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Sabnis N, Raut S, Nagarajan B, Kapic A, Dossou AS, Lothstein L, Fudala R, Bunnell BA, Lacko AG. A Spontaneous Assembling Lipopeptide Nanoconjugate Transporting the Anthracycline Drug N-Benzyladriamycin-14-valerate for Personalized Therapy of Ewing Sarcoma. Bioconjug Chem 2024; 35:187-202. [PMID: 38318778 DOI: 10.1021/acs.bioconjchem.3c00429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
To meet the current need for a tumor-selective, targeted therapy regimen associated with reduced toxicity, our laboratory has developed a spontaneously assembled nanostructure that resembles high-density lipoproteins (HDLs). These myristoyl-5A (MYR-5A) nanotransporters are designed to safely transport lipophilic pharmaceuticals, including a novel anthracycline drug (N-benzyladriamycin-14-valerate (AD198)). This formulation has been found to enhance the therapeutic efficacy and reduced toxicity of drugs in preclinical studies of 2D and 3D models of Ewing sarcoma (EWS) and cardiomyocytes. Our findings indicate that the MYR-5A/AD198 nanocomplex delivers its payload selectively to cancer cells via the scavenger receptor type B1 (SR-B1), thus providing a solid proof of concept for the development of an improved and highly effective, potentially personalized therapy for EWS while protecting against treatment-associated cardiotoxicity.
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Affiliation(s)
- Nirupama Sabnis
- Lipoprotein Drug Delivery Research Laboratory, Department of Microbiology, Immunology & Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - Sangram Raut
- Department of Physiology and Anatomy, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - Bhavani Nagarajan
- North Texas Research Eye Institute, Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - Ammar Kapic
- Lipoprotein Drug Delivery Research Laboratory, Department of Microbiology, Immunology & Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - Akpedje Serena Dossou
- Lipoprotein Drug Delivery Research Laboratory, Department of Microbiology, Immunology & Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - Leonard Lothstein
- Department of Pathology and Laboratory Medicine, The University of Tennessee Health Science Center, Memphis, Tennessee 38103, United States
| | - Rafal Fudala
- Lipoprotein Drug Delivery Research Laboratory, Department of Microbiology, Immunology & Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - Bruce A Bunnell
- Lipoprotein Drug Delivery Research Laboratory, Department of Microbiology, Immunology & Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - Andras G Lacko
- Lipoprotein Drug Delivery Research Laboratory, Department of Microbiology, Immunology & Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
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Eghtedari AR, Vaezi MA, Safari E, Salimi V, Safizadeh B, Babaheidarian P, Abiri A, Mahdinia E, Alireza Mirzaei, Mokhles P, Tavakoli-Yaraki M. The expression changes of PD-L1 and immune response mediators are related to the severity of primary bone tumors. Sci Rep 2023; 13:20474. [PMID: 37993664 PMCID: PMC10665336 DOI: 10.1038/s41598-023-47996-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 11/21/2023] [Indexed: 11/24/2023] Open
Abstract
The expression pattern, diagnostic value, and association of PD-L1, IFN-γ and TGF-β with bone tumor type, severity, and relapse are determined in this study. 300 human samples from patients with osteosarcoma, Ewing sarcoma, and GCT were enrolled. The PD-L1 gene and protein expression were assessed by qRT-PCR and immunohistochemistry, respectively. ELISA and flow cytometry was used to detect cytokines and CD4/CD8 T cell percentages, respectively. A considerable increase in PD-L1 level was detected in bone tumor tissues at both gene and protein levels that was considerable in osteosarcoma and Ewing sarcoma. A positive correlation was detected regarding the PD-L1 and tumor metastasis and recurrence in osteosarcoma and Ewing sarcoma. The increased IFN-γ level was detected in patients with metastatic, and recurrent osteosarcoma tumors that were in accordance with the level of TGF-β in these samples. The simultaneous elevation of IFN-γ and TGF-β was detected in Ewing sarcoma and GCT, also the CD4 + /CD8 + ratio was decreased significantly in patients with osteosarcoma compared to GCT tumors. The elevated levels of PD-L1, TGF- β, and IFN-γ were associated with bone tumor severity that can provide insights into the possible role of this axis in promoting immune system escape, suppression, and tumor invasion.
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Affiliation(s)
- Amir Reza Eghtedari
- Department of Biochemistry, School of Medicine, Iran University of Medical Sciences, P.O. Box: 1449614535, Tehran, Iran
| | - Mohammad Amin Vaezi
- Department of Biochemistry, School of Medicine, Iran University of Medical Sciences, P.O. Box: 1449614535, Tehran, Iran
| | - Elaheh Safari
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Vahid Salimi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Banafsheh Safizadeh
- Department of Biochemistry, School of Medicine, Iran University of Medical Sciences, P.O. Box: 1449614535, Tehran, Iran
| | - Pegah Babaheidarian
- Department of Pathology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Amene Abiri
- Department of Obstetrics and Gynecology, Tehran University of Medical Sciences, Tehran, Iran
| | - Elmira Mahdinia
- Department of Biochemistry, School of Medicine, Iran University of Medical Sciences, P.O. Box: 1449614535, Tehran, Iran
| | - Alireza Mirzaei
- Bone and Joint Reconstruction Research Center, Shafa Orthopedic Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Parisa Mokhles
- School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Masoumeh Tavakoli-Yaraki
- Department of Biochemistry, School of Medicine, Iran University of Medical Sciences, P.O. Box: 1449614535, Tehran, Iran.
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3
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Mancarella C, Morrione A, Scotlandi K. PROTAC-Based Protein Degradation as a Promising Strategy for Targeted Therapy in Sarcomas. Int J Mol Sci 2023; 24:16346. [PMID: 38003535 PMCID: PMC10671294 DOI: 10.3390/ijms242216346] [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: 10/13/2023] [Revised: 11/10/2023] [Accepted: 11/11/2023] [Indexed: 11/26/2023] Open
Abstract
Sarcomas are heterogeneous bone and soft tissue cancers representing the second most common tumor type in children and adolescents. Histology and genetic profiling discovered more than 100 subtypes, which are characterized by peculiar molecular vulnerabilities. However, limited therapeutic options exist beyond standard therapy and clinical benefits from targeted therapies were observed only in a minority of patients with sarcomas. The rarity of these tumors, paucity of actionable mutations, and limitations in the chemical composition of current targeted therapies hindered the use of these approaches in sarcomas. Targeted protein degradation (TPD) is an innovative pharmacological modality to directly alter protein abundance with promising clinical potential in cancer, even for undruggable proteins. TPD is based on the use of small molecules called degraders or proteolysis-targeting chimeras (PROTACs), which trigger ubiquitin-dependent degradation of protein of interest. In this review, we will discuss major features of PROTAC and PROTAC-derived genetic systems for target validation and cancer treatment and focus on the potential of these approaches to overcome major issues connected to targeted therapies in sarcomas, including drug resistance, target specificity, and undruggable targets. A deeper understanding of these strategies might provide new fuel to drive molecular and personalized medicine to sarcomas.
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Affiliation(s)
- Caterina Mancarella
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
| | - Andrea Morrione
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA;
| | - Katia Scotlandi
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
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4
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Dupuy M, Lamoureux F, Mullard M, Postec A, Regnier L, Baud’huin M, Georges S, Brounais-Le Royer B, Ory B, Rédini F, Verrecchia F. Ewing sarcoma from molecular biology to the clinic. Front Cell Dev Biol 2023; 11:1248753. [PMID: 37752913 PMCID: PMC10518617 DOI: 10.3389/fcell.2023.1248753] [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: 06/27/2023] [Accepted: 08/30/2023] [Indexed: 09/28/2023] Open
Abstract
In Europe, with an incidence of 7.5 cases per million, Ewing sarcoma (ES) is the second most common primary malignant bone tumor in children, adolescents and young adults, after osteosarcoma. Since the 1980s, conventional treatment has been based on the use of neoadjuvant and adjuvant chemotherapeutic agents combined with surgical resection of the tumor when possible. These treatments have increased the patient survival rate to 70% for localized forms, which drops drastically to less than 30% when patients are resistant to chemotherapy or when pulmonary metastases are present at diagnosis. However, the lack of improvement in these survival rates over the last decades points to the urgent need for new therapies. Genetically, ES is characterized by a chromosomal translocation between a member of the FET family and a member of the ETS family. In 85% of cases, the chromosomal translocation found is (11; 22) (q24; q12), between the EWS RNA-binding protein and the FLI1 transcription factor, leading to the EWS-FLI1 fusion protein. This chimeric protein acts as an oncogenic factor playing a crucial role in the development of ES. This review provides a non-exhaustive overview of ES from a clinical and biological point of view, describing its main clinical, cellular and molecular aspects.
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Affiliation(s)
- Maryne Dupuy
- Nantes Université, Inserm UMR 1307, CNRS UMR 6075, CRCI2NA, Université d'Angers, Nantes, France
| | | | | | | | | | | | | | | | | | | | - Franck Verrecchia
- Nantes Université, Inserm UMR 1307, CNRS UMR 6075, CRCI2NA, Université d'Angers, Nantes, France
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Wood GE, Graves LA, Rubin EM, Reed DR, Riedel RF, Strauss SJ. Bad to the Bone: Emerging Approaches to Aggressive Bone Sarcomas. Am Soc Clin Oncol Educ Book 2023; 43:e390306. [PMID: 37220319 DOI: 10.1200/edbk_390306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Bone sarcomas are rare heterogeneous tumors that affect patients of all ages including children, adolescent young adults, and older adults. They include many aggressive subtypes and patient groups with poor outcomes, poor access to clinical trials, and lack of defined standard therapeutic strategies. Conventional chondrosarcoma remains a surgical disease, with no defined role for cytotoxic therapy and no approved targeted systemic therapies. Here, we discuss promising novel targets and strategies undergoing evaluation in clinical trials. Multiagent chemotherapy has greatly improved outcomes for patients with Ewing sarcoma (ES) and osteosarcoma, but management of those with high-risk or recurrent disease remains challenging and controversial. We describe the impact of international collaborative trials, such as the rEECur study, that aim to define optimal treatment strategies for those with recurrent, refractory ES, and evidence for high-dose chemotherapy with stem-cell support. We also discuss current and emerging strategies for other small round cell sarcomas, such as CIC-rearranged, BCOR-rearranged tumors, and the evaluation of emerging novel therapeutics and trial designs that may offer a new paradigm to improve survival in these aggressive tumors with notoriously bad (to the bone) outcomes.
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Affiliation(s)
- Georgina E Wood
- Department of Oncology, University College London Hospitals NHS Trust, UCL Cancer Institute, London, United Kingdom
| | - Laurie A Graves
- Division of Hematology/Oncology, Department of Pediatrics, Duke University, Durham, NC
| | - Elyssa M Rubin
- Division of Oncology, Children's Hospital of Orange County, Orange, CA
| | - Damon R Reed
- Department of Individualized Cancer Management, Moffitt Cancer Center, Tampa, FL
| | - Richard F Riedel
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, Durham, NC
| | - Sandra J Strauss
- Department of Oncology, University College London Hospitals NHS Trust, UCL Cancer Institute, London, United Kingdom
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6
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Anderson PM, Tu ZJ, Kilpatrick SE, Trucco M, Hanna R, Chan T. Routine EWS Fusion Analysis in the Oncology Clinic to Identify Cancer-Specific Peptide Sequence Patterns That Span Breakpoints in Ewing Sarcoma and DSRCT. Cancers (Basel) 2023; 15:cancers15051623. [PMID: 36900411 PMCID: PMC10001040 DOI: 10.3390/cancers15051623] [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: 01/18/2023] [Revised: 02/14/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
(1) Background: EWS fusion genes are associated with Ewing sarcoma and other Ewing family tumors including desmoplastic small round tumor, DSRCT. We utilize a clinical genomics workflow to reveal real-world frequencies of EWS fusion events, cataloging events that are similar, or divergent at the EWS breakpoint. (2) Methods: EWS fusion events from our next-generation sequencing panel (NGS) samples were first sorted by breakpoint or fusion junctions to map out the frequency of breakpoints. Fusion results were illustrated as in-frame fusion peptides involving EWS and a partner gene. (3) Results: From 2471 patient pool samples for fusion analysis at the Cleveland Clinic Molecular Pathology Laboratory, we identified 182 fusion samples evolved with the EWS gene. They are clustered in several breakpoints: chr22:29683123 (65.9%), and chr22:29688595 (2.7%). About 3/4 of Ewing sarcoma and DSRCT tumors have an identical EWS breakpoint motif at Exon 7 (SQQSSSYGQQ-) fused to a specific part of FLI1 (NPSYDSVRRG or-SSLLAYNTSS), ERG (NLPYEPPRRS), FEV (NPVGDGLFKD) or WT1 (SEKPYQCDFK). Our method also worked with Caris transcriptome data, too. Our primary clinical utility is to use this information to identify neoantigens for therapeutic purposes. (4) Conclusions and future perspectives: our method allows interpretation of what peptides result from the in-frame translation of EWS fusion junctions. These sequences, coupled with HLA-peptide binding data, are used to identify potential sequences of cancer-specific immunogenic peptides for Ewing sarcoma or DSRCT patients. This information may also be useful for immune monitoring (e.g., circulating T-cells with fusion-peptide specificity) to detect vaccine candidates, responses, or residual disease.
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Affiliation(s)
- Peter M. Anderson
- Pediatric Hematology and Bone Marrow Transplant, Pediatric and Taussig Cancer Institutes, Cleveland Clinic, Cleveland, OH 44195, USA
- Correspondence: ; Tel.: +1-216-308-2706
| | - Zheng Jin Tu
- Bioinformatics, Molecular Pathology and Cytogenomics, Department of Laboratory Medicine, Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Scott E. Kilpatrick
- Orthopedic Pathology and Center for ePathology, Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Matteo Trucco
- Pediatric Hematology and Bone Marrow Transplant, Pediatric and Taussig Cancer Institutes, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Rabi Hanna
- Pediatric Hematology and Bone Marrow Transplant, Pediatric and Taussig Cancer Institutes, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Timothy Chan
- Center for Immuno-Oncology, Department of Radiation Oncology, Taussig Cancer Institute and Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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7
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Therapeutic targeting the oncogenic driver EWSR1::FLI1 in Ewing sarcoma through inhibition of the FACT complex. Oncogene 2023; 42:11-25. [PMID: 36357572 DOI: 10.1038/s41388-022-02533-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 11/12/2022]
Abstract
EWS/ETS fusion transcription factors, most commonly EWSR1::FLI1, drives initiation and progression of Ewing sarcoma (EwS). Even though direct targeting EWSR1::FLI1 is a formidable challenge, epigenetic/transcriptional modulators have been proved to be promising therapeutic targets for indirectly disrupting its expression and/or function. Here, we identified structure-specific recognition protein 1 (SSRP1), a subunit of the Facilitates Chromatin Transcription (FACT) complex, to be an essential tumor-dependent gene directly induced by EWSR1::FLI1 in EwS. The FACT-targeted drug CBL0137 exhibits potent therapeutic efficacy against multiple EwS preclinical models both in vitro and in vivo. Mechanistically, SSRP1 and EWSR1::FLI1 form oncogenic positive feedback loop via mutual transcriptional regulation and activation, and cooperatively promote cell cycle/DNA replication process and IGF1R-PI3K-AKT-mTOR pathway to drive EwS oncogenesis. The FACT inhibitor drug CBL0137 effectively targets the EWSR1::FLI1-FACT circuit, resulting in transcriptional disruption of EWSR1::FLI1, SSRP1 and their downstream effector oncogenic signatures. Our study illustrates a crucial role of the FACT complex in facilitating the expression and function of EWSR1::FLI1 and demonstrates FACT inhibition as a novel and effective epigenetic/transcriptional-targeted therapeutic strategy against EwS, providing preclinical support for adding EwS to CBL0137's future clinical trials.
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8
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Weiss KR, Bailey KM. A Druggable Rheostat for Ewing Sarcoma? Clin Cancer Res 2022; 28:4360-4362. [PMID: 35921177 PMCID: PMC9588653 DOI: 10.1158/1078-0432.ccr-22-1794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/16/2022] [Accepted: 07/25/2022] [Indexed: 01/26/2023]
Abstract
The posterior HOXD enhancer is an EWSR1::FLI1-dependent regulator of HOXD13 expression in Ewing sarcoma. HOXD13 expression promotes a mesenchymal cell state. Through antagonistic transcriptional programs, EWSR1::FLI1 and HOXD13 serve as master regulators of Ewing cell plasticity. Targeting Ewing cells as they exist in/transition between mesenchymal states is a priority. See related article by Apfelbaum et al., p. 4466.
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Affiliation(s)
- Kurt R. Weiss
- Department of Orthopedic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kelly M. Bailey
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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9
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Cancer: A pathologist's journey from morphology to molecular. Med J Armed Forces India 2022; 78:255-263. [DOI: 10.1016/j.mjafi.2022.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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10
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Hamilton G. Comparative characteristics of small cell lung cancer and Ewing's sarcoma: a narrative review. Transl Lung Cancer Res 2022; 11:1185-1198. [PMID: 35832443 PMCID: PMC9271444 DOI: 10.21037/tlcr-22-58] [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: 01/19/2022] [Accepted: 05/23/2022] [Indexed: 12/24/2022]
Abstract
Background and Objective Small cell lung cancer (SCLC) and Ewing's sarcoma (ES) at the disseminated stage are not amenable to therapy and have a dismal prognosis with low survival rates. Despite representing different tumor entities, treatment for both malignancies relies on cytotoxic chemotherapy that has not considerably changed for the past decades. The genomic background has been extensively studied and found to comprise inactivation of p53 and RB1 in case of SCLC and EWSR1/FLI1 rearrangement in case of ES resulting in aggressive tumors in adults with heavy tobacco consumption and as bone tumor in juveniles, respectively. New therapeutic modalities are urgently needed to improve the outcomes of both tumor entities, especially in patients with metastatic disease or recurrences. This review summarizes the common cell biologic and clinical characteristics of difficult-to-treat SCLC and ES and discusses their refractoriness and options to improve the therapeutic efficacy. Methods PubMed and Euro PMC were searched from January 1st, 2012 to January 16th, 2022 using the following key words: "SCLC", "Ewing´s sarcoma", "Genomics" and "Chemoresistance" as well as own work. Key Content and Findings Therapy of SCLC and ES involves the use of undirected cytotoxic drugs in multimodal chemotherapy and administration of topotecan for 2nd line SCLC regimens. Despite highly aggressive chemotherapies, outcomes are dismal for patients with disseminated tumors. A host of unrelated drugs and targeted therapeutics have failed to result in progress for the patients and the underlying mechanisms of chemoresistance are still not clear. Identification of chemoresistance-reversing modulators in vitro and patient-derived xenografts of SCLC and ES has not translated into new therapies. Conclusions The global chemoresistance of SCLC and ES may be explained by physiological resistance at the tumor level and formation of larger spheroids that contain quiescent and hypoxic tumor cells in regions that occlude therapeutics. This type of chemoresistance is difficult to overcome and prevent the accumulation of effective drug concentration at the tumor cell level to a significant degree leaving therapeutic interventions of any kind ineffective.
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Affiliation(s)
- Gerhard Hamilton
- Institute of Pharmacology, Medical University of Vienna, Vienna, Austria
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11
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Hartung M, Anastasi E, Mamdouh ZM, Nogales C, Schmidt HHHW, Baumbach J, Zolotareva O, List M. Cancer driver drug interaction explorer. Nucleic Acids Res 2022; 50:W138-W144. [PMID: 35580047 PMCID: PMC9252786 DOI: 10.1093/nar/gkac384] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/06/2022] [Accepted: 04/29/2022] [Indexed: 12/16/2022] Open
Abstract
Cancer is a heterogeneous disease characterized by unregulated cell growth and promoted by mutations in cancer driver genes some of which encode suitable drug targets. Since the distinct set of cancer driver genes can vary between and within cancer types, evidence-based selection of drugs is crucial for targeted therapy following the precision medicine paradigm. However, many putative cancer driver genes can not be targeted directly, suggesting an indirect approach that considers alternative functionally related targets in the gene interaction network. Once potential drug targets have been identified, it is essential to consider all available drugs. Since tools that offer support for systematic discovery of drug repurposing candidates in oncology are lacking, we developed CADDIE, a web application integrating six human gene-gene and four drug-gene interaction databases, information regarding cancer driver genes, cancer-type specific mutation frequencies, gene expression information, genetically related diseases, and anticancer drugs. CADDIE offers access to various network algorithms for identifying drug targets and drug repurposing candidates. It guides users from the selection of seed genes to the identification of therapeutic targets or drug candidates, making network medicine algorithms accessible for clinical research. CADDIE is available at https://exbio.wzw.tum.de/caddie/ and programmatically via a python package at https://pypi.org/project/caddiepy/.
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Affiliation(s)
- Michael Hartung
- Institute for Computational Systems Biology, University of Hamburg, 22607 Hamburg, Germany
| | - Elisa Anastasi
- School of Computing, Newcastle University, 2308 Newcastle upon Tyne, UK
| | - Zeinab M Mamdouh
- Department of Pharmacology and Personalised Medicine, Maastricht University, 6229 Maastricht, Netherlands.,Department of Pharmacology and Toxicology, Faculty of Pharmacy, Zagazig University, 44519 Zagazig, Egypt
| | - Cristian Nogales
- Department of Pharmacology and Personalised Medicine, Maastricht University, 6229 Maastricht, Netherlands
| | - Harald H H W Schmidt
- Department of Pharmacology and Personalised Medicine, Maastricht University, 6229 Maastricht, Netherlands
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, 22607 Hamburg, Germany.,Computational Biomedicine Lab, Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark
| | - Olga Zolotareva
- Institute for Computational Systems Biology, University of Hamburg, 22607 Hamburg, Germany.,Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Markus List
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
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