1
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Mariella E, Grasso G, Miotto M, Buzo K, Reilly NM, Andrei P, Vitiello PP, Crisafulli G, Arena S, Rospo G, Corti G, Lorenzato A, Cancelliere C, Barault L, Gionfriddo G, Linnebacher M, Russo M, Di Nicolantonio F, Bardelli A. Transcriptome-wide gene expression outlier analysis pinpoints therapeutic vulnerabilities in colorectal cancer. Mol Oncol 2024; 18:1460-1485. [PMID: 38468448 PMCID: PMC11161737 DOI: 10.1002/1878-0261.13622] [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: 01/25/2024] [Accepted: 02/20/2024] [Indexed: 03/13/2024] Open
Abstract
Multiple strategies are continuously being explored to expand the drug target repertoire in solid tumors. We devised a novel computational workflow for transcriptome-wide gene expression outlier analysis that allows the systematic identification of both overexpression and underexpression events in cancer cells. Here, it was applied to expression values obtained through RNA sequencing in 226 colorectal cancer (CRC) cell lines that were also characterized by whole-exome sequencing and microarray-based DNA methylation profiling. We found cell models displaying an abnormally high or low expression level for 3533 and 965 genes, respectively. Gene expression abnormalities that have been previously associated with clinically relevant features of CRC cell lines were confirmed. Moreover, by integrating multi-omics data, we identified both genetic and epigenetic alternations underlying outlier expression values. Importantly, our atlas of CRC gene expression outliers can guide the discovery of novel drug targets and biomarkers. As a proof of concept, we found that CRC cell lines lacking expression of the MTAP gene are sensitive to treatment with a PRMT5-MTA inhibitor (MRTX1719). Finally, other tumor types may also benefit from this approach.
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Affiliation(s)
- Elisa Mariella
- Department of Oncology, Molecular Biotechnology CenterUniversity of TorinoItaly
- IFOM ETS, The AIRC Institute of Molecular OncologyMilanItaly
| | - Gaia Grasso
- Department of Oncology, Molecular Biotechnology CenterUniversity of TorinoItaly
- IFOM ETS, The AIRC Institute of Molecular OncologyMilanItaly
| | - Martina Miotto
- Department of Oncology, Molecular Biotechnology CenterUniversity of TorinoItaly
- IFOM ETS, The AIRC Institute of Molecular OncologyMilanItaly
| | - Kristi Buzo
- Department of OncologyUniversity of TorinoCandiolo (TO)Italy
- Candiolo Cancer InstituteFPO‐IRCCSCandiolo (TO)Italy
| | | | - Pietro Andrei
- Department of OncologyUniversity of TorinoCandiolo (TO)Italy
| | - Pietro Paolo Vitiello
- Department of Oncology, Molecular Biotechnology CenterUniversity of TorinoItaly
- IFOM ETS, The AIRC Institute of Molecular OncologyMilanItaly
| | | | - Sabrina Arena
- Department of OncologyUniversity of TorinoCandiolo (TO)Italy
- Candiolo Cancer InstituteFPO‐IRCCSCandiolo (TO)Italy
| | - Giuseppe Rospo
- Department of OncologyUniversity of TorinoCandiolo (TO)Italy
- Present address:
Boehringer Ingelheim RCV GmbH & Co KGViennaAustria
| | - Giorgio Corti
- Department of Oncology, Molecular Biotechnology CenterUniversity of TorinoItaly
| | - Annalisa Lorenzato
- Department of Oncology, Molecular Biotechnology CenterUniversity of TorinoItaly
| | | | - Ludovic Barault
- Department of OncologyUniversity of TorinoCandiolo (TO)Italy
| | | | - Michael Linnebacher
- Clinic of General Surgery, Molecular Oncology and ImmunotherapyUniversity of RostockGermany
| | - Mariangela Russo
- Department of Oncology, Molecular Biotechnology CenterUniversity of TorinoItaly
- IFOM ETS, The AIRC Institute of Molecular OncologyMilanItaly
| | - Federica Di Nicolantonio
- Department of OncologyUniversity of TorinoCandiolo (TO)Italy
- Candiolo Cancer InstituteFPO‐IRCCSCandiolo (TO)Italy
| | - Alberto Bardelli
- Department of Oncology, Molecular Biotechnology CenterUniversity of TorinoItaly
- IFOM ETS, The AIRC Institute of Molecular OncologyMilanItaly
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2
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Battuello P, Corti G, Bartolini A, Lorenzato A, Sogari A, Russo M, Di Nicolantonio F, Bardelli A, Crisafulli G. Mutational signatures of colorectal cancers according to distinct computational workflows. Brief Bioinform 2024; 25:bbae249. [PMID: 38783705 PMCID: PMC11116831 DOI: 10.1093/bib/bbae249] [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: 02/20/2024] [Revised: 04/15/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024] Open
Abstract
Tumor mutational signatures have gained prominence in cancer research, yet the lack of standardized methods hinders reproducibility and robustness. Leveraging colorectal cancer (CRC) as a model, we explored the influence of computational parameters on mutational signature analyses across 230 CRC cell lines and 152 CRC patients. Results were validated in three independent datasets: 483 endometrial cancer patients stratified by mismatch repair (MMR) status, 35 lung cancer patients by smoking status and 12 patient-derived organoids (PDOs) annotated for colibactin exposure. Assessing various bioinformatic tools, reference datasets and input data sizes including whole genome sequencing, whole exome sequencing and a pan-cancer gene panel, we demonstrated significant variability in the results. We report that the use of distinct algorithms and references led to statistically different results, highlighting how arbitrary choices may induce variability in the mutational signature contributions. Furthermore, we found a differential contribution of mutational signatures between coding and intergenic regions and defined the minimum number of somatic variants required for reliable mutational signature assignment. To facilitate the identification of the most suitable workflows, we developed Comparative Mutational Signature analysis on Coding and Extragenic Regions (CoMSCER), a bioinformatic tool which allows researchers to easily perform comparative mutational signature analysis by coupling the results from several tools and public reference datasets and to assess mutational signature contributions in coding and non-coding genomic regions. In conclusion, our study provides a comparative framework to elucidate the impact of distinct computational workflows on mutational signatures.
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Affiliation(s)
- Paolo Battuello
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
- Genomics of Cancer and Targeted Therapies Unit, IFOM ETS, The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Giorgio Corti
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
- Candiolo Cancer Institute, FPO - IRCCS, Strada Provinciale 142 - km 3.95, 10060, Candiolo, Turin, Italy
| | - Alice Bartolini
- Candiolo Cancer Institute, FPO - IRCCS, Strada Provinciale 142 - km 3.95, 10060, Candiolo, Turin, Italy
| | - Annalisa Lorenzato
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
| | - Alberto Sogari
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
- Genomics of Cancer and Targeted Therapies Unit, IFOM ETS, The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Mariangela Russo
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
- Genomics of Cancer and Targeted Therapies Unit, IFOM ETS, The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Federica Di Nicolantonio
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
- Candiolo Cancer Institute, FPO - IRCCS, Strada Provinciale 142 - km 3.95, 10060, Candiolo, Turin, Italy
| | - Alberto Bardelli
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
- Genomics of Cancer and Targeted Therapies Unit, IFOM ETS, The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Giovanni Crisafulli
- Genomics of Cancer and Targeted Therapies Unit, IFOM ETS, The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
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3
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López L, Morosi LG, La Terza F, Bourdely P, Rospo G, Amadio R, Piperno GM, Russo V, Volponi C, Vodret S, Joshi S, Giannese F, Lazarevic D, Germano G, Stoitzner P, Bardelli A, Dalod M, Pace L, Caronni N, Guermonprez P, Benvenuti F. Dendritic cell-targeted therapy expands CD8 T cell responses to bona-fide neoantigens in lung tumors. Nat Commun 2024; 15:2280. [PMID: 38480738 PMCID: PMC10937682 DOI: 10.1038/s41467-024-46685-y] [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: 03/29/2023] [Accepted: 03/06/2024] [Indexed: 03/17/2024] Open
Abstract
Cross-presentation by type 1 DCs (cDC1) is critical to induce and sustain antitumoral CD8 T cell responses to model antigens, in various tumor settings. However, the impact of cross-presenting cDC1 and the potential of DC-based therapies in tumors carrying varied levels of bona-fide neoantigens (neoAgs) remain unclear. Here we develop a hypermutated model of non-small cell lung cancer in female mice, encoding genuine MHC-I neoepitopes to study neoAgs-specific CD8 T cell responses in spontaneous settings and upon Flt3L + αCD40 (DC-therapy). We find that cDC1 are required to generate broad CD8 responses against a range of diverse neoAgs. DC-therapy promotes immunogenicity of weaker neoAgs and strongly inhibits the growth of high tumor-mutational burden (TMB) tumors. In contrast, low TMB tumors respond poorly to DC-therapy, generating mild CD8 T cell responses that are not sufficient to block progression. scRNA transcriptional analysis, immune profiling and functional assays unveil the changes induced by DC-therapy in lung tissues, which comprise accumulation of cDC1 with increased immunostimulatory properties and less exhausted effector CD8 T cells. We conclude that boosting cDC1 activity is critical to broaden the diversity of anti-tumoral CD8 T cell responses and to leverage neoAgs content for therapeutic advantage.
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Affiliation(s)
- Lucía López
- Cellular Immunology, International Centre for Genetic Engineering and Biotechnology, ICGEB, Trieste, Italy
| | - Luciano Gastón Morosi
- Cellular Immunology, International Centre for Genetic Engineering and Biotechnology, ICGEB, Trieste, Italy
| | - Federica La Terza
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Pierre Bourdely
- Université Paris Cité, Institut Cochin, INSERM 1016, Paris, France
- Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, VIB, KU Leuven, Leuven, Belgium
| | - Giuseppe Rospo
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Turin, Italy
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Roberto Amadio
- Cellular Immunology, International Centre for Genetic Engineering and Biotechnology, ICGEB, Trieste, Italy
| | - Giulia Maria Piperno
- Cellular Immunology, International Centre for Genetic Engineering and Biotechnology, ICGEB, Trieste, Italy
| | - Valentina Russo
- G. Armenise-Harvard Immune Regulation Unit, IIGM, Candiolo, TO, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy
| | - Camilla Volponi
- Cellular Immunology, International Centre for Genetic Engineering and Biotechnology, ICGEB, Trieste, Italy
- Cellular and Molecular Oncoimmunology, IRCCS Humanitas Research Hospital, Rozzano, Italy
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy
| | - Simone Vodret
- Cellular Immunology, International Centre for Genetic Engineering and Biotechnology, ICGEB, Trieste, Italy
| | - Sonal Joshi
- Cellular Immunology, International Centre for Genetic Engineering and Biotechnology, ICGEB, Trieste, Italy
| | - Francesca Giannese
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milano, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Dejan Lazarevic
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milano, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Giovanni Germano
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Turin, Italy
- IFOM ETS - The AIRC Institute of Molecular Oncology, 20139, Milan, Italy
| | - Patrizia Stoitzner
- Department of Dermatology, Venereology & Allergology, Medical University of Innsbruck, Innsbruck, Austria
| | - Alberto Bardelli
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Turin, Italy
- IFOM ETS - The AIRC Institute of Molecular Oncology, 20139, Milan, Italy
| | - Marc Dalod
- Aix-Marseille University, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Turing Center for Living Systems, Marseille, France
| | - Luigia Pace
- G. Armenise-Harvard Immune Regulation Unit, IIGM, Candiolo, TO, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy
| | - Nicoletta Caronni
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Federica Benvenuti
- Cellular Immunology, International Centre for Genetic Engineering and Biotechnology, ICGEB, Trieste, Italy.
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4
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Rospo G, Chilà R, Matafora V, Basso V, Lamba S, Bartolini A, Bachi A, Di Nicolantonio F, Mondino A, Germano G, Bardelli A. Non-canonical antigens are the largest fraction of peptides presented by MHC class I in mismatch repair deficient murine colorectal cancer. Genome Med 2024; 16:15. [PMID: 38243308 PMCID: PMC10797964 DOI: 10.1186/s13073-023-01275-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/12/2023] [Indexed: 01/21/2024] Open
Abstract
BACKGROUND Immunotherapy based on checkpoint inhibitors is highly effective in mismatch repair deficient (MMRd) colorectal cancer (CRC). These tumors carry a high number of mutations, which are predicted to translate into a wide array of neoepitopes; however, a systematic classification of the neoantigen repertoire in MMRd CRC is lacking. Mass spectrometry peptidomics has demonstrated the existence of MHC class I associated peptides (MAPs) originating from non-coding DNA regions. Based on these premises we investigated DNA genomic regions responsible for generating MMRd-induced peptides. METHODS We exploited mouse CRC models in which the MMR gene Mlh1 was genetically inactivated. Isogenic cell lines CT26 Mlh1+/+ and Mlh1-/- were inoculated in immunocompromised and immunocompetent mice. Whole genome and RNA sequencing data were generated from samples obtained before and after injection in murine hosts. First, peptide databases were built from transcriptomes of isogenic cell lines. We then compiled a database of peptides lost after tumor cells injection in immunocompetent mice, likely due to immune editing. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) and matched next-generation sequencing databases were employed to identify the DNA regions from which the immune-targeted MAPs originated. Finally, we adopted in vitro T cell assays to verify whether MAP-specific T cells were part of the in vivo immune response against Mlh1-/- cells. RESULTS Whole genome sequencing analyses revealed an unbalanced distribution of immune edited alterations across the genome in Mlh1-/- cells grown in immunocompetent mice. Specifically, untranslated (UTR) and coding regions exhibited the largest fraction of mutations leading to highly immunogenic peptides. Moreover, the integrated computational and LC-MS/MS analyses revealed that MAPs originate mainly from atypical translational events in both Mlh1+/+ and Mlh1-/- tumor cells. In addition, mutated MAPs-derived from UTRs and out-of-frame translation of coding regions-were highly enriched in Mlh1-/- cells. The MAPs trigger T-cell activation in mice primed with Mlh1-/- cells. CONCLUSIONS Our results suggest that-in comparison to MMR proficient CRC-MMRd tumors generate a significantly higher number of non-canonical mutated peptides able to elicit T cell responses. These results reveal the importance of evaluating the diversity of neoepitope repertoire in MMRd tumors.
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Affiliation(s)
- Giuseppe Rospo
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Turin, Italy
- Present address: Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Rosaria Chilà
- IFOM ETS - The AIRC Institute of Molecular Oncology, 20139, Milan, Italy
| | - Vittoria Matafora
- IFOM ETS - The AIRC Institute of Molecular Oncology, 20139, Milan, Italy
| | - Veronica Basso
- Lymphocyte Activation Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute Via Olgettina, 58, 20132, Milan, Italy
| | - Simona Lamba
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Turin, Italy
| | - Alice Bartolini
- Candiolo Cancer Institute, FPO-IRCCS, 10060, Candiolo, TO, Italy
| | - Angela Bachi
- IFOM ETS - The AIRC Institute of Molecular Oncology, 20139, Milan, Italy
| | - Federica Di Nicolantonio
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Turin, Italy
- Candiolo Cancer Institute, FPO-IRCCS, 10060, Candiolo, TO, Italy
| | - Anna Mondino
- Lymphocyte Activation Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute Via Olgettina, 58, 20132, Milan, Italy
| | - Giovanni Germano
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Turin, Italy.
- IFOM ETS - The AIRC Institute of Molecular Oncology, 20139, Milan, Italy.
| | - Alberto Bardelli
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Turin, Italy.
- IFOM ETS - The AIRC Institute of Molecular Oncology, 20139, Milan, Italy.
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5
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De Bacco F, Orzan F, Crisafulli G, Prelli M, Isella C, Casanova E, Albano R, Reato G, Erriquez J, D'Ambrosio A, Panero M, Dall'Aglio C, Casorzo L, Cominelli M, Pagani F, Melcarne A, Zeppa P, Altieri R, Morra I, Cassoni P, Garbossa D, Cassisa A, Bartolini A, Pellegatta S, Comoglio PM, Finocchiaro G, Poliani PL, Boccaccio C. Coexisting cancer stem cells with heterogeneous gene amplifications, transcriptional profiles, and malignancy are isolated from single glioblastomas. Cell Rep 2023; 42:112816. [PMID: 37505981 DOI: 10.1016/j.celrep.2023.112816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 04/05/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023] Open
Abstract
Glioblastoma (GBM) is known as an intractable, highly heterogeneous tumor encompassing multiple subclones, each supported by a distinct glioblastoma stem cell (GSC). The contribution of GSC genetic and transcriptional heterogeneity to tumor subclonal properties is debated. In this study, we describe the systematic derivation, propagation, and characterization of multiple distinct GSCs from single, treatment-naive GBMs (GSC families). The tumorigenic potential of each GSC better correlates with its transcriptional profile than its genetic make-up, with classical GSCs being inherently more aggressive and mesenchymal more dependent on exogenous growth factors across multiple GBMs. These GSCs can segregate and recapitulate different histopathological aspects of the same GBM, as shown in a paradigmatic tumor with two histopathologically distinct components, including a conventional GBM and a more aggressive primitive neuronal component. This study provides a resource for investigating how GSCs with distinct genetic and/or phenotypic features contribute to individual GBM heterogeneity and malignant escalation.
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Affiliation(s)
- Francesca De Bacco
- Laboratory of Cancer Stem Cell Research, Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; Department of Oncology, University of Turin, 10060 Candiolo, Italy
| | - Francesca Orzan
- Laboratory of Cancer Stem Cell Research, Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy
| | | | - Marta Prelli
- Laboratory of Cancer Stem Cell Research, Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; Department of Oncology, University of Turin, 10060 Candiolo, Italy
| | - Claudio Isella
- Department of Oncology, University of Turin, 10060 Candiolo, Italy; Laboratory of Oncogenomics, Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy
| | - Elena Casanova
- Laboratory of Cancer Stem Cell Research, Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy
| | - Raffaella Albano
- Core Facilities, Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy
| | - Gigliola Reato
- Laboratory of Cancer Stem Cell Research, Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; Department of Oncology, University of Turin, 10060 Candiolo, Italy
| | - Jessica Erriquez
- Core Facilities, Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy
| | - Antonio D'Ambrosio
- Laboratory of Cancer Stem Cell Research, Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy
| | - Mara Panero
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy
| | - Carmine Dall'Aglio
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy
| | - Laura Casorzo
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy
| | - Manuela Cominelli
- Pathology Unit, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Francesca Pagani
- Pathology Unit, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Antonio Melcarne
- Neurosurgery Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy
| | - Pietro Zeppa
- Neurosurgery Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy; Department of Neurosciences, University of Turin, 10126 Turin, Italy
| | - Roberto Altieri
- Department of Neurosciences, University of Turin, 10126 Turin, Italy
| | - Isabella Morra
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy
| | - Paola Cassoni
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy
| | - Diego Garbossa
- Neurosurgery Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy; Department of Neurosciences, University of Turin, 10126 Turin, Italy
| | - Anna Cassisa
- Laboratory of Oncogenomics, Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy
| | - Alice Bartolini
- Core Facilities, Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy
| | - Serena Pellegatta
- Unit of Immunotherapy of Brain Tumors, Fondazione IRCCS Istituto Neurologico C. Besta, 20133 Milan, Italy
| | - Paolo M Comoglio
- IFOM ETS - The AIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | | | - Pietro L Poliani
- Pathology Unit, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Carla Boccaccio
- Laboratory of Cancer Stem Cell Research, Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; Department of Oncology, University of Turin, 10060 Candiolo, Italy.
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6
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Manganaro L, Bianco S, Bironzo P, Cipollini F, Colombi D, Corà D, Corti G, Doronzo G, Errico L, Falco P, Gandolfi L, Guerrera F, Monica V, Novello S, Papotti M, Parab S, Pittaro A, Primo L, Righi L, Sabbatini G, Sandri A, Vattakunnel S, Bussolino F, Scagliotti GV. Consensus clustering methodology to improve molecular stratification of non-small cell lung cancer. Sci Rep 2023; 13:7759. [PMID: 37173325 PMCID: PMC10182023 DOI: 10.1038/s41598-023-33954-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Recent advances in machine learning research, combined with the reduced sequencing costs enabled by modern next-generation sequencing, paved the way to the implementation of precision medicine through routine multi-omics molecular profiling of tumours. Thus, there is an emerging need of reliable models exploiting such data to retrieve clinically useful information. Here, we introduce an original consensus clustering approach, overcoming the intrinsic instability of common clustering methods based on molecular data. This approach is applied to the case of non-small cell lung cancer (NSCLC), integrating data of an ongoing clinical study (PROMOLE) with those made available by The Cancer Genome Atlas, to define a molecular-based stratification of the patients beyond, but still preserving, histological subtyping. The resulting subgroups are biologically characterized by well-defined mutational and gene-expression profiles and are significantly related to disease-free survival (DFS). Interestingly, it was observed that (1) cluster B, characterized by a short DFS, is enriched in KEAP1 and SKP2 mutations, that makes it an ideal candidate for further studies with inhibitors, and (2) over- and under-representation of inflammation and immune systems pathways in squamous-cell carcinomas subgroups could be potentially exploited to stratify patients treated with immunotherapy.
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Affiliation(s)
- L Manganaro
- aizoOn Technology Consulting S.R.L, Torino, Italy
| | - S Bianco
- aizoOn Technology Consulting S.R.L, Torino, Italy
| | - P Bironzo
- Medical Oncology Division at San Luigi Hospital, Department of Oncology, University of Torino, Orbassano (TO), Italy
| | - F Cipollini
- aizoOn Technology Consulting S.R.L, Torino, Italy
| | - D Colombi
- aizoOn Technology Consulting S.R.L, Torino, Italy
| | - D Corà
- Department of Translational Medicine, Piemonte Orientale University, Novara, Italy
- Center for Translational Research on Autoimmune and Allergic Diseases-CAAD, Novara, Italy
| | - G Corti
- Department of Oncology, University of Torino, 10060, Candiolo, Italy
- Candiolo Cancer Institute-IRCCS-FPO, 10060, Candiolo, Italy
| | - G Doronzo
- Department of Oncology, University of Torino, 10060, Candiolo, Italy
- Candiolo Cancer Institute-IRCCS-FPO, 10060, Candiolo, Italy
| | - L Errico
- Division of Thoracic Surgery at AOU San Luigi, Department of Oncology, University of Torino, Orbassano (TO), Italy
| | - P Falco
- aizoOn Technology Consulting S.R.L, Torino, Italy
| | - L Gandolfi
- Department of Oncology, University of Torino, 10060, Candiolo, Italy
- Candiolo Cancer Institute-IRCCS-FPO, 10060, Candiolo, Italy
| | - F Guerrera
- Division of Thoracic Surgery at AOU Città della Salute e della Scienza, Department of Surgical Sciences, University of Torino, Torino, Italy
| | - V Monica
- Department of Oncology, University of Torino, 10060, Candiolo, Italy
- Candiolo Cancer Institute-IRCCS-FPO, 10060, Candiolo, Italy
| | - S Novello
- Medical Oncology Division at San Luigi Hospital, Department of Oncology, University of Torino, Orbassano (TO), Italy
| | - M Papotti
- Pathology Division at AOU Città della Salute e della Scienza, Department of Oncology, University of Torino, Torino, Italy
| | - S Parab
- Department of Oncology, University of Torino, 10060, Candiolo, Italy
- Candiolo Cancer Institute-IRCCS-FPO, 10060, Candiolo, Italy
| | - A Pittaro
- Pathology Division at AOU Città della Salute e della Scienza, Department of Oncology, University of Torino, Torino, Italy
| | - L Primo
- Department of Oncology, University of Torino, 10060, Candiolo, Italy
- Candiolo Cancer Institute-IRCCS-FPO, 10060, Candiolo, Italy
| | - L Righi
- Pathology Division at AOU San Luigi, Department of Oncology, University of Torino, Orbassano (TO), Italy
| | - G Sabbatini
- aizoOn Technology Consulting S.R.L, Torino, Italy
| | - A Sandri
- Division of Thoracic Surgery at AOU San Luigi, Department of Oncology, University of Torino, Orbassano (TO), Italy
| | | | - F Bussolino
- Department of Oncology, University of Torino, 10060, Candiolo, Italy
- Candiolo Cancer Institute-IRCCS-FPO, 10060, Candiolo, Italy
| | - G V Scagliotti
- Medical Oncology Division at San Luigi Hospital, Department of Oncology, University of Torino, Orbassano (TO), Italy.
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7
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Abbes S, Baldi S, Sellami H, Amedei A, Keskes L. Molecular methods for colorectal cancer screening: Progress with next-generation sequencing evolution. World J Gastrointest Oncol 2023; 15:425-442. [PMID: 37009313 PMCID: PMC10052664 DOI: 10.4251/wjgo.v15.i3.425] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/02/2023] [Accepted: 02/15/2023] [Indexed: 03/14/2023] Open
Abstract
Currently, colorectal cancer (CRC) represents the third most common malignancy and the second most deadly cancer worldwide, with a higher incidence in developed countries. Like other solid tumors, CRC is a heterogeneous genomic disease in which various alterations, such as point mutations, genomic rearrangements, gene fusions or chromosomal copy number alterations, can contribute to the disease development. However, because of its orderly natural history, easily accessible onset location and high lifetime incidence, CRC is ideally suited for preventive intervention, but the many screening efforts of the last decades have been compromised by performance limitations and low penetrance of the standard screening tools. The advent of next-generation sequencing (NGS) has both facilitated the identification of previously unrecognized CRC features such as its relationship with gut microbial pathogens and revolutionized the speed and throughput of cataloguing CRC-related genomic alterations. Hence, in this review, we summarized the several diagnostic tools used for CRC screening in the past and the present, focusing on recent NGS approaches and their revolutionary role in the identification of novel genomic CRC characteristics, the advancement of understanding the CRC carcinogenesis and the screening of clinically actionable targets for personalized medicine.
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Affiliation(s)
- Salma Abbes
- Laboratory of Parasitic and Fungal Molecular Biology, University of Sfax, Sfax 3029, Tunisia
| | - Simone Baldi
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50134, Italy
| | - Hayet Sellami
- Drosophila Research Unit-Parasitology and Mycologie Laboratory, University of Sfax, Sfax 3029, Tunisia
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50134, Italy
- SOD of Interdisciplinary Internal Medicine, Careggi University Hospital, Florence 50134, Italy
| | - Leila Keskes
- Laboratory of Human Molecular Genetic, University of Sfax, Sfax 3029, Tunisia
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8
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Durinikova E, Reilly NM, Buzo K, Mariella E, Chilà R, Lorenzato A, Dias JML, Grasso G, Pisati F, Lamba S, Corti G, Degasperi A, Cancelliere C, Mauri G, Andrei P, Linnebacher M, Marsoni S, Siena S, Sartore-Bianchi A, Nik-Zainal S, Di Nicolantonio F, Bardelli A, Arena S. Targeting the DNA Damage Response Pathways and Replication Stress in Colorectal Cancer. Clin Cancer Res 2022; 28:3874-3889. [PMID: 35881546 PMCID: PMC9433963 DOI: 10.1158/1078-0432.ccr-22-0875] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/05/2022] [Accepted: 07/01/2022] [Indexed: 12/04/2022]
Abstract
PURPOSE Genomic instability is a hallmark of cancer and targeting DNA damage response (DDR) is emerging as a promising therapeutic strategy in different solid tumors. The effectiveness of targeting DDR in colorectal cancer has not been extensively explored. EXPERIMENTAL DESIGN We challenged 112 cell models recapitulating the genomic landscape of metastatic colorectal cancer with ATM, ATR, CHK1, WEE1, and DNA-PK inhibitors, in parallel with chemotherapeutic agents. We focused then on ATR inhibitors (ATRi) and, to identify putative biomarkers of response and resistance, we analyzed at multiple levels colorectal cancer models highly sensitive or resistant to these drugs. RESULTS We found that around 30% of colorectal cancers, including those carrying KRAS and BRAF mutations and unresponsive to targeted agents, are sensitive to at least one DDR inhibitor. By investigating potential biomarkers of response to ATRi, we found that ATRi-sensitive cells displayed reduced phospho-RPA32 foci at basal level, while ATRi-resistant cells showed increased RAD51 foci formation in response to replication stress. Lack of ATM and RAD51C expression was associated with ATRi sensitivity. Analysis of mutational signatures and HRDetect score identified a subgroup of ATRi-sensitive models. Organoids derived from patients with metastatic colorectal cancer recapitulated findings obtained in cell lines. CONCLUSIONS In conclusion, a subset of colorectal cancers refractory to current therapies could benefit from inhibitors of DDR pathways and replication stress. A composite biomarker involving phospho-RPA32 and RAD51 foci, lack of ATM and RAD51C expression, as well as analysis of mutational signatures could be used to identify colorectal cancers likely to respond to ATRi.
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Affiliation(s)
| | - Nicole M. Reilly
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Italy
| | - Kristi Buzo
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Italy
| | - Elisa Mariella
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Italy
| | - Rosaria Chilà
- Department of Oncology, University of Torino, Candiolo, Italy
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Annalisa Lorenzato
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Italy
| | - João M. L. Dias
- Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
- Early Cancer Institute, University of Cambridge, Cambridge, United Kingdom
| | - Gaia Grasso
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Italy
| | | | - Simona Lamba
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy
| | - Giorgio Corti
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Italy
| | - Andrea Degasperi
- Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
- Early Cancer Institute, University of Cambridge, Cambridge, United Kingdom
| | | | - Gianluca Mauri
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Pietro Andrei
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Italy
| | - Michael Linnebacher
- Clinic of General Surgery, Molecular Oncology and Immunotherapy, University of Rostock, Rostock, Germany
| | - Silvia Marsoni
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Salvatore Siena
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Andrea Sartore-Bianchi
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Serena Nik-Zainal
- Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
- Early Cancer Institute, University of Cambridge, Cambridge, United Kingdom
| | - Federica Di Nicolantonio
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Italy
| | - Alberto Bardelli
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Italy
| | - Sabrina Arena
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Italy
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9
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Merlini A, Centomo ML, Ferrero G, Chiabotto G, Miglio U, Berrino E, Giordano G, Brusco S, Pisacane A, Maldi E, Sarotto I, Capozzi F, Lano C, Isella C, Crisafulli G, Aglietta M, Dei Tos AP, Sbaraglia M, Sangiolo D, D’Ambrosio L, Bardelli A, Pignochino Y, Grignani G. DNA damage response and repair genes in advanced bone and soft tissue sarcomas: An 8-gene signature as a candidate predictive biomarker of response to trabectedin and olaparib combination. Front Oncol 2022; 12:844250. [PMID: 36110934 PMCID: PMC9469659 DOI: 10.3389/fonc.2022.844250] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 07/26/2022] [Indexed: 11/21/2022] Open
Abstract
Background Advanced and unresectable bone and soft tissue sarcomas (BSTS) still represent an unmet medical need. We demonstrated that the alkylating agent trabectedin and the PARP1-inhibitor olaparib display antitumor activity in BSTS preclinical models. Moreover, in a phase Ib clinical trial (NCT02398058), feasibility, tolerability and encouraging results have been observed and the treatment combination is currently under study in a phase II trial (NCT03838744). Methods Differential expression of genes involved in DNA Damage Response and Repair was evaluated by Nanostring® technology, extracting RNA from pre-treatment tumor samples of 16 responder (≥6-month progression free survival) and 16 non-responder patients. Data validation was performed by quantitative real-time PCR, RNA in situ hybridization, and immunohistochemistry. The correlation between the identified candidate genes and both progression-free survival and overall survival was investigated in the publicly available dataset “Sarcoma (TCGA, The Cancer Genome Atlas)”. Results Differential RNA expression analysis revealed an 8-gene signature (CDKN2A, PIK3R1, SLFN11, ATM, APEX2, BLM, XRCC2, MAD2L2) defining patients with better outcome upon trabectedin+olaparib treatment. In responder vs. non-responder patients, a significant differential expression of these genes was further confirmed by RNA in situ hybridization and by qRT-PCR and immunohistochemistry in selected experiments. Correlation between survival outcomes and genetic alterations in the identified genes was shown in the TCGA sarcoma dataset. Conclusions This work identified an 8-gene expression signature to improve prediction of response to trabectedin+olaparib combination in BSTS. The predictive role of these potential biomarkers warrants further investigation.
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Affiliation(s)
- Alessandra Merlini
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Department of Oncology, University of Torino, Turin, Italy
| | - Maria Laura Centomo
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Department of Oncology, University of Torino, Turin, Italy
| | - Giulio Ferrero
- Department of Clinical and Biological Sciences, University of Torino, Turin, Italy
- Department of Computer Science, University of Torino, Turin, Italy
| | - Giulia Chiabotto
- Department of Medical Sciences, University of Torino, Turin, Italy
| | | | - Enrico Berrino
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Giorgia Giordano
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Department of Oncology, University of Torino, Turin, Italy
| | - Silvia Brusco
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Department of Oncology, University of Torino, Turin, Italy
| | | | - Elena Maldi
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
| | | | | | - Cristina Lano
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Department of Oncology, University of Torino, Turin, Italy
| | - Claudio Isella
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Department of Oncology, University of Torino, Turin, Italy
| | - Giovanni Crisafulli
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Department of Oncology, University of Torino, Turin, Italy
| | - Massimo Aglietta
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Department of Oncology, University of Torino, Turin, Italy
| | - Angelo Paolo Dei Tos
- Department of Pathology, Azienda Ospedale-Università Padova, Padua, Italy
- Department of Medicine (DIMED), University of Padua School of Medicine, Padua, Italy
| | - Marta Sbaraglia
- Department of Pathology, Azienda Ospedale-Università Padova, Padua, Italy
| | - Dario Sangiolo
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Department of Oncology, University of Torino, Turin, Italy
| | - Lorenzo D’Ambrosio
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Department of Oncology, University of Torino, Turin, Italy
- Medical Oncology, AOU San Luigi Gonzaga, Orbassano (TO), Italy
| | - Alberto Bardelli
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Department of Oncology, University of Torino, Turin, Italy
| | - Ymera Pignochino
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Department of Clinical and Biological Sciences, University of Torino, Turin, Italy
- *Correspondence: Ymera Pignochino, ; Giovanni Grignani,
| | - Giovanni Grignani
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- *Correspondence: Ymera Pignochino, ; Giovanni Grignani,
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10
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Crisafulli G, Sartore-Bianchi A, Lazzari L, Pietrantonio F, Amatu A, Macagno M, Barault L, Cassingena A, Bartolini A, Luraghi P, Mauri G, Battuello P, Personeni N, Zampino MG, Pessei V, Vitiello PP, Tosi F, Idotta L, Morano F, Valtorta E, Bonoldi E, Germano G, Di Nicolantonio F, Marsoni S, Siena S, Bardelli A. Temozolomide Treatment Alters Mismatch Repair and Boosts Mutational Burden in Tumor and Blood of Colorectal Cancer Patients. Cancer Discov 2022; 12:1656-1675. [PMID: 35522273 PMCID: PMC9394384 DOI: 10.1158/2159-8290.cd-21-1434] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 04/16/2022] [Accepted: 05/04/2022] [Indexed: 01/07/2023]
Abstract
The majority of metastatic colorectal cancers (mCRC) are mismatch repair (MMR) proficient and unresponsive to immunotherapy, whereas MMR-deficient (MMRd) tumors often respond to immune-checkpoint blockade. We previously reported that the treatment of colorectal cancer preclinical models with temozolomide (TMZ) leads to MMR deficiency, increased tumor mutational burden (TMB), and sensitization to immunotherapy. To clinically translate these findings, we designed the ARETHUSA clinical trial whereby O6-methylguanine-DNA-methyltransferase (MGMT)-deficient, MMR-proficient, RAS-mutant mCRC patients received priming therapy with TMZ. Analysis of tissue biopsies and circulating tumor DNA (ctDNA) revealed the emergence of a distinct mutational signature and increased TMB after TMZ treatment. Multiple alterations in the nucleotide context favored by the TMZ signature emerged in MMR genes, and the p.T1219I MSH6 variant was detected in ctDNA and tissue of 94% (16/17) of the cases. A subset of patients whose tumors displayed the MSH6 mutation, the TMZ mutational signature, and increased TMB achieved disease stabilization upon pembrolizumab treatment. SIGNIFICANCE MMR-proficient mCRCs are unresponsive to immunotherapy. We provide the proof of concept that inactivation of MMR genes can be achieved pharmacologically with TMZ and molecularly monitored in the tissue and blood of patients with mCRC. This strategy deserves additional evaluation in mCRC patients whose tumors are no longer responsive to standard-of-care treatments. See related commentary by Willis and Overman, p. 1612. This article is highlighted in the In This Issue feature, p. 1599.
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Affiliation(s)
- Giovanni Crisafulli
- Department of Oncology, University of Torino, Candiolo, Italy.,Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Italy
| | - Andrea Sartore-Bianchi
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy.,Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
| | - Luca Lazzari
- The FIRC Institute of Molecular Oncology, Milan, Italy
| | - Filippo Pietrantonio
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Alessio Amatu
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Marco Macagno
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Italy
| | - Ludovic Barault
- Department of Oncology, University of Torino, Candiolo, Italy.,Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Italy
| | - Andrea Cassingena
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | | | - Paolo Luraghi
- The FIRC Institute of Molecular Oncology, Milan, Italy
| | - Gianluca Mauri
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy.,The FIRC Institute of Molecular Oncology, Milan, Italy
| | - Paolo Battuello
- Department of Oncology, University of Torino, Candiolo, Italy
| | - Nicola Personeni
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy.,Medical Oncology and Hematology Unit, Humanitas Cancer Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Maria Giulia Zampino
- Division of Gastrointestinal Medical Oncology and Neuroendocrine Tumors, European Institute of Oncology, IRCCS, Milan, Italy
| | | | - Pietro Paolo Vitiello
- Department of Oncology, University of Torino, Candiolo, Italy.,Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Italy
| | - Federica Tosi
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Laura Idotta
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Federica Morano
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Emanuele Valtorta
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Emanuela Bonoldi
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Giovanni Germano
- Department of Oncology, University of Torino, Candiolo, Italy.,Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Italy
| | - Federica Di Nicolantonio
- Department of Oncology, University of Torino, Candiolo, Italy.,Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Italy
| | | | - Salvatore Siena
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy.,Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
| | - Alberto Bardelli
- Department of Oncology, University of Torino, Candiolo, Italy.,Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Italy.,Corresponding Author: Alberto Bardelli, University of Turin, Department of Oncology, Candiolo Cancer Institute, FPO - IRCCS, Str.Prov.le 142, km 3.95, 10060, Candiolo, Torino, Italy. Phone/Fax: 39-011-993-3235; E-mail:
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11
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Dlamini Z, Skepu A, Kim N, Mkhabele M, Khanyile R, Molefi T, Mbatha S, Setlai B, Mulaudzi T, Mabongo M, Bida M, Kgoebane-Maseko M, Mathabe K, Lockhat Z, Kgokolo M, Chauke-Malinga N, Ramagaga S, Hull R. AI and precision oncology in clinical cancer genomics: From prevention to targeted cancer therapies-an outcomes based patient care. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.100965] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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12
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Luo D, Yang J, Liu J, Yong X, Wang Z. Identification of four novel hub genes as monitoring biomarkers for colorectal cancer. Hereditas 2022; 159:11. [PMID: 35093172 PMCID: PMC8801129 DOI: 10.1186/s41065-021-00216-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/29/2021] [Indexed: 11/30/2022] Open
Abstract
Background It must be admitted that the incidence of colorectal cancer (CRC) was on the rise all over the world, but the related treatment had not caught up. Further research on the underlying pathogenesis of CRC was conducive to improving the survival status of current CRC patients. Methods Differentially expressed genes (DEGs) screening were conducted based on “limma” and “RobustRankAggreg” package of R software. Weighted gene co-expression network analysis (WGCNA) was performed in the integrated DEGs that from The Cancer Genome Atlas (TCGA), and all samples of validation were from Gene Expression Omnlbus (GEO) dataset. Results The terms obtained in the functional annotation for primary DEGs indicated that they were associated with CRC. The MEyellow stand out whereby showed the significant correlation with clinical feature (disease), and 4 hub genes, including ABCC13, AMPD1, SCNN1B and TMIGD1, were identified in yellow module. Nine datasets from Gene Expression Omnibus database confirmed these four genes were significantly down-regulated and the survival estimates for the low-expression group of these genes were lower than for the high-expression group in Kaplan-Meier survival analysis section. MEXPRESS suggested that down-regulation of some top hub genes may be caused by hypermethylation. Receiver operating characteristic curves indicated that these genes had certain diagnostic efficacy. Moreover, tumor-infiltrating immune cells and gene set enrichment analysis for hub genes suggested that there were some associations between these genes and the pathogenesis of CRC. Conclusion This study identified modules that were significantly associated with CRC, four novel hub genes, and further analysis of these genes. This may provide a little new insights and directions into the potential pathogenesis of CRC. Supplementary Information The online version contains supplementary material available at 10.1186/s41065-021-00216-7.
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13
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Circulating tumor DNA to guide rechallenge with panitumumab in metastatic colorectal cancer: the phase 2 CHRONOS trial. Nat Med 2022; 28:1612-1618. [PMID: 35915157 PMCID: PMC9386661 DOI: 10.1038/s41591-022-01886-0] [Citation(s) in RCA: 84] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 06/01/2022] [Indexed: 01/09/2023]
Abstract
Anti-epidermal growth factor receptor (EGFR) monoclonal antibodies are approved for the treatment of RAS wild-type (WT) metastatic colorectal cancer (mCRC), but the emergence of resistance mutations restricts their efficacy. We previously showed that RAS, BRAF and EGFR mutant alleles, which appear in circulating tumor DNA (ctDNA) during EGFR blockade, decline upon therapy withdrawal. We hypothesized that monitoring resistance mutations in blood could rationally guide subsequent therapy with anti-EGFR antibodies. We report here the results of CHRONOS, an open-label, single-arm phase 2 clinical trial exploiting blood-based identification of RAS/BRAF/EGFR mutations levels to tailor a chemotherapy-free anti-EGFR rechallenge with panitumumab (ClinicalTrials.gov: NCT03227926 ; EudraCT 2016-002597-12). The primary endpoint was objective response rate. Secondary endpoints were progression-free survival, overall survival, safety and tolerability of this strategy. In CHRONOS, patients with tissue-RAS WT tumors after a previous treatment with anti-EGFR-based regimens underwent an interventional ctDNA-based screening. Of 52 patients, 16 (31%) carried at least one mutation conferring resistance to anti-EGFR therapy and were excluded. The primary endpoint of the trial was met; and, of 27 enrolled patients, eight (30%) achieved partial response and 17 (63%) disease control, including two unconfirmed responses. These clinical results favorably compare with standard third-line treatments and show that interventional liquid biopsies can be effectively and safely exploited in a timely manner to guide anti-EGFR rechallenge therapy with panitumumab in patients with mCRC. Further larger and randomized trials are warranted to formally compare panitumumab rechallenge with standard-of-care therapies in this patient setting.
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14
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Pignochino Y, Crisafulli G, Giordano G, Merlini A, Berrino E, Centomo ML, Chiabotto G, Brusco S, Basiricò M, Maldi E, Pisacane A, Leuci V, Sangiolo D, D’Ambrosio L, Aglietta M, Kasper B, Bardelli A, Grignani G. PARP1 Inhibitor and Trabectedin Combination Does Not Increase Tumor Mutational Burden in Advanced Sarcomas-A Preclinical and Translational Study. Cancers (Basel) 2021; 13:cancers13246295. [PMID: 34944915 PMCID: PMC8699802 DOI: 10.3390/cancers13246295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 11/25/2022] Open
Abstract
Simple Summary Immunotherapy has revolutionized cancer treatment, but not for all tumor types. Indeed, sarcomas are considered “immune-cold” tumors, which are relatively unresponsive to immunotherapy. One strategy to potentiate immunotherapy efficacy is to increase tumor immunogenicity, for instance by boosting the number of candidate targets (neoantigens) to be recognized by the immune system. Tumor mutational burden indicates the number of somatic mutations identified in the tumor and normalized per megabase. Tumor mutational burden is considered as an acceptable, measurable surrogate of tumor neoantigens. Here, we explored whether the combination of two DNA-damaging agents, trabectedin and olaparib, could increase tumor mutational burden in sarcomas, to prime subsequent immunotherapy. We found no variation in tumor mutational burden after trabectedin + olaparib in preclinical and clinical samples. Therefore, other aspects should be considered to increase sarcoma immunogenicity, by exploiting different pathways such as the potential modulation of the tumor microenvironment induced by trabectedin + olaparib. Abstract Drug-induced tumor mutational burden (TMB) may contribute to unleashing the immune response in relatively “immune-cold” tumors, such as sarcomas. We previously showed that PARP1 inhibition perpetuates the DNA damage induced by the chemotherapeutic agent trabectedin in both preclinical models and sarcoma patients. In the present work, we explored acquired genetic changes in DNA repair genes, mutational signatures, and TMB in a translational platform composed of cell lines, xenografts, and tumor samples from patients treated with trabectedin and olaparib combination, compared to cells treated with temozolomide, an alkylating agent that induces hypermutation. Whole-exome and targeted panel sequencing data analyses revealed that three cycles of trabectedin and olaparib combination neither affected the mutational profiles, DNA repair gene status, or copy number alterations, nor increased TMB both in homologous recombinant-defective and proficient cells or in xenografts. Moreover, TMB was not increased in tumor specimens derived from trabectedin- and olaparib-treated patients (5–6 cycles) when compared to pre-treatment biopsies. Conversely, repeated treatments with temozolomide induced a massive TMB increase in the SJSA-1 osteosarcoma model. In conclusion, a trabectedin and olaparib combination did not show mutagenic effects and is unlikely to prime subsequent immune-therapeutic interventions based on TMB increase. On the other hand, these findings are reassuring in the increasing warning of treatment-induced hematologic malignancies correlated to PARP1 inhibitor use.
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Affiliation(s)
- Ymera Pignochino
- Department of Clinical and Biological Sciences, University of Torino, 10100 Torino, Italy;
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (G.C.); (G.G.); (E.B.); (M.L.C.); (S.B.); (M.B.); (E.M.); (A.P.); (V.L.); (D.S.); (L.D.); (M.A.); (A.B.); (G.G.)
| | - Giovanni Crisafulli
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (G.C.); (G.G.); (E.B.); (M.L.C.); (S.B.); (M.B.); (E.M.); (A.P.); (V.L.); (D.S.); (L.D.); (M.A.); (A.B.); (G.G.)
- Department of Oncology, University of Torino, 10100 Torino, Italy
| | - Giorgia Giordano
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (G.C.); (G.G.); (E.B.); (M.L.C.); (S.B.); (M.B.); (E.M.); (A.P.); (V.L.); (D.S.); (L.D.); (M.A.); (A.B.); (G.G.)
- Department of Oncology, University of Torino, 10100 Torino, Italy
| | - Alessandra Merlini
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (G.C.); (G.G.); (E.B.); (M.L.C.); (S.B.); (M.B.); (E.M.); (A.P.); (V.L.); (D.S.); (L.D.); (M.A.); (A.B.); (G.G.)
- Department of Oncology, University of Torino, 10100 Torino, Italy
- Correspondence: ; Tel.: +39-0119933623
| | - Enrico Berrino
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (G.C.); (G.G.); (E.B.); (M.L.C.); (S.B.); (M.B.); (E.M.); (A.P.); (V.L.); (D.S.); (L.D.); (M.A.); (A.B.); (G.G.)
- Department of Medical Sciences, University of Torino, 10100 Torino, Italy;
| | - Maria Laura Centomo
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (G.C.); (G.G.); (E.B.); (M.L.C.); (S.B.); (M.B.); (E.M.); (A.P.); (V.L.); (D.S.); (L.D.); (M.A.); (A.B.); (G.G.)
- Department of Oncology, University of Torino, 10100 Torino, Italy
| | - Giulia Chiabotto
- Department of Medical Sciences, University of Torino, 10100 Torino, Italy;
| | - Silvia Brusco
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (G.C.); (G.G.); (E.B.); (M.L.C.); (S.B.); (M.B.); (E.M.); (A.P.); (V.L.); (D.S.); (L.D.); (M.A.); (A.B.); (G.G.)
- Department of Oncology, University of Torino, 10100 Torino, Italy
| | - Marco Basiricò
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (G.C.); (G.G.); (E.B.); (M.L.C.); (S.B.); (M.B.); (E.M.); (A.P.); (V.L.); (D.S.); (L.D.); (M.A.); (A.B.); (G.G.)
| | - Elena Maldi
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (G.C.); (G.G.); (E.B.); (M.L.C.); (S.B.); (M.B.); (E.M.); (A.P.); (V.L.); (D.S.); (L.D.); (M.A.); (A.B.); (G.G.)
| | - Alberto Pisacane
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (G.C.); (G.G.); (E.B.); (M.L.C.); (S.B.); (M.B.); (E.M.); (A.P.); (V.L.); (D.S.); (L.D.); (M.A.); (A.B.); (G.G.)
| | - Valeria Leuci
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (G.C.); (G.G.); (E.B.); (M.L.C.); (S.B.); (M.B.); (E.M.); (A.P.); (V.L.); (D.S.); (L.D.); (M.A.); (A.B.); (G.G.)
| | - Dario Sangiolo
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (G.C.); (G.G.); (E.B.); (M.L.C.); (S.B.); (M.B.); (E.M.); (A.P.); (V.L.); (D.S.); (L.D.); (M.A.); (A.B.); (G.G.)
- Department of Oncology, University of Torino, 10100 Torino, Italy
| | - Lorenzo D’Ambrosio
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (G.C.); (G.G.); (E.B.); (M.L.C.); (S.B.); (M.B.); (E.M.); (A.P.); (V.L.); (D.S.); (L.D.); (M.A.); (A.B.); (G.G.)
- Cardinal Massaia Hospital, 14100 Asti, Italy
| | - Massimo Aglietta
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (G.C.); (G.G.); (E.B.); (M.L.C.); (S.B.); (M.B.); (E.M.); (A.P.); (V.L.); (D.S.); (L.D.); (M.A.); (A.B.); (G.G.)
- Department of Oncology, University of Torino, 10100 Torino, Italy
| | - Bernd Kasper
- Sarcoma Unit, Mannheim University Medical Center, University of Heidelberg, 68167 Mannheim, Germany;
| | - Alberto Bardelli
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (G.C.); (G.G.); (E.B.); (M.L.C.); (S.B.); (M.B.); (E.M.); (A.P.); (V.L.); (D.S.); (L.D.); (M.A.); (A.B.); (G.G.)
- Department of Oncology, University of Torino, 10100 Torino, Italy
| | - Giovanni Grignani
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (G.C.); (G.G.); (E.B.); (M.L.C.); (S.B.); (M.B.); (E.M.); (A.P.); (V.L.); (D.S.); (L.D.); (M.A.); (A.B.); (G.G.)
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15
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Picco G, Cattaneo CM, van Vliet EJ, Crisafulli G, Rospo G, Consonni S, Vieira SF, Rodríguez IS, Cancelliere C, Banerjee R, Schipper LJ, Oddo D, Dijkstra KK, Cinatl J, Michaelis M, Yang F, Di Nicolantonio F, Sartore-Bianchi A, Siena S, Arena S, Voest EE, Bardelli A, Garnett MJ. Werner Helicase Is a Synthetic-Lethal Vulnerability in Mismatch Repair-Deficient Colorectal Cancer Refractory to Targeted Therapies, Chemotherapy, and Immunotherapy. Cancer Discov 2021; 11:1923-1937. [PMID: 33837064 DOI: 10.1158/2159-8290.cd-20-1508] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 03/03/2021] [Accepted: 03/29/2021] [Indexed: 11/16/2022]
Abstract
Targeted therapies, chemotherapy, and immunotherapy are used to treat patients with mismatch repair-deficient (dMMR)/microsatellite instability-high (MSI-H) colorectal cancer. The clinical effectiveness of targeted therapy and chemotherapy is limited by resistance and drug toxicities, and about half of patients receiving immunotherapy have disease that is refractory to immune checkpoint inhibitors. Loss of Werner syndrome ATP-dependent helicase (WRN) is a synthetic lethality in dMMR/MSI-H cells. To inform the development of WRN as a therapeutic target, we performed WRN knockout or knockdown in 60 heterogeneous dMMR colorectal cancer preclinical models, demonstrating that WRN dependency is an almost universal feature and a robust marker for patient selection. Furthermore, models of resistance to clinically relevant targeted therapy, chemotherapy, and immunotherapy retain WRN dependency. These data show the potential of therapeutically targeting WRN in patients with dMMR/MSI-H colorectal cancer and support WRN as a therapeutic option for patients with dMMR/MSI-H cancers refractory to current treatment strategies. SIGNIFICANCE: We found that a large, diverse set of dMMR/MSI-H colorectal cancer preclinical models, including models of treatment-refractory disease, are WRN-dependent. Our results support WRN as a promising synthetic-lethal target in dMMR/MSI-H colorectal cancer tumors as a monotherapy or in combination with targeted agents, chemotherapy, or immunotherapy.This article is highlighted in the In This Issue feature, p. 1861.
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Affiliation(s)
| | - Chiara M Cattaneo
- Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands.,Oncode Institute, Amsterdam, the Netherlands
| | | | - Giovanni Crisafulli
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo (TO), Italy.,Department of Oncology, University of Torino, Candiolo, Italy
| | - Giuseppe Rospo
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo (TO), Italy.,Department of Oncology, University of Torino, Candiolo, Italy
| | | | - Sara F Vieira
- Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Iñigo Sánchez Rodríguez
- Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands.,Oncode Institute, Amsterdam, the Netherlands
| | | | - Ruby Banerjee
- Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Luuk J Schipper
- Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands.,Oncode Institute, Amsterdam, the Netherlands
| | - Daniele Oddo
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo (TO), Italy.,Department of Oncology, University of Torino, Candiolo, Italy
| | - Krijn K Dijkstra
- Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands.,Oncode Institute, Amsterdam, the Netherlands
| | - Jindrich Cinatl
- Institute for Medical Virology, Goethe-University, Frankfurt am Main, Germany
| | - Martin Michaelis
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | | | - Federica Di Nicolantonio
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo (TO), Italy.,Department of Oncology, University of Torino, Candiolo, Italy
| | - Andrea Sartore-Bianchi
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milano, Italy.,Dipartimento di Oncologia ed Emato-Oncologia, Università degli Studi di Milano (La Statale), Milano, Italy
| | - Salvatore Siena
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milano, Italy.,Dipartimento di Oncologia ed Emato-Oncologia, Università degli Studi di Milano (La Statale), Milano, Italy
| | - Sabrina Arena
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo (TO), Italy.,Department of Oncology, University of Torino, Candiolo, Italy
| | - Emile E Voest
- Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands.,Oncode Institute, Amsterdam, the Netherlands
| | - Alberto Bardelli
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo (TO), Italy.,Department of Oncology, University of Torino, Candiolo, Italy
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16
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Germano G, Lu S, Rospo G, Lamba S, Rousseau B, Fanelli S, Stenech D, Le DT, Hays J, Totaro MG, Amodio V, Chilà R, Mondino A, Diaz LA, Di Nicolantonio F, Bardelli A. CD4 T Cell-Dependent Rejection of Beta-2 Microglobulin Null Mismatch Repair-Deficient Tumors. Cancer Discov 2021; 11:1844-1859. [PMID: 33653693 DOI: 10.1158/2159-8290.cd-20-0987] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 01/09/2021] [Accepted: 02/25/2021] [Indexed: 11/16/2022]
Abstract
Inactivation of beta-2 microglobulin (B2M) is considered a determinant of resistance to immune checkpoint inhibitors (ICPi) in melanoma and lung cancers. In contrast, B2M loss does not appear to affect response to ICPis in mismatch repair-deficient (MMRd) colorectal tumors where biallelic inactivation of B2M is frequently observed. We inactivated B2m in multiple murine MMRd cancer models. Although MMRd cells would not readily grow in immunocompetent mice, MMRd B2m null cells were tumorigenic and regressed when treated with anti-PD-1 and anti-CTLA4. The efficacy of ICPis against MMRd B2m null tumors did not require CD8+ T cells but relied on the presence of CD4+ T cells. Human tumors expressing low levels of B2M display increased intratumoral CD4+ T cells. We conclude that B2M inactivation does not blunt the efficacy of ICPi in MMRd tumors, and we identify a unique role for CD4+ T cells in tumor rejection. SIGNIFICANCE: B2M alterations, which impair antigen presentation, occur frequently in microsatellite-unstable colorectal cancers. Although in melanoma and lung cancers B2M loss is a mechanism of resistance to immune checkpoint blockade, we show that MMRd tumors respond to ICPis through CD4+ T-cell activation.This article is highlighted in the In This Issue feature, p. 1601.
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Affiliation(s)
- Giovanni Germano
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy. .,Department of Oncology, University of Torino, Candiolo, Turin, Italy
| | - Steve Lu
- Ludwig Center and Howard Hughes Medical Institute at Johns Hopkins, Baltimore, Maryland
| | - Giuseppe Rospo
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy.,Department of Oncology, University of Torino, Candiolo, Turin, Italy
| | - Simona Lamba
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Benoit Rousseau
- Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sonia Fanelli
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy.,Department of Oncology, University of Torino, Candiolo, Turin, Italy
| | - Denise Stenech
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy.,Department of Oncology, University of Torino, Candiolo, Turin, Italy
| | - Dung T Le
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | - John Hays
- Division of Medical Oncology, Wexner Medical Center and James Cancer Hospital, The Ohio State University, Columbus, Ohio
| | | | - Vito Amodio
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy.,Department of Oncology, University of Torino, Candiolo, Turin, Italy
| | - Rosaria Chilà
- Department of Oncology, University of Torino, Candiolo, Turin, Italy.,IFOM-the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Anna Mondino
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Luis A Diaz
- Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Federica Di Nicolantonio
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy.,Department of Oncology, University of Torino, Candiolo, Turin, Italy
| | - Alberto Bardelli
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy. .,Department of Oncology, University of Torino, Candiolo, Turin, Italy
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17
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Badic B, Tixier F, Cheze Le Rest C, Hatt M, Visvikis D. Radiogenomics in Colorectal Cancer. Cancers (Basel) 2021; 13:cancers13050973. [PMID: 33652647 PMCID: PMC7956421 DOI: 10.3390/cancers13050973] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 02/07/2021] [Accepted: 02/20/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Colorectal carcinoma is characterized by intratumoral heterogeneity that can be assessed by radiogenomics. Radiomics, high-throughput quantitative data extracted from medical imaging, combined with molecular analysis, through genomic and transcriptomic data, is expected to lead to significant advances in personalized medicine. However, a radiogenomics approach in colorectal cancer is still in its early stages and many problems remain to be solved. Here we review the progress and challenges in this field at its current stage, as well as future developments. Abstract The steady improvement of high-throughput technologies greatly facilitates the implementation of personalized precision medicine. Characterization of tumor heterogeneity through image-derived features—radiomics and genetic profile modifications—genomics, is a rapidly evolving field known as radiogenomics. Various radiogenomics studies have been dedicated to colorectal cancer so far, highlighting the potential of these approaches to enhance clinical decision-making. In this review, a general outline of colorectal radiogenomics literature is provided, discussing the current limitations and suggested further developments.
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Affiliation(s)
- Bogdan Badic
- National Institute of Health and Medical Research, LaTIM—Laboratory of Medical Information Processing (INSERM LaTIM), UMR 1101, Université Bretagne Occidentale, 29238 Brest, France; (F.T.); (C.C.L.R.); (M.H.); (D.V.)
- Correspondence: ; Tel.: +33-298-347-215
| | - Florent Tixier
- National Institute of Health and Medical Research, LaTIM—Laboratory of Medical Information Processing (INSERM LaTIM), UMR 1101, Université Bretagne Occidentale, 29238 Brest, France; (F.T.); (C.C.L.R.); (M.H.); (D.V.)
| | - Catherine Cheze Le Rest
- National Institute of Health and Medical Research, LaTIM—Laboratory of Medical Information Processing (INSERM LaTIM), UMR 1101, Université Bretagne Occidentale, 29238 Brest, France; (F.T.); (C.C.L.R.); (M.H.); (D.V.)
- Department of Nuclear Medicine, University Hospital of Poitiers, 86021 Poitiers, France
| | - Mathieu Hatt
- National Institute of Health and Medical Research, LaTIM—Laboratory of Medical Information Processing (INSERM LaTIM), UMR 1101, Université Bretagne Occidentale, 29238 Brest, France; (F.T.); (C.C.L.R.); (M.H.); (D.V.)
| | - Dimitris Visvikis
- National Institute of Health and Medical Research, LaTIM—Laboratory of Medical Information Processing (INSERM LaTIM), UMR 1101, Université Bretagne Occidentale, 29238 Brest, France; (F.T.); (C.C.L.R.); (M.H.); (D.V.)
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18
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Nikmanesh F, Sarhadi S, Dadashpour M, Asgari Y, Zarghami N. Omics Integration Analysis Unravel the Landscape of Driving Mechanisms of Colorectal Cancer. Asian Pac J Cancer Prev 2020; 21:3539-3549. [PMID: 33369450 PMCID: PMC8046321 DOI: 10.31557/apjcp.2020.21.12.3539] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 11/30/2020] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most malignant cancers and results in a substantial rate of morbidity and mortality. Diagnosis of this malignancy in early stages increases the chance of effective treatment. High-throughput data analyses reveal omics signatures and also provide the possibility of developing computational models for early detection of this disease. Such models would be able to use as complementary tools for early detection of different types of cancers including CRC. In this study, using gene expression data, the Flux balance analysis (FBA) applied to decode metabolic fluxes in cancer and normal cells. Moreover, transcriptome and genome analyses revealed driver agents of CRC in a biological network scheme. By applying comprehensive publicly available data from TCGA, different aspect of CRC regulome including the regulatory effect of gene expression, methylation, microRNA, copy number aberration and point mutation profile over protein levels investigated and the results provide a regulatory picture underlying CRC. Compiling omics profiles indicated snapshots of changes in different omics levels and flux rate of CRC. In conclusion, considering obtained CRC signatures and their role in biological operating systems of cells, the results suggest reliable driver regulatory modules that could potentially serve as biomarkers and therapeutic targets and furthermore expand our understanding of driving mechanisms of this disease. .
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Affiliation(s)
- Fatemeh Nikmanesh
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.
- Iranian Blood Transfusion Organization-Research Center, Iranian Blood Transfusion Organization, IBTO blg., Hemmat Exp. Way, Teheran, Iran.
| | - Shamim Sarhadi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Mehdi Dadashpour
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Yazdan Asgari
- Iranian Blood Transfusion Organization-Research Center, Iranian Blood Transfusion Organization, IBTO blg., Hemmat Exp. Way, Teheran, Iran.
| | - Nosratollah Zarghami
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
- Department of Clinical Biochemistry and Laboratory Medicine, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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19
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Crisafulli G, Mussolin B, Cassingena A, Montone M, Bartolini A, Barault L, Martinetti A, Morano F, Pietrantonio F, Sartore-Bianchi A, Siena S, Di Nicolantonio F, Marsoni S, Bardelli A, Siravegna G. Whole exome sequencing analysis of urine trans-renal tumour DNA in metastatic colorectal cancer patients. ESMO Open 2020; 4:S2059-7029(20)30089-2. [PMID: 32149725 PMCID: PMC7001107 DOI: 10.1136/esmoopen-2019-000572] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/19/2019] [Accepted: 09/21/2019] [Indexed: 12/22/2022] Open
Abstract
Background The analysis of circulating free tumour DNA (ctDNA) in blood, commonly referred as liquid biopsy, is being used to characterise patients with solid cancers. Tumour-specific genetic variants can also be present in DNA isolated from other body fluids, such as urine. Unlike blood, urine sampling is non-invasive, can be self-performed, and allows recurrent longitudinal monitoring. The features of tumour DNA that clears from the glomerular filtration barrier, named trans-renal tumour DNA (trtDNA), are largely unexplored. Patients and methods Specimens were collected from 24 patients with KRAS or BRAF mutant metastatic colorectal cancer (mCRC). Driver mutations were assessed by droplet digital PCR (ddPCR) in ctDNA from plasma and trtDNA from urine. Whole exome sequencing (WES) was performed in DNA isolated from tissue, plasma and urine. Results Out of the 24 CRC cases, only four had sufficient DNA to allow WES analyses in urine and plasma. We found that tumour alterations primarily reside in low molecular weight fragments (less than 112 bp). In patients whose trtDNA was more than 2.69% of the urine derived DNA, cancer-specific molecular alterations, mutational signatures and copy number profiles identified in urine DNA are comparable with those detected in plasma ctDNA. Conclusions With current technologies, WES analysis of trtDNA is feasible in a small fraction of mCRC patients. Tumour-related genetic information is mainly present in low molecular weight DNA fragments. Although the limited amounts of trtDNA poses analytical challenges, enrichment of low molecular weight DNAs and optimised computational tools can improve the detection of tumour-specific genetic information in urine.
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Affiliation(s)
- Giovanni Crisafulli
- University of Turin, Department of Oncology, Candiolo (TO), Italy.,Candiolo Cancer Institute, FPO - IRCCS, Candiolo TO, Italy
| | | | - Andrea Cassingena
- Niguarda Cancer Center, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Monica Montone
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo TO, Italy
| | | | - Ludovic Barault
- University of Turin, Department of Oncology, Candiolo (TO), Italy.,Candiolo Cancer Institute, FPO - IRCCS, Candiolo TO, Italy
| | | | - Federica Morano
- Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | | | - Salvatore Siena
- Niguarda Cancer Center, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Federica Di Nicolantonio
- University of Turin, Department of Oncology, Candiolo (TO), Italy.,Candiolo Cancer Institute, FPO - IRCCS, Candiolo TO, Italy
| | - Silvia Marsoni
- IFOM - the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Alberto Bardelli
- University of Turin, Department of Oncology, Candiolo (TO), Italy.,Candiolo Cancer Institute, FPO - IRCCS, Candiolo TO, Italy
| | - Giulia Siravegna
- University of Turin, Department of Oncology, Candiolo (TO), Italy .,Candiolo Cancer Institute, FPO - IRCCS, Candiolo TO, Italy
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20
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Arena S, Corti G, Durinikova E, Montone M, Reilly NM, Russo M, Lorenzato A, Arcella P, Lazzari L, Rospo G, Pagani M, Cancelliere C, Negrino C, Isella C, Bartolini A, Cassingena A, Amatu A, Mauri G, Sartore-Bianchi A, Mittica G, Medico E, Marsoni S, Linnebacher M, Abrignani S, Siena S, Di Nicolantonio F, Bardelli A. A Subset of Colorectal Cancers with Cross-Sensitivity to Olaparib and Oxaliplatin. Clin Cancer Res 2019; 26:1372-1384. [PMID: 31831554 DOI: 10.1158/1078-0432.ccr-19-2409] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 11/06/2019] [Accepted: 12/05/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Defects in the homologous recombination (HR) repair pathway are of clinical interest due to sensitivity of HR-deficient cells to PARP inhibitors. We were interested in defining PARP vulnerability in patients with metastatic colorectal cancer (mCRC) carrying KRAS and BRAF mutations who display poor prognosis, have limited therapeutic options, and represent an unmet clinical need. EXPERIMENTAL DESIGN We tested colorectal cancer cell lines, patient-derived organoids (PDO), and patient-derived xenografts (PDX) enriched for KRAS and BRAF mutations for sensitivity to the PARP inhibitor olaparib, and the chemotherapeutic agents oxaliplatin and 5-fluorouracil (5-FU). Genomic profiles and DNA repair proficiency of colorectal cancer models were compared with pharmacologic response. RESULTS Thirteen of 99 (around 13%) colorectal cancer cell lines were highly sensitive to clinically active concentrations of olaparib and displayed functional deficiency in HR. Response to PARP blockade was positively correlated with sensitivity to oxaliplatin in colorectal cancer cell lines as well as patient-derived organoids. Treatment of PDXs with olaparib impaired tumor growth and maintenance therapy with PARP blockade after initial oxaliplatin response delayed disease progression in mice. CONCLUSIONS These results indicate that a colorectal cancer subset characterized by poor prognosis and limited therapeutic options is vulnerable to PARP inhibition and suggest that PDO-based drug-screening assays can be used to identify patients with colorectal cancer likely to benefit from olaparib. As patients with mCRC almost invariably receive therapies based on oxaliplatin, "maintenance" treatment with PARP inhibitors warrants further clinical investigation.
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Affiliation(s)
- Sabrina Arena
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy.,Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Giorgio Corti
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy
| | | | - Monica Montone
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy
| | - Nicole M Reilly
- Fondazione Piemontese per la Ricerca sul Cancro ONLUS, Candiolo, Torino, Italy
| | - Mariangela Russo
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy.,Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Annalisa Lorenzato
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy.,Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Pamela Arcella
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy.,Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Luca Lazzari
- IFOM, The FIRC Institute of Molecular Oncology, Milan, Italy
| | - Giuseppe Rospo
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy
| | - Massimiliano Pagani
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy.,Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
| | | | - Carola Negrino
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy.,Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Claudio Isella
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy
| | - Alice Bartolini
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy
| | - Andrea Cassingena
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Alessio Amatu
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Gianluca Mauri
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy.,Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
| | - Andrea Sartore-Bianchi
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy.,Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
| | - Gloria Mittica
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy
| | - Enzo Medico
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy.,Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Silvia Marsoni
- IFOM, The FIRC Institute of Molecular Oncology, Milan, Italy.,Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Michael Linnebacher
- Department of General Surgery, Molecular Oncology and Immunotherapy, University of Rostock, Rostock, Germany
| | - Sergio Abrignani
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy.,Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Salvatore Siena
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy.,Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
| | - Federica Di Nicolantonio
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy. .,Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Alberto Bardelli
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy. .,Department of Oncology, University of Torino, Candiolo, Torino, Italy
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21
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Russo M, Crisafulli G, Sogari A, Reilly NM, Arena S, Lamba S, Bartolini A, Amodio V, Magrì A, Novara L, Sarotto I, Nagel ZD, Piett CG, Amatu A, Sartore-Bianchi A, Siena S, Bertotti A, Trusolino L, Corigliano M, Gherardi M, Lagomarsino MC, Di Nicolantonio F, Bardelli A. Adaptive mutability of colorectal cancers in response to targeted therapies. Science 2019; 366:1473-1480. [PMID: 31699882 DOI: 10.1126/science.aav4474] [Citation(s) in RCA: 245] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 07/24/2019] [Accepted: 10/26/2019] [Indexed: 12/13/2022]
Abstract
The emergence of drug resistance limits the efficacy of targeted therapies in human tumors. The prevalent view is that resistance is a fait accompli: when treatment is initiated, cancers already contain drug-resistant mutant cells. Bacteria exposed to antibiotics transiently increase their mutation rates (adaptive mutability), thus improving the likelihood of survival. We investigated whether human colorectal cancer (CRC) cells likewise exploit adaptive mutability to evade therapeutic pressure. We found that epidermal growth factor receptor (EGFR)/BRAF inhibition down-regulates mismatch repair (MMR) and homologous recombination DNA-repair genes and concomitantly up-regulates error-prone polymerases in drug-tolerant (persister) cells. MMR proteins were also down-regulated in patient-derived xenografts and tumor specimens during therapy. EGFR/BRAF inhibition induced DNA damage, increased mutability, and triggered microsatellite instability. Thus, like unicellular organisms, tumor cells evade therapeutic pressures by enhancing mutability.
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Affiliation(s)
- Mariangela Russo
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo (TO) 10060, Italy. .,Department of Oncology, University of Torino, Candiolo (TO) 10060, Italy
| | - Giovanni Crisafulli
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo (TO) 10060, Italy.,Department of Oncology, University of Torino, Candiolo (TO) 10060, Italy
| | - Alberto Sogari
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo (TO) 10060, Italy.,Department of Oncology, University of Torino, Candiolo (TO) 10060, Italy
| | - Nicole M Reilly
- Fondazione Piemontese per la Ricerca sul Cancro ONLUS, Candiolo (TO) 10060, Italy
| | - Sabrina Arena
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo (TO) 10060, Italy.,Department of Oncology, University of Torino, Candiolo (TO) 10060, Italy
| | - Simona Lamba
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo (TO) 10060, Italy
| | - Alice Bartolini
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo (TO) 10060, Italy
| | - Vito Amodio
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo (TO) 10060, Italy.,Department of Oncology, University of Torino, Candiolo (TO) 10060, Italy
| | - Alessandro Magrì
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo (TO) 10060, Italy.,Department of Oncology, University of Torino, Candiolo (TO) 10060, Italy
| | - Luca Novara
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo (TO) 10060, Italy
| | - Ivana Sarotto
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo (TO) 10060, Italy
| | - Zachary D Nagel
- Department of Environmental Health, JBL Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Cortt G Piett
- Department of Environmental Health, JBL Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Alessio Amatu
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy.,Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, 20133 Milan, Italy
| | - Andrea Sartore-Bianchi
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy.,Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, 20133 Milan, Italy
| | - Salvatore Siena
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy.,Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, 20133 Milan, Italy
| | - Andrea Bertotti
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo (TO) 10060, Italy.,Department of Oncology, University of Torino, Candiolo (TO) 10060, Italy
| | - Livio Trusolino
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo (TO) 10060, Italy.,Department of Oncology, University of Torino, Candiolo (TO) 10060, Italy
| | - Mattia Corigliano
- IFOM-FIRC Institute of Molecular Oncology, 20139 Milan, Italy.,Department of Physics, Università degli Studi di Milano, and I.N.F.N., 20133 Milan, Italy
| | - Marco Gherardi
- IFOM-FIRC Institute of Molecular Oncology, 20139 Milan, Italy.,Department of Physics, Università degli Studi di Milano, and I.N.F.N., 20133 Milan, Italy
| | - Marco Cosentino Lagomarsino
- IFOM-FIRC Institute of Molecular Oncology, 20139 Milan, Italy.,Department of Physics, Università degli Studi di Milano, and I.N.F.N., 20133 Milan, Italy
| | - Federica Di Nicolantonio
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo (TO) 10060, Italy.,Department of Oncology, University of Torino, Candiolo (TO) 10060, Italy
| | - Alberto Bardelli
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo (TO) 10060, Italy. .,Department of Oncology, University of Torino, Candiolo (TO) 10060, Italy
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22
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Kastrisiou M, Zarkavelis G, Pentheroudakis G, Magklara A. Clinical Application of Next-Generation Sequencing as A Liquid Biopsy Technique in Advanced Colorectal Cancer: A Trick or A Treat? Cancers (Basel) 2019; 11:E1573. [PMID: 31623125 PMCID: PMC6826585 DOI: 10.3390/cancers11101573] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/01/2019] [Accepted: 10/13/2019] [Indexed: 12/24/2022] Open
Abstract
Owing to its advantages over prior relevant technologies, massive parallel or next-generation sequencing (NGS) is rapidly evolving, with growing applications in a wide range of human diseases. The burst in actionable molecular alterations in many cancer types advocates for the practicality of using NGS in the clinical setting, as it permits the parallel characterization of multiple genes in a cost- and time-effective way, starting from low-input DNA. In advanced clinical practice, the oncological management of colorectal cancer requires prior knowledge of KRAS, NRAS, and BRAF status, for the design of appropriate therapeutic strategies, with more gene mutations still surfacing as potential biomarkers. Tumor heterogeneity, as well as the need for serial gene profiling due to tumor evolution and the emergence of novel genetic alterations, have promoted the use of liquid biopsies-especially in the form of circulating tumor DNA (ctDNA)-as a promising alternative to tissue molecular analysis. This review discusses recent studies that have used plasma NGS in advanced colorectal cancer and summarizes the clinical applications, as well as the technical challenges involved in adopting this technique in a clinically beneficial oncological practice.
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Affiliation(s)
- Myrto Kastrisiou
- Laboratory of Clinical Chemistry, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece.
- Department of Medical Oncology, University General Hospital of Ioannina, 45500 Ioannina, Greece.
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), 45444 Ioannina, Greece.
| | - George Zarkavelis
- Department of Medical Oncology, University General Hospital of Ioannina, 45500 Ioannina, Greece.
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), 45444 Ioannina, Greece.
| | - George Pentheroudakis
- Department of Medical Oncology, University General Hospital of Ioannina, 45500 Ioannina, Greece.
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), 45444 Ioannina, Greece.
| | - Angeliki Magklara
- Laboratory of Clinical Chemistry, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece.
- Department of Biomedical Research, Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology-Hellas, 45110 Ioannina, Greece.
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23
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Siravegna G, Mussolin B, Venesio T, Marsoni S, Seoane J, Dive C, Papadopoulos N, Kopetz S, Corcoran RB, Siu LL, Bardelli A. How liquid biopsies can change clinical practice in oncology. Ann Oncol 2019; 30:1580-1590. [PMID: 31373349 DOI: 10.1093/annonc/mdz227] [Citation(s) in RCA: 215] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Cell-free DNA fragments are shed into the bloodstream by tumor cells. The analysis of circulating tumor DNA (ctDNA), commonly known as liquid biopsy, can be exploited for a variety of clinical applications. ctDNA is being used to genotype solid cancers non-invasively, to track tumor dynamics and to detect the emergence of drug resistance. In a few settings, liquid biopsies have already entered clinical practice. For example, ctDNA is used to guide treatment in a subset of lung cancers. In this review, we discuss how recent improvements in the sensitivity and accuracy of ctDNA analyses have led to unprecedented advances in this research field. We further consider what is required for the routine deployment of liquid biopsies in the clinical diagnostic space. We pinpoint technical hurdles that liquid biopsies have yet to overcome, including preanalytical and analytical challenges. We foresee how liquid biopsies will transform clinical practice: by complementing (or replacing) imaging to monitor treatment response and by detecting minimal residual disease after surgery with curative intent.
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Affiliation(s)
- G Siravegna
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy; Department of Oncology, University of Torino, Candiolo, Turin, Italy
| | - B Mussolin
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - T Venesio
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - S Marsoni
- IFOM, Istituto FIRC di Oncología Molecolare, Milan, Italy
| | - J Seoane
- Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital and Universitat Autonoma de Barcelona, CIBERONC, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - C Dive
- Clinical and Experimental Pharmacology Group and Manchester Centre for Cancer Biomarker Sciences, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - N Papadopoulos
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, USA; Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, USA
| | - S Kopetz
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - R B Corcoran
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, USA
| | - L L Siu
- Princess Margaret Cancer Centre, University of Toronto, Toronto, Canada
| | - A Bardelli
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy; Department of Oncology, University of Torino, Candiolo, Turin, Italy.
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24
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Lazzari L, Corti G, Picco G, Isella C, Montone M, Arcella P, Durinikova E, Zanella ER, Novara L, Barbosa F, Cassingena A, Cancelliere C, Medico E, Sartore-Bianchi A, Siena S, Garnett MJ, Bertotti A, Trusolino L, Di Nicolantonio F, Linnebacher M, Bardelli A, Arena S. Patient-Derived Xenografts and Matched Cell Lines Identify Pharmacogenomic Vulnerabilities in Colorectal Cancer. Clin Cancer Res 2019; 25:6243-6259. [PMID: 31375513 DOI: 10.1158/1078-0432.ccr-18-3440] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 06/13/2019] [Accepted: 07/29/2019] [Indexed: 12/21/2022]
Abstract
PURPOSE Patient-derived xenograft (PDX) models accurately recapitulate the tumor of origin in terms of histopathology, genomic landscape, and therapeutic response, but some limitations due to costs associated with their maintenance and restricted amenability for large-scale screenings still exist. To overcome these issues, we established a platform of 2D cell lines (xeno-cell lines, XL), derived from PDXs of colorectal cancer with matched patient germline gDNA available. EXPERIMENTAL DESIGN Whole-exome and transcriptome sequencing analyses were performed. Biomarkers of response and resistance to anti-HER therapy were annotated. Dependency on the WRN helicase gene was assessed in MSS, MSI-H, and MSI-like XLs using a reverse genetics functional approach. RESULTS XLs recapitulated the entire spectrum of colorectal cancer transcriptional subtypes. Exome and RNA-seq analyses delineated several molecular biomarkers of response and resistance to EGFR and HER2 blockade. Genotype-driven responses observed in vitro in XLs were confirmed in vivo in the matched PDXs. MSI-H models were dependent upon WRN gene expression, while loss of WRN did not affect MSS XLs growth. Interestingly, one MSS XL with transcriptional MSI-like traits was sensitive to WRN depletion. CONCLUSIONS The XL platform represents a preclinical tool for functional gene validation and proof-of-concept studies to identify novel druggable vulnerabilities in colorectal cancer.
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Affiliation(s)
- Luca Lazzari
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Giorgio Corti
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy
| | | | - Claudio Isella
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy
| | - Monica Montone
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy
| | - Pamela Arcella
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy
| | | | | | - Luca Novara
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy
| | - Fabiane Barbosa
- Department of Interventional Radiology, Ospedale Niguarda Ca' Granda, Milan, Italy
| | - Andrea Cassingena
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | | | - Enzo Medico
- Department of Oncology, University of Torino, Candiolo, Torino, Italy.,Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy
| | - Andrea Sartore-Bianchi
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy.,Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
| | - Salvatore Siena
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy.,Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
| | | | - Andrea Bertotti
- 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
| | - Federica Di Nicolantonio
- Department of Oncology, University of Torino, Candiolo, Torino, Italy.,Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy
| | - Michael Linnebacher
- Department of General Surgery, Molecular Oncology and Immunotherapy, University of Rostock, Rostock, Germany
| | - Alberto Bardelli
- Department of Oncology, University of Torino, Candiolo, Torino, Italy.,Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy
| | - Sabrina Arena
- Department of Oncology, University of Torino, Candiolo, Torino, Italy. .,Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy
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25
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Evolving neoantigen profiles in colorectal cancers with DNA repair defects. Genome Med 2019; 11:42. [PMID: 31253177 PMCID: PMC6599263 DOI: 10.1186/s13073-019-0654-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 06/13/2019] [Indexed: 12/21/2022] Open
Abstract
Background Neoantigens that arise as a consequence of tumor-specific mutations can be recognized by T lymphocytes leading to effective immune surveillance. In colorectal cancer (CRC) and other tumor types, a high number of neoantigens is associated with patient response to immune therapies. The molecular processes governing the generation of neoantigens and their turnover in cancer cells are poorly understood. We exploited CRC as a model system to understand how alterations in DNA repair pathways modulate neoantigen profiles over time. Methods We performed whole exome sequencing (WES) and RNA sequencing (RNAseq) in CRC cell lines, in vitro and in vivo, and in CRC patient-derived xenografts (PDXs) to track longitudinally genomic profiles, clonal evolution, mutational signatures, and predicted neoantigens. Results The majority of CRC models showed remarkably stable mutational and neoantigen profiles; however, those carrying defects in DNA repair genes continuously diversified. Rapidly evolving and evolutionary stable CRCs displayed characteristic genomic signatures and transcriptional profiles. Downregulation of molecules implicated in antigen presentation occurred selectively in highly mutated and rapidly evolving CRC. Conclusions These results indicate that CRCs carrying alterations in DNA repair pathways display dynamic neoantigen patterns that fluctuate over time. We define CRC subsets characterized by slow and fast evolvability and link this phenotype to downregulation of antigen-presenting cellular mechanisms. Longitudinal monitoring of the neoantigen landscape could be relevant in the context of precision medicine. Electronic supplementary material The online version of this article (10.1186/s13073-019-0654-6) contains supplementary material, which is available to authorized users.
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