cell biology and genetics. However, these methods require enormous, often slow, efforts to identify and validate novel therapeutic targets. Systems biology can complement and accelerate discoveries in this field. One example of such an approach is Boolean networks, which make complex biological problems tractable by modeling data (“nodes”) connected by logical operators. Here, we focus on virus-induced cellular plasticity and cell reprogramming in mammals, and how Boolean networks could provide novel insights into the ability of some viruses to trigger uncontrolled cell proliferation and EMT, two key hallmarks of cancer.
Collapse
Affiliation(s)
- Jenny Paola Alfaro-García
- Molecular and Translation Medicine Group, Faculty of Medicine, University of Antioquia, Medellin 050010, Colombia; (J.P.A.-G.); (M.C.G.-A.)
| | - María Camila Granados-Alzate
- Molecular and Translation Medicine Group, Faculty of Medicine, University of Antioquia, Medellin 050010, Colombia; (J.P.A.-G.); (M.C.G.-A.)
| | - Miguel Vicente-Manzanares
- Molecular Mechanisms Program, Centro de Investigación del Cáncer, Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007 Salamanca, Spain
- Correspondence: (M.V.-M.); (J.C.G.-G.)
| | - Juan Carlos Gallego-Gómez
- Molecular and Translation Medicine Group, Faculty of Medicine, University of Antioquia, Medellin 050010, Colombia; (J.P.A.-G.); (M.C.G.-A.)
- Correspondence: (M.V.-M.); (J.C.G.-G.)
| |
Collapse
|