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Zhang YW, Gvozdenovic A, Aceto N. A Molecular Voyage: Multiomics Insights into Circulating Tumor Cells. Cancer Discov 2024; 14:920-933. [PMID: 38581442 DOI: 10.1158/2159-8290.cd-24-0218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/08/2024] [Accepted: 03/13/2024] [Indexed: 04/08/2024]
Abstract
Circulating tumor cells (CTCs) play a pivotal role in metastasis, the leading cause of cancer-associated death. Recent improvements of CTC isolation tools, coupled with a steady development of multiomics technologies at single-cell resolution, have enabled an extensive exploration of CTC biology, unlocking insights into their molecular profiles. A detailed molecular portrait requires CTC interrogation across various levels encompassing genomic, epigenetic, transcriptomic, proteomic and metabolic features. Here, we review how state-of-the-art multiomics applied to CTCs are shedding light on how cancer spreads. Further, we highlight the potential implications of CTC profiling for clinical applications aimed at enhancing cancer diagnosis and treatment. SIGNIFICANCE Exploring the complexity of cancer progression through cutting-edge multiomics studies holds the promise of uncovering novel aspects of cancer biology and identifying therapeutic vulnerabilities to suppress metastasis.
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Affiliation(s)
- Yu Wei Zhang
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich, Switzerland
| | - Ana Gvozdenovic
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich, Switzerland
| | - Nicola Aceto
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich, Switzerland
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2
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Ferrer CM, Cho HM, Boon R, Bernasocchi T, Wong LP, Cetinbas M, Haggerty ER, Mitsiades I, Wojtkiewicz GR, McLoughlin DE, Aboushousha R, Abdelhamid H, Kugel S, Rheinbay E, Sadreyev R, Juric D, Janssen-Heininger YMW, Mostoslavsky R. The glutathione S-transferase Gstt1 drives survival and dissemination in metastases. Nat Cell Biol 2024; 26:975-990. [PMID: 38862786 DOI: 10.1038/s41556-024-01426-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 04/18/2024] [Indexed: 06/13/2024]
Abstract
Identifying the adaptive mechanisms of metastatic cancer cells remains an elusive question in the treatment of metastatic disease, particularly in pancreatic cancer (pancreatic adenocarcinoma, PDA). A loss-of-function shRNA targeted screen in metastatic-derived cells identified Gstt1, a member of the glutathione S-transferase superfamily, as uniquely required for dissemination and metastasis, but dispensable for primary tumour growth. Gstt1 is expressed in latent disseminated tumour cells (DTCs), is retained within a subpopulation of slow-cycling cells within existing metastases, and its inhibition leads to complete regression of macrometastatic tumours. This distinct Gstt1high population is highly metastatic and retains slow-cycling phenotypes, epithelial-mesenchymal transition features and DTC characteristics compared to the Gstt1low population. Mechanistic studies indicate that in this subset of cancer cells, Gstt1 maintains metastases by binding and glutathione-modifying intracellular fibronectin, in turn promoting its secretion and deposition into the metastatic microenvironment. We identified Gstt1 as a mediator of metastasis, highlighting the importance of heterogeneity and its influence on the metastatic tumour microenvironment.
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Affiliation(s)
- Christina M Ferrer
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA.
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- University of Maryland School of Medicine and the Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA.
| | - Hyo Min Cho
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ruben Boon
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Galapagos NV, 2800 Mechelen, Belgium
| | - Tiziano Bernasocchi
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lai Ping Wong
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Murat Cetinbas
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Elizabeth R Haggerty
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Irene Mitsiades
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | | | - Daniel E McLoughlin
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Termeer Center for Targeted Therapies, Massachusetts General Hospital, Boston, MA, USA
| | - Reem Aboushousha
- University of Vermont Larner College of Medicine, Burlington, VT, USA
| | - Hend Abdelhamid
- University of Vermont Larner College of Medicine, Burlington, VT, USA
| | - Sita Kugel
- Fred Hutchison Cancer Research Center, Seattle, WA, USA
| | - Esther Rheinbay
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Dejan Juric
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Termeer Center for Targeted Therapies, Massachusetts General Hospital, Boston, MA, USA
| | | | - Raul Mostoslavsky
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA.
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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3
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Rotatori S, Zhang Y, Madden-Hennessey K, Mohammed C, Yang CH, Urbani J, Shrestha P, Pettinelli J, Wang D, Liu X, Zhao Q. Live cell pool and rare cell isolation using Enrich TROVO system. N Biotechnol 2024; 80:12-20. [PMID: 38176452 DOI: 10.1016/j.nbt.2023.12.013] [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: 05/02/2023] [Revised: 12/12/2023] [Accepted: 12/30/2023] [Indexed: 01/06/2024]
Abstract
Although several technologies have been developed to isolate cells of interest from a heterogenous sample, clogging and impaired cell viability limit such isolation. We have developed the Enrich TROVO system as a novel, nonfluidic technology to sort live cells. The TROVO system combines imaging-based cell selection and photo-crosslinking of (gelatin methacrylate) gelMA-hydrogel to capture cells. After capture, cells are released by enzymatic digestion of the hydrogel and then retrieved for downstream analysis or further cell culturing. The system can capture cells with a recovery rate of 48% while maintaining 90% viability. Moreover, TROVO can enrich rare cells 506-fold with 93% efficiency using single step isolation from a 1:104 cell mixture, and can also capture one target cell from 1 million cells, reaching an enrichment ratio of 9128. In addition, 100% purity and 49% recovery rate can be achieved by a following negative isolation process. Compared to existing technologies, the TROVO system is clog-resistant, highly biocompatible, and can process a wide range of sample sizes.
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Affiliation(s)
- Stephen Rotatori
- Enrich Biosystems Inc., 21 Business Park Drive. STE. 4, Branford, CT 06405, USA
| | - Yichong Zhang
- Enrich Biosystems Inc., 21 Business Park Drive. STE. 4, Branford, CT 06405, USA.
| | | | - Christina Mohammed
- Enrich Biosystems Inc., 21 Business Park Drive. STE. 4, Branford, CT 06405, USA
| | - Chi-Han Yang
- Enrich Biosystems Inc., 21 Business Park Drive. STE. 4, Branford, CT 06405, USA
| | - Jordan Urbani
- Enrich Biosystems Inc., 21 Business Park Drive. STE. 4, Branford, CT 06405, USA
| | - Prem Shrestha
- Enrich Biosystems Inc., 21 Business Park Drive. STE. 4, Branford, CT 06405, USA
| | - Joseph Pettinelli
- Enrich Biosystems Inc., 21 Business Park Drive. STE. 4, Branford, CT 06405, USA
| | - Dong Wang
- Enrich Biosystems Inc., 21 Business Park Drive. STE. 4, Branford, CT 06405, USA
| | - Xueqi Liu
- Enrich Biosystems Inc., 21 Business Park Drive. STE. 4, Branford, CT 06405, USA
| | - Qi Zhao
- Enrich Biosystems Inc., 21 Business Park Drive. STE. 4, Branford, CT 06405, USA.
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4
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Wang Z, Wang H, Lin S, Angers S, Sargent EH, Kelley SO. Phenotypic targeting using magnetic nanoparticles for rapid characterization of cellular proliferation regulators. SCIENCE ADVANCES 2024; 10:eadj1468. [PMID: 38718125 PMCID: PMC11078187 DOI: 10.1126/sciadv.adj1468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 04/03/2024] [Indexed: 05/12/2024]
Abstract
Genome-wide CRISPR screens have provided a systematic way to identify essential genetic regulators of a phenotype of interest with single-cell resolution. However, most screens use live/dead readout of viability to identify factors of interest. Here, we describe an approach that converts cell proliferation into the degree of magnetization, enabling downstream microfluidic magnetic sorting to be performed. We performed a head-to-head comparison and verified that the magnetic workflow can identify the same hits from a traditional screen while reducing the screening period from 4 weeks to 1 week. Taking advantage of parallelization and performance, we screened multiple mesenchymal cancer cell lines for their dependency on cell proliferation. We found and validated pan- and cell-specific potential therapeutic targets. The method presented provides a nanoparticle-enabled approach means to increase the breadth of data collected in CRISPR screens, enabling the rapid discovery of drug targets for treatment.
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Affiliation(s)
- Zongjie Wang
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2, Canada
| | - Hansen Wang
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2, Canada
| | - Sichun Lin
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto M5S 3E1, Canada
| | - Stephane Angers
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto M5S 3E1, Canada
| | - Edward H. Sargent
- The Edward S. Rogers Sr. Department of Electrical & Computer Engineering, University of Toronto, Toronto M5S 3G4, Canada
- Department of Chemistry, Weinberg College of Arts and Science, Northwestern University, Evanston, IL 60208, USA
- Department of Electrical and Computer Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, Evanston, IL 60208, USA
| | - Shana O. Kelley
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2, Canada
- The Edward S. Rogers Sr. Department of Electrical & Computer Engineering, University of Toronto, Toronto M5S 3G4, Canada
- Department of Chemistry, Weinberg College of Arts and Science, Northwestern University, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, Evanston, IL 60208, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
- Simpson Querrey Institute, Northwestern University, Chicago, IL 60611, USA
- Chan Zuckerberg Biohub Chicago, Chicago, IL 60607, USA
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5
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Karras P, Black JRM, McGranahan N, Marine JC. Decoding the interplay between genetic and non-genetic drivers of metastasis. Nature 2024; 629:543-554. [PMID: 38750233 DOI: 10.1038/s41586-024-07302-6] [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: 06/24/2022] [Accepted: 03/12/2024] [Indexed: 05/18/2024]
Abstract
Metastasis is a multistep process by which cancer cells break away from their original location and spread to distant organs, and is responsible for the vast majority of cancer-related deaths. Preventing early metastatic dissemination would revolutionize the ability to fight cancer. Unfortunately, the relatively poor understanding of the molecular underpinnings of metastasis has hampered the development of effective anti-metastatic drugs. Although it is now accepted that disseminating tumour cells need to acquire multiple competencies to face the many obstacles they encounter before reaching their metastatic site(s), whether these competencies are acquired through an accumulation of metastasis-specific genetic alterations and/or non-genetic events is often debated. Here we review a growing body of literature highlighting the importance of both genetic and non-genetic reprogramming events during the metastatic cascade, and discuss how genetic and non-genetic processes act in concert to confer metastatic competencies. We also describe how recent technological advances, and in particular the advent of single-cell multi-omics and barcoding approaches, will help to better elucidate the cross-talk between genetic and non-genetic mechanisms of metastasis and ultimately inform innovative paths for the early detection and interception of this lethal process.
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Affiliation(s)
- Panagiotis Karras
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - James R M Black
- Cancer Genome Evolution Research Group, UCL Cancer Institute, London, UK
| | | | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium.
- Department of Oncology, KU Leuven, Leuven, Belgium.
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6
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Johnson GA, Gould SI, Sánchez-Rivera FJ. Deconstructing cancer with precision genome editing. Biochem Soc Trans 2024; 52:803-819. [PMID: 38629716 PMCID: PMC11088927 DOI: 10.1042/bst20230984] [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: 02/01/2024] [Revised: 03/25/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024]
Abstract
Recent advances in genome editing technologies are allowing investigators to engineer and study cancer-associated mutations in their endogenous genetic contexts with high precision and efficiency. Of these, base editing and prime editing are quickly becoming gold-standards in the field due to their versatility and scalability. Here, we review the merits and limitations of these precision genome editing technologies, their application to modern cancer research, and speculate how these could be integrated to address future directions in the field.
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Affiliation(s)
- Grace A. Johnson
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02142, MA, U.S.A
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge 02142, MA, U.S.A
| | - Samuel I. Gould
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02142, MA, U.S.A
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge 02142, MA, U.S.A
| | - Francisco J. Sánchez-Rivera
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02142, MA, U.S.A
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge 02142, MA, U.S.A
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7
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Toriseva M, Björkgren I, Junnila A, Mehmood A, Mattsson J, Raimoranta I, Kim B, Laiho A, Nees M, Elo L, Poutanen M, Breton S, Sipilä P. RUNX transcription factors are essential in maintaining epididymal epithelial differentiation. Cell Mol Life Sci 2024; 81:183. [PMID: 38630262 PMCID: PMC11023966 DOI: 10.1007/s00018-024-05211-5] [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: 09/04/2023] [Revised: 01/06/2024] [Accepted: 03/18/2024] [Indexed: 04/19/2024]
Abstract
Apart from the androgen receptor, transcription factors (TFs) that are required for the development and formation of the different segments of the epididymis have remained unknown. We identified TF families expressed in the developing epididymides, of which many showed segment specificity. From these TFs, down-regulation of runt related transcription factors (RUNXs) 1 and 2 expression coincides with epithelial regression in Dicer1 cKO mice. Concomitant deletion of both Runx1 and Runx2 in a mouse epididymal epithelial cell line affected cell morphology, adhesion and mobility in vitro. Furthermore, lack of functional RUNXs severely disturbed the formation of 3D epididymal organoid-like structures. Transcriptomic analysis of the epididymal cell organoid-like structures indicated that RUNX1 and RUNX2 are involved in the regulation of MAPK signaling, NOTCH pathway activity, and EMT-related gene expression. This suggests that RUNXs are master regulators of several essential signaling pathways, and necessary for the maintenance of proper differentiation of the epididymal epithelium.
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Affiliation(s)
- Mervi Toriseva
- Institute of Biomedicine, Cancer Research Unit and FICAN West Cancer Centre Laboratory, University of Turku and Turku University Hospital, Turku, Finland
| | - Ida Björkgren
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, Turku Center for Disease Modeling, University of Turku, Turku, Finland
| | - Arttu Junnila
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, Turku Center for Disease Modeling, University of Turku, Turku, Finland
| | - Arfa Mehmood
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Jesse Mattsson
- Institute of Biomedicine, Cancer Research Unit and FICAN West Cancer Centre Laboratory, University of Turku and Turku University Hospital, Turku, Finland
| | - Inka Raimoranta
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, Turku Center for Disease Modeling, University of Turku, Turku, Finland
| | - Bongki Kim
- Program in Membrane Biology/Division of Nephrology, Massachusetts General Hospital, Simches Research Center, Boston, MA, 02114, USA
- Department of Animal Resources Science, Kongju National University, Chungcheongnam-do, Yesan, 32439, Republic of Korea
| | - Asta Laiho
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Matthias Nees
- Institute of Biomedicine, Cancer Research Unit and FICAN West Cancer Centre Laboratory, University of Turku and Turku University Hospital, Turku, Finland
| | - Laura Elo
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, Turku Center for Disease Modeling, University of Turku, Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Matti Poutanen
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, Turku Center for Disease Modeling, University of Turku, Turku, Finland
- Institute of Medicine, The Sahlgrenska Academy, Gothenburg University, Göteborg, Sweden
| | - Sylvie Breton
- Program in Membrane Biology/Division of Nephrology, Massachusetts General Hospital, Simches Research Center, Boston, MA, 02114, USA
- Department of Obstetrics, Gynecology and Reproduction, Faculty of Medicine, Research Center-CHU de Québec, Université Laval, Québec, QC, Canada
| | - Petra Sipilä
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, Turku Center for Disease Modeling, University of Turku, Turku, Finland.
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