1
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Russo M, Chen M, Mariella E, Peng H, Rehman SK, Sancho E, Sogari A, Toh TS, Balaban NQ, Batlle E, Bernards R, Garnett MJ, Hangauer M, Leucci E, Marine JC, O'Brien CA, Oren Y, Patton EE, Robert C, Rosenberg SM, Shen S, Bardelli A. Cancer drug-tolerant persister cells: from biological questions to clinical opportunities. Nat Rev Cancer 2024:10.1038/s41568-024-00737-z. [PMID: 39223250 DOI: 10.1038/s41568-024-00737-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/29/2024] [Indexed: 09/04/2024]
Abstract
The emergence of drug resistance is the most substantial challenge to the effectiveness of anticancer therapies. Orthogonal approaches have revealed that a subset of cells, known as drug-tolerant 'persister' (DTP) cells, have a prominent role in drug resistance. Although long recognized in bacterial populations which have acquired resistance to antibiotics, the presence of DTPs in various cancer types has come to light only in the past two decades, yet several aspects of their biology remain enigmatic. Here, we delve into the biological characteristics of DTPs and explore potential strategies for tracking and targeting them. Recent findings suggest that DTPs exhibit remarkable plasticity, being capable of transitioning between different cellular states, resulting in distinct DTP phenotypes within a single tumour. However, defining the biological features of DTPs has been challenging, partly due to the complex interplay between clonal dynamics and tissue-specific factors influencing their phenotype. Moreover, the interactions between DTPs and the tumour microenvironment, including their potential to evade immune surveillance, remain to be discovered. Finally, the mechanisms underlying DTP-derived drug resistance and their correlation with clinical outcomes remain poorly understood. This Roadmap aims to provide a comprehensive overview of the field of DTPs, encompassing past achievements and current endeavours in elucidating their biology. We also discuss the prospect of future advancements in technologies in helping to unveil the features of DTPs and propose novel therapeutic strategies that could lead to their eradication.
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Affiliation(s)
- Mariangela Russo
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Torino, Italy.
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milano, Italy.
| | - Mengnuo Chen
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Elisa Mariella
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Torino, Italy
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milano, Italy
| | - Haoning Peng
- Institute of Thoracic Oncology and National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, China
| | - Sumaiyah K Rehman
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Elena Sancho
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Alberto Sogari
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Torino, Italy
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milano, Italy
| | - Tzen S Toh
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Nathalie Q Balaban
- Racah Institute of Physics, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Rene Bernards
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Matthew Hangauer
- Department of Dermatology, University of California San Diego, San Diego, CA, USA
| | | | - Jean-Christophe Marine
- Department of Oncology, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
| | - Catherine A O'Brien
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Surgery, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Yaara Oren
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - E Elizabeth Patton
- MRC Human Genetics Unit, and CRUK Scotland Centre and Edinburgh Cancer Research, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Caroline Robert
- Oncology Department, Dermatology Unit, Villejuif, France
- Oncology Department and INSERM U981, Villejuif, France
- Paris Saclay University, Villejuif, France
| | - Susan M Rosenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shensi Shen
- Institute of Thoracic Oncology and National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, China
| | - Alberto Bardelli
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Torino, Italy.
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milano, Italy.
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2
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Cañellas-Socias A, Sancho E, Batlle E. Mechanisms of metastatic colorectal cancer. Nat Rev Gastroenterol Hepatol 2024; 21:609-625. [PMID: 38806657 DOI: 10.1038/s41575-024-00934-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/17/2024] [Indexed: 05/30/2024]
Abstract
Despite extensive research and improvements in understanding colorectal cancer (CRC), its metastatic form continues to pose a substantial challenge, primarily owing to limited therapeutic options and a poor prognosis. This Review addresses the emerging focus on metastatic CRC (mCRC), which has historically been under-studied compared with primary CRC despite its lethality. We delve into two crucial aspects: the molecular and cellular determinants facilitating CRC metastasis and the principles guiding the evolution of metastatic disease. Initially, we examine the genetic alterations integral to CRC metastasis, connecting them to clinically marked characteristics of advanced CRC. Subsequently, we scrutinize the role of cellular heterogeneity and plasticity in metastatic spread and therapy resistance. Finally, we explore how the tumour microenvironment influences metastatic disease, emphasizing the effect of stromal gene programmes and the immune context. The ongoing research in these fields holds immense importance, as its future implications are projected to revolutionize the treatment of patients with mCRC, hopefully offering a promising outlook for their survival.
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Affiliation(s)
- Adrià Cañellas-Socias
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
| | - Elena Sancho
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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3
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Leto SM, Grassi E, Avolio M, Vurchio V, Cottino F, Ferri M, Zanella ER, Borgato S, Corti G, di Blasio L, Somale D, Vara-Messler M, Galimi F, Sassi F, Lupo B, Catalano I, Pinnelli M, Viviani M, Sperti L, Mellano A, Ferrero A, Zingaretti CC, Puliafito A, Primo L, Bertotti A, Trusolino L. XENTURION is a population-level multidimensional resource of xenografts and tumoroids from metastatic colorectal cancer patients. Nat Commun 2024; 15:7495. [PMID: 39209908 PMCID: PMC11362617 DOI: 10.1038/s41467-024-51909-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 08/19/2024] [Indexed: 09/04/2024] Open
Abstract
The breadth and depth at which cancer models are interrogated contribute to the successful clinical translation of drug discovery efforts. In colorectal cancer (CRC), model availability is limited by a dearth of large-scale collections of patient-derived xenografts (PDXs) and paired tumoroids from metastatic disease, where experimental therapies are typically tested. Here we introduce XENTURION, an open-science resource offering a platform of 128 PDX models from patients with metastatic CRC, along with matched PDX-derived tumoroids. Multidimensional omics analyses indicate that tumoroids retain extensive molecular fidelity with parental PDXs. A tumoroid-based trial with the anti-EGFR antibody cetuximab reveals variable sensitivities that are consistent with clinical response biomarkers, mirror tumor growth changes in matched PDXs, and recapitulate EGFR genetic deletion outcomes. Inhibition of adaptive signals upregulated by EGFR blockade increases the magnitude of cetuximab response. These findings illustrate the potential of large living biobanks, providing avenues for molecularly informed preclinical research in oncology.
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Affiliation(s)
| | - Elena Grassi
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Marco Avolio
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Valentina Vurchio
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | | | - Martina Ferri
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | | | - Sofia Borgato
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Giorgio Corti
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Laura di Blasio
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Desiana Somale
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, Torino, Italy
- Aptuit, an Evotec Company, Verona, Italy
| | - Marianela Vara-Messler
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
- Sanofi Belgium, Zwijnaarde, Belgium
| | - Francesco Galimi
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Francesco Sassi
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, Torino, Italy
| | - Barbara Lupo
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Irene Catalano
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, Torino, Italy
| | - Marika Pinnelli
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Marco Viviani
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Luca Sperti
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Alfredo Mellano
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, Torino, Italy
| | | | | | - Alberto Puliafito
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Luca Primo
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Andrea Bertotti
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, Torino, Italy.
- Department of Oncology, University of Torino, Candiolo, Torino, Italy.
| | - Livio Trusolino
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, Torino, Italy.
- Department of Oncology, University of Torino, Candiolo, Torino, Italy.
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4
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Tape CJ. Plastic persisters: revival stem cells in colorectal cancer. Trends Cancer 2024; 10:185-195. [PMID: 38071119 DOI: 10.1016/j.trecan.2023.11.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 03/16/2024]
Abstract
Colorectal cancer (CRC) is traditionally considered to be a genetically driven disease. However, nongenetic plasticity has recently emerged as a major driver of tumour initiation, metastasis, and therapy response in CRC. Central to these processes is a recently discovered cell type, the revival colonic stem cell (revCSC). In contrast to traditional proliferative CSCs (proCSCs), revCSCs prioritise survival over propagation. revCSCs play an essential role in primary tumour formation, metastatic dissemination, and nongenetic chemoresistance. Current evidence suggests that CRC tumours leverage intestinal stem cell plasticity to both proliferate (via proCSCs) when unchallenged and survive (via revCSCs) in response to cell-extrinsic pressures. Although revCSCs likely represent a major source of therapeutic failure in CRC, our increasing knowledge of this important stem cell fate provides novel opportunities for therapeutic intervention.
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Affiliation(s)
- Christopher J Tape
- Cell Communication Lab, Department of Oncology, University College London Cancer Institute, 72 Huntley Street, London, WC1E 6DD, UK.
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5
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Sakahara M, Okamoto T, Srivastava U, Natsume Y, Yamanaka H, Suzuki Y, Obama K, Nagayama S, Yao R. Paneth-like cells produced from OLFM4 + stem cells support OLFM4 + stem cell growth in advanced colorectal cancer. Commun Biol 2024; 7:27. [PMID: 38182890 PMCID: PMC10770338 DOI: 10.1038/s42003-023-05504-8] [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: 11/15/2022] [Accepted: 10/25/2023] [Indexed: 01/07/2024] Open
Abstract
Tumor tissues consist of heterogeneous cells that originate from stem cells; however, their cell fate determination program remains incompletely understood. Using patient-derived organoids established from patients with advanced colorectal cancer (CRC), we evaluated the potential of olfactomedin 4 (OLFM4)+ stem cells to produce a bifurcated lineage of progenies with absorptive and secretory properties. In the early phases of organoid reconstruction, OLFM4+ cells preferentially gave rise to secretory cells. Additionally, we found that Paneth-like cells, which do not exist in the normal colon, were induced in response to Notch signaling inhibition. Video recordings of single OLFM4+ cells revealed that organoids containing Paneth-like cells were effectively propagated and that their selective ablation led to organoid collapse. In tumor tissues, Paneth-like cells were identified only in the region where tumor cells lost cell adhesion. These findings indicate that Paneth-like cells are directly produced by OLFM4+ stem cells and that their interaction contributes to tumor formation by providing niche factors. This study reveals the importance of the cell fate specification program for building a complete tumor cellular ecosystem, which might be targeted with novel therapeutics.
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Affiliation(s)
- Mizuho Sakahara
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Takuya Okamoto
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Upasna Srivastava
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Child Study Center, Yale School of Medicine, New Haven, CT, USA
| | - Yasuko Natsume
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Hitomi Yamanaka
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Kazutaka Obama
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Satoshi Nagayama
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Surgery, Uji-Tokushukai Medical Center, Kyoto, Japan
| | - Ryoji Yao
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan.
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6
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Plattner C, Lamberti G, Blattmann P, Kirchmair A, Rieder D, Loncova Z, Sturm G, Scheidl S, Ijsselsteijn M, Fotakis G, Noureen A, Lisandrelli R, Böck N, Nemati N, Krogsdam A, Daum S, Finotello F, Somarakis A, Schäfer A, Wilflingseder D, Gonzalez Acera M, Öfner D, Huber LA, Clevers H, Becker C, Farin HF, Greten FR, Aebersold R, de Miranda NF, Trajanoski Z. Functional and spatial proteomics profiling reveals intra- and intercellular signaling crosstalk in colorectal cancer. iScience 2023; 26:108399. [PMID: 38047086 PMCID: PMC10692669 DOI: 10.1016/j.isci.2023.108399] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/21/2023] [Accepted: 11/02/2023] [Indexed: 12/05/2023] Open
Abstract
Precision oncology approaches for patients with colorectal cancer (CRC) continue to lag behind other solid cancers. Functional precision oncology-a strategy that is based on perturbing primary tumor cells from cancer patients-could provide a road forward to personalize treatment. We extend this paradigm to measuring proteome activity landscapes by acquiring quantitative phosphoproteomic data from patient-derived organoids (PDOs). We show that kinase inhibitors induce inhibitor- and patient-specific off-target effects and pathway crosstalk. Reconstruction of the kinase networks revealed that the signaling rewiring is modestly affected by mutations. We show non-genetic heterogeneity of the PDOs and upregulation of stemness and differentiation genes by kinase inhibitors. Using imaging mass-cytometry-based profiling of the primary tumors, we characterize the tumor microenvironment (TME) and determine spatial heterocellular crosstalk and tumor-immune cell interactions. Collectively, we provide a framework for inferring tumor cell intrinsic signaling and external signaling from the TME to inform precision (immuno-) oncology in CRC.
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Affiliation(s)
- Christina Plattner
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Giorgia Lamberti
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Peter Blattmann
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Alexander Kirchmair
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Dietmar Rieder
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Zuzana Loncova
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Gregor Sturm
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Stefan Scheidl
- Department of Visceral, Transplant and Thoracic Surgery, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Marieke Ijsselsteijn
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Georgios Fotakis
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Asma Noureen
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Rebecca Lisandrelli
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Nina Böck
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Niloofar Nemati
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Anne Krogsdam
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Sophia Daum
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Francesca Finotello
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Antonios Somarakis
- Department of Radiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Alexander Schäfer
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Doris Wilflingseder
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Miguel Gonzalez Acera
- Department of Medicine 1, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Dietmar Öfner
- Department of Visceral, Transplant and Thoracic Surgery, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Lukas A. Huber
- Biocenter, Institute of Cell Biology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Hans Clevers
- Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Christoph Becker
- Department of Medicine 1, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Henner F. Farin
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, 60596 Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), partner site Frankfurt/Mainz, a partnership with DKFZ Heidelberg, Frankfurt/Mainz, Germany
| | - Florian R. Greten
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, 60596 Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), partner site Frankfurt/Mainz, a partnership with DKFZ Heidelberg, Frankfurt/Mainz, Germany
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Noel F.C.C. de Miranda
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Zlatko Trajanoski
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
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7
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Dobbs Spendlove M, M. Gibson T, McCain S, Stone BC, Gill T, Pickett BE. Pathway2Targets: an open-source pathway-based approach to repurpose therapeutic drugs and prioritize human targets. PeerJ 2023; 11:e16088. [PMID: 37790614 PMCID: PMC10544355 DOI: 10.7717/peerj.16088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/22/2023] [Indexed: 10/05/2023] Open
Abstract
Background Recent efforts to repurpose existing drugs to different indications have been accompanied by a number of computational methods, which incorporate protein-protein interaction networks and signaling pathways, to aid with prioritizing existing targets and/or drugs. However, many of these existing methods are focused on integrating additional data that are only available for a small subset of diseases or conditions. Methods We have designed and implemented a new R-based open-source target prioritization and repurposing method that integrates both canonical intracellular signaling information from five public pathway databases and target information from public sources including OpenTargets.org. The Pathway2Targets algorithm takes a list of significant pathways as input, then retrieves and integrates public data for all targets within those pathways for a given condition. It also incorporates a weighting scheme that is customizable by the user to support a variety of use cases including target prioritization, drug repurposing, and identifying novel targets that are biologically relevant for a different indication. Results As a proof of concept, we applied this algorithm to a public colorectal cancer RNA-sequencing dataset with 144 case and control samples. Our analysis identified 430 targets and ~700 unique drugs based on differential gene expression and signaling pathway enrichment. We found that our highest-ranked predicted targets were significantly enriched in targets with FDA-approved therapeutics for colorectal cancer (p-value < 0.025) that included EGFR, VEGFA, and PTGS2. Interestingly, there was no statistically significant enrichment of targets for other cancers in this same list suggesting high specificity of the results. We also adjusted the weighting scheme to prioritize more novel targets for CRC. This second analysis revealed epidermal growth factor receptor (EGFR), phosphoinositide-3-kinase (PI3K), and two mitogen-activated protein kinases (MAPK14 and MAPK3). These observations suggest that our open-source method with a customizable weighting scheme can accurately prioritize targets that are specific and relevant to the disease or condition of interest, as well as targets that are at earlier stages of development. We anticipate that this method will complement other approaches to repurpose drugs for a variety of indications, which can contribute to the improvement of the quality of life and overall health of such patients.
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Affiliation(s)
- Mauri Dobbs Spendlove
- Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Trenton M. Gibson
- Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Shaney McCain
- Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Benjamin C. Stone
- Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | | | - Brett E. Pickett
- Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
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8
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Beekhof R, Bertotti A, Böttger F, Vurchio V, Cottino F, Zanella ER, Migliardi G, Viviani M, Grassi E, Lupo B, Henneman AA, Knol JC, Pham TV, de Goeij-de Haas R, Piersma SR, Labots M, Verheul HMW, Trusolino L, Jimenez CR. Phosphoproteomics of patient-derived xenografts identifies targets and markers associated with sensitivity and resistance to EGFR blockade in colorectal cancer. Sci Transl Med 2023; 15:eabm3687. [PMID: 37585503 DOI: 10.1126/scitranslmed.abm3687] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 07/25/2023] [Indexed: 08/18/2023]
Abstract
Epidermal growth factor receptor (EGFR) is a well-exploited therapeutic target in metastatic colorectal cancer (mCRC). Unfortunately, not all patients benefit from current EGFR inhibitors. Mass spectrometry-based proteomics and phosphoproteomics were performed on 30 genomically and pharmacologically characterized mCRC patient-derived xenografts (PDXs) to investigate the molecular basis of response to EGFR blockade and identify alternative drug targets to overcome resistance. Both the tyrosine and global phosphoproteome as well as the proteome harbored distinctive response signatures. We found that increased pathway activity related to mitogen-activated protein kinase (MAPK) inhibition and abundant tyrosine phosphorylation of cell junction proteins, such as CXADR and CLDN1/3, in sensitive tumors, whereas epithelial-mesenchymal transition and increased MAPK and AKT signaling were more prevalent in resistant tumors. Furthermore, the ranking of kinase activities in single samples confirmed the driver activity of ERBB2, EGFR, and MET in cetuximab-resistant tumors. This analysis also revealed high kinase activity of several members of the Src and ephrin kinase family in 2 CRC PDX models with genomically unexplained resistance. Inhibition of these hyperactive kinases, alone or in combination with cetuximab, resulted in growth inhibition of ex vivo PDX-derived organoids and in vivo PDXs. Together, these findings highlight the potential value of phosphoproteomics to improve our understanding of anti-EGFR treatment and response prediction in mCRC and bring to the forefront alternative drug targets in cetuximab-resistant tumors.
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Affiliation(s)
- Robin Beekhof
- Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, Netherlands
- Amsterdam UMC, Vrije Universiteit Amsterdam, OncoProteomics Laboratory, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, Netherlands
| | - Andrea Bertotti
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, 10060 Torino, Italy
- Department of Oncology, University of Torino, Candiolo, 10060 Torino, Italy
| | - Franziska Böttger
- Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, Netherlands
- Amsterdam UMC, Vrije Universiteit Amsterdam, OncoProteomics Laboratory, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, Netherlands
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Oncode Institute, 1066 CX Amsterdam, Netherlands
| | - Valentina Vurchio
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, 10060 Torino, Italy
- Department of Oncology, University of Torino, Candiolo, 10060 Torino, Italy
| | - Francesca Cottino
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, 10060 Torino, Italy
| | - Eugenia R Zanella
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, 10060 Torino, Italy
| | - Giorgia Migliardi
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, 10060 Torino, Italy
- Department of Oncology, University of Torino, Candiolo, 10060 Torino, Italy
| | - Marco Viviani
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, 10060 Torino, Italy
- Department of Oncology, University of Torino, Candiolo, 10060 Torino, Italy
| | - Elena Grassi
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, 10060 Torino, Italy
- Department of Oncology, University of Torino, Candiolo, 10060 Torino, Italy
| | - Barbara Lupo
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, 10060 Torino, Italy
| | - Alex A Henneman
- Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, Netherlands
- Amsterdam UMC, Vrije Universiteit Amsterdam, OncoProteomics Laboratory, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, Netherlands
| | - Jaco C Knol
- Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, Netherlands
- Amsterdam UMC, Vrije Universiteit Amsterdam, OncoProteomics Laboratory, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, Netherlands
| | - Thang V Pham
- Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, Netherlands
- Amsterdam UMC, Vrije Universiteit Amsterdam, OncoProteomics Laboratory, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, Netherlands
| | - Richard de Goeij-de Haas
- Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, Netherlands
- Amsterdam UMC, Vrije Universiteit Amsterdam, OncoProteomics Laboratory, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, Netherlands
| | - Sander R Piersma
- Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, Netherlands
- Amsterdam UMC, Vrije Universiteit Amsterdam, OncoProteomics Laboratory, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, Netherlands
| | - Mariette Labots
- Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, Netherlands
| | - Henk M W Verheul
- Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, Netherlands
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD Rotterdam, Netherlands
| | - Livio Trusolino
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, 10060 Torino, Italy
- Department of Oncology, University of Torino, Candiolo, 10060 Torino, Italy
| | - Connie R Jimenez
- Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, Netherlands
- Amsterdam UMC, Vrije Universiteit Amsterdam, OncoProteomics Laboratory, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, Netherlands
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9
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Pérez-González A, Bévant K, Blanpain C. Cancer cell plasticity during tumor progression, metastasis and response to therapy. NATURE CANCER 2023; 4:1063-1082. [PMID: 37537300 PMCID: PMC7615147 DOI: 10.1038/s43018-023-00595-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 06/01/2023] [Indexed: 08/05/2023]
Abstract
Cell plasticity represents the ability of cells to be reprogrammed and to change their fate and identity, enabling homeostasis restoration and tissue regeneration following damage. Cell plasticity also contributes to pathological conditions, such as cancer, enabling cells to acquire new phenotypic and functional features by transiting across distinct cell states that contribute to tumor initiation, progression, metastasis and resistance to therapy. Here, we review the intrinsic and extrinsic mechanisms driving cell plasticity that promote tumor growth and proliferation as well as metastasis and drug tolerance. Finally, we discuss how cell plasticity could be exploited for anti-cancer therapy.
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Affiliation(s)
- Andrea Pérez-González
- Laboratory of Stem Cells and Cancer, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Kevin Bévant
- Laboratory of Stem Cells and Cancer, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Cédric Blanpain
- Laboratory of Stem Cells and Cancer, Université Libre de Bruxelles (ULB), Brussels, Belgium.
- WELBIO, ULB, Bruxelles, Belgium.
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10
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Apollonio M, Bellazzo A, Franco N, Lombardi S, Senigagliesi B, Casalis L, Parisse P, Thalhammer A, Baj G, De Florian Fania R, Del Sal G, Collavin L. The Tumor Suppressor DAB2IP Is Regulated by Cell Contact and Contributes to YAP/TAZ Inhibition in Confluent Cells. Cancers (Basel) 2023; 15:3379. [PMID: 37444489 DOI: 10.3390/cancers15133379] [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: 05/13/2023] [Revised: 06/17/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
External and internal mechanical forces modulate cell morphology, movement, proliferation and metabolism, and represent crucial inputs for tissue homeostasis. The transcriptional regulators YAP and TAZ are important effectors of mechanical signaling and are frequently activated in solid tumors, correlating with metastasis, chemoresistance, and shorter patient survival. YAP/TAZ activity is controlled by various pathways that sense cell shape, polarity, contacts, and mechanical tension. In tumors, aberrant YAP/TAZ activation may result from cancer-related alterations of such regulatory networks. The tumor suppressor DAB2IP is a Ras-GAP and scaffold protein that negatively modulates multiple oncogenic pathways and is frequently downregulated or inactivated in solid tumors. Here, we provide evidence that DAB2IP expression is sustained by cell confluency. We also find that DAB2IP depletion in confluent cells alters their morphology, reducing cell packing while increasing cell stiffness. Finally, we find that DAB2IP depletion in confluent cells favors YAP/TAZ nuclear localization and transcriptional activity, while its ectopic expression in subconfluent cells increases YAP/TAZ retention in the cytoplasm. Together, these data suggest that DAB2IP may function as a sensor of cell interactions, contributing to dampening cellular responses to oncogenic inputs in confluent cells and that DAB2IP loss-of-function would facilitate YAP/TAZ activation in intact epithelia, accelerating oncogenic transformation.
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Affiliation(s)
- Mattia Apollonio
- Department of Life Sciences, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
| | - Arianna Bellazzo
- Department of Life Sciences, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
| | - Nicoletta Franco
- Department of Life Sciences, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
| | - Silvia Lombardi
- Department of Life Sciences, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
| | | | - Loredana Casalis
- Elettra-Sincrotrone Trieste, Area Science Park Basovizza, 34149 Trieste, Italy
| | - Pietro Parisse
- Elettra-Sincrotrone Trieste, Area Science Park Basovizza, 34149 Trieste, Italy
- Institute of Materials (IOM), Italian National Research Council (CNR), Area Science Park Basovizza, 34149 Trieste, Italy
| | - Agnes Thalhammer
- Department of Life Sciences, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
| | - Gabriele Baj
- Department of Life Sciences, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
| | | | - Giannino Del Sal
- Department of Life Sciences, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
- ICGEB-Area Science Park Padriciano, 34149 Trieste, Italy
- Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), 20139 Milan, Italy
| | - Licio Collavin
- Department of Life Sciences, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
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11
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Liu Y, Wu W, Cai C, Zhang H, Shen H, Han Y. Patient-derived xenograft models in cancer therapy: technologies and applications. Signal Transduct Target Ther 2023; 8:160. [PMID: 37045827 PMCID: PMC10097874 DOI: 10.1038/s41392-023-01419-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/21/2023] [Indexed: 04/14/2023] Open
Abstract
Patient-derived xenograft (PDX) models, in which tumor tissues from patients are implanted into immunocompromised or humanized mice, have shown superiority in recapitulating the characteristics of cancer, such as the spatial structure of cancer and the intratumor heterogeneity of cancer. Moreover, PDX models retain the genomic features of patients across different stages, subtypes, and diversified treatment backgrounds. Optimized PDX engraftment procedures and modern technologies such as multi-omics and deep learning have enabled a more comprehensive depiction of the PDX molecular landscape and boosted the utilization of PDX models. These irreplaceable advantages make PDX models an ideal choice in cancer treatment studies, such as preclinical trials of novel drugs, validating novel drug combinations, screening drug-sensitive patients, and exploring drug resistance mechanisms. In this review, we gave an overview of the history of PDX models and the process of PDX model establishment. Subsequently, the review presents the strengths and weaknesses of PDX models and highlights the integration of novel technologies in PDX model research. Finally, we delineated the broad application of PDX models in chemotherapy, targeted therapy, immunotherapy, and other novel therapies.
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Affiliation(s)
- Yihan Liu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
| | - Wantao Wu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
| | - Changjing Cai
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
| | - Hao Zhang
- Department of Neurosurgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Hong Shen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China.
| | - Ying Han
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China.
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12
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Dormancy, stemness, and therapy resistance: interconnected players in cancer evolution. Cancer Metastasis Rev 2023; 42:197-215. [PMID: 36757577 PMCID: PMC10014678 DOI: 10.1007/s10555-023-10092-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/26/2023] [Indexed: 02/10/2023]
Abstract
The biological complexity of cancer represents a tremendous clinical challenge, resulting in the frequent failure of current treatment protocols. In the rapidly evolving scenario of a growing tumor, anticancer treatments impose a drastic perturbation not only to cancer cells but also to the tumor microenvironment, killing a portion of the cells and inducing a massive stress response in the survivors. Consequently, treatments can act as a double-edged sword by inducing a temporary response while laying the ground for therapy resistance and subsequent disease progression. Cancer cell dormancy (or quiescence) is a central theme in tumor evolution, being tightly linked to the tumor's ability to survive cytotoxic challenges, metastasize, and resist immune-mediated attack. Accordingly, quiescent cancer cells (QCCs) have been detected in virtually all the stages of tumor development. In recent years, an increasing number of studies have focused on the characterization of quiescent/therapy resistant cancer cells, unveiling QCCs core transcriptional programs, metabolic plasticity, and mechanisms of immune escape. At the same time, our partial understanding of tumor quiescence reflects the difficulty to identify stable QCCs biomarkers/therapeutic targets and to control cancer dormancy in clinical settings. This review focuses on recent discoveries in the interrelated fields of dormancy, stemness, and therapy resistance, discussing experimental evidences in the frame of a nonlinear dynamics approach, and exploring the possibility that tumor quiescence may represent not only a peril but also a potential therapeutic resource.
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13
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Falcinelli M, Dell'Omo G, Grassi E, Mariella E, Leto SM, Scardellato S, Lorenzato A, Arena S, Bertotti A, Trusolino L, Bardelli A, d'Adda di Fagagna F. Colorectal cancer patient-derived organoids and cell lines harboring ATRX and/or DAXX mutations lack Alternative Lengthening of Telomeres (ALT). Cell Death Dis 2023; 14:96. [PMID: 36759506 PMCID: PMC9911751 DOI: 10.1038/s41419-023-05640-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/19/2023] [Accepted: 02/01/2023] [Indexed: 02/11/2023]
Abstract
Telomere maintenance is necessary to maintain cancer cell unlimited viability. However, the mechanisms maintaining telomere length in colorectal cancer (CRC) have not been extensively investigated. Telomere maintenance mechanisms (TMM) include the re-expression of telomerase or alternative lengthening of telomeres (ALT). ALT is genetically associated with somatic alterations in alpha-thalassemia/mental retardation X-linked (ATRX) and death domain-associated protein (DAXX) genes. Cells displaying ALT present distinctive features including C-circles made of telomeric DNA, long and heterogenous telomeric tracts, and telomeric DNA co-localized with promyelocytic leukemia (PML) bodies forming so-called ALT-associated PML bodies (APBs). Here, we identified mutations in ATRX and/or DAXX genes in an extensive collection of CRC samples including 119 patient-derived organoids (PDOs) and 232 established CRC cell lines. C-circles measured in CRC PDOs and cell lines showed low levels overall. We also observed that CRC PDOs and cell lines did not display a significant accumulation of APBs or long telomeres with no appreciable differences between wild-type and mutated ATRX/DAXX samples. Overall, our extensive analyses indicate that CRC is not prone to engage ALT, even when carrying genetic lesions in ATRX and/or DAXX, and support the notion that ATRX/DAXX genomic footprints are not reliable predictors of ALT.
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Affiliation(s)
- Marta Falcinelli
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Giulia Dell'Omo
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Elena Grassi
- Department of Oncology, University of Torino, 1060 Candiolo, Torino, Italy
- Candiolo Cancer Institute - FPO IRCCs, 10060 Candiolo, Torino, Italy
| | - Elisa Mariella
- Department of Oncology, University of Torino, 1060 Candiolo, Torino, Italy
- Candiolo Cancer Institute - FPO IRCCs, 10060 Candiolo, Torino, Italy
| | | | | | - Annalisa Lorenzato
- Department of Oncology, University of Torino, 1060 Candiolo, Torino, Italy
- Candiolo Cancer Institute - FPO IRCCs, 10060 Candiolo, Torino, Italy
| | - Sabrina Arena
- Department of Oncology, University of Torino, 1060 Candiolo, Torino, Italy
- Candiolo Cancer Institute - FPO IRCCs, 10060 Candiolo, Torino, Italy
| | - Andrea Bertotti
- Department of Oncology, University of Torino, 1060 Candiolo, Torino, Italy
- Candiolo Cancer Institute - FPO IRCCs, 10060 Candiolo, Torino, Italy
| | - Livio Trusolino
- Department of Oncology, University of Torino, 1060 Candiolo, Torino, Italy
- Candiolo Cancer Institute - FPO IRCCs, 10060 Candiolo, Torino, Italy
| | - Alberto Bardelli
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
- Department of Oncology, University of Torino, 1060 Candiolo, Torino, Italy
- Candiolo Cancer Institute - FPO IRCCs, 10060 Candiolo, Torino, Italy
| | - Fabrizio d'Adda di Fagagna
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy.
- Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza", Pavia, Italy.
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14
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Song Y, Wang Y, Guan A, Xue J, Li B, Huang Z, Zheng Z, Liang N, Yang Y, Li S. Footprints: Stamping hallmarks of lung cancer with patient-derived models, from molecular mechanisms to clinical translation. Front Bioeng Biotechnol 2023; 11:1132940. [PMID: 36911198 PMCID: PMC9993089 DOI: 10.3389/fbioe.2023.1132940] [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: 12/28/2022] [Accepted: 02/13/2023] [Indexed: 02/24/2023] Open
Abstract
The conventional two-dimensional (2D) tumor cell lines in Petri dishes have played an important role in revealing the molecular biological mechanism of lung cancer. However, they cannot adequately recapitulate the complex biological systems and clinical outcomes of lung cancer. The three-dimensional (3D) cell culture enables the possible 3D cell interactions and the complex 3D systems with co-culture of different cells mimicking the tumor microenvironments (TME). In this regard, patient-derived models, mainly patient-derived tumor xenograft (PDX) and patient-derived organoids discussed hereby, are with higher biological fidelity of lung cancer, and regarded as more faithful preclinical models. The significant Hallmarks of Cancer is believed to be the most comprehensive coverage of current research on tumor biological characteristics. Therefore, this review aims to present and discuss the application of different patient-derived lung cancer models from molecular mechanisms to clinical translation with regards to the dimensions of different hallmarks, and to look to the prospects of these patient-derived lung cancer models.
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Affiliation(s)
- Yang Song
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Yadong Wang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Ai Guan
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Jianchao Xue
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Bowen Li
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhicheng Huang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhibo Zheng
- Department of International Medical Services, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Naixin Liang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Yanlian Yang
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China
| | - Shanqing Li
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
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15
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Piccolo S, Panciera T, Contessotto P, Cordenonsi M. YAP/TAZ as master regulators in cancer: modulation, function and therapeutic approaches. NATURE CANCER 2023; 4:9-26. [PMID: 36564601 PMCID: PMC7614914 DOI: 10.1038/s43018-022-00473-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 10/31/2022] [Indexed: 12/24/2022]
Abstract
Our understanding of the function of the transcriptional regulators YAP and TAZ (YAP/TAZ) in cancer is advancing. In this Review, we provide an update on recent progress in YAP/TAZ biology, their regulation by Hippo signaling and mechanotransduction and highlight open questions. YAP/TAZ signaling is an addiction shared by multiple tumor types and their microenvironments, providing many malignant attributes. As such, it represents an important vulnerability that may offer a broad window of therapeutic efficacy, and here we give an overview of the current treatment strategies and pioneering clinical trials.
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Affiliation(s)
- Stefano Piccolo
- Department of Molecular Medicine, University of Padua, Padua, Italy.
- IFOM-ETS, the AIRC Institute of Molecular Oncology, Milan, Italy.
| | - Tito Panciera
- Department of Molecular Medicine, University of Padua, Padua, Italy
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16
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Metastatic recurrence in colorectal cancer arises from residual EMP1+ cells. Nature 2022; 611:603-613. [DOI: 10.1038/s41586-022-05402-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 09/30/2022] [Indexed: 11/10/2022]
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17
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Recent advances in the development of transplanted colorectal cancer mouse models. Transl Res 2022; 249:128-143. [PMID: 35850446 DOI: 10.1016/j.trsl.2022.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 06/13/2022] [Accepted: 07/11/2022] [Indexed: 11/22/2022]
Abstract
Despite progress in prevention and treatment, colorectal cancer (CRC) remains the third most common malignancy worldwide and the second most common cause of cancer death in 2020. To evaluate various characteristics of human CRC, a variety of mouse models have been established. Transplant mouse models have distinct advantages in studying the clinical behavior and therapeutic progress of CRC. Host, xenograft, and transplantation routes are the basis of transplant mouse models. As the effects of the tumor microenvironment and the systemic environment on cancer cells are gradually revealed, 3 key elements of transplanted CRC mouse models have been revolutionized. This has led to the development of humanized mice, patient-derived xenografts, and orthotopic transplants that reflect the human systemic environment, patient's tumor of origin, and tumor growth microenvironments in immunodeficient mice, respectively. These milestone events have allowed for great progress in tumor biology and the treatment of CRC. This article reviews the evolution of these events and points out their strengths and weaknesses as innovative and useful preclinical tools to study CRC progression and metastasis and to exploit novel treatment schedules by establishing a testing platform. This review article depicts the optimal transplanted CRC mouse models and emphasizes the significance of surgical models in the study of CRC behavior and treatment response.
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18
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Wang N, Cao Y, Si C, Shao P, Su G, Wang K, Bao J, Yang L. Emerging Role of ERBB2 in Targeted Therapy for Metastatic Colorectal Cancer: Signaling Pathways to Therapeutic Strategies. Cancers (Basel) 2022; 14:5160. [PMID: 36291943 PMCID: PMC9600272 DOI: 10.3390/cancers14205160] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/16/2022] [Accepted: 10/18/2022] [Indexed: 12/24/2022] Open
Abstract
Despite recent improvements in the comprehensive therapy of malignancy, metastatic colorectal cancer (mCRC) continues to have a poor prognosis. Notably, 5% of mCRC cases harbor Erb-B2 receptor tyrosine kinase 2 (ERBB2) alterations. ERBB2, commonly referred to as human epidermal growth factor receptor 2, is a member of the human epidermal growth factor receptor family of protein tyrosine kinases. In addition to being a recognized therapeutic target in the treatment of gastric and breast malignancies, it is considered crucial in the management of CRC. In this review, we describe the molecular biology of ERBB2 from the perspective of biomarkers for mCRC-targeted therapy, including receptor structures, signaling pathways, gene alterations, and their detection methods. We also discuss the relationship between ERBB2 aberrations and the underlying mechanisms of resistance to anti-EGFR therapy and immunotherapy tolerance in these patients with a focus on novel targeted therapeutics and ongoing clinical trials. This may aid the development of a new standard of care in patients with ERBB2-positive mCRC.
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Affiliation(s)
- Nannan Wang
- Department of Colorectal Surgery, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 210009, China
| | - Yuepeng Cao
- Department of Colorectal Surgery, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 210009, China
| | - Chengshuai Si
- Department of Colorectal Surgery, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 210009, China
| | - Peng Shao
- Department of Colorectal Surgery, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 210009, China
| | - Guoqing Su
- Department of Colorectal Surgery, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 210009, China
| | - Ke Wang
- Department of Colorectal Surgery, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 210009, China
| | - Jun Bao
- Department of Medical Oncology, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 210009, China
| | - Liu Yang
- Department of Colorectal Surgery, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 210009, China
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19
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Zanella ER, Grassi E, Trusolino L. Towards precision oncology with patient-derived xenografts. Nat Rev Clin Oncol 2022; 19:719-732. [PMID: 36151307 DOI: 10.1038/s41571-022-00682-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2022] [Indexed: 11/09/2022]
Abstract
Under the selective pressure of therapy, tumours dynamically evolve multiple adaptive mechanisms that make static interrogation of genomic alterations insufficient to guide treatment decisions. Clinical research does not enable the assessment of how various regulatory circuits in tumours are affected by therapeutic insults over time and space. Likewise, testing different precision oncology approaches informed by composite and ever-changing molecular information is hard to achieve in patients. Therefore, preclinical models that incorporate the biology and genetics of human cancers, facilitate analyses of complex variables and enable adequate population throughput are needed to pinpoint randomly distributed response predictors. Patient-derived xenograft (PDX) models are dynamic entities in which cancer evolution can be monitored through serial propagation in mice. PDX models can also recapitulate interpatient diversity, thus enabling the identification of response biomarkers and therapeutic targets for molecularly defined tumour subgroups. In this Review, we discuss examples from the past decade of the use of PDX models for precision oncology, from translational research to drug discovery. We elaborate on how and to what extent preclinical observations in PDX models have confirmed and/or anticipated findings in patients. Finally, we illustrate emerging methodological efforts that could broaden the application of PDX models by honing their predictive accuracy or improving their versatility.
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Affiliation(s)
| | - Elena Grassi
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, Italy.,Department of Oncology, University of Torino, Candiolo, Italy
| | - Livio Trusolino
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, Italy. .,Department of Oncology, University of Torino, Candiolo, Italy.
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20
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Álvarez-Varela A, Novellasdemunt L, Barriga FM, Hernando-Momblona X, Cañellas-Socias A, Cano-Crespo S, Sevillano M, Cortina C, Stork D, Morral C, Turon G, Slebe F, Jiménez-Gracia L, Caratù G, Jung P, Stassi G, Heyn H, Tauriello DVF, Mateo L, Tejpar S, Sancho E, Stephan-Otto Attolini C, Batlle E. Mex3a marks drug-tolerant persister colorectal cancer cells that mediate relapse after chemotherapy. NATURE CANCER 2022; 3:1052-1070. [PMID: 35773527 DOI: 10.1038/s43018-022-00402-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Colorectal cancer (CRC) patient-derived organoids predict responses to chemotherapy. Here we used them to investigate relapse after treatment. Patient-derived organoids expand from highly proliferative LGR5+ tumor cells; however, we discovered that lack of optimal growth conditions specifies a latent LGR5+ cell state. This cell population expressed the gene MEX3A, is chemoresistant and regenerated the organoid culture after treatment. In CRC mouse models, Mex3a+ cells contributed marginally to metastatic outgrowth; however, after chemotherapy, Mex3a+ cells produced large cell clones that regenerated the disease. Lineage-tracing analysis showed that persister Mex3a+ cells downregulate the WNT/stem cell gene program immediately after chemotherapy and adopt a transient state reminiscent to that of YAP+ fetal intestinal progenitors. In contrast, Mex3a-deficient cells differentiated toward a goblet cell-like phenotype and were unable to resist chemotherapy. Our findings reveal that adaptation of cancer stem cells to suboptimal niche environments protects them from chemotherapy and identify a candidate cell of origin of relapse after treatment in CRC.
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Affiliation(s)
- Adrián Álvarez-Varela
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Laura Novellasdemunt
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Francisco M Barriga
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xavier Hernando-Momblona
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Adrià Cañellas-Socias
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Sara Cano-Crespo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marta Sevillano
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Carme Cortina
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Diana Stork
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Clara Morral
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Gemma Turon
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Felipe Slebe
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Laura Jiménez-Gracia
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ginevra Caratù
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Peter Jung
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Partner site Munich, Institute of Pathology, Ludwig Maximilian University, Munich, Germany
| | - Giorgio Stassi
- Department of Surgical Oncological and Stomatological Sciences, University of Palermo, Palermo, Italy
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Daniele V F Tauriello
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Lidia Mateo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Sabine Tejpar
- Molecular Digestive Oncology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Elena Sancho
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Camille Stephan-Otto Attolini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.
- ICREA, Barcelona, Spain.
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21
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Russo M, Pompei S, Sogari A, Corigliano M, Crisafulli G, Puliafito A, Lamba S, Erriquez J, Bertotti A, Gherardi M, Di Nicolantonio F, Bardelli A, Cosentino Lagomarsino M. A modified fluctuation-test framework characterizes the population dynamics and mutation rate of colorectal cancer persister cells. Nat Genet 2022; 54:976-984. [PMID: 35817983 PMCID: PMC9279152 DOI: 10.1038/s41588-022-01105-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 05/25/2022] [Indexed: 12/16/2022]
Abstract
Compelling evidence shows that cancer persister cells represent a major limit to the long-term efficacy of targeted therapies. However, the phenotype and population dynamics of cancer persister cells remain unclear. We developed a quantitative framework to study persisters by combining experimental characterization and mathematical modeling. We found that, in colorectal cancer, a fraction of persisters slowly replicates. Clinically approved targeted therapies induce a switch to drug-tolerant persisters and a temporary 7- to 50-fold increase of their mutation rate, thus increasing the number of persister-derived resistant cells. These findings reveal that treatment may influence persistence and mutability in cancer cells and pinpoint inhibition of error-prone DNA polymerases as a strategy to restrict tumor recurrence.
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Affiliation(s)
- Mariangela Russo
- Department of Oncology, University of Turin, Candiolo, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Simone Pompei
- IFOM Foundation, FIRC Institute of Molecular Oncology, Milan, Italy
| | - Alberto Sogari
- Department of Oncology, University of Turin, Candiolo, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Mattia Corigliano
- IFOM Foundation, FIRC Institute of Molecular Oncology, Milan, Italy
- Department of Physics, University of Milan and INFN, Milan, Italy
| | - Giovanni Crisafulli
- Department of Oncology, University of Turin, Candiolo, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Alberto Puliafito
- Department of Oncology, University of Turin, Candiolo, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Simona Lamba
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | | | - Andrea Bertotti
- Department of Oncology, University of Turin, Candiolo, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Marco Gherardi
- IFOM Foundation, FIRC Institute of Molecular Oncology, Milan, Italy
- Department of Physics, University of Milan and INFN, Milan, Italy
| | - Federica Di Nicolantonio
- Department of Oncology, University of Turin, Candiolo, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Alberto Bardelli
- Department of Oncology, University of Turin, Candiolo, Italy.
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.
| | - Marco Cosentino Lagomarsino
- IFOM Foundation, FIRC Institute of Molecular Oncology, Milan, Italy.
- Department of Physics, University of Milan and INFN, Milan, Italy.
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22
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Bent A, Raghavan S, Dasari A, Kopetz S. The Future of ctDNA-Defined Minimal Residual Disease: Personalizing Adjuvant Therapy in Colorectal Cancer. Clin Colorectal Cancer 2022; 21:89-95. [PMID: 35450837 PMCID: PMC9149115 DOI: 10.1016/j.clcc.2022.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 03/17/2022] [Indexed: 12/24/2022]
Abstract
Our understanding of the diagnostic and prognostic use of circulating tumor DNA (ctDNA) in colorectal cancer (CRC) has broadly expanded over the past few years. The utilization of ctDNA to detect minimal residual disease is currently being employed across the continuum of cancer care. The lead-time of ctDNA positivity to radiographic recurrence in stage I to III CRC is up to 9 months on average, which provides a therapeutic window for a group of high-risk patients who will ultimately recur. There are several ongoing prospective clinical trials that investigate whether ctDNA can be used as an integral biomarker to risk stratify CRC patients and guide adjuvant treatment decisions. In this review, we summarize the evidence supporting the promise of ctDNA-defined MRD in CRC and highlight the current ctDNA guided adjuvant prospective clinical trials.
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Affiliation(s)
- Alisha Bent
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX.
| | - Shreya Raghavan
- Department of Biomedical Engineering, Texas A&M University, College Station, TX
| | - Arvind Dasari
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX.
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23
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Rau A, Janssen N, Kühl L, Sell T, Kalmykova S, Mürdter TE, Dahlke MH, Sers C, Morkel M, Schwab M, Kontermann RE, Olayioye MA. Triple Targeting of HER Receptors Overcomes Heregulin-mediated Resistance to EGFR Blockade in Colorectal Cancer. Mol Cancer Ther 2022; 21:799-809. [PMID: 35247930 DOI: 10.1158/1535-7163.mct-21-0818] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 01/12/2022] [Accepted: 02/10/2022] [Indexed: 11/16/2022]
Abstract
Current treatment options for patients with advanced colorectal cancers include anti-EGFR/HER1 therapy with the blocking antibody cetuximab. Although a subset of patients with KRAS WT disease initially respond to the treatment, resistance develops in almost all cases. Relapse has been associated with the production of the ligand heregulin (HRG) and/or compensatory signaling involving the receptor tyrosine kinases HER2 and HER3. Here, we provide evidence that triple-HER receptor blockade based on a newly developed bispecific EGFR×HER3-targeting antibody (scDb-Fc) together with the HER2-blocking antibody trastuzumab effectively inhibited HRG-induced HER receptor phosphorylation, downstream signaling, proliferation, and stem cell expansion of DiFi and LIM1215 colorectal cancer cells. Comparative analyses revealed that the biological activity of scDb-Fc plus trastuzumab was sometimes even superior to that of the combination of the parental antibodies, with PI3K/Akt pathway inhibition correlating with improved therapeutic response and apoptosis induction as seen by single-cell analysis. Importantly, growth suppression by triple-HER targeting was recapitulated in primary KRAS WT patient-derived organoid cultures exposed to HRG. Collectively, our results provide strong support for a pan-HER receptor blocking approach to combat anti-EGFR therapy resistance of KRAS WT colorectal cancer tumors mediated by the upregulation of HRG and/or HER2/HER3 signaling.
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Affiliation(s)
- Alexander Rau
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
| | - Nicole Janssen
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tübingen, Tübingen, Germany
| | - Lennart Kühl
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
| | - Thomas Sell
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,IRI Life Sciences and Institute of Theoretical Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Svetlana Kalmykova
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,IRI Life Sciences and Institute of Theoretical Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Thomas E Mürdter
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tübingen, Tübingen, Germany
| | - Marc-H Dahlke
- Department of General and Visceral Surgery, Robert-Bosch-Hospital, Stuttgart, Germany
| | - Christine Sers
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), Partner Site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Markus Morkel
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), Partner Site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany.,German Cancer Consortium (DKTK), Partner Site Tübingen and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Departments of Clinical Pharmacology, and of Biochemistry and Pharmacy, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen, Germany
| | - Roland E Kontermann
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany.,Stuttgart Research Center Systems Biology (SRCSB), University of Stuttgart, Stuttgart, Germany
| | - Monilola A Olayioye
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany.,Stuttgart Research Center Systems Biology (SRCSB), University of Stuttgart, Stuttgart, Germany
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24
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Herpers B, Eppink B, James MI, Cortina C, Cañellas-Socias A, Boj SF, Hernando-Momblona X, Glodzik D, Roovers RC, van de Wetering M, Bartelink-Clements C, Zondag-van der Zande V, Mateos JG, Yan K, Salinaro L, Basmeleh A, Fatrai S, Maussang D, Lammerts van Bueren JJ, Chicote I, Serna G, Cabellos L, Ramírez L, Nuciforo P, Salazar R, Santos C, Villanueva A, Stephan-Otto Attolini C, Sancho E, Palmer HG, Tabernero J, Stratton MR, de Kruif J, Logtenberg T, Clevers H, Price LS, Vries RGJ, Batlle E, Throsby M. Functional patient-derived organoid screenings identify MCLA-158 as a therapeutic EGFR × LGR5 bispecific antibody with efficacy in epithelial tumors. NATURE CANCER 2022; 3:418-436. [PMID: 35469014 DOI: 10.1038/s43018-022-00359-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 03/04/2022] [Indexed: 12/19/2022]
Abstract
Patient-derived organoids (PDOs) recapitulate tumor architecture, contain cancer stem cells and have predictive value supporting personalized medicine. Here we describe a large-scale functional screen of dual-targeting bispecific antibodies (bAbs) on a heterogeneous colorectal cancer PDO biobank and paired healthy colonic mucosa samples. More than 500 therapeutic bAbs generated against Wingless-related integration site (WNT) and receptor tyrosine kinase (RTK) targets were functionally evaluated by high-content imaging to capture the complexity of PDO responses. Our drug discovery strategy resulted in the generation of MCLA-158, a bAb that specifically triggers epidermal growth factor receptor degradation in leucine-rich repeat-containing G-protein-coupled receptor 5-positive (LGR5+) cancer stem cells but shows minimal toxicity toward healthy LGR5+ colon stem cells. MCLA-158 exhibits therapeutic properties such as growth inhibition of KRAS-mutant colorectal cancers, blockade of metastasis initiation and suppression of tumor outgrowth in preclinical models for several epithelial cancer types.
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Affiliation(s)
- Bram Herpers
- OcellO BV, Leiden, The Netherlands
- Crown Bioscience Netherlands BV, Leiden, The Netherlands
| | | | - Mark I James
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Carme Cortina
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain
- CIBERONC, Madrid, Spain
| | - Adrià Cañellas-Socias
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain
- CIBERONC, Madrid, Spain
| | - Sylvia F Boj
- Hubrecht Organoid Technology (HUB), Utrecht, the Netherlands
| | - Xavier Hernando-Momblona
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain
- CIBERONC, Madrid, Spain
| | - Dominik Glodzik
- Wellcome Sanger Institute, Hinxton, UK
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Marc van de Wetering
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Hubrecht Institute, Utrecht, the Netherlands
| | | | | | - Jara García Mateos
- OcellO BV, Leiden, The Netherlands
- Crown Bioscience Netherlands BV, Leiden, The Netherlands
| | - Kuan Yan
- OcellO BV, Leiden, The Netherlands
- Crown Bioscience Netherlands BV, Leiden, The Netherlands
| | | | | | | | | | | | - Irene Chicote
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Garazi Serna
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Laia Cabellos
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Medical Oncology Department, Vall d'Hebron University Hospital (HUVH), Barcelona, Spain
| | - Lorena Ramírez
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Medical Oncology Department, Vall d'Hebron University Hospital (HUVH), Barcelona, Spain
| | - Paolo Nuciforo
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Ramon Salazar
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL)-CIBERONC, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Cristina Santos
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL)-CIBERONC, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Alberto Villanueva
- Chemoresistance and Predictive Factors Group, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
- Xenopat SL, Parc Cientific de Barcelona (PCB), Barcelona, Spain
| | - Camille Stephan-Otto Attolini
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Elena Sancho
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain
- CIBERONC, Madrid, Spain
| | - Hector G Palmer
- CIBERONC, Madrid, Spain
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Medical Oncology Department, Vall d'Hebron University Hospital (HUVH), Barcelona, Spain
| | - Josep Tabernero
- CIBERONC, Madrid, Spain
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Medical Oncology Department, Vall d'Hebron University Hospital (HUVH), Barcelona, Spain
| | | | | | | | - Hans Clevers
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Hubrecht Institute, Utrecht, the Netherlands
| | - Leo S Price
- OcellO BV, Leiden, The Netherlands
- Crown Bioscience Netherlands BV, Leiden, The Netherlands
| | | | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain.
- CIBERONC, Madrid, Spain.
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
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25
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Huang W, Chen Y, Chang W, Ren L, Tang W, Zheng P, Wu Q, Liu T, Liu Y, Wei Y, Xu J. HER2 positivity as a biomarker for poor prognosis and unresponsiveness to anti-EGFR therapy in colorectal cancer. J Cancer Res Clin Oncol 2022; 148:993-1002. [PMID: 34156520 DOI: 10.1007/s00432-021-03655-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/27/2021] [Indexed: 01/27/2023]
Abstract
PURPOSE To investigate the role of HER2 positivity in prognosis and unresponsiveness to anti-EGFR therapy for colorectal cancer. METHODS Patients who underwent primary CRC tumor resection were included. HER2 status of CRC was confirmed by immunohistochemistry and fluorescence in situ hybridization tests. Comparison of survival analysis between HER2 positivity and negativity was evaluated by a stratified log-rank test and summarized with the use of Kaplan-Meier and Cox proportional hazards methods. The treatment effects of cetuximab were further compared in full subgroup analyses. RESULT 1240 patients were enrolled, including 763 with stage I-III CRC and 477 with stage IV CRC. 57 (4.6%) CRC patients presented HER2 positivity in the entire cohort. The survival analysis showed that patients with HER2 positivity had significantly worse disease-free survival and overall survival in stage III and IV CRC. The multivariable analysis also confirmed that HER2 positivity was a significantly independent risk factor in stage III and IV CRC. Univariate and multivariable survival analysis showed no prognostic significance of HER2 positivity in stage I-II CRC patients. Prespecified subgroup analysis showed no favorable trends in progression-free survival and overall survival for cetuximab in the patients with HER2 positivity, KRAS/NRAS/BRAF wild-type metastatic CRC (interaction P values = 0.005 and 0.014). CONCLUSION For stage III and IV CRC patients, HER2 positivity was confirmed as an independent prognostic risk factor. It could help predict the unresponsiveness to anti-EGFR therapy for metastatic CRC.
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Affiliation(s)
- Wenbai Huang
- Department of General Surgery, Colorectal Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, People's Republic of China
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yijiao Chen
- Department of General Surgery, Colorectal Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, People's Republic of China
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wenju Chang
- Department of General Surgery, Colorectal Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, People's Republic of China
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Colorectal Cancer Minimally Invasive, Shanghai, China
| | - Li Ren
- Department of General Surgery, Colorectal Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, People's Republic of China
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Colorectal Cancer Minimally Invasive, Shanghai, China
- Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wentao Tang
- Department of General Surgery, Colorectal Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, People's Republic of China
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Peng Zheng
- Department of General Surgery, Colorectal Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, People's Republic of China
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qi Wu
- Department of General Surgery, Colorectal Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, People's Republic of China
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Tianyu Liu
- Department of General Surgery, Colorectal Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, People's Republic of China
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yu Liu
- Department of General Surgery, Colorectal Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, People's Republic of China
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ye Wei
- Department of General Surgery, Colorectal Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, People's Republic of China.
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.
- Shanghai Engineering Research Center of Colorectal Cancer Minimally Invasive, Shanghai, China.
- Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Jianmin Xu
- Department of General Surgery, Colorectal Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, People's Republic of China.
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.
- Shanghai Engineering Research Center of Colorectal Cancer Minimally Invasive, Shanghai, China.
- Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China.
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26
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Tedesco M, Giannese F, Lazarević D, Giansanti V, Rosano D, Monzani S, Catalano I, Grassi E, Zanella ER, Botrugno OA, Morelli L, Panina Bordignon P, Caravagna G, Bertotti A, Martino G, Aldrighetti L, Pasqualato S, Trusolino L, Cittaro D, Tonon G. Chromatin Velocity reveals epigenetic dynamics by single-cell profiling of heterochromatin and euchromatin. Nat Biotechnol 2022; 40:235-244. [PMID: 34635836 DOI: 10.1038/s41587-021-01031-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 07/22/2021] [Indexed: 02/08/2023]
Abstract
Recent efforts have succeeded in surveying open chromatin at the single-cell level, but high-throughput, single-cell assessment of heterochromatin and its underlying genomic determinants remains challenging. We engineered a hybrid transposase including the chromodomain (CD) of the heterochromatin protein-1α (HP-1α), which is involved in heterochromatin assembly and maintenance through its binding to trimethylation of the lysine 9 on histone 3 (H3K9me3), and developed a single-cell method, single-cell genome and epigenome by transposases sequencing (scGET-seq), that, unlike single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq), comprehensively probes both open and closed chromatin and concomitantly records the underlying genomic sequences. We tested scGET-seq in cancer-derived organoids and human-derived xenograft (PDX) models and identified genetic events and plasticity-driven mechanisms contributing to cancer drug resistance. Next, building upon the differential enrichment of closed and open chromatin, we devised a method, Chromatin Velocity, that identifies the trajectories of epigenetic modifications at the single-cell level. Chromatin Velocity uncovered paths of epigenetic reorganization during stem cell reprogramming and identified key transcription factors driving these developmental processes. scGET-seq reveals the dynamics of genomic and epigenetic landscapes underlying any cellular processes.
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Affiliation(s)
- Martina Tedesco
- Università Vita-Salute San Raffaele, Milano, Italy
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | | | - Dejan Lazarević
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milano, Italy
| | - Valentina Giansanti
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milano, Italy
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milano, Italy
| | - Dalia Rosano
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Silvia Monzani
- Biochemistry and Structural Biology Unit, Department of Experimental Oncology, IEO, IRCCS European Institute of Oncology, Milano, Italy
| | - Irene Catalano
- Department of Oncology, University of Torino School of Medicine, Candiolo, Torino, Italy
- Candiolo Cancer Institute FPO- IRCCS, Candiolo, Torino, Italy
| | - Elena Grassi
- Department of Oncology, University of Torino School of Medicine, Candiolo, Torino, Italy
- Candiolo Cancer Institute FPO- IRCCS, Candiolo, Torino, Italy
| | | | - Oronza A Botrugno
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Leonardo Morelli
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milano, Italy
| | - Paola Panina Bordignon
- Università Vita-Salute San Raffaele, Milano, Italy
- Neuroimmunology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Hospital, Milano, Italy
| | - Giulio Caravagna
- Department of Mathematics and Geosciences, University of Trieste, Trieste, Italy
| | - Andrea Bertotti
- Department of Oncology, University of Torino School of Medicine, Candiolo, Torino, Italy
- Candiolo Cancer Institute FPO- IRCCS, Candiolo, Torino, Italy
| | - Gianvito Martino
- Università Vita-Salute San Raffaele, Milano, Italy
- Neuroimmunology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Hospital, Milano, Italy
| | - Luca Aldrighetti
- Hepatobiliary Surgery Division, IRCCS San Raffaele Hospital, Milano, Italy
| | - Sebastiano Pasqualato
- Biochemistry and Structural Biology Unit, Department of Experimental Oncology, IEO, IRCCS European Institute of Oncology, Milano, Italy
| | - Livio Trusolino
- Department of Oncology, University of Torino School of Medicine, Candiolo, Torino, Italy
- Candiolo Cancer Institute FPO- IRCCS, Candiolo, Torino, Italy
| | - Davide Cittaro
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milano, Italy.
| | - Giovanni Tonon
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy.
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milano, Italy.
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27
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Mouillet-Richard S. ERBB2 in anti-EGFR-resistant colorectal cancer: cancer stem cells come into play. Gut 2022; 71:4-5. [PMID: 33619166 DOI: 10.1136/gutjnl-2020-323924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 12/08/2022]
Affiliation(s)
- Sophie Mouillet-Richard
- INSERM-U1138, Centre de Recherche des Cordeliers, Sorbonne Université, Université de Paris, Paris, France
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28
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Uhlitz F, Bischoff P, Peidli S, Sieber A, Trinks A, Lüthen M, Obermayer B, Blanc E, Ruchiy Y, Sell T, Mamlouk S, Arsie R, Wei T, Klotz‐Noack K, Schwarz RF, Sawitzki B, Kamphues C, Beule D, Landthaler M, Sers C, Horst D, Blüthgen N, Morkel M. Mitogen-activated protein kinase activity drives cell trajectories in colorectal cancer. EMBO Mol Med 2021; 13:e14123. [PMID: 34409732 PMCID: PMC8495451 DOI: 10.15252/emmm.202114123] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 07/27/2021] [Accepted: 07/30/2021] [Indexed: 01/07/2023] Open
Abstract
In colorectal cancer, oncogenic mutations transform a hierarchically organized and homeostatic epithelium into invasive cancer tissue lacking visible organization. We sought to define transcriptional states of colorectal cancer cells and signals controlling their development by performing single-cell transcriptome analysis of tumors and matched non-cancerous tissues of twelve colorectal cancer patients. We defined patient-overarching colorectal cancer cell clusters characterized by differential activities of oncogenic signaling pathways such as mitogen-activated protein kinase and oncogenic traits such as replication stress. RNA metabolic labeling and assessment of RNA velocity in patient-derived organoids revealed developmental trajectories of colorectal cancer cells organized along a mitogen-activated protein kinase activity gradient. This was in contrast to normal colon organoid cells developing along graded Wnt activity. Experimental targeting of EGFR-BRAF-MEK in cancer organoids affected signaling and gene expression contingent on predictive KRAS/BRAF mutations and induced cell plasticity overriding default developmental trajectories. Our results highlight directional cancer cell development as a driver of non-genetic cancer cell heterogeneity and re-routing of trajectories as a response to targeted therapy.
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Affiliation(s)
- Florian Uhlitz
- Institute of PathologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- IRI Life SciencesHumboldt University of BerlinBerlinGermany
- German Cancer Consortium (DKTK) Partner Site BerlinGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Philip Bischoff
- Institute of PathologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
| | - Stefan Peidli
- Institute of PathologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- IRI Life SciencesHumboldt University of BerlinBerlinGermany
| | - Anja Sieber
- Institute of PathologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- IRI Life SciencesHumboldt University of BerlinBerlinGermany
| | - Alexandra Trinks
- Institute of PathologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- BIH Bioportal Single CellsBerlin Institute of Health at Charité – Universitätsmedizin BerlinBerlinGermany
| | - Mareen Lüthen
- Institute of PathologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- German Cancer Consortium (DKTK) Partner Site BerlinGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Benedikt Obermayer
- Core Unit Bioinformatics (CUBI)Berlin Institute of Health at Charité Universitätsmedizin – BerlinBerlinGermany
| | - Eric Blanc
- Core Unit Bioinformatics (CUBI)Berlin Institute of Health at Charité Universitätsmedizin – BerlinBerlinGermany
| | - Yana Ruchiy
- Institute of PathologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
| | - Thomas Sell
- Institute of PathologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- IRI Life SciencesHumboldt University of BerlinBerlinGermany
| | - Soulafa Mamlouk
- Institute of PathologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- German Cancer Consortium (DKTK) Partner Site BerlinGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Roberto Arsie
- Max Delbrück Center for Molecular MedicineBerlin Institute for Medical Systems Biology (BIMSB)BerlinGermany
| | - Tzu‐Ting Wei
- Institute of PathologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- Max Delbrück Center for Molecular MedicineBerlin Institute for Medical Systems Biology (BIMSB)BerlinGermany
| | - Kathleen Klotz‐Noack
- Institute of PathologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- Institute of Medical ImmunologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
| | - Roland F Schwarz
- Max Delbrück Center for Molecular MedicineBerlin Institute for Medical Systems Biology (BIMSB)BerlinGermany
- BIFOLD – Berlin Institute for the Foundations of Learning and DataBerlinGermany
| | - Birgit Sawitzki
- Institute of Medical ImmunologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
| | - Carsten Kamphues
- German Cancer Consortium (DKTK) Partner Site BerlinGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Department of SurgeryCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
| | - Dieter Beule
- Core Unit Bioinformatics (CUBI)Berlin Institute of Health at Charité Universitätsmedizin – BerlinBerlinGermany
| | - Markus Landthaler
- Max Delbrück Center for Molecular MedicineBerlin Institute for Medical Systems Biology (BIMSB)BerlinGermany
| | - Christine Sers
- Institute of PathologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- German Cancer Consortium (DKTK) Partner Site BerlinGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - David Horst
- Institute of PathologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- German Cancer Consortium (DKTK) Partner Site BerlinGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Nils Blüthgen
- Institute of PathologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- IRI Life SciencesHumboldt University of BerlinBerlinGermany
- German Cancer Consortium (DKTK) Partner Site BerlinGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Markus Morkel
- Institute of PathologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- German Cancer Consortium (DKTK) Partner Site BerlinGerman Cancer Research Center (DKFZ)HeidelbergGermany
- BIH Bioportal Single CellsBerlin Institute of Health at Charité – Universitätsmedizin BerlinBerlinGermany
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29
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Thankamony AP, Subbalakshmi AR, Jolly MK, Nair R. Lineage Plasticity in Cancer: The Tale of a Skin-Walker. Cancers (Basel) 2021; 13:3602. [PMID: 34298815 PMCID: PMC8306016 DOI: 10.3390/cancers13143602] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/04/2021] [Accepted: 07/14/2021] [Indexed: 12/11/2022] Open
Abstract
Lineage plasticity, the switching of cells from one lineage to another, has been recognized as a cardinal property essential for embryonic development, tissue repair and homeostasis. However, such a highly regulated process goes awry when cancer cells exploit this inherent ability to their advantage, resulting in tumorigenesis, relapse, metastasis and therapy resistance. In this review, we summarize our current understanding on the role of lineage plasticity in tumor progression and therapeutic resistance in multiple cancers. Lineage plasticity can be triggered by treatment itself and is reported across various solid as well as liquid tumors. Here, we focus on the importance of lineage switching in tumor progression and therapeutic resistance of solid tumors such as the prostate, lung, hepatocellular and colorectal carcinoma and the myeloid and lymphoid lineage switch observed in leukemias. Besides this, we also discuss the role of epithelial-mesenchymal transition (EMT) in facilitating the lineage switch in biphasic cancers such as aggressive carcinosarcomas. We also discuss the mechanisms involved, current therapeutic approaches and challenges that lie ahead in taming the scourge of lineage plasticity in cancer.
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Affiliation(s)
- Archana P. Thankamony
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Kerala 695014, India;
- Manipal Academy of Higher Education (MAHE), Manipal 576104, India
| | - Ayalur Raghu Subbalakshmi
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India;
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India;
| | - Radhika Nair
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Kerala 695014, India;
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30
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Rizzo G, Bertotti A, Leto SM, Vetrano S. Patient-derived tumor models: a more suitable tool for pre-clinical studies in colorectal cancer. J Exp Clin Cancer Res 2021; 40:178. [PMID: 34074330 PMCID: PMC8168319 DOI: 10.1186/s13046-021-01970-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/02/2021] [Indexed: 12/15/2022] Open
Abstract
Colorectal cancer (CRC), despite the advances in screening and surveillance, remains the second most common cause of cancer death worldwide. The biological inadequacy of pre-clinical models to fully recapitulate the multifactorial etiology and the complexity of tumor microenvironment and human CRC's genetic heterogeneity has limited cancer treatment development. This has led to the development of Patient-derived models able to phenocopy as much as possible the original inter- and intra-tumor heterogeneity of CRC, reflecting the tumor microenvironment's cellular interactions. Implantation of patient tissue into immunodeficient mice hosts and the culture of tumor organoids have allowed advances in cancer biology and metastasis. This review highlights the advantages and limits of Patient-derived models as innovative and valuable pre-clinical tools to study progression and metastasis of CRC, develop novel therapeutic strategies by creating a drug screening platform, and predict the efficacy of clinical response to therapy.
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Affiliation(s)
- Giulia Rizzo
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini, Pieve Emanuele, 20090, Milan, Italy
| | - Andrea Bertotti
- Laboratory of Translational Cancer Medicine, Candiolo Cancer Institute - FPO IRCCs, Candiolo, 10060, Torino, Italy
- Department of Oncology, University of Torino School of Medicine, Candiolo, 10060, Torino, Italy
| | - Simonetta Maria Leto
- Laboratory of Translational Cancer Medicine, Candiolo Cancer Institute - FPO IRCCs, Candiolo, 10060, Torino, Italy
| | - Stefania Vetrano
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini, Pieve Emanuele, 20090, Milan, Italy.
- IBD Center, Department of Gastroenterology, Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy.
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31
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Avolio M, Trusolino L. Rational Treatment of Metastatic Colorectal Cancer: A Reverse Tale of Men, Mice, and Culture Dishes. Cancer Discov 2021; 11:1644-1660. [PMID: 33820776 DOI: 10.1158/2159-8290.cd-20-1531] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/04/2021] [Accepted: 02/01/2021] [Indexed: 11/16/2022]
Abstract
Stratification of colorectal cancer into subgroups with different response to therapy was initially guided by descriptive associations between specific biomarkers and treatment outcome. Recently, preclinical models based on propagatable patient-derived tumor samples have yielded an improved understanding of disease biology, which has facilitated the functional validation of correlative information and the discovery of novel response determinants, therapeutic targets, and mechanisms of tumor adaptation and drug resistance. We review the contribution of patient-derived models to advancing colorectal cancer characterization, discuss their influence on clinical decision-making, and highlight emerging challenges in the interpretation and clinical transferability of results obtainable with such approaches. SIGNIFICANCE: Association studies in patients with colorectal cancer have led to the identification of response biomarkers, some of which have been implemented as companion diagnostics for therapeutic decisions. By enabling biological investigation in a clinically relevant experimental context, patient-derived colorectal cancer models have proved useful to examine the causal role of such biomarkers in dictating drug sensitivity and are providing fresh knowledge on new actionable targets, dynamics of tumor evolution and adaptation, and mechanisms of drug resistance.
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Affiliation(s)
- Marco Avolio
- Department of Oncology, University of Torino, Candiolo, Torino, Italy.,Candiolo Cancer Institute - FPO IRCCS, Candiolo, Torino, Italy
| | - Livio Trusolino
- Department of Oncology, University of Torino, Candiolo, Torino, Italy. .,Candiolo Cancer Institute - FPO IRCCS, Candiolo, Torino, Italy
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32
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Quantifying single-cell ERK dynamics in colorectal cancer organoids reveals EGFR as an amplifier of oncogenic MAPK pathway signalling. Nat Cell Biol 2021; 23:377-390. [PMID: 33795873 PMCID: PMC7610573 DOI: 10.1038/s41556-021-00654-5] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 02/24/2021] [Indexed: 02/07/2023]
Abstract
Direct targeting of the downstream mitogen-activated protein kinase (MAPK) pathway to suppress extracellular-regulated kinase (ERK) activation in KRAS and BRAF mutant colorectal cancer (CRC) has proven clinically unsuccessful, but promising results have been obtained with combination therapies including epidermal growth factor receptor (EGFR) inhibition. To elucidate the interplay between EGF signalling and ERK activation in tumours, we used patient-derived organoids (PDOs) from KRAS and BRAF mutant CRCs. PDOs resemble in vivo tumours, model treatment response and are compatible with live-cell microscopy. We established real-time, quantitative drug response assessment in PDOs with single-cell resolution, using our improved fluorescence resonance energy transfer (FRET)-based ERK biosensor EKAREN5. We show that oncogene-driven signalling is strikingly limited without EGFR activity and insufficient to sustain full proliferative potential. In PDOs and in vivo, upstream EGFR activity rigorously amplifies signal transduction efficiency in KRAS or BRAF mutant MAPK pathways. Our data provide a mechanistic understanding of the effectivity of EGFR inhibitors within combination therapies against KRAS and BRAF mutant CRC.
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33
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Chen Q, Suzuki K, Sifuentes-Dominguez L, Miyata N, Song J, Lopez A, Starokadomskyy P, Gopal P, Dozmorov I, Tan S, Ge B, Burstein E. Paneth cell-derived growth factors support tumorigenesis in the small intestine. Life Sci Alliance 2020; 4:4/3/e202000934. [PMID: 33372038 PMCID: PMC7772774 DOI: 10.26508/lsa.202000934] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 12/17/2022] Open
Abstract
Paneth cells, known for their production of antimicrobial peptides and growth factors in the gut epithelium, are found to play a key role in intestinal tumor formation through secretion of Wnt3. Paneth cells (PCs) are small intestinal epithelial cells that secrete antimicrobial peptides and growth factors, such as Wnt ligands. Intriguingly, the context in which PC-derived Wnt secretion is relevant in vivo remains unknown as intestinal epithelial ablation of Wnt does not affect homeostatic proliferation or restitution after irradiation injury. Considering the importance of growth factors in tumor development, we explored here the role of PCs in intestinal carcinogenesis using a genetic model of PC depletion through conditional expression of diphtheria toxin-α subunit. PC depletion in ApcMin mice impaired adenoma development in the small intestine and led to decreased Wnt3 expression in small bowel adenomas. To determine if PC-derived Wnt3 was required for adenoma development, we examined tumor formation after PC-specific ablation of Wnt3. We found that this was sufficient to decrease small intestinal adenoma formation; moreover, organoids derived from these tumors displayed slower growth capacity. Overall, we report that PC-derived Wnt3 is required to sustain early tumorigenesis in the small bowel and identify a clear role for PC-derived Wnt production in intestinal pathology.
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Affiliation(s)
- Qing Chen
- Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Internal Medicine, University of Texas (UT) Southwestern Medical Center, Dallas, TX, USA
| | - Kohei Suzuki
- Department of Internal Medicine, University of Texas (UT) Southwestern Medical Center, Dallas, TX, USA
| | - Luis Sifuentes-Dominguez
- Department of Internal Medicine, University of Texas (UT) Southwestern Medical Center, Dallas, TX, USA.,Department of Pediatrics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Naoteru Miyata
- Department of Internal Medicine, University of Texas (UT) Southwestern Medical Center, Dallas, TX, USA
| | - Jie Song
- Department of Internal Medicine, University of Texas (UT) Southwestern Medical Center, Dallas, TX, USA
| | - Adam Lopez
- Department of Internal Medicine, University of Texas (UT) Southwestern Medical Center, Dallas, TX, USA
| | - Petro Starokadomskyy
- Department of Internal Medicine, University of Texas (UT) Southwestern Medical Center, Dallas, TX, USA
| | - Purva Gopal
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Igor Dozmorov
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Shuai Tan
- Department of Internal Medicine, University of Texas (UT) Southwestern Medical Center, Dallas, TX, USA
| | - Bujun Ge
- Department of General Surgery, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ezra Burstein
- Department of Internal Medicine, University of Texas (UT) Southwestern Medical Center, Dallas, TX, USA .,Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
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34
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Yalcin GD, Danisik N, Baygin RC, Acar A. Systems Biology and Experimental Model Systems of Cancer. J Pers Med 2020; 10:E180. [PMID: 33086677 PMCID: PMC7712848 DOI: 10.3390/jpm10040180] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/13/2020] [Accepted: 10/16/2020] [Indexed: 12/29/2022] Open
Abstract
Over the past decade, we have witnessed an increasing number of large-scale studies that have provided multi-omics data by high-throughput sequencing approaches. This has particularly helped with identifying key (epi)genetic alterations in cancers. Importantly, aberrations that lead to the activation of signaling networks through the disruption of normal cellular homeostasis is seen both in cancer cells and also in the neighboring tumor microenvironment. Cancer systems biology approaches have enabled the efficient integration of experimental data with computational algorithms and the implementation of actionable targeted therapies, as the exceptions, for the treatment of cancer. Comprehensive multi-omics data obtained through the sequencing of tumor samples and experimental model systems will be important in implementing novel cancer systems biology approaches and increasing their efficacy for tailoring novel personalized treatment modalities in cancer. In this review, we discuss emerging cancer systems biology approaches based on multi-omics data derived from bulk and single-cell genomics studies in addition to existing experimental model systems that play a critical role in understanding (epi)genetic heterogeneity and therapy resistance in cancer.
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Affiliation(s)
| | | | | | - Ahmet Acar
- Department of Biological Sciences, Middle East Technical University, Universiteler Mah. Dumlupınar Bulvarı 1, Çankaya, Ankara 06800, Turkey; (G.D.Y.); (N.D.); (R.C.B.)
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