1
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Fasano C, Lepore Signorile M, De Marco K, Forte G, Disciglio V, Sanese P, Grossi V, Simone C. In Silico Deciphering of the Potential Impact of Variants of Uncertain Significance in Hereditary Colorectal Cancer Syndromes. Cells 2024; 13:1314. [PMID: 39195204 DOI: 10.3390/cells13161314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/23/2024] [Accepted: 08/03/2024] [Indexed: 08/29/2024] Open
Abstract
Colorectal cancer (CRC) ranks third in terms of cancer incidence worldwide and is responsible for 8% of all deaths globally. Approximately 10% of CRC cases are caused by inherited pathogenic mutations in driver genes involved in pathways that are crucial for CRC tumorigenesis and progression. These hereditary mutations significantly increase the risk of initial benign polyps or adenomas developing into cancer. In recent years, the rapid and accurate sequencing of CRC-specific multigene panels by next-generation sequencing (NGS) technologies has enabled the identification of several recurrent pathogenic variants with established functional consequences. In parallel, rare genetic variants that are not characterized and are, therefore, called variants of uncertain significance (VUSs) have also been detected. The classification of VUSs is a challenging task because each amino acid has specific biochemical properties and uniquely contributes to the structural stability and functional activity of proteins. In this scenario, the ability to computationally predict the effect of a VUS is crucial. In particular, in silico prediction methods can provide useful insights to assess the potential impact of a VUS and support additional clinical evaluation. This approach can further benefit from recent advances in artificial intelligence-based technologies. In this review, we describe the main in silico prediction tools that can be used to evaluate the structural and functional impact of VUSs and provide examples of their application in the analysis of gene variants involved in hereditary CRC syndromes.
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Affiliation(s)
- Candida Fasano
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, 70013 Castellana Grotte, Italy
| | - Martina Lepore Signorile
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, 70013 Castellana Grotte, Italy
| | - Katia De Marco
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, 70013 Castellana Grotte, Italy
| | - Giovanna Forte
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, 70013 Castellana Grotte, Italy
| | - Vittoria Disciglio
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, 70013 Castellana Grotte, Italy
| | - Paola Sanese
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, 70013 Castellana Grotte, Italy
| | - Valentina Grossi
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, 70013 Castellana Grotte, Italy
| | - Cristiano Simone
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, 70013 Castellana Grotte, Italy
- Medical Genetics, Department of Precision and Regenerative Medicine and Jonic Area (DiMePRe-J), University of Bari Aldo Moro, 70124 Bari, Italy
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2
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Rashid M, Rashid R, Gadewal N, Carethers JM, Koi M, Brim H, Ashktorab H. High-throughput sequencing and in-silico analysis confirm pathogenicity of novel MSH3 variants in African American colorectal cancer. Neoplasia 2024; 49:100970. [PMID: 38281411 PMCID: PMC10840101 DOI: 10.1016/j.neo.2024.100970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/19/2023] [Accepted: 01/08/2024] [Indexed: 01/30/2024]
Abstract
The maintenance of DNA sequence integrity is critical to avoid accumulation of cancer-causing mutations. Inactivation of DNA Mismatch Repair (MMR) genes (e.g., MLH1 and MSH2) is common among many cancers, including colorectal cancer (CRC) and is the driver of classic microsatellite instability (MSI) in tumors. Somatic MSH3 alterations have been linked to a specific form of MSI called elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) that is associated with patient poor prognosis and elevated among African American (AA) rectal cancer patients. Genetic variants of MSH3 and their pathogenicity vary among different populations, such as among AA, which are not well-represented in publicly available databases. Targeted exome sequencing of MSH3 among AA CRC samples followed by computational bioinformatic pipeline and molecular dynamic simulation analysis approach confirmed six identified MSH3 variants (c.G1237A, c.C2759T, c.G1397A, c.G2926A, c.C3028T, c.G3241A) that corresponded to MSH3 amino-acid changes (p.E413K; p.S466N; p.S920F; p.E976K; p.H1010Y; p.E1081K). All identified MSH3 variants were non-synonymous, novel, pathogenic, and show loss or gain of hydrogen bonding, ionic bonding, hydrophobic bonding, and disulfide bonding and have a deleterious effect on the structure of MSH3 protein. Some variants were located within the ATPase site of MSH3, affecting ATP hydrolysis that is critical for MSH3's function. Other variants were in the MSH3-MSH2 interacting domain, important for MSH3's binding to MSH2. Overall, our data suggest that these variants among AA CRC patients affect the function of MSH3 making them pathogenic and likely contributing to the development or advancement of CRC among AA. Further clarifying functional studies will be necessary to fully understand the impact of these variants on MSH3 function and CRC development in AA patients.
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Affiliation(s)
- Mudasir Rashid
- Department of Medicine, Gastroenterology Division, Department of Pathology and Cancer Center, Howard University College of Medicine, Washington, DC 20059, USA
| | - Rumaisa Rashid
- Department of Medicine, Gastroenterology Division, Department of Pathology and Cancer Center, Howard University College of Medicine, Washington, DC 20059, USA
| | - Nikhil Gadewal
- Bioinformatics and Computational Biology Facility, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH 410210, India
| | - John M Carethers
- Division of Gastroenterology and Hepatology, Department of Medicine, UC San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA; Moores Cancer Center, and Herbert Wertheim School of Public Health and Human Longevity Science, UC San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Minoru Koi
- Division of Gastroenterology and Hepatology, Department of Medicine, UC San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Hassan Brim
- Department of Medicine, Gastroenterology Division, Department of Pathology and Cancer Center, Howard University College of Medicine, Washington, DC 20059, USA
| | - Hassan Ashktorab
- Department of Medicine, Gastroenterology Division, Department of Pathology and Cancer Center, Howard University College of Medicine, Washington, DC 20059, USA.
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3
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Oncotherapeutic Strategies in Early Onset Colorectal Cancer. Cancers (Basel) 2023; 15:cancers15020552. [PMID: 36672501 PMCID: PMC9856676 DOI: 10.3390/cancers15020552] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
Early onset colorectal cancer (EOCRC), defined as colorectal cancers in patients aged less than 50 years, is becoming an increasingly common issue, globally. Since 1994, the incidence of this condition has been rising by 2% annually. Approximately one in five patients under 50 years of age diagnosed with colorectal cancer have an underlying genetic predisposition syndrome. The detection of cancer among the other 80% of patients poses a considerable task, as there is no family history to advocate for commencing early screening in this group. Patients with EOCRC have distinct social, spiritual, fertility, and financial needs from their older counterparts that need to be addressed. This review discusses the risk factors associated with the development of EOCRC and current best practice for the management of this disease.
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4
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Sibilio P, Belardinilli F, Licursi V, Paci P, Giannini G. An integrative in-silico analysis discloses a novel molecular subset of colorectal cancer possibly eligible for immune checkpoint immunotherapy. Biol Direct 2022; 17:10. [PMID: 35534873 PMCID: PMC9082922 DOI: 10.1186/s13062-022-00324-y] [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: 02/16/2022] [Accepted: 04/23/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Historically, the molecular classification of colorectal cancer (CRC) was based on the global genomic status, which identified microsatellite instability in mismatch repair (MMR) deficient CRC, and chromosomal instability in MMR proficient CRC. With the introduction of immune checkpoint inhibitors, the microsatellite and chromosomal instability classification regained momentum as the microsatellite instability condition predicted sensitivity to immune checkpoint inhibitors, possibly due to both high tumor mutation burden (TMB) and high levels of infiltrating lymphocytes. Conversely, proficient MMR CRC are mostly resistant to immunotherapy. To better understand the relationship between the microsatellite and chromosomal instability classification, and eventually discover additional CRC subgroups relevant for therapeutic decisions, we developed a computational pipeline that include molecular integrative analysis of genomic, epigenomic and transcriptomic data. RESULTS The first step of the pipeline was based on unsupervised hierarchical clustering analysis of copy number variations (CNVs) versus hypermutation status that identified a first CRC cluster with few CNVs enriched in Hypermutated and microsatellite instability samples, a second CRC cluster with a high number of CNVs mostly including non-HM and microsatellite stable samples, and a third cluster (7.8% of the entire dataset) with low CNVs and low TMB, which shared clinical-pathological features with Hypermutated CRCs and thus defined Hypermutated-like CRCs. The mutational features, DNA methylation profile and base substitution fingerprints of these tumors revealed that Hypermutated-like patients are molecularly distinct from Hypermutated and non-Hypermutated tumors and are likely to develop and progress through different genetic events. Transcriptomic analysis highlighted further differences amongst the three groups and revealed an inflamed tumor microenvironment and modulation Immune Checkpoint Genes in Hypermutated-like CRCs. CONCLUSION Therefore, our work highlights Hypermutated-like tumors as a distinct and previously unidentified CRC subgroup possibly responsive to immune checkpoint inhibitors. If further validated, these findings can lead to expanding the fraction of patients eligible to immunotherapy.
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Affiliation(s)
- Pasquale Sibilio
- Department of Translational and Precision Medicine, University La Sapienza, 00161, Rome, Italy.,Institute for Systems Analysis and Computer Science Antonio Ruberti, National Research Council, 00185, Rome, Italy
| | | | - Valerio Licursi
- Department of Biology and Biotechnologies "Charles Darwin", University La Sapienza, 00185, Rome, Italy.,Institute of Molecular Biology and Pathology, National Research Council of Italy, Via degli Apuli, 4, 00185, Rome, Italy
| | - Paola Paci
- Institute for Systems Analysis and Computer Science Antonio Ruberti, National Research Council, 00185, Rome, Italy.,Department of Computer Engineering, Automation and Management, University La Sapienza, 00161, Rome, Italy
| | - Giuseppe Giannini
- Department of Molecular Medicine, University La Sapienza, 00161, Rome, Italy. .,Istituto Pasteur-Fondazione Cenci Bolognetti, 00161, Rome, Italy.
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5
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Wang Z, Zhao T, Zhang S, Wang J, Chen Y, Zhao H, Yang Y, Shi S, Chen Q, Liu K. The Wnt signaling pathway in tumorigenesis, pharmacological targets, and drug development for cancer therapy. Biomark Res 2021; 9:68. [PMID: 34488905 PMCID: PMC8422786 DOI: 10.1186/s40364-021-00323-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/20/2021] [Indexed: 12/12/2022] Open
Abstract
Wnt signaling was initially recognized to be vital for tissue development and homeostasis maintenance. Further studies revealed that this pathway is also important for tumorigenesis and progression. Abnormal expression of signaling components through gene mutation or epigenetic regulation is closely associated with tumor progression and poor prognosis in several tissues. Additionally, Wnt signaling also influences the tumor microenvironment and immune response. Some strategies and drugs have been proposed to target this pathway, such as blocking receptors/ligands, targeting intracellular molecules, beta-catenin/TCF4 complex and its downstream target genes, or tumor microenvironment and immune response. Here we discuss the roles of these components in Wnt signaling pathway in tumorigenesis and cancer progression, the underlying mechanisms that is responsible for the activation of Wnt signaling, and a series of drugs targeting the Wnt pathway provide multiple therapeutic values. Although some of these drugs exhibit exciting anti-cancer effect, clinical trials and systematic evaluation should be strictly performed along with multiple-omics technology.
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Affiliation(s)
- Zhuo Wang
- Central Laboratory, Xiang'an Hospital of Xiamen University, Xiamen, Fujian, 361102, P. R. China.,School of Medicine, Xiamen University, Xiamen, Fujian, 361102, P. R. China
| | - Tingting Zhao
- Central Laboratory, Xiang'an Hospital of Xiamen University, Xiamen, Fujian, 361102, P. R. China.,School of Medicine, Xiamen University, Xiamen, Fujian, 361102, P. R. China
| | - Shihui Zhang
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, EH164UU, UK
| | - Junkai Wang
- Central Laboratory, Xiang'an Hospital of Xiamen University, Xiamen, Fujian, 361102, P. R. China
| | - Yunyun Chen
- Central Laboratory, Xiang'an Hospital of Xiamen University, Xiamen, Fujian, 361102, P. R. China.,School of Medicine, Xiamen University, Xiamen, Fujian, 361102, P. R. China
| | - Hongzhou Zhao
- Central Laboratory, Xiang'an Hospital of Xiamen University, Xiamen, Fujian, 361102, P. R. China.,School of Medicine, Xiamen University, Xiamen, Fujian, 361102, P. R. China
| | - Yaxin Yang
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Songlin Shi
- School of Medicine, Xiamen University, Xiamen, Fujian, 361102, P. R. China
| | - Qiang Chen
- Cancer Centre, Faculty of Health Sciences, University of Macau, Macau, SAR, China
| | - Kuancan Liu
- Central Laboratory, Xiang'an Hospital of Xiamen University, Xiamen, Fujian, 361102, P. R. China. .,School of Medicine, Xiamen University, Xiamen, Fujian, 361102, P. R. China.
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6
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Belardinilli F, Pernazza A, Mahdavian Y, Cerbelli B, Bassi M, Gradilone A, Coppa A, Pignataro MG, Anile M, Venuta F, Della Rocca C, Giannini G, d'Amati G. A multidisciplinary approach for the differential diagnosis between multiple primary lung adenocarcinomas and intrapulmonary metastases. Pathol Res Pract 2021; 220:153387. [PMID: 33647865 DOI: 10.1016/j.prp.2021.153387] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/13/2021] [Indexed: 11/26/2022]
Abstract
PURPOSE The distinction between multiple primary lung cancers (MPLCs) and intrapulmonary metastases has a significant impact on tumor staging and therapeutic choices. Several criteria have been proposed to solve this diagnostic issue, but a definitive consensus is still missing. We tested the efficacy of a combined clinical, histopathological and molecular ("real world") approach for the correct classification of multiple lung tumors in a selected cohort of patients. METHODS 24 multiple lung tumors with a diagnosis of adenocarcinoma from 10 patients were retrospectively reviewed. Radiological, pathological and clinical information, including follow-up, were integrated with molecular profiling via a routine multigene panel sequencing. RESULTS Comprehensive histologic assessment revealed readily distinguishable histologic patterns between multiple tumors suggesting unrelated lesions in 7 cases, in agreement with clinical, radiological and molecular data, thus leading to final diagnosis of MPLCs. In the remaining 3 cases, the differential diagnosis between MPLCs and intrapulmonary metastases was challenging, since the histologic features of the lesions were similar or identical. The final interpretation (2 MPLCs and 1 most likely intrapulmonary metastases) was reached thanks to the integration of all available data, and was confirmed by follow-up. CONCLUSIONS A multidisciplinary approach including a routinely affordable multigene panel sequencing is a useful tool to discriminate MPLCs from intrapulmonary metastases in multiple lung nodules sharing the adenocarcinoma histotype.
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Affiliation(s)
- Francesca Belardinilli
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161, Rome, Italy
| | - Angelina Pernazza
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University, Latina, 04100, Italy
| | - Yasaman Mahdavian
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161, Rome, Italy
| | - Bruna Cerbelli
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University, Latina, 04100, Italy
| | - Massimiliano Bassi
- Department of General and Specialist Surgery "P. Stefanini" Sapienza University, Rome, 00161, Italy
| | - Angela Gradilone
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161, Rome, Italy
| | | | - Maria Gemma Pignataro
- Department of Radiological, Oncological and Pathological Sciences, Sapienza University, Rome, 00161, Italy
| | - Marco Anile
- Department of General and Specialist Surgery "P. Stefanini" Sapienza University, Rome, 00161, Italy
| | - Federico Venuta
- Department of General and Specialist Surgery "P. Stefanini" Sapienza University, Rome, 00161, Italy
| | - Carlo Della Rocca
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University, Latina, 04100, Italy
| | - Giuseppe Giannini
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161, Rome, Italy.
| | - Giulia d'Amati
- Department of Radiological, Oncological and Pathological Sciences, Sapienza University, Rome, 00161, Italy.
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7
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Goeman F, De Nicola F, Amoreo CA, Scalera S, Marinelli D, Sperati F, Mazzotta M, Terrenato I, Pallocca M, Ciuffreda L, Sperandio E, Barba M, Pizzuti L, Sergi D, Amodio A, Paoletti G, Krasniqi E, Vici P, Casini B, Gallo E, Buglioni S, Diodoro MG, Pescarmona E, Vitale I, De Maria R, Grazi GL, Ciliberto G, Fanciulli M, Maugeri-Saccà M. Multicohort and cross-platform validation of a prognostic Wnt signature in colorectal cancer. Clin Transl Med 2020; 10:e199. [PMID: 33377637 PMCID: PMC7770515 DOI: 10.1002/ctm2.199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 09/23/2020] [Indexed: 11/15/2022] Open
Affiliation(s)
- Frauke Goeman
- Oncogenomic and Epigenetic Unit, IRCCS "Regina Elena" National Cancer Institute, Rome, Italy
| | - Francesca De Nicola
- SAFU Laboratory, Department of Research, Advanced Diagnostic, and Technological Innovation, IRCCS "Regina Elena" National Cancer Institute, Rome, Italy
| | - Carla Azzurra Amoreo
- Department of Pathology, IRCCS "Regina Elena" National Cancer Institute, Rome, Italy
| | - Stefano Scalera
- SAFU Laboratory, Department of Research, Advanced Diagnostic, and Technological Innovation, IRCCS "Regina Elena" National Cancer Institute, Rome, Italy
| | - Daniele Marinelli
- Medical Oncology Unit, Department of Clinical and Molecular Medicine, Sant'Andrea Hospital, "Sapienza" University of Rome, Rome, Italy
| | - Francesca Sperati
- Biostatistics Unit, San Gallicano Dermatological Institute IRCCS, Rome, Italy
| | - Marco Mazzotta
- Division of Medical Oncology 2, IRCCS "Regina Elena" National Cancer Institute, Rome, Italy
| | - Irene Terrenato
- Biostatistics-Scientific Direction, IRCCS "Regina Elena" National Cancer Institute, Rome, Italy
| | - Matteo Pallocca
- SAFU Laboratory, Department of Research, Advanced Diagnostic, and Technological Innovation, IRCCS "Regina Elena" National Cancer Institute, Rome, Italy
| | - Ludovica Ciuffreda
- SAFU Laboratory, Department of Research, Advanced Diagnostic, and Technological Innovation, IRCCS "Regina Elena" National Cancer Institute, Rome, Italy
| | - Eleonora Sperandio
- SAFU Laboratory, Department of Research, Advanced Diagnostic, and Technological Innovation, IRCCS "Regina Elena" National Cancer Institute, Rome, Italy
| | - Maddalena Barba
- Division of Medical Oncology 2, IRCCS "Regina Elena" National Cancer Institute, Rome, Italy
| | - Laura Pizzuti
- Division of Medical Oncology 2, IRCCS "Regina Elena" National Cancer Institute, Rome, Italy
| | - Domenico Sergi
- Division of Medical Oncology 2, IRCCS "Regina Elena" National Cancer Institute, Rome, Italy
| | - Antonella Amodio
- Division of Medical Oncology 2, IRCCS "Regina Elena" National Cancer Institute, Rome, Italy
| | - Giancarlo Paoletti
- Division of Medical Oncology 2, IRCCS "Regina Elena" National Cancer Institute, Rome, Italy
| | - Eriseld Krasniqi
- Division of Medical Oncology 2, IRCCS "Regina Elena" National Cancer Institute, Rome, Italy
| | - Patrizia Vici
- Division of Medical Oncology 2, IRCCS "Regina Elena" National Cancer Institute, Rome, Italy
| | - Beatrice Casini
- Department of Pathology, IRCCS "Regina Elena" National Cancer Institute, Rome, Italy
| | - Enzo Gallo
- Department of Pathology, IRCCS "Regina Elena" National Cancer Institute, Rome, Italy
| | - Simonetta Buglioni
- Department of Pathology, IRCCS "Regina Elena" National Cancer Institute, Rome, Italy
| | - Maria Grazia Diodoro
- Department of Pathology, IRCCS "Regina Elena" National Cancer Institute, Rome, Italy
| | - Edoardo Pescarmona
- Department of Pathology, IRCCS "Regina Elena" National Cancer Institute, Rome, Italy
| | - Ilio Vitale
- Italian Institute for Genomic Medicine (IIGM), IRCSS Candiolo, Turin, Italy.,Candiolo Cancer Institute, FPO - IRCCS, Turin, Italy
| | - Ruggero De Maria
- Institute of General Pathology, Catholic University of the Sacred Heart, Rome, Italy.,Institute of General Pathology, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy
| | - Gian Luca Grazi
- Hepato-Pancreato-Biliary Surgery, IRCCS "Regina Elena" National Cancer Institute, Rome, Italy
| | - Gennaro Ciliberto
- Scientific Direction, IRCCS "Regina Elena" National Cancer Institute, Rome, Italy
| | - Maurizio Fanciulli
- SAFU Laboratory, Department of Research, Advanced Diagnostic, and Technological Innovation, IRCCS "Regina Elena" National Cancer Institute, Rome, Italy
| | - Marcello Maugeri-Saccà
- Division of Medical Oncology 2, IRCCS "Regina Elena" National Cancer Institute, Rome, Italy
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8
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Belardinilli F, Capalbo C, Malapelle U, Pisapia P, Raimondo D, Milanetti E, Yasaman M, Liccardi C, Paci P, Sibilio P, Pepe F, Bonfiglio C, Mezi S, Magri V, Coppa A, Nicolussi A, Gradilone A, Petroni M, Di Giulio S, Fabretti F, Infante P, Coni S, Canettieri G, Troncone G, Giannini G. Clinical Multigene Panel Sequencing Identifies Distinct Mutational Association Patterns in Metastatic Colorectal Cancer. Front Oncol 2020; 10:560. [PMID: 32457828 PMCID: PMC7221020 DOI: 10.3389/fonc.2020.00560] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 03/27/2020] [Indexed: 12/12/2022] Open
Abstract
Extensive molecular characterization of human colorectal cancer (CRC) via Next Generation Sequencing (NGS) indicated that genetic or epigenetic dysregulation of a relevant, but limited, number of molecular pathways typically occurs in this tumor. The molecular picture of the disease is significantly complicated by the frequent occurrence of individually rare genetic aberrations, which expand tumor heterogeneity. Inter- and intratumor molecular heterogeneity is very likely responsible for the remarkable individual variability in the response to conventional and target-driven first-line therapies, in metastatic CRC (mCRC) patients, whose median overall survival remains unsatisfactory. Implementation of an extensive molecular characterization of mCRC in the clinical routine does not yet appear feasible on a large scale, while multigene panel sequencing of most commonly mutated oncogene/oncosuppressor hotspots is more easily achievable. Here, we report that clinical multigene panel sequencing performed for anti-EGFR therapy predictive purposes in 639 formalin-fixed paraffin-embedded (FFPE) mCRC specimens revealed previously unknown pairwise mutation associations and a high proportion of cases carrying actionable gene mutations. Most importantly, a simple principal component analysis directed the delineation of a new molecular stratification of mCRC patients in eight groups characterized by non-random, specific mutational association patterns (MAPs), aggregating samples with similar biology. These data were validated on a The Cancer Genome Atlas (TCGA) CRC dataset. The proposed stratification may provide great opportunities to direct more informed therapeutic decisions in the majority of mCRC cases.
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Affiliation(s)
| | - Carlo Capalbo
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | | | - Pasquale Pisapia
- Department of Public Health, University Federico II, Naples, Italy
| | - Domenico Raimondo
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | | | - Mahdavian Yasaman
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | - Carlotta Liccardi
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | - Paola Paci
- Institute for System Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Pasquale Sibilio
- Institute for System Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Francesco Pepe
- Department of Public Health, University Federico II, Naples, Italy
| | - Caterina Bonfiglio
- National Institute of Gastroenterology-Research Hospital, IRCCS "S. de Bellis", Bari, Italy
| | - Silvia Mezi
- Department of Radiological Oncological and Pathological Sciences, University La Sapienza, Rome, Italy
| | - Valentina Magri
- Department of Surgery Pietro Valdoni, Faculty of Medicine and Dentistry, Sapienza University of Rome, Rome, Italy
| | - Anna Coppa
- Department of Experimental Medicine, University La Sapienza, Rome, Italy
| | - Arianna Nicolussi
- Department of Experimental Medicine, University La Sapienza, Rome, Italy
| | - Angela Gradilone
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | - Marialaura Petroni
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Stefano Di Giulio
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | | | - Paola Infante
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Sonia Coni
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | - Gianluca Canettieri
- Department of Molecular Medicine, University La Sapienza, Rome, Italy.,Pasteur Institute-Cenci Bolognetti Foundation, Rome, Italy
| | | | - Giuseppe Giannini
- Department of Molecular Medicine, University La Sapienza, Rome, Italy.,Pasteur Institute-Cenci Bolognetti Foundation, Rome, Italy
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9
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Capalbo C, Belardinilli F, Raimondo D, Milanetti E, Malapelle U, Pisapia P, Magri V, Prete A, Pecorari S, Colella M, Coppa A, Bonfiglio C, Nicolussi A, Valentini V, Tessitore A, Cardinali B, Petroni M, Infante P, Santoni M, Filetti M, Colicchia V, Paci P, Mezi S, Longo F, Cortesi E, Marchetti P, Troncone G, Bellavia D, Canettieri G, Giannini G. A Simplified Genomic Profiling Approach Predicts Outcome in Metastatic Colorectal Cancer. Cancers (Basel) 2019; 11:cancers11020147. [PMID: 30691222 PMCID: PMC6406354 DOI: 10.3390/cancers11020147] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 01/19/2019] [Accepted: 01/22/2019] [Indexed: 12/22/2022] Open
Abstract
The response of metastatic colorectal cancer (mCRC) to the first-line conventional combination therapy is highly variable, reflecting the elevated heterogeneity of the disease. The genetic alterations underlying this heterogeneity have been thoroughly characterized through omic approaches requiring elevated efforts and costs. In order to translate the knowledge of CRC molecular heterogeneity into a practical clinical approach, we utilized a simplified Next Generation Sequencing (NGS) based platform to screen a cohort of 77 patients treated with first-line conventional therapy. Samples were sequenced using a panel of hotspots and targeted regions of 22 genes commonly involved in CRC. This revealed 51 patients carrying actionable gene mutations, 22 of which carried druggable alterations. These mutations were frequently associated with additional genetic alterations. To take into account this molecular complexity and assisted by an unbiased bioinformatic analysis, we defined three subgroups of patients carrying distinct molecular patterns. We demonstrated these three molecular subgroups are associated with a different response to first-line conventional combination therapies. The best outcome was achieved in patients exclusively carrying mutations on TP53 and/or RAS genes. By contrast, in patients carrying mutations in any of the other genes, alone or associated with mutations of TP53/RAS, the expected response is much worse compared to patients with exclusive TP53/RAS mutations. Additionally, our data indicate that the standard approach has limited efficacy in patients without any mutations in the genes included in the panel. In conclusion, we identified a reliable and easy-to-use approach for a simplified molecular-based stratification of mCRC patients that predicts the efficacy of the first-line conventional combination therapy.
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Affiliation(s)
- Carlo Capalbo
- Department of Molecular Medicine, University La Sapienza, 00161 Rome, Italy.
- Department of Medical Oncology Sant' Andrea Hospital, I-00189 Rome, Italy.
| | | | - Domenico Raimondo
- Department of Molecular Medicine, University La Sapienza, 00161 Rome, Italy.
| | | | - Umberto Malapelle
- Department of Public Health, University Federico II, 80131 Naples, Italy.
| | - Pasquale Pisapia
- Department of Public Health, University Federico II, 80131 Naples, Italy.
| | - Valentina Magri
- Department of Radiological Oncological and Pathological Sciences, University La Sapienza, 00161 Rome, Italy.
| | - Alessandra Prete
- Department of Radiological Oncological and Pathological Sciences, University La Sapienza, 00161 Rome, Italy.
| | - Silvia Pecorari
- Department of Radiological Oncological and Pathological Sciences, University La Sapienza, 00161 Rome, Italy.
| | | | - Anna Coppa
- Department of Experimental Medicine, University La Sapienza, 00161 Rome, Italy.
| | - Caterina Bonfiglio
- National Institute of Gastroenterology-Research Hospital, IRCCS "S. de Bellis", Castellana Grotte, 70013 Bari, Italy.
| | - Arianna Nicolussi
- Department of Experimental Medicine, University La Sapienza, 00161 Rome, Italy.
| | - Virginia Valentini
- Department of Molecular Medicine, University La Sapienza, 00161 Rome, Italy.
| | - Alessandra Tessitore
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, 67100 L'Aquila, Italy.
| | - Beatrice Cardinali
- Institute of Cell Biology and Neurobiology, National Research Council, Campus A. Buzzati-Traverso, 00015 Monterotondo Scalo, Italy.
| | - Marialaura Petroni
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, 00161 Rome, Italy.
| | - Paola Infante
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, 00161 Rome, Italy.
| | - Matteo Santoni
- Oncology Unit, Macerata Hospital, 62012 Macerata, Italy.
| | - Marco Filetti
- Department of Medical Oncology Sant' Andrea Hospital, I-00189 Rome, Italy.
| | - Valeria Colicchia
- Department of Molecular Medicine, University La Sapienza, 00161 Rome, Italy.
| | - Paola Paci
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, 00185 Rome, Italy.
| | - Silvia Mezi
- Department of Radiological Oncological and Pathological Sciences, University La Sapienza, 00161 Rome, Italy.
| | - Flavia Longo
- Department of Radiological Oncological and Pathological Sciences, University La Sapienza, 00161 Rome, Italy.
| | - Enrico Cortesi
- Department of Radiological Oncological and Pathological Sciences, University La Sapienza, 00161 Rome, Italy.
| | - Paolo Marchetti
- Department of Medical Oncology Sant' Andrea Hospital, I-00189 Rome, Italy.
| | - Giancarlo Troncone
- Department of Public Health, University Federico II, 80131 Naples, Italy.
| | - Diana Bellavia
- Department of Molecular Medicine, University La Sapienza, 00161 Rome, Italy.
| | - Gianluca Canettieri
- Department of Molecular Medicine, University La Sapienza, 00161 Rome, Italy.
- Pasteur Institute-Cenci Bolognetti Foundation, 00161 Rome, Italy.
| | - Giuseppe Giannini
- Department of Molecular Medicine, University La Sapienza, 00161 Rome, Italy.
- Pasteur Institute-Cenci Bolognetti Foundation, 00161 Rome, Italy.
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