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Esteban-Medina M, de la Oliva Roque VM, Herráiz-Gil S, Peña-Chilet M, Dopazo J, Loucera C. drexml: A command line tool and Python package for drug repurposing. Comput Struct Biotechnol J 2024; 23:1129-1143. [PMID: 38510973 PMCID: PMC10950807 DOI: 10.1016/j.csbj.2024.02.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 03/22/2024] Open
Abstract
We introduce drexml, a command line tool and Python package for rational data-driven drug repurposing. The package employs machine learning and mechanistic signal transduction modeling to identify drug targets capable of regulating a particular disease. In addition, it employs explainability tools to contextualize potential drug targets within the functional landscape of the disease. The methodology is validated in Fanconi Anemia and Familial Melanoma, two distinct rare diseases where there is a pressing need for solutions. In the Fanconi Anemia case, the model successfully predicts previously validated repurposed drugs, while in the Familial Melanoma case, it identifies a promising set of drugs for further investigation.
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Affiliation(s)
- Marina Esteban-Medina
- Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Seville, Spain
| | - Víctor Manuel de la Oliva Roque
- Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Seville, Spain
| | - Sara Herráiz-Gil
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII), U714, Madrid, Spain
- Departamento de Bioingeniería, Universidad Carlos III de Madrid (UC3M), Madrid, Spain
- Regenerative Medicine and Tissue Engineering Group, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital (IIS-FJD), Madrid, Spain
- Epithelial Biomedicine Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - María Peña-Chilet
- Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Platform of Big Data, AI and Biostatistics, Health Research Institute La Fe (IISLAFE), Valencia, Spain
| | - Joaquín Dopazo
- Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII), U715, Seville, Spain
- FPS/ELIXIR-es, Hospital Virgen del Rocío, Seville, Spain
| | - Carlos Loucera
- Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII), U715, Seville, Spain
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Esteban-Medina M, Loucera C, Rian K, Velasco S, Olivares-González L, Rodrigo R, Dopazo J, Peña-Chilet M. The mechanistic functional landscape of retinitis pigmentosa: a machine learning-driven approach to therapeutic target discovery. J Transl Med 2024; 22:139. [PMID: 38321543 PMCID: PMC10848380 DOI: 10.1186/s12967-024-04911-7] [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: 07/13/2023] [Accepted: 01/20/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND Retinitis pigmentosa is the prevailing genetic cause of blindness in developed nations with no effective treatments. In the pursuit of unraveling the intricate dynamics underlying this complex disease, mechanistic models emerge as a tool of proven efficiency rooted in systems biology, to elucidate the interplay between RP genes and their mechanisms. The integration of mechanistic models and drug-target interactions under the umbrella of machine learning methodologies provides a multifaceted approach that can boost the discovery of novel therapeutic targets, facilitating further drug repurposing in RP. METHODS By mapping Retinitis Pigmentosa-related genes (obtained from Orphanet, OMIM and HPO databases) onto KEGG signaling pathways, a collection of signaling functional circuits encompassing Retinitis Pigmentosa molecular mechanisms was defined. Next, a mechanistic model of the so-defined disease map, where the effects of interventions can be simulated, was built. Then, an explainable multi-output random forest regressor was trained using normal tissue transcriptomic data to learn causal connections between targets of approved drugs from DrugBank and the functional circuits of the mechanistic disease map. Selected target genes involvement were validated on rd10 mice, a murine model of Retinitis Pigmentosa. RESULTS A mechanistic functional map of Retinitis Pigmentosa was constructed resulting in 226 functional circuits belonging to 40 KEGG signaling pathways. The method predicted 109 targets of approved drugs in use with a potential effect over circuits corresponding to nine hallmarks identified. Five of those targets were selected and experimentally validated in rd10 mice: Gabre, Gabra1 (GABARα1 protein), Slc12a5 (KCC2 protein), Grin1 (NR1 protein) and Glr2a. As a result, we provide a resource to evaluate the potential impact of drug target genes in Retinitis Pigmentosa. CONCLUSIONS The possibility of building actionable disease models in combination with machine learning algorithms to learn causal drug-disease interactions opens new avenues for boosting drug discovery. Such mechanistically-based hypotheses can guide and accelerate the experimental validations prioritizing drug target candidates. In this work, a mechanistic model describing the functional disease map of Retinitis Pigmentosa was developed, identifying five promising therapeutic candidates targeted by approved drug. Further experimental validation will demonstrate the efficiency of this approach for a systematic application to other rare diseases.
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Affiliation(s)
- Marina Esteban-Medina
- Andalusian Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Systems and Computational Medicine Group, Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013, Seville, Spain
| | - Carlos Loucera
- Andalusian Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Systems and Computational Medicine Group, Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013, Seville, Spain
| | - Kinza Rian
- Andalusian Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Systems and Computational Medicine Group, Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013, Seville, Spain
| | - Sheyla Velasco
- Group of Pathophysiology and Therapies for Vision Disorders, Príncipe Felipe Research Center (CIPF), 46012, Valencia, Spain
| | - Lorena Olivares-González
- Group of Pathophysiology and Therapies for Vision Disorders, Príncipe Felipe Research Center (CIPF), 46012, Valencia, Spain
| | - Regina Rodrigo
- Group of Pathophysiology and Therapies for Vision Disorders, Príncipe Felipe Research Center (CIPF), 46012, Valencia, Spain
- Biomedical Research Networking Center in Rare Diseases (CIBERER), Health Institute Carlos III, 28029, Madrid, Spain
- Department of Physiology, University of Valencia (UV), 46100, Burjassot, Spain
- Department of Anatomy and Physiology, Catholic University of Valencia San Vicente Mártir, 46001, Valencia, Spain
- Joint Research Unit on Endocrinology, Nutrition and Clinical Dietetics UV-IIS La Fe, 46026, Valencia, Spain
| | - Joaquin Dopazo
- Andalusian Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain.
- Systems and Computational Medicine Group, Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013, Seville, Spain.
- Biomedical Research Networking Center in Rare Diseases (CIBERER), Health Institute Carlos III, 28029, Madrid, Spain.
| | - Maria Peña-Chilet
- Andalusian Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain.
- Systems and Computational Medicine Group, Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013, Seville, Spain.
- Biomedical Research Networking Center in Rare Diseases (CIBERER), Health Institute Carlos III, 28029, Madrid, Spain.
- BigData, AI, Biostatistics & Bioinformatics Platform, Health Research Institute La Fe (IISLaFe), 46026, Valencia, Spain.
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Payá-Milans M, Peña-Chilet M, Loucera C, Esteban-Medina M, Dopazo J. Functional Profiling of Soft Tissue Sarcoma Using Mechanistic Models. Int J Mol Sci 2023; 24:14732. [PMID: 37834179 PMCID: PMC10572617 DOI: 10.3390/ijms241914732] [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: 08/10/2023] [Revised: 09/08/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Soft tissue sarcoma is an umbrella term for a group of rare cancers that are difficult to treat. In addition to surgery, neoadjuvant chemotherapy has shown the potential to downstage tumors and prevent micrometastases. However, finding effective therapeutic targets remains a research challenge. Here, a previously developed computational approach called mechanistic models of signaling pathways has been employed to unravel the impact of observed changes at the gene expression level on the ultimate functional behavior of cells. In the context of such a mechanistic model, RNA-Seq counts sourced from the Recount3 resource, from The Cancer Genome Atlas (TCGA) Sarcoma project, and non-diseased sarcomagenic tissues from the Genotype-Tissue Expression (GTEx) project were utilized to investigate signal transduction activity through signaling pathways. This approach provides a precise view of the relationship between sarcoma patient survival and the signaling landscape in tumors and their environment. Despite the distinct regulatory alterations observed in each sarcoma subtype, this study identified 13 signaling circuits, or elementary sub-pathways triggering specific cell functions, present across all subtypes, belonging to eight signaling pathways, which served as predictors for patient survival. Additionally, nine signaling circuits from five signaling pathways that highlighted the modifications tumor samples underwent in comparison to normal tissues were found. These results describe the protective role of the immune system, suggesting an anti-tumorigenic effect in the tumor microenvironment, in the process of tumor cell detachment and migration, or the dysregulation of ion homeostasis. Also, the analysis of signaling circuit intermediary proteins suggests multiple strategies for therapy.
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Affiliation(s)
- Miriam Payá-Milans
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain; (M.P.-M.); (M.P.-C.); (C.L.); (M.E.-M.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocío, 41013 Seville, Spain
- Institute of Biomedicine of Seville, IBiS/University Hospital Virgen del Rocío/CSIC/University of Sevilla, 41013 Sevilla, Spain
| | - María Peña-Chilet
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain; (M.P.-M.); (M.P.-C.); (C.L.); (M.E.-M.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocío, 41013 Seville, Spain
- Institute of Biomedicine of Seville, IBiS/University Hospital Virgen del Rocío/CSIC/University of Sevilla, 41013 Sevilla, Spain
| | - Carlos Loucera
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain; (M.P.-M.); (M.P.-C.); (C.L.); (M.E.-M.)
- Institute of Biomedicine of Seville, IBiS/University Hospital Virgen del Rocío/CSIC/University of Sevilla, 41013 Sevilla, Spain
| | - Marina Esteban-Medina
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain; (M.P.-M.); (M.P.-C.); (C.L.); (M.E.-M.)
- Institute of Biomedicine of Seville, IBiS/University Hospital Virgen del Rocío/CSIC/University of Sevilla, 41013 Sevilla, Spain
| | - Joaquín Dopazo
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain; (M.P.-M.); (M.P.-C.); (C.L.); (M.E.-M.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocío, 41013 Seville, Spain
- Institute of Biomedicine of Seville, IBiS/University Hospital Virgen del Rocío/CSIC/University of Sevilla, 41013 Sevilla, Spain
- FPS/ELIXIR-ES, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocío, 41013 Sevilla, Spain
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Errazquin R, Page A, Suñol A, Segrelles C, Carrasco E, Peral J, Garrido-Aranda A, Del Marro S, Ortiz J, Lorz C, Minguillon J, Surralles J, Belendez C, Alvarez M, Balmaña J, Bravo A, Ramirez A, Garcia-Escudero R. Development of a mouse model for spontaneous oral squamous cell carcinoma in Fanconi anemia. Oral Oncol 2022; 134:106184. [PMID: 36191479 DOI: 10.1016/j.oraloncology.2022.106184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/21/2022] [Accepted: 09/24/2022] [Indexed: 11/29/2022]
Abstract
Fanconi anemia (FA) patients frequently develop oral squamous cell carcinoma (OSCC). This cancer in FA patients is diagnosed within the first 3-4 decades of life, very often preceded by lesions that suffer a malignant transformation. In addition, they respond poorly to current treatments due to toxicity or multiple recurrences. Translational research on new chemopreventive agents and therapeutic strategies has been unsuccessful partly due to scarcity of disease models or failure to fully reproduce the disease. Here we report that Fanca gene knockout mice (Fanca-/-) frequently display pre-malignant lesions in the oral cavity. Moreover, when these animals were crossed with animals having conditional deletion of Trp53 gene in oral mucosa (K14cre;Trp53F2-10/F2-10), they spontaneously developed OSCC with high penetrance and a median latency of less than ten months. Tumors were well differentiated and expressed markers of squamous differentiation, such as keratins K5 and K10. In conclusion, Fanca and Trp53 genes cooperate to suppress oral cancer in mice, and Fanca-/-;K14cre;Trp53F2-10/F2-10 mice constitute the first animal model of spontaneous OSCC in FA.
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Affiliation(s)
- Ricardo Errazquin
- Research Institute Hospital 12 de Octubre (imas12), University Hospital "12 de Octubre", Av Córdoba s/n, 28041 Madrid, Spain
| | - Angustias Page
- Research Institute Hospital 12 de Octubre (imas12), University Hospital "12 de Octubre", Av Córdoba s/n, 28041 Madrid, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; Biomedical Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Avenida Complutense 40, 28040 Madrid, Spain
| | - Anna Suñol
- Hereditary Cancer Genetics Group and Medical Oncology Department, VHIO, Barcelona, Spain
| | - Carmen Segrelles
- Research Institute Hospital 12 de Octubre (imas12), University Hospital "12 de Octubre", Av Córdoba s/n, 28041 Madrid, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; Biomedical Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Avenida Complutense 40, 28040 Madrid, Spain
| | - Estela Carrasco
- Hereditary Cancer Genetics Group and Medical Oncology Department, VHIO, Barcelona, Spain
| | - Jorge Peral
- Biomedical Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Avenida Complutense 40, 28040 Madrid, Spain
| | | | - Sonia Del Marro
- Biomedical Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Avenida Complutense 40, 28040 Madrid, Spain
| | - Jessica Ortiz
- Biomedical Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Avenida Complutense 40, 28040 Madrid, Spain
| | - Corina Lorz
- Research Institute Hospital 12 de Octubre (imas12), University Hospital "12 de Octubre", Av Córdoba s/n, 28041 Madrid, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; Biomedical Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Avenida Complutense 40, 28040 Madrid, Spain
| | - Jordi Minguillon
- Join Research Unit on Genomic Medicine UAB-Sant Pau Biomedical Research Institute (IIB Sant Pau), Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain; Centro de Investigación Biomédica en Enfermedades Raras (CIBERER), 28029 Madrid, Spain
| | - Jordi Surralles
- Join Research Unit on Genomic Medicine UAB-Sant Pau Biomedical Research Institute (IIB Sant Pau), Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain; Centro de Investigación Biomédica en Enfermedades Raras (CIBERER), 28029 Madrid, Spain
| | - Cristina Belendez
- Centro de Investigación Biomédica en Enfermedades Raras (CIBERER), 28029 Madrid, Spain; Pediatric Hematology and Oncology, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Facultad de Medicina, Universidad Complutense de Madrid, Spain; Instituto Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Martina Alvarez
- Centro de Investigaciones Médico-Sanitarias (CIMES), Malaga, Spain
| | - Judith Balmaña
- Hereditary Cancer Genetics Group and Medical Oncology Department, VHIO, Barcelona, Spain
| | - Ana Bravo
- Department of Anatomy, Animal Production and Veterinary Clinical Sciences, Laboratory of Pathology Phenotyping of Genetically Engineered Mice, Faculty of Veterinary Medicine, University of Santiago de Compostela, 27002 Lugo, Spain
| | - Angel Ramirez
- Research Institute Hospital 12 de Octubre (imas12), University Hospital "12 de Octubre", Av Córdoba s/n, 28041 Madrid, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; Biomedical Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Avenida Complutense 40, 28040 Madrid, Spain
| | - Ramon Garcia-Escudero
- Research Institute Hospital 12 de Octubre (imas12), University Hospital "12 de Octubre", Av Córdoba s/n, 28041 Madrid, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; Biomedical Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Avenida Complutense 40, 28040 Madrid, Spain.
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Long Z, Grandis JR, Johnson DE. Emerging tyrosine kinase inhibitors for head and neck cancer. Expert Opin Emerg Drugs 2022; 27:333-344. [PMID: 36131561 PMCID: PMC9987561 DOI: 10.1080/14728214.2022.2125954] [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: 06/17/2022] [Accepted: 09/14/2022] [Indexed: 01/09/2023]
Abstract
INTRODUCTION Conventional regimens for head and neck squamous cell carcinoma (HNSCC) are limited in efficacy and are associated with adverse toxicities. Food and Drug Administration (FDA) approved molecular targeting agents include the HER1 (EGFR)-directed monoclonal antibody cetuximab and the immune checkpoint inhibitors nivolumab and pembrolizumab. However, clinical benefit is only seen in roughly 15-20% of HNSCC patients treated with these agents. New molecular targeting agents are needed that either act with monotherapeutic activity against HNSCC tumors or enhance the activities of current therapies, particularly immunotherapy. Small-molecule tyrosine kinase inhibitors (TKIs) represent a viable option toward this goal. AREAS COVERED This review provides an update on TKIs currently under investigation in HNSCC. We focus our review on data obtained and trials underway in HNSCC, including salivary gland cancers and nasopharyngeal carcinomas, but excluding thyroid cancer and esophageal cancer. EXPERT OPINION While some emerging TKIs have shown clinical benefit, the positive effects have, largely, been modest. The design of clinical trials of TKIs has been hampered by a lack of understanding of biomarkers that can be used to define patient populations most likely to respond. Further preclinical and translational studies to define biomarkers of TKI response will be critically important.
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Affiliation(s)
- Zhen Long
- Department of Otolaryngology – Head and Neck Surgery, University of California, San Francisco, California, USA
| | - Jennifer R. Grandis
- Department of Otolaryngology – Head and Neck Surgery, University of California, San Francisco, California, USA
| | - Daniel E. Johnson
- Department of Otolaryngology – Head and Neck Surgery, University of California, San Francisco, California, USA
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Li H, Peyser ND, Zeng Y, Ha PK, Johnson DE, Grandis JR. NSAIDs Overcome PIK3CA Mutation-Mediated Resistance to EGFR Inhibition in Head and Neck Cancer Preclinical Models. Cancers (Basel) 2022; 14:cancers14030506. [PMID: 35158773 PMCID: PMC8833811 DOI: 10.3390/cancers14030506] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/20/2021] [Accepted: 01/04/2022] [Indexed: 02/04/2023] Open
Abstract
Epidermal growth factor receptor (EGFR) inhibitors are approved by the Food and Drug Administration (FDA) but remain under active clinical investigation for the treatment of both newly diagnosed and recurrent/metastatic head and neck squamous cell carcinoma (HNSCC). Despite EGFR expression in the majority of HNSCC tumors, the levels of total or phosphorylated EGFR have not consistently been correlated with a response to EGFR targeting agents. The lack of predictive biomarkers represents a major obstacle to successful use of these drugs. Activation of phosphatidylinositol 3-kinase (PI3K) signaling by mutation of the PIK3CA oncogene represents a plausible mechanism for EGFR inhibitor drug resistance. We compared the impact of EGFR inhibitors, alone or in combination with non-steroidal anti-inflammatory drugs (NSAIDs), in preclinical HNSCC models harboring mutant versus wild-type PIK3CA. Our results demonstrate additive or synergistic effects of NSAIDs and EGFR inhibitors in vitro and in vivo in PIK3CA-mutated HNSCC models. These findings suggest that the addition of NSAIDs to EGFR inhibitors for the treatment of HNSCC may represent a promising therapeutic strategy in PIK3CA-mutated cancers.
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CDK5RAP3, a New BRCA2 Partner That Regulates DNA Repair, Is Associated with Breast Cancer Survival. Cancers (Basel) 2022; 14:cancers14020353. [PMID: 35053516 PMCID: PMC8773632 DOI: 10.3390/cancers14020353] [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: 09/27/2021] [Revised: 10/27/2021] [Accepted: 10/30/2021] [Indexed: 02/01/2023] Open
Abstract
BRCA2 is essential for homologous recombination DNA repair. BRCA2 mutations lead to genome instability and increased risk of breast and ovarian cancer. Similarly, mutations in BRCA2-interacting proteins are also known to modulate sensitivity to DNA damage agents and are established cancer risk factors. Here we identify the tumor suppressor CDK5RAP3 as a novel BRCA2 helical domain-interacting protein. CDK5RAP3 depletion induced DNA damage resistance, homologous recombination and single-strand annealing upregulation, and reduced spontaneous and DNA damage-induced genomic instability, suggesting that CDK5RAP3 negatively regulates double-strand break repair in the S-phase. Consistent with this cellular phenotype, analysis of transcriptomic data revealed an association between low CDK5RAP3 tumor expression and poor survival of breast cancer patients. Finally, we identified common genetic variations in the CDK5RAP3 locus as potentially associated with breast and ovarian cancer risk in BRCA1 and BRCA2 mutation carriers. Our results uncover CDK5RAP3 as a critical player in DNA repair and breast cancer outcomes.
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Roohollahi K, de Jong Y, Pai G, Zaini MA, de Lint K, Sie D, Rooimans MA, Rockx D, Hoskins EE, Ameziane N, Wolthuis R, Joenje H, Wells SI, Dorsman J. BIRC2-BIRC3 amplification: a potentially druggable feature of a subset of head and neck cancers in patients with Fanconi anemia. Sci Rep 2022; 12:45. [PMID: 34997070 PMCID: PMC8742043 DOI: 10.1038/s41598-021-04042-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 12/10/2021] [Indexed: 12/13/2022] Open
Abstract
Head-and-neck squamous cell carcinomas (HNSCCs) are relatively common in patients with Fanconi anemia (FA), a hereditary chromosomal instability disorder. Standard chemo-radiation therapy is not tolerated in FA due to an overall somatic hypersensitivity to such treatment. The question is how to find a suitable alternative treatment. We used whole-exome and whole genome mRNA sequencing to identify major genomic and transcriptomic events associated with FA-HNSCC. CRISPR-engineered FA-knockout models were used to validate a number of top hits that were likely to be druggable. We identified deletion of 18q21.2 and amplification of 11q22.2 as prevailing copy-number alterations in FA HNSCCs, the latter of which was associated with strong overexpression of the cancer-related genes YAP1, BIRC2, BIRC3 (at 11q22.1-2). We then found the drug AZD5582, a known small molecule inhibitor of BIRC2-3, to selectively kill FA tumor cells that overexpressed BIRC2-3. This occurred at drug concentrations that did not affect the viability of untransformed FA cells. Our data indicate that 11q22.2 amplifications are relatively common oncogenic events in FA-HNSCCs, as holds for non FA-HNSCC. Therefore, chemotherapeutic inhibition of overexpressed BIRC2-3 may provide the basis for an approach to develop a clinically realistic treatment of FA-HNSCCs that carry 11q22.2 amplifications.
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Affiliation(s)
- Khashayar Roohollahi
- Department of Clinical Genetics, Amsterdam UMC, Location VUMC, De Boelelaan 1117, 1118, 1081 HV, Amsterdam, The Netherlands.
| | - Yvonne de Jong
- Department of Clinical Genetics, Amsterdam UMC, Location VUMC, De Boelelaan 1117, 1118, 1081 HV, Amsterdam, The Netherlands
| | - Govind Pai
- Department of Clinical Genetics, Amsterdam UMC, Location VUMC, De Boelelaan 1117, 1118, 1081 HV, Amsterdam, The Netherlands
| | - Mohamad Amr Zaini
- Department of Clinical Genetics, Amsterdam UMC, Location VUMC, De Boelelaan 1117, 1118, 1081 HV, Amsterdam, The Netherlands
| | - Klaas de Lint
- Department of Clinical Genetics, Amsterdam UMC, Location VUMC, De Boelelaan 1117, 1118, 1081 HV, Amsterdam, The Netherlands
| | - Daoud Sie
- Department of Clinical Genetics, Amsterdam UMC, Location VUMC, De Boelelaan 1117, 1118, 1081 HV, Amsterdam, The Netherlands
| | - Martin A Rooimans
- Department of Clinical Genetics, Amsterdam UMC, Location VUMC, De Boelelaan 1117, 1118, 1081 HV, Amsterdam, The Netherlands
| | - Davy Rockx
- Department of Clinical Genetics, Amsterdam UMC, Location VUMC, De Boelelaan 1117, 1118, 1081 HV, Amsterdam, The Netherlands
| | | | - Najim Ameziane
- Department of Clinical Genetics, Amsterdam UMC, Location VUMC, De Boelelaan 1117, 1118, 1081 HV, Amsterdam, The Netherlands
| | - Rob Wolthuis
- Department of Clinical Genetics, Amsterdam UMC, Location VUMC, De Boelelaan 1117, 1118, 1081 HV, Amsterdam, The Netherlands
| | - Hans Joenje
- Department of Clinical Genetics, Amsterdam UMC, Location VUMC, De Boelelaan 1117, 1118, 1081 HV, Amsterdam, The Netherlands
| | - Susanne I Wells
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Josephine Dorsman
- Department of Clinical Genetics, Amsterdam UMC, Location VUMC, De Boelelaan 1117, 1118, 1081 HV, Amsterdam, The Netherlands.
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Moreno OM, Paredes AC, Suarez-Obando F, Rojas A. An update on Fanconi anemia: Clinical, cytogenetic and molecular approaches (Review). Biomed Rep 2021; 15:74. [PMID: 34405046 PMCID: PMC8329995 DOI: 10.3892/br.2021.1450] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/11/2021] [Indexed: 12/25/2022] Open
Abstract
Fanconi anemia is a genetic syndrome clinically characterized by congenital malformations that affect several human systems, leads to progressive bone marrow failure and predisposes an individual to cancer, particularly in the urogenital area as well as the head and neck. It is commonly caused by the biallelic compromise of one of 22 genes involved in the FA/BRCA repair pathway in most cases. The diagnosis is based on clinical suspicion and confirmation using genetic analysis, where the chromosomal breakage test is considered the gold standard. Other diagnostic methods used include western blotting, multiplex ligation-dependent probe amplification and next-generation sequencing. This genetic condition has variable expressiveness, which makes early diagnosis difficult in certain cases. Although early diagnosis does not currently allow for improved cure rates for this condition, it does enable healthcare professionals to perform a specific systematic follow-up and, if indicated, a bone marrow transplantation that improves the mobility and mortality of affected individuals. The present review article is a theoretical revision of the pathophysiology, clinical manifestations and diagnosis methods intended for different specialists and general practitioners to improve the diagnosis of this condition.
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Affiliation(s)
- Olga María Moreno
- Institute of Human Genetics, School of Medicine, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Angela Camila Paredes
- Institute of Human Genetics, School of Medicine, Pontificia Universidad Javeriana, Bogotá 110231, Colombia.,Genetics Department, Hospital Universitario San Ignacio, Bogotá 110231, Colombia
| | - Fernando Suarez-Obando
- Institute of Human Genetics, School of Medicine, Pontificia Universidad Javeriana, Bogotá 110231, Colombia.,Genetics Department, Hospital Universitario San Ignacio, Bogotá 110231, Colombia
| | - Adriana Rojas
- Institute of Human Genetics, School of Medicine, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
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10
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Lee RH, Kang H, Yom SS, Smogorzewska A, Johnson DE, Grandis JR. Treatment of Fanconi Anemia-Associated Head and Neck Cancer: Opportunities to Improve Outcomes. Clin Cancer Res 2021; 27:5168-5187. [PMID: 34045293 DOI: 10.1158/1078-0432.ccr-21-1259] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/06/2021] [Accepted: 05/20/2021] [Indexed: 11/16/2022]
Abstract
Fanconi anemia, the most frequent genetic cause of bone marrow failure, is characterized by an extreme predilection toward multiple malignancies, including a greater than 500-fold incidence of head and neck squamous cell carcinoma (HNSCC) relative to the general population. Fanconi anemia-associated HNSCC and esophageal SCC (FA-HNSCC) often present at advanced stages with poor survival. Surgical resection remains the primary treatment for FA-HNSCC, and there is often great reluctance to administer systemic agents and/or radiotherapy to these patients given their susceptibility to DNA damage. The paucity of FA-HNSCC case reports limits evidence-based management, and such cases have not been analyzed collectively in detail. We present a systematic review of FA-HNSCC treatments reported from 1966 to 2020, defining a cohort of 119 patients with FA-HNSCC including 16 esophageal SCCs (131 total primary tumors), who were treated with surgery, radiotherapy, systemic therapy (including cytotoxic agents, EGFR inhibitors, or immune checkpoint inhibitors), or a combination of modalities. We summarize the clinical responses and regimen-associated toxicities by treatment modality. The collective evidence suggests that when possible, surgical resection with curative intent should remain the primary treatment modality for FA-HNSCC. Radiation can be administered with acceptable toxicity in the majority of cases, including patients who have undergone stem cell transplantation. Although there is little justification for cytotoxic chemotherapy, EGFR inhibitors and tyrosine kinase inhibitors may be both safe and effective. Immunotherapy may also be considered. Most oncologists have little personal experience with FA-HNSCC. This review is intended as a comprehensive resource for clinicians.
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Affiliation(s)
- Rex H Lee
- Department of Otolaryngology - Head and Neck Surgery, University of California San Francisco, San Francisco, California
| | - Hyunseok Kang
- Department of Medicine, University of California San Francisco, San Francisco, California
| | - Sue S Yom
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York, New York
| | - Daniel E Johnson
- Department of Otolaryngology - Head and Neck Surgery, University of California San Francisco, San Francisco, California
| | - Jennifer R Grandis
- Department of Otolaryngology - Head and Neck Surgery, University of California San Francisco, San Francisco, California
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11
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Rian K, Hidalgo MR, Çubuk C, Falco MM, Loucera C, Esteban-Medina M, Alamo-Alvarez I, Peña-Chilet M, Dopazo J. Genome-scale mechanistic modeling of signaling pathways made easy: A bioconductor/cytoscape/web server framework for the analysis of omic data. Comput Struct Biotechnol J 2021; 19:2968-2978. [PMID: 34136096 PMCID: PMC8170118 DOI: 10.1016/j.csbj.2021.05.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/21/2021] [Accepted: 05/11/2021] [Indexed: 12/13/2022] Open
Abstract
Genome-scale mechanistic models of pathways are gaining importance for genomic data interpretation because they provide a natural link between genotype measurements (transcriptomics or genomics data) and the phenotype of the cell (its functional behavior). Moreover, mechanistic models can be used to predict the potential effect of interventions, including drug inhibitions. Here, we present the implementation of a mechanistic model of cell signaling for the interpretation of transcriptomic data as an R/Bioconductor package, a Cytoscape plugin and a web tool with enhanced functionality which includes building interpretable predictors, estimation of the effect of perturbations and assessment of the effect of mutations in complex scenarios.
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Affiliation(s)
- Kinza Rian
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
- Laboratory of Innovative Technologies (LTI), National School of Applied Sciences in Tangier, UAE, Morocco
| | - Marta R. Hidalgo
- Bioinformatics and Biostatistics Unit, Centro de Investigación Príncipe Felipe (CIPF), 46012 Valencia, Spain
| | - Cankut Çubuk
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
| | - Matias M. Falco
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
- Bioinformatics in RareDiseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Sevilla 41013, Spain
| | - Carlos Loucera
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
- Computational Systems Medicine. Institute of Biomedicine of Seville (IBiS), Sevilla 41013, Spain
| | - Marina Esteban-Medina
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
- Computational Systems Medicine. Institute of Biomedicine of Seville (IBiS), Sevilla 41013, Spain
| | - Inmaculada Alamo-Alvarez
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
- Computational Systems Medicine. Institute of Biomedicine of Seville (IBiS), Sevilla 41013, Spain
| | - María Peña-Chilet
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
- Bioinformatics in RareDiseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Sevilla 41013, Spain
- Computational Systems Medicine. Institute of Biomedicine of Seville (IBiS), Sevilla 41013, Spain
| | - Joaquín Dopazo
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
- Bioinformatics in RareDiseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Sevilla 41013, Spain
- Computational Systems Medicine. Institute of Biomedicine of Seville (IBiS), Sevilla 41013, Spain
- Functional Genomics Node (INB-ELIXIR-es), Sevilla, Spain
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12
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Deng S, Ye W, Zhang S, Zhu G, Zhang P, Song Y, Duan F, Lang J, Lu S. Oral Tongue Cancer in a Patient with Fanconi Anemia: A Case Report and Literature Review. Cancer Manag Res 2021; 13:3145-3154. [PMID: 33883933 PMCID: PMC8053604 DOI: 10.2147/cmar.s301582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 03/17/2021] [Indexed: 02/05/2023] Open
Abstract
Purpose Fanconi anemia (FA) is a rare genetic disorder characterized by congenital anomalies, progressive bone marrow failure and high susceptibility to solid tumors, especially head and neck squamous cell carcinoma (HNSCC). Management of FA patients with head and neck cancer is a challenge due to increased risk of surgery, poor tolerance of chemotherapy, and severe myelotoxicity of radiotherapy. Patients and Methods We present a case of a 33-year-old man with carcinoma of oral tongue (T1N2M0), who experienced prolonged and profound bone marrow failure as a consequence of concurrent cisplatin/radiation. The young patient who developed HNSCC without risk factors, the myelotoxicity after exposure to platinum-based agent cisplatin and the further evaluation of phenotypic characteristics raised suspicion of FA. Whole exome sequencing performed for the patient and parents ultimately established the diagnosis of FA. Results Genetic testing in 23 FANC genes revealed two novel heterozygous mutations, c.367C>T and c.3971_3972delCGinsTT in FANCA gene of the patient, which were inherited from his father and mother, respectively. Radiotherapy with reduced dose has successfully alleviated the symptoms of tumor invasion and progression, and the radiation-related side effects were acceptable. Unfortunately, the patient eventually died of locoregional disease progression. Conclusion This case highlights the importance of considering the diagnosis of FA in young patients who develop HNSCC in the absence of risk factors, thus permitting more effective oncological treatment strategies and improved outcomes. In conclusion, any decision on different modalities of management in such patients should be based on a balance between locoregional control and therapeutic toxicity.
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Affiliation(s)
- Siyao Deng
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
| | - Wenjing Ye
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
| | - Shichuan Zhang
- Department of Radiation Oncology, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, People's Republic of China.,Radiation Oncology Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Guiquan Zhu
- State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, Department of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, Chengdu, People's Republic of China
| | - Peng Zhang
- Department of Radiation Oncology, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
| | - Yanqiong Song
- Department of Radiation Oncology, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
| | - Fanglei Duan
- Radiation Oncology Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Jinyi Lang
- Department of Radiation Oncology, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, People's Republic of China.,Radiation Oncology Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Shun Lu
- Department of Radiation Oncology, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, People's Republic of China.,Radiation Oncology Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
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13
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Errazquin R, Sieiro E, Moreno P, Ramirez MJ, Lorz C, Peral J, Ortiz J, Casado JA, Roman-Rodriguez FJ, Hanenberg H, Río P, Surralles J, Segrelles C, Garcia-Escudero R. Generating New FANCA-Deficient HNSCC Cell Lines by Genomic Editing Recapitulates the Cellular Phenotypes of Fanconi Anemia. Genes (Basel) 2021; 12:548. [PMID: 33918752 PMCID: PMC8069753 DOI: 10.3390/genes12040548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 03/30/2021] [Accepted: 04/07/2021] [Indexed: 01/22/2023] Open
Abstract
Fanconi anemia (FA) patients have an exacerbated risk of head and neck squamous cell carcinoma (HNSCC). Treatment is challenging as FA patients display enhanced toxicity to standard treatments, including radio/chemotherapy. Therefore, better therapies as well as new disease models are urgently needed. We have used CRISPR/Cas9 editing tools in order to interrupt the human FANCA gene by the generation of insertions/deletions (indels) in exon 4 in two cancer cell lines from sporadic HNSCC having no mutation in FA-genes: CAL27 and CAL33 cells. Our approach allowed efficient editing, subsequent purification of single-cell clones, and Sanger sequencing validation at the edited locus. Clones having frameshift indels in homozygosis did not express FANCA protein and were selected for further analysis. When compared with parental CAL27 and CAL33, FANCA-mutant cell clones displayed a FA-phenotype as they (i) are highly sensitive to DNA interstrand crosslink (ICL) agents such as mitomycin C (MMC) or cisplatin, (ii) do not monoubiquitinate FANCD2 upon MMC treatment and therefore (iii) do not form FANCD2 nuclear foci, and (iv) they display increased chromosome fragility and G2 arrest after diepoxybutane (DEB) treatment. These FANCA-mutant clones display similar growth rates as their parental cells. Interestingly, mutant cells acquire phenotypes associated with more aggressive disease, such as increased migration in wound healing assays. Therefore, CAL27 and CAL33 cells with FANCA mutations are phenocopies of FA-HNSCC cells.
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Affiliation(s)
- Ricardo Errazquin
- Biomedical Research Institute I+12, University Hospital 12 de Octubre, 28041 Madrid, Spain; (R.E.); (C.L.); (C.S.)
- Molecular Oncology Unit, CIEMAT, 28040 Madrid, Spain; (E.S.); (P.M.); (J.P.); (J.O.)
| | - Esther Sieiro
- Molecular Oncology Unit, CIEMAT, 28040 Madrid, Spain; (E.S.); (P.M.); (J.P.); (J.O.)
| | - Pilar Moreno
- Molecular Oncology Unit, CIEMAT, 28040 Madrid, Spain; (E.S.); (P.M.); (J.P.); (J.O.)
| | - María José Ramirez
- Join Research Unit on Genomic Medicine UAB-Sant Pau Biomedical Research Institute, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain; (M.J.R.); (J.S.)
- Centro de Investigación Biomédica en Enfermedades Raras (CIBERER), 28029 Madrid, Spain; (J.A.C.); (F.J.R.-R.); (P.R.)
| | - Corina Lorz
- Biomedical Research Institute I+12, University Hospital 12 de Octubre, 28041 Madrid, Spain; (R.E.); (C.L.); (C.S.)
- Molecular Oncology Unit, CIEMAT, 28040 Madrid, Spain; (E.S.); (P.M.); (J.P.); (J.O.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Jorge Peral
- Molecular Oncology Unit, CIEMAT, 28040 Madrid, Spain; (E.S.); (P.M.); (J.P.); (J.O.)
| | - Jessica Ortiz
- Molecular Oncology Unit, CIEMAT, 28040 Madrid, Spain; (E.S.); (P.M.); (J.P.); (J.O.)
| | - José Antonio Casado
- Centro de Investigación Biomédica en Enfermedades Raras (CIBERER), 28029 Madrid, Spain; (J.A.C.); (F.J.R.-R.); (P.R.)
- Hematopoietic Innovative Therapies Division, CIEMAT, 28040 Madrid, Spain
- Instituto de Investigaciones Sanitarias de la Fundación Jiménez Díaz, 28040 Madrid, Spain
| | - Francisco J. Roman-Rodriguez
- Centro de Investigación Biomédica en Enfermedades Raras (CIBERER), 28029 Madrid, Spain; (J.A.C.); (F.J.R.-R.); (P.R.)
- Hematopoietic Innovative Therapies Division, CIEMAT, 28040 Madrid, Spain
- Instituto de Investigaciones Sanitarias de la Fundación Jiménez Díaz, 28040 Madrid, Spain
| | - Helmut Hanenberg
- University Children’s Hospital Essen, University of Duisburg-Essen, 47057 Essen, Germany;
- Department of Otorhinolaryngology & Head/Neck Surgery, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Paula Río
- Centro de Investigación Biomédica en Enfermedades Raras (CIBERER), 28029 Madrid, Spain; (J.A.C.); (F.J.R.-R.); (P.R.)
- Hematopoietic Innovative Therapies Division, CIEMAT, 28040 Madrid, Spain
- Instituto de Investigaciones Sanitarias de la Fundación Jiménez Díaz, 28040 Madrid, Spain
| | - Jordi Surralles
- Join Research Unit on Genomic Medicine UAB-Sant Pau Biomedical Research Institute, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain; (M.J.R.); (J.S.)
- Centro de Investigación Biomédica en Enfermedades Raras (CIBERER), 28029 Madrid, Spain; (J.A.C.); (F.J.R.-R.); (P.R.)
| | - Carmen Segrelles
- Biomedical Research Institute I+12, University Hospital 12 de Octubre, 28041 Madrid, Spain; (R.E.); (C.L.); (C.S.)
- Molecular Oncology Unit, CIEMAT, 28040 Madrid, Spain; (E.S.); (P.M.); (J.P.); (J.O.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Ramon Garcia-Escudero
- Biomedical Research Institute I+12, University Hospital 12 de Octubre, 28041 Madrid, Spain; (R.E.); (C.L.); (C.S.)
- Molecular Oncology Unit, CIEMAT, 28040 Madrid, Spain; (E.S.); (P.M.); (J.P.); (J.O.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
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14
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Usman S, Jamal A, Teh MT, Waseem A. Major Molecular Signaling Pathways in Oral Cancer Associated With Therapeutic Resistance. FRONTIERS IN ORAL HEALTH 2021; 1:603160. [PMID: 35047986 PMCID: PMC8757854 DOI: 10.3389/froh.2020.603160] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 12/29/2020] [Indexed: 12/12/2022] Open
Abstract
Oral cancer is a sub-category of head and neck cancers that primarily initiates in the oral cavity. The primary treatment option for oral cancer remains surgery but it is associated with massive disfigurement, inability to carry out normal oral functions, psycho-social stress and exhaustive rehabilitation. Other treatment options such as chemotherapy and radiotherapy have their own limitations in terms of toxicity, intolerance and therapeutic resistance. Immunological treatments to enhance the body's ability to recognize cancer tissue as a foreign entity are also being used but they are new and underdeveloped. Although substantial progress has been made in the treatment of oral cancer, its complex heterogeneous nature still needs to be explored, to elucidate the molecular basis for developing resistance to therapeutic agents and how to overcome it, with the aim of improving the chances of patients' survival and their quality of life. This review provides an overview of up-to-date information on the complex role of the major molecules and associated signaling, epigenetic changes, DNA damage repair systems, cancer stem cells and micro RNAs in the development of therapeutic resistance and treatment failure in oral cancer. We have also summarized the current strategies being developed to overcome these therapeutic challenges. This review will help not only researchers but also oral oncologists in the management of the disease and in developing new therapeutic modalities.
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Affiliation(s)
| | | | | | - Ahmad Waseem
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
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15
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Canonical and Noncanonical Roles of Fanconi Anemia Proteins: Implications in Cancer Predisposition. Cancers (Basel) 2020; 12:cancers12092684. [PMID: 32962238 PMCID: PMC7565043 DOI: 10.3390/cancers12092684] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/11/2020] [Accepted: 09/17/2020] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Fanconi anemia (FA) is a genetic disorder that is characterized by bone marrow failure (BMF), developmental abnormalities, and predisposition to cancer. In this review, we present an overview of both canonical (regulation of interstrand cross-links repair, ICLs) and noncanonical roles of FA proteins. We divide noncanonical alternative functions in two types: nuclear (outside ICLs such as FA action in replication stress or DSB repair) and cytosolic (such as in mitochondrial quality control or selective autophagy). We further discuss the involvement of FA genes in the predisposition to develop different types of cancers and we examine current DNA damage response-targeted therapies. Finally, we promote an insightful perspective regarding the clinical implication of the cytosolic noncanonical roles of FA proteins in cancer predisposition, suggesting that these alternative roles could be of critical importance for disease progression. Abstract Fanconi anemia (FA) is a clinically and genetically heterogeneous disorder characterized by the variable presence of congenital somatic abnormalities, bone marrow failure (BMF), and a predisposition to develop cancer. Monoallelic germline mutations in at least five genes involved in the FA pathway are associated with the development of sporadic hematological and solid malignancies. The key function of the FA pathway is to orchestrate proteins involved in the repair of interstrand cross-links (ICLs), to prevent genomic instability and replication stress. Recently, many studies have highlighted the importance of FA genes in noncanonical pathways, such as mitochondria homeostasis, inflammation, and virophagy, which act, in some cases, independently of DNA repair processes. Thus, primary defects in DNA repair mechanisms of FA patients are typically exacerbated by an impairment of other cytoprotective pathways that contribute to the multifaceted clinical phenotype of this disease. In this review, we summarize recent advances in the understanding of the pathogenesis of FA, with a focus on the cytosolic noncanonical roles of FA genes, discussing how they may contribute to cancer development, thus suggesting opportunities to envisage novel therapeutic approaches.
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16
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Anderson AN, McClanahan D, Jacobs J, Jeng S, Vigoda M, Blucher AS, Zheng C, Yoo YJ, Hale C, Ouyang X, Clayburgh D, Andersen P, Tyner JW, Bar A, Lucero OM, Leitenberger JJ, McWeeney SK, Kulesz-Martin M. Functional genomic analysis identifies drug targetable pathways in invasive and metastatic cutaneous squamous cell carcinoma. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005439. [PMID: 32843430 PMCID: PMC7476409 DOI: 10.1101/mcs.a005439] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/09/2020] [Indexed: 12/20/2022] Open
Abstract
Although cutaneous squamous cell carcinoma (cSCC) is treatable in the majority of cases, deadly invasive and metastatic cases do occur. To date there are neither reliable predictive biomarkers of disease progression nor FDA-approved targeted therapies as standard of care. To address these issues, we screened patient-derived primary cultured cells from invasive/metastatic cSCC with 107 small-molecule inhibitors. In-house bioinformatics tools were used to cross-analyze drug responses and DNA mutations in tumors detected by whole-exome sequencing (WES). Aberrations in molecular pathways with evidence of potential drug targets were identified, including the Eph-ephrin and neutrophil degranulation signaling pathways. Using a screening panel of siRNAs, we identified EPHA6 and EPHA7 as targets within the Eph-ephrin pathway responsible for mitigating decreased cell viability. These studies form a plausible foundation for detecting biomarkers of high-risk progressive disease applicable in dermatopathology and for patient-specific therapeutic options for invasive/metastatic cSCC.
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Affiliation(s)
- Ashley N Anderson
- Department of Dermatology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Danielle McClanahan
- Department of Dermatology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - James Jacobs
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University Knight Cancer Institute, Portland, Oregon 97239, USA
| | - Sophia Jeng
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University Knight Cancer Institute, Portland, Oregon 97239, USA.,Oregon Clinical and Translational Research Institute, Oregon Health and Science University, Portland, Oregon 97339, USA
| | - Myles Vigoda
- Department of Dermatology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Aurora S Blucher
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University Knight Cancer Institute, Portland, Oregon 97239, USA
| | - Christina Zheng
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University Knight Cancer Institute, Portland, Oregon 97239, USA
| | - Yeon Jung Yoo
- Department of Dermatology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Carolyn Hale
- Department of Dermatology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Xiaoming Ouyang
- Department of Dermatology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Daniel Clayburgh
- Department of Otolaryngology, Oregon Health & Science University, Portland, Oregon 97239, USA.,Operative Care Division, Veterans Affairs Medical Center, Portland, Oregon 97239, USA
| | - Peter Andersen
- Department of Otolaryngology, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Jeffrey W Tyner
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University Knight Cancer Institute, Portland, Oregon 97239, USA.,Division of Hematology and Medical Oncology, Oregon Health and Science University Knight Cancer Institute, Portland, Oregon 97239, USA
| | - Anna Bar
- Department of Dermatology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Olivia M Lucero
- Department of Dermatology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Justin J Leitenberger
- Department of Dermatology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Shannon K McWeeney
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University Knight Cancer Institute, Portland, Oregon 97239, USA
| | - Molly Kulesz-Martin
- Department of Dermatology, Oregon Health and Science University, Portland, Oregon 97239, USA.,Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University Knight Cancer Institute, Portland, Oregon 97239, USA
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17
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Montanuy H, Camps-Fajol C, Carreras-Puigvert J, Häggblad M, Lundgren B, Aza-Carmona M, Helleday T, Minguillón J, Surrallés J. High content drug screening for Fanconi anemia therapeutics. Orphanet J Rare Dis 2020; 15:170. [PMID: 32605631 PMCID: PMC7325660 DOI: 10.1186/s13023-020-01437-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 06/15/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fanconi anemia is a rare disease clinically characterized by malformations, bone marrow failure and an increased risk of solid tumors and hematologic malignancies. The only therapies available are hematopoietic stem cell transplantation for bone marrow failure or leukemia, and surgical resection for solid tumors. Therefore, there is still an urgent need for new therapeutic options. With this aim, we developed a novel high-content cell-based screening assay to identify drugs with therapeutic potential in FA. RESULTS A TALEN-mediated FANCA-deficient U2OS cell line was stably transfected with YFP-FANCD2 fusion protein. These cells were unable to form fluorescent foci or to monoubiquitinate endogenous or exogenous FANCD2 upon DNA damage and were more sensitive to mitomycin C when compared to the parental wild type counterpart. FANCA correction by retroviral infection restored the cell line's ability to form FANCD2 foci and ubiquitinate FANCD2. The feasibility of this cell-based system was interrogated in a high content screening of 3802 compounds, including a Prestwick library of 1200 FDA-approved drugs. The potential hits identified were then individually tested for their ability to rescue FANCD2 foci and monoubiquitination, and chromosomal stability in the absence of FANCA. CONCLUSIONS While, unfortunately, none of the compounds tested were able to restore cellular FANCA-deficiency, our study shows the potential capacity to screen large compound libraries in the context of Fanconi anemia therapeutics in an optimized and cost-effective platform.
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Affiliation(s)
- Helena Montanuy
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Cristina Camps-Fajol
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain.,Join Research Unit on Genomic Medicine UAB-Sant Pau, Biomedical Research Institute, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Jordi Carreras-Puigvert
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain.,Join Research Unit on Genomic Medicine UAB-Sant Pau, Biomedical Research Institute, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades raras, Barcelona, Spain
| | - Maria Häggblad
- Division of Translational Medicine and Chemical Biology, Science for Life Laboratory, Department of Molecular Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Currently at Division of Genome Biology, Science for Life Laboratory, Department of Molecular Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Bo Lundgren
- Department of Biochemistry and Biophysics, SciLifelab, Stockholm University, Stockholm, SE, Sweden
| | - Miriam Aza-Carmona
- Institute of Medical and Molecular Genetics and Skeletal dysplasia multidisciplinary Unit, Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPaz, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
| | - Thomas Helleday
- Division of Translational Medicine and Chemical Biology, Science for Life Laboratory, Department of Molecular Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jordi Minguillón
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades raras, Barcelona, Spain.,Genetics Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Jordi Surrallés
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain. .,Join Research Unit on Genomic Medicine UAB-Sant Pau, Biomedical Research Institute, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades raras, Barcelona, Spain. .,Genetics Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.
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Association of the Epithelial-Mesenchymal Transition (EMT) with Cisplatin Resistance. Int J Mol Sci 2020; 21:ijms21114002. [PMID: 32503307 PMCID: PMC7312011 DOI: 10.3390/ijms21114002] [Citation(s) in RCA: 147] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/14/2020] [Accepted: 05/26/2020] [Indexed: 02/08/2023] Open
Abstract
Therapy resistance is a characteristic of cancer cells that significantly reduces the effectiveness of drugs. Despite the popularity of cisplatin (CP) as a chemotherapeutic agent, which is widely used in the treatment of various types of cancer, resistance of cancer cells to CP chemotherapy has been extensively observed. Among various reported mechanism(s), the epithelial–mesenchymal transition (EMT) process can significantly contribute to chemoresistance by converting the motionless epithelial cells into mobile mesenchymal cells and altering cell–cell adhesion as well as the cellular extracellular matrix, leading to invasion of tumor cells. By analyzing the impact of the different molecular pathways such as microRNAs, long non-coding RNAs, nuclear factor-κB (NF-ĸB), phosphoinositide 3-kinase-related protein kinase (PI3K)/Akt, mammalian target rapamycin (mTOR), and Wnt, which play an important role in resistance exhibited to CP therapy, we first give an introduction about the EMT mechanism and its role in drug resistance. We then focus specifically on the molecular pathways involved in drug resistance and the pharmacological strategies that can be used to mitigate this resistance. Overall, we highlight the various targeted signaling pathways that could be considered in future studies to pave the way for the inhibition of EMT-mediated resistance displayed by tumor cells in response to CP exposure.
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