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Wang S, Tong S, Jin X, Li N, Dang P, Sui Y, Liu Y, Wang D. Single-cell RNA sequencing analysis of the retina under acute high intraocular pressure. Neural Regen Res 2024; 19:2522-2531. [PMID: 38526288 PMCID: PMC11090430 DOI: 10.4103/1673-5374.389363] [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: 05/24/2023] [Revised: 07/27/2023] [Accepted: 09/13/2023] [Indexed: 03/26/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202419110-00032/figure1/v/2024-03-08T184507Z/r/image-tiff High intraocular pressure causes retinal ganglion cell injury in primary and secondary glaucoma diseases, yet the molecular landscape characteristics of retinal cells under high intraocular pressure remain unknown. Rat models of acute hypertension ocular pressure were established by injection of cross-linked hyaluronic acid hydrogel (Healaflow®). Single-cell RNA sequencing was then used to describe the cellular composition and molecular profile of the retina following high intraocular pressure. Our results identified a total of 12 cell types, namely retinal pigment epithelial cells, rod-photoreceptor cells, bipolar cells, Müller cells, microglia, cone-photoreceptor cells, retinal ganglion cells, endothelial cells, retinal progenitor cells, oligodendrocytes, pericytes, and fibroblasts. The single-cell RNA sequencing analysis of the retina under acute high intraocular pressure revealed obvious changes in the proportions of various retinal cells, with ganglion cells decreased by 23%. Hematoxylin and eosin staining and TUNEL staining confirmed the damage to retinal ganglion cells under high intraocular pressure. We extracted data from retinal ganglion cells and analyzed the retinal ganglion cell cluster with the most distinct expression. We found upregulation of the B3gat2 gene, which is associated with neuronal migration and adhesion, and downregulation of the Tsc22d gene, which participates in inhibition of inflammation. This study is the first to reveal molecular changes and intercellular interactions in the retina under high intraocular pressure. These data contribute to understanding of the molecular mechanism of retinal injury induced by high intraocular pressure and will benefit the development of novel therapies.
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Affiliation(s)
- Shaojun Wang
- Division of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, China
| | - Siti Tong
- Division of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, China
| | - Xin Jin
- Division of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, China
| | - Na Li
- Division of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, China
| | - Pingxiu Dang
- Division of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, China
| | - Yang Sui
- Division of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, China
| | - Ying Liu
- Department of Ophthalmology, Beijing Rehabilitation Hospital, Capital Medical University, Beijing, China
| | - Dajiang Wang
- Division of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, China
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2
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Luo W, Hoang H, Miller KE, Zhu H, Xu S, Mo X, Garfinkle EAR, Costello H, Wijeratne S, Chemnitz W, Gandhi R, Liao Y, Ayello J, Gardenswartz A, Rosenblum JM, Cassady KA, Mardis ER, Lee DA, Cripe TP, Cairo MS. Combinatorial macrophage induced innate immunotherapy against Ewing sarcoma: Turning "Two Keys" simultaneously. J Exp Clin Cancer Res 2024; 43:193. [PMID: 38992659 PMCID: PMC11238356 DOI: 10.1186/s13046-024-03093-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Accepted: 06/06/2024] [Indexed: 07/13/2024] Open
Abstract
BACKGROUND Macrophages play important roles in phagocytosing tumor cells. However, tumors escape macrophage phagocytosis in part through the expression of anti-phagocytic signals, most commonly CD47. In Ewing sarcoma (ES), we found that tumor cells utilize dual mechanisms to evade macrophage clearance by simultaneously over-expressing CD47 and down-regulating cell surface calreticulin (csCRT), the pro-phagocytic signal. Here, we investigate the combination of a CD47 blockade (magrolimab, MAG) to inhibit the anti-phagocytic signal and a chemotherapy regimen (doxorubicin, DOX) to enhance the pro-phagocytic signal to induce macrophage phagocytosis of ES cells in vitro and inhibit tumor growth and metastasis in vivo. METHODS Macrophages were derived from human peripheral blood monocytes by granulocyte-macrophage colony-stimulating factor (GM-CSF) and macrophage colony-stimulating factor (M-CSF). Flow cytometry- and microscopy-based in-vitro phagocytosis assays were performed to evaluate macrophage phagocytosis of ES cells. Annexin-V assay was performed to evaluate apoptosis. CD47 was knocked out by CRISPR/Cas9 approach. ES cell-based and patient-derived-xenograft (PDX)-based mouse models were utilized to assess the effects of MAG and/or DOX on ES tumor development and animal survival. RNA-Seq combined with CIBERSORTx analysis was utilized to identify changes in tumor cell transcriptome and tumor infiltrating immune cell profiling in MAG and/or DOX treated xenograft tumors. RESULTS We found that MAG significantly increased macrophage phagocytosis of ES cells in vitro (p < 0.01) and had significant effect on reducing tumor burden (p < 0.01) and increasing survival in NSG mouse model (p < 0.001). The csCRT level on ES cells was significantly enhanced by DOX in a dose- and time-dependent manner (p < 0.01). Importantly, DOX combined with MAG significantly enhanced macrophage phagocytosis of ES cells in vitro (p < 0.01) and significantly decreased tumor burden (p < 0.01) and lung metastasis (p < 0.0001) and extended animal survival in vivo in two different mouse models of ES (p < 0.0001). Furthermore, we identified CD38, CD209, CD163 and CD206 as potential markers for ES-phagocytic macrophages. Moreover, we found increased M2 macrophage infiltration and decreased expression of Cd209 in the tumor microenvironment of MAG and DOX combinatorial therapy treated tumors. CONCLUSIONS By turning "two keys" simultaneously to reactivate macrophage phagocytic activity, our data demonstrated an effective and highly translatable alternative therapeutic approach utilizing innate (tumor associated macrophages) immunotherapy against high-risk metastatic ES.
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Affiliation(s)
- Wen Luo
- Department of Pediatrics, New York Medical College, 15 Dana Road, Valhalla, NY, 10595, USA.
- Department of Pathology, Immunology and Microbiology, New York Medical College, Valhalla, NY, 10595, USA.
| | - Hai Hoang
- Department of Pediatrics, New York Medical College, 15 Dana Road, Valhalla, NY, 10595, USA
| | - Katherine E Miller
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Hongwen Zhu
- Department of Pediatrics, New York Medical College, 15 Dana Road, Valhalla, NY, 10595, USA
| | - Serena Xu
- James J. Peters Veterans Affairs Medical Center, Bronx, NY, USA
| | - Xiaokui Mo
- Department of Biomedical Informatics, Center for Biostatistics, The Ohio State University, Columbus, OH, USA
| | - Elizabeth A R Garfinkle
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Heather Costello
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Saranga Wijeratne
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Wiebke Chemnitz
- Department of Medicine, New York Medical College, Valhalla, NY, USA
| | | | - Yanling Liao
- Department of Pediatrics, New York Medical College, 15 Dana Road, Valhalla, NY, 10595, USA
| | - Janet Ayello
- Department of Pediatrics, New York Medical College, 15 Dana Road, Valhalla, NY, 10595, USA
| | - Aliza Gardenswartz
- Department of Pediatrics, New York Medical College, 15 Dana Road, Valhalla, NY, 10595, USA
| | - Jeremy M Rosenblum
- Department of Pediatrics, New York Medical College, 15 Dana Road, Valhalla, NY, 10595, USA
| | - Kevin A Cassady
- Center for Childhood Cancer Research, Nationwide Children's Hospital, Columbus, OH, USA
| | - Elaine R Mardis
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
- Department of Neurosurgery, The Ohio State University, Columbus, OH, USA
| | - Dean A Lee
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Timothy P Cripe
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
- Center for Childhood Cancer Research, Nationwide Children's Hospital, Columbus, OH, USA
| | - Mitchell S Cairo
- Department of Pediatrics, New York Medical College, 15 Dana Road, Valhalla, NY, 10595, USA.
- Department of Pathology, Immunology and Microbiology, New York Medical College, Valhalla, NY, 10595, USA.
- Department of Medicine, New York Medical College, Valhalla, NY, USA.
- Department of Cell Biology and Anatomy, New York Medical College, Valhalla, NY, USA.
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3
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Doll S, Schweizer L, Bollwein C, Steiger K, Pfarr N, Walker M, Wörtler K, Knebel C, von Eisenhart-Rothe R, Hartmann W, Weichert W, Mann M, Kuhn PH, Specht K. Proteomic Characterization of Undifferentiated Small Round Cell Sarcomas With EWSR1 and CIC::DUX4 Translocations Reveals Diverging Tumor Biology and Distinct Diagnostic Markers. Mod Pathol 2024; 37:100511. [PMID: 38705279 DOI: 10.1016/j.modpat.2024.100511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 04/11/2024] [Accepted: 04/26/2024] [Indexed: 05/07/2024]
Abstract
Undifferentiated small round cell sarcomas (USRS) of bone and soft tissue are a group of tumors with heterogenic genomic alterations sharing similar morphology. In the present study, we performed a comparative large-scale proteomic analysis of USRS (n = 42) with diverse genomic translocations including classic Ewing sarcomas with EWSR1::FLI1 fusions (n = 24) or EWSR1::ERG fusions (n = 4), sarcomas with an EWSR1 rearrangement (n = 2), CIC::DUX4 fusion (n = 8), as well as tumors classified as USRS with no genetic data available (n = 4). Proteins extracted from formalin-fixed, paraffin-embedded pretherapeutic biopsies were analyzed qualitatively and quantitatively using shotgun mass spectrometry (MS). More than 8000 protein groups could be quantified using data-independent acquisition. Unsupervised hierarchical cluster analysis based on proteomic data allowed stratification of the 42 cases into distinct groups reflecting the different molecular genotypes. Protein signatures that significantly correlated with the respective genomic translocations were identified and used to generate a heatmap of all 42 sarcomas with assignment of cases with unknown molecular genetic data to either the EWSR1- or CIC-rearranged groups. MS-based prediction of sarcoma subtypes was molecularly confirmed in 2 cases where next-generation sequencing was technically feasible. MS also detected proteins routinely used in the immunohistochemical approach for the differential diagnosis of USRS. BCL11B highly expressed in Ewing sarcomas, and BACH2 as well as ETS-1 highly expressed in CIC::DUX4-associated sarcomas, were among proteins identified by the present proteomic study, and were chosen for immunohistochemical confirmation of MS data in our study cohort. Differential expressions of these 3 markers in the 2 genetic groups were further validated in an independent cohort of n = 34 USRS. Finally, our proteomic results point toward diverging signaling pathways in the different USRS subgroups.
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Affiliation(s)
- Sophia Doll
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Bavaria, Germany; OmicEra Diagnostics GmbH, Planegg, Bavaria, Germany
| | - Lisa Schweizer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Bavaria, Germany
| | | | - Katja Steiger
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Nicole Pfarr
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Maria Walker
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Klaus Wörtler
- Musculoskeletal Radiology Section, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Carolin Knebel
- Department of Orthopaedic Surgery, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | | | | | - Wilko Weichert
- Institute of Pathology, Technical University of Munich, Munich, Germany; German Cancer Consortium (DKTK), Partner-site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Bavaria, Germany
| | - Peer-Hendrik Kuhn
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Katja Specht
- Institute of Pathology, Technical University of Munich, Munich, Germany.
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4
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Fonódi M, Nagy L, Boratkó A. Role of Protein Phosphatases in Tumor Angiogenesis: Assessing PP1, PP2A, PP2B and PTPs Activity. Int J Mol Sci 2024; 25:6868. [PMID: 38999976 PMCID: PMC11241275 DOI: 10.3390/ijms25136868] [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: 05/16/2024] [Revised: 06/19/2024] [Accepted: 06/20/2024] [Indexed: 07/14/2024] Open
Abstract
Tumor angiogenesis, the formation of new blood vessels to support tumor growth and metastasis, is a complex process regulated by a multitude of signaling pathways. Dysregulation of signaling pathways involving protein kinases has been extensively studied, but the role of protein phosphatases in angiogenesis within the tumor microenvironment remains less explored. However, among angiogenic pathways, protein phosphatases play critical roles in modulating signaling cascades. This review provides a comprehensive overview of the involvement of protein phosphatases in tumor angiogenesis, highlighting their diverse functions and mechanisms of action. Protein phosphatases are key regulators of cellular signaling pathways by catalyzing the dephosphorylation of proteins, thereby modulating their activity and function. This review aims to assess the activity of the protein tyrosine phosphatases and serine/threonine phosphatases. These phosphatases exert their effects on angiogenic signaling pathways through various mechanisms, including direct dephosphorylation of angiogenic receptors and downstream signaling molecules. Moreover, protein phosphatases also crosstalk with other signaling pathways involved in angiogenesis, further emphasizing their significance in regulating tumor vascularization, including endothelial cell survival, sprouting, and vessel maturation. In conclusion, this review underscores the pivotal role of protein phosphatases in tumor angiogenesis and accentuate their potential as therapeutic targets for anti-angiogenic therapy in cancer.
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Affiliation(s)
| | | | - Anita Boratkó
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (M.F.); (L.N.)
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5
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Gonzalez-Llerena JL, Espinosa-Rodriguez BA, Treviño-Almaguer D, Mendez-Lopez LF, Carranza-Rosales P, Gonzalez-Barranco P, Guzman-Delgado NE, Romo-Mancillas A, Balderas-Renteria I. Cordycepin Triphosphate as a Potential Modulator of Cellular Plasticity in Cancer via cAMP-Dependent Pathways: An In Silico Approach. Int J Mol Sci 2024; 25:5692. [PMID: 38891880 PMCID: PMC11171877 DOI: 10.3390/ijms25115692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/14/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
Cordycepin, or 3'-deoxyadenosine, is an adenosine analog with a broad spectrum of biological activity. The key structural difference between cordycepin and adenosine lies in the absence of a hydroxyl group at the 3' position of the ribose ring. Upon administration, cordycepin can undergo an enzymatic transformation in specific tissues, forming cordycepin triphosphate. In this study, we conducted a comprehensive analysis of the structural features of cordycepin and its derivatives, contrasting them with endogenous purine-based metabolites using chemoinformatics and bioinformatics tools in addition to molecular dynamics simulations. We tested the hypothesis that cordycepin triphosphate could bind to the active site of the adenylate cyclase enzyme. The outcomes of our molecular dynamics simulations revealed scores that are comparable to, and superior to, those of adenosine triphosphate (ATP), the endogenous ligand. This interaction could reduce the production of cyclic adenosine monophosphate (cAMP) by acting as a pseudo-ATP that lacks a hydroxyl group at the 3' position, essential to carry out nucleotide cyclization. We discuss the implications in the context of the plasticity of cancer and other cells within the tumor microenvironment, such as cancer-associated fibroblast, endothelial, and immune cells. This interaction could awaken antitumor immunity by preventing phenotypic changes in the immune cells driven by sustained cAMP signaling. The last could be an unreported molecular mechanism that helps to explain more details about cordycepin's mechanism of action.
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Affiliation(s)
- Jose Luis Gonzalez-Llerena
- Laboratory of Molecular Pharmacology and Biological Models, School of Chemistry, Autonomous University of Nuevo Leon, San Nicolas de los Garza 66451, Mexico; (J.L.G.-L.); (B.A.E.-R.); (D.T.-A.); (P.G.-B.)
- Center for Research on Nutrition and Public Health, School of Public Health and Nutrition, Autonomous University of Nuevo Leon, Monterrey 66460, Mexico;
| | - Bryan Alejandro Espinosa-Rodriguez
- Laboratory of Molecular Pharmacology and Biological Models, School of Chemistry, Autonomous University of Nuevo Leon, San Nicolas de los Garza 66451, Mexico; (J.L.G.-L.); (B.A.E.-R.); (D.T.-A.); (P.G.-B.)
| | - Daniela Treviño-Almaguer
- Laboratory of Molecular Pharmacology and Biological Models, School of Chemistry, Autonomous University of Nuevo Leon, San Nicolas de los Garza 66451, Mexico; (J.L.G.-L.); (B.A.E.-R.); (D.T.-A.); (P.G.-B.)
| | - Luis Fernando Mendez-Lopez
- Center for Research on Nutrition and Public Health, School of Public Health and Nutrition, Autonomous University of Nuevo Leon, Monterrey 66460, Mexico;
| | - Pilar Carranza-Rosales
- Laboratory of Cell Biology, Northeast Biomedical Research Center, Mexican Social Security Institute, Monterrey 64720, Mexico;
| | - Patricia Gonzalez-Barranco
- Laboratory of Molecular Pharmacology and Biological Models, School of Chemistry, Autonomous University of Nuevo Leon, San Nicolas de los Garza 66451, Mexico; (J.L.G.-L.); (B.A.E.-R.); (D.T.-A.); (P.G.-B.)
| | - Nancy Elena Guzman-Delgado
- Health Research Division, High Specialty Medical Unit, Cardiology Hospital N. 34. Mexican Social Security Institute, Monterrey 64360, Mexico;
| | - Antonio Romo-Mancillas
- Computer Aided Drug Design and Synthesis Group, School of Chemistry, Autonomous University of Queretaro, Queretaro 76010, Mexico
| | - Isaias Balderas-Renteria
- Laboratory of Molecular Pharmacology and Biological Models, School of Chemistry, Autonomous University of Nuevo Leon, San Nicolas de los Garza 66451, Mexico; (J.L.G.-L.); (B.A.E.-R.); (D.T.-A.); (P.G.-B.)
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6
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Zhang H, Liu Y, Liu J, Chen J, Wang J, Hua H, Jiang Y. cAMP-PKA/EPAC signaling and cancer: the interplay in tumor microenvironment. J Hematol Oncol 2024; 17:5. [PMID: 38233872 PMCID: PMC10792844 DOI: 10.1186/s13045-024-01524-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024] Open
Abstract
Cancer is a complex disease resulting from abnormal cell growth that is induced by a number of genetic and environmental factors. The tumor microenvironment (TME), which involves extracellular matrix, cancer-associated fibroblasts (CAF), tumor-infiltrating immune cells and angiogenesis, plays a critical role in tumor progression. Cyclic adenosine monophosphate (cAMP) is a second messenger that has pleiotropic effects on the TME. The downstream effectors of cAMP include cAMP-dependent protein kinase (PKA), exchange protein activated by cAMP (EPAC) and ion channels. While cAMP can activate PKA or EPAC and promote cancer cell growth, it can also inhibit cell proliferation and survival in context- and cancer type-dependent manner. Tumor-associated stromal cells, such as CAF and immune cells, can release cytokines and growth factors that either stimulate or inhibit cAMP production within the TME. Recent studies have shown that targeting cAMP signaling in the TME has therapeutic benefits in cancer. Small-molecule agents that inhibit adenylate cyclase and PKA have been shown to inhibit tumor growth. In addition, cAMP-elevating agents, such as forskolin, can not only induce cancer cell death, but also directly inhibit cell proliferation in some cancer types. In this review, we summarize current understanding of cAMP signaling in cancer biology and immunology and discuss the basis for its context-dependent dual role in oncogenesis. Understanding the precise mechanisms by which cAMP and the TME interact in cancer will be critical for the development of effective therapies. Future studies aimed at investigating the cAMP-cancer axis and its regulation in the TME may provide new insights into the underlying mechanisms of tumorigenesis and lead to the development of novel therapeutic strategies.
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Affiliation(s)
- Hongying Zhang
- Cancer Center, Laboratory of Oncogene, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yongliang Liu
- Cancer Center, Laboratory of Oncogene, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jieya Liu
- Cancer Center, Laboratory of Oncogene, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jinzhu Chen
- Cancer Center, Laboratory of Oncogene, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jiao Wang
- School of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China
| | - Hui Hua
- Laboratory of Stem Cell Biology, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Yangfu Jiang
- Cancer Center, Laboratory of Oncogene, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
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7
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Luo W, Hoang H, Liao Y, Pan J, Ayello J, Cairo MS. A humanized orthotopic mouse model for preclinical evaluation of immunotherapy in Ewing sarcoma. Front Immunol 2023; 14:1277987. [PMID: 37868989 PMCID: PMC10587429 DOI: 10.3389/fimmu.2023.1277987] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 09/19/2023] [Indexed: 10/24/2023] Open
Abstract
The advent of novel cancer immunotherapy approaches is revolutionizing the treatment for cancer. Current small animal models for most cancers are syngeneic or genetically engineered mouse models or xenograft models based on immunodeficient mouse strains. These models have been limited in evaluating immunotherapy regimens due to the lack of functional human immune system. Development of animal models for bone cancer faces another challenge in the accessibility of tumor engraftment sites. Here, we describe a protocol to develop an orthotopic humanized mouse model for a bone and soft tissue sarcoma, Ewing sarcoma, by transplanting fresh human cord blood CD34+ hematopoietic stem cells into young NSG-SGM3 mice combined with subsequent Ewing sarcoma patient derived cell engraftment in the tibia of the humanized mice. We demonstrated early and robust reconstitution of human CD45+ leukocytes including T cells, B cells, natural killer cells and monocytes. Ewing sarcoma xenograft tumors successfully orthotopically engrafted in the humanized mice with minimal invasive procedures. We validated the translational utility of this orthotopic humanized model by evaluating the safety and efficacy of an immunotherapy antibody, magrolimab. Treatment with magrolimab induces CD47 blockade resulting in significantly decreased primary tumor growth, decreased lung metastasis and prolonged animal survival in the established humanized model. Furthermore, the humanized model recapitulated the dose dependent toxicity associated with the CD47 blockade as observed in patients in clinical trials. In conclusion, this orthotopic humanized mouse model of Ewing sarcoma represents an improved platform for evaluating immunotherapy in bone and soft tissue sarcoma, such as Ewing sarcoma. With careful design and optimization, this model is generalizable for other bone malignancies.
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Affiliation(s)
- Wen Luo
- Department of Pediatrics, New York Medical College, Valhalla, NY, United States
- Department of Pathology, Immunology and Microbiology, New York Medical College, Valhalla, NY, United States
| | - Hai Hoang
- Department of Pediatrics, New York Medical College, Valhalla, NY, United States
| | - Yanling Liao
- Department of Pediatrics, New York Medical College, Valhalla, NY, United States
| | - Jian Pan
- Department of Pediatrics, New York Medical College, Valhalla, NY, United States
| | - Janet Ayello
- Department of Pediatrics, New York Medical College, Valhalla, NY, United States
| | - Mitchell S. Cairo
- Department of Pediatrics, New York Medical College, Valhalla, NY, United States
- Department of Pathology, Immunology and Microbiology, New York Medical College, Valhalla, NY, United States
- Department of Medicine, New York Medical College, Valhalla, NY, United States
- Department of Cell Biology and Anatomy, New York Medical College, Valhalla, NY, United States
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8
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Magnusson MI, Agnarsson BA, Jonasson JG, Tryggvason T, Aeffner F, le Roux L, Magnusdottir DN, Gunnarsdottir HS, Alexíusdóttir KK, Gunnarsdottir K, Söebech E, Runarsdottir H, Jonsdottir EM, Kristinsdottir BS, Olafsson S, Knutsdottir H, Thorsteinsdottir U, Ulfarsson MO, Gudbjartsson DF, Saemundsdottir J, Magnusson OT, Norddahl GL, Watson JEV, Rafnar T, Lund SH, Stefansson K. Histopathology and levels of proteins in plasma associate with survival after colorectal cancer diagnosis. Br J Cancer 2023; 129:1142-1151. [PMID: 37596405 PMCID: PMC10539279 DOI: 10.1038/s41416-023-02374-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/15/2023] [Accepted: 07/18/2023] [Indexed: 08/20/2023] Open
Abstract
BACKGROUND The TNM system is used to assess prognosis after colorectal cancer (CRC) diagnosis. Other prognostic factors reported include histopathological assessments of the tumour, tumour mutations and proteins in the blood. As some of these factors are strongly correlated, it is important to evaluate the independent effects they may have on survival. METHODS Tumour samples from 2162 CRC patients were visually assessed for amount of tumour stroma, severity of lymphocytic infiltrate at the tumour margins and the presence of lymphoid follicles. Somatic mutations in the tumour were assessed for 2134 individuals. Pre-surgical levels of 4963 plasma proteins were measured in 128 individuals. The associations between these features and prognosis were inspected by a Cox Proportional Hazards Model (CPH). RESULTS Levels of stroma, lymphocytic infiltration and presence of lymphoid follicles all associate with prognosis, along with high tumour mutation burden, high microsatellite instability and TP53 and BRAF mutations. The somatic mutations are correlated with the histopathology and none of the somatic mutations associate with survival in a multivariate analysis. Amount of stroma and lymphocytic infiltration associate with local invasion of tumours. Elevated levels of two plasma proteins, CA-125 and PPP1R1A, associate with a worse prognosis. CONCLUSIONS Tumour stroma and lymphocytic infiltration variables are strongly associated with prognosis of CRC and capture the prognostic effects of tumour mutation status. CA-125 and PPP1R1A may be useful prognostic biomarkers in CRC.
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Affiliation(s)
- Magnus I Magnusson
- deCODE genetics/Amgen, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Bjarni A Agnarsson
- Department of Pathology, Landspitali University Hospital, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Jon G Jonasson
- Department of Pathology, Landspitali University Hospital, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Thordur Tryggvason
- Department of Pathology, Landspitali University Hospital, Reykjavik, Iceland
| | | | | | | | | | | | | | | | | | - Erna M Jonsdottir
- Department of Pathology, Landspitali University Hospital, Reykjavik, Iceland
| | | | | | | | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Magnus O Ulfarsson
- deCODE genetics/Amgen, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | | | | | - Sigrun H Lund
- deCODE genetics/Amgen, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE genetics/Amgen, Reykjavik, Iceland.
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland.
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9
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Wen J, Yi L, Wan L, Dong X. Prognostic value of GLCE and infiltrating immune cells in Ewing sarcoma. Heliyon 2023; 9:e19357. [PMID: 37662777 PMCID: PMC10474439 DOI: 10.1016/j.heliyon.2023.e19357] [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: 02/26/2023] [Revised: 08/10/2023] [Accepted: 08/20/2023] [Indexed: 09/05/2023] Open
Abstract
Background The prognostic value of D-glucuronyl C5-epimerase (GLCE) and mast cell infiltration in Ewing sarcoma (ES) has not been well specified and highlighted, which may facilitate survival prediction and treatment. Methods Several qualified datasets were downloaded from the GEO website. Common differentially expressed genes between normal subjects and ES patients in GSE17679, GSE45544, and GSE68776 were identified and screened by multiple algorithms to find hub genes with prognostic value. The prognostic value of 64 infiltrating cells was also explored. A prognostic model was established and then validated with GSE63155 and GSE63156. Finally, functional analysis was performed. Results GLCE and mast cell infiltration were screened as two indicators for a prognostic model. The Kaplan‒Meier analysis showed that patients in the low GLCE expression, mast cell infiltration and risk score groups had poorer outcomes than patients in the high GLCE expression, mast cell infiltration and risk score groups, both in the training and validation sets. Scatter plots and heatmaps also indicated the same results. The concordance indices and calibration analyses indicated a high prediction accuracy of the model in the training and validation sets. The time-dependent receiver operating characteristic analyses suggested high sensitivity and specificity of the model, with area under the curve values between 0.76 and 0.98. The decision curve analyses suggested a significantly higher net benefit by the model than the treat-all and treat-none strategies. Functional analyses suggested that glycosaminoglycan biosynthesis-heparan sulfate/heparin, the cell cycle and microRNAs in cancer were upregulated in ES patients. Conclusions GLCE and mast cell infiltration are potential prognostic indicators in ES. GLCE may affect the proliferation, angiogenesis and metastasis of ES by affecting the biosynthesis of heparan sulfate and heparin.
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Affiliation(s)
- Jian Wen
- Medical College of Nanchang University, Nanchang, Jiangxi, 330006, China
- Department of Orthopedics, JXHC Key Laboratory of Digital Orthopedics, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, 152 Aiguo Road, Nanchang, Jiangxi, 330006, China
| | - Lijun Yi
- Central Laboratory, Jiangxi Provincial Children's Hospital, Yangming Rd, Nanchang, Jiangxi, 330006, China
| | - Lijia Wan
- Department of Child Healthcare, Hunan Provincial Maternal and Child Health Hospital, Changsha, Hunan, 410008, China
| | - Xieping Dong
- Medical College of Nanchang University, Nanchang, Jiangxi, 330006, China
- Department of Orthopedics, JXHC Key Laboratory of Digital Orthopedics, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, 152 Aiguo Road, Nanchang, Jiangxi, 330006, China
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10
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Gong H, Xue B, Ru J, Pei G, Li Y. Targeted Therapy for EWS-FLI1 in Ewing Sarcoma. Cancers (Basel) 2023; 15:4035. [PMID: 37627063 PMCID: PMC10452796 DOI: 10.3390/cancers15164035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 08/05/2023] [Accepted: 08/06/2023] [Indexed: 08/27/2023] Open
Abstract
Ewing sarcoma (EwS) is a rare and predominantly pediatric malignancy of bone and soft tissue in children and adolescents. Although international collaborations have greatly improved the prognosis of most EwS, the occurrence of macrometastases or relapse remains challenging. The prototypic oncogene EWS-FLI1 acts as an aberrant transcription factor that drives the cellular transformation of EwS. In addition to its involvement in RNA splicing and the DNA damage response, this chimeric protein directly binds to GGAA repeats, thereby modifying the transcriptional profile of EwS. Direct pharmacological targeting of EWS-FLI1 is difficult because of its intrinsically disordered structure. However, targeting the EWS-FLI1 protein complex or downstream pathways provides additional therapeutic options. This review describes the EWS-FLI1 protein partners and downstream pathways, as well as the related target therapies for the treatment of EwS.
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Affiliation(s)
- Helong Gong
- Department of Orthopaedic Surgery, Shengjing Hospital, China Medical University, No. 36 Sanhao Street, Heping District, Shenyang 110004, China;
| | - Busheng Xue
- Department of Hematology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China;
| | - Jinlong Ru
- Institute of Virology, Helmholtz Centre Munich, German Research Centre for Environmental Health, 85764 Neuherberg, Germany;
| | - Guoqing Pei
- Department of Orthopedics, Xijing Hospital, Air Force Medical University, Xi’an 710032, China;
| | - Yan Li
- Department of Orthopaedic Surgery, Shengjing Hospital, China Medical University, No. 36 Sanhao Street, Heping District, Shenyang 110004, China;
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11
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Daher M, Zalaquett Z, Chalhoub R, Abi Farraj S, Abdo M, Sebaaly A, Kourie HR, Ghanem I. Molecular and biologic biomarkers of Ewing sarcoma: A systematic review. J Bone Oncol 2023; 40:100482. [PMID: 37180735 PMCID: PMC10173001 DOI: 10.1016/j.jbo.2023.100482] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/23/2023] [Accepted: 04/23/2023] [Indexed: 05/16/2023] Open
Abstract
With an annual incidence of less than 1%, Ewing sarcoma mainly occurs in children and young adults. It is not a frequent tumor but is the second most common bone malignancy in children. It has a 5-year survival rate of 65-75%; however, it has a poor prognosis when it relapses in patients. A genomic profile of this tumor can potentially help identify poor prognosis patients earlier and guide their treatment. A systematic review of the articles concerning genetic biomarkers in Ewing sarcoma was conducted using the Google Scholar, Cochrane, and PubMed database. There were 71 articles discovered. Numerous diagnostic, prognostic, and predictive biomarkers were found. However, more research is necessary to confirm the role of some of the mentioned biomarkers. .
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Affiliation(s)
- Mohammad Daher
- Orthopedic Department, Faculty of Medicine, Saint Joseph University of Beirut, Lebanon
- Corresponding author at: Hotel Dieu de France, Beirut, Lebanon.
| | - Ziad Zalaquett
- Hematology-Oncology Department, Faculty of Medicine, Saint Joseph University of Beirut, Lebanon
| | - Ralph Chalhoub
- Hematology-Oncology Department, Faculty of Medicine, Saint Joseph University of Beirut, Lebanon
| | - Sami Abi Farraj
- Orthopedic Department, Faculty of Medicine, Saint Joseph University of Beirut, Lebanon
| | - Majd Abdo
- Hematology-Oncology Department, Faculty of Medicine, Saint Joseph University of Beirut, Lebanon
| | - Amer Sebaaly
- Orthopedic Department, Faculty of Medicine, Saint Joseph University of Beirut, Lebanon
| | - Hampig-Raphaël Kourie
- Hematology-Oncology Department, Faculty of Medicine, Saint Joseph University of Beirut, Lebanon
| | - Ismat Ghanem
- Orthopedic Department, Faculty of Medicine, Saint Joseph University of Beirut, Lebanon
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12
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Identification of Methylation Signatures and Rules for Sarcoma Subtypes by Machine Learning Methods. BIOMED RESEARCH INTERNATIONAL 2022; 2022:5297235. [PMID: 36619306 PMCID: PMC9812612 DOI: 10.1155/2022/5297235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/28/2022] [Accepted: 12/08/2022] [Indexed: 12/31/2022]
Abstract
Sarcoma, the second common type of solid tumor in children and adolescents, has a wide variety of subtypes that are often not properly diagnosed at an early stage, leading to late metastases and causing serious loss of life and property to patients and families. It exhibits a high degree of heterogeneity at the cellular, molecular, and epigenetic levels, where DNA methylation has been proposed to play a role in the diagnosis of sarcoma subtypes. Thus, this study is aimed at finding potential biomarkers at the DNA methylation level to distinguish different sarcoma subtypes. A machine learning process was designed to analyse sarcoma samples, each of which was represented by lots of methylation sites. Irrelevant sites were removed using the Boruta method, and remaining sites related to the target variables were kept for further analyses. Afterward, three feature ranking methods (LASSO, LightGBM, and MCFS) were adopted to rank these features, and six classification models were constructed by combining incremental feature selection and two classification algorithms (decision tree and random forest). Among these models, the performance of RF model was higher than that of DT model under all three ranking conditions. The specific expression of genes obtained from the annotation of highly correlated methylation site features, such as PRKAR1B, INPP5A, and GLI3, was proven to be associated with sarcoma by publications. Moreover, the quantitative rules obtained by decision tree algorithm helped us to understand the essential differences between various sarcoma types and classify sarcoma subtypes, providing a new means of clinical identification and determining new therapeutic targets.
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13
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Orth MF, Surdez D, Faehling T, Ehlers AC, Marchetto A, Grossetête S, Volckmann R, Zwijnenburg DA, Gerke JS, Zaidi S, Alonso J, Sastre A, Baulande S, Sill M, Cidre-Aranaz F, Ohmura S, Kirchner T, Hauck SM, Reischl E, Gymrek M, Pfister SM, Strauch K, Koster J, Delattre O, Grünewald TGP. Systematic multi-omics cell line profiling uncovers principles of Ewing sarcoma fusion oncogene-mediated gene regulation. Cell Rep 2022; 41:111761. [PMID: 36476851 DOI: 10.1016/j.celrep.2022.111761] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 08/25/2022] [Accepted: 11/08/2022] [Indexed: 12/12/2022] Open
Abstract
Ewing sarcoma (EwS) is characterized by EWSR1-ETS fusion transcription factors converting polymorphic GGAA microsatellites (mSats) into potent neo-enhancers. Although the paucity of additional mutations makes EwS a genuine model to study principles of cooperation between dominant fusion oncogenes and neo-enhancers, this is impeded by the limited number of well-characterized models. Here we present the Ewing Sarcoma Cell Line Atlas (ESCLA), comprising whole-genome, DNA methylation, transcriptome, proteome, and chromatin immunoprecipitation sequencing (ChIP-seq) data of 18 cell lines with inducible EWSR1-ETS knockdown. The ESCLA shows hundreds of EWSR1-ETS-targets, the nature of EWSR1-ETS-preferred GGAA mSats, and putative indirect modes of EWSR1-ETS-mediated gene regulation, converging in the duality of a specific but plastic EwS signature. We identify heterogeneously regulated EWSR1-ETS-targets as potential prognostic EwS biomarkers. Our freely available ESCLA (http://r2platform.com/escla/) is a rich resource for EwS research and highlights the power of comprehensive datasets to unravel principles of heterogeneous gene regulation by chimeric transcription factors.
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Affiliation(s)
- Martin F Orth
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, 80337 Munich, Germany
| | - Didier Surdez
- INSERM Unit 830 "Genetics and Biology of Cancers," Institut Curie Research Center, 75005 Paris, France; Balgrist University Hospital, Faculty of Medicine, University of Zürich, 8008 Zürich, Switzerland
| | - Tobias Faehling
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Anna C Ehlers
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Aruna Marchetto
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, 80337 Munich, Germany
| | - Sandrine Grossetête
- INSERM Unit 830 "Genetics and Biology of Cancers," Institut Curie Research Center, 75005 Paris, France
| | - Richard Volckmann
- Department of Oncogenomics, Amsterdam University Medical Centers (AUMC), 1105 Amsterdam, the Netherlands
| | - Danny A Zwijnenburg
- Department of Oncogenomics, Amsterdam University Medical Centers (AUMC), 1105 Amsterdam, the Netherlands
| | - Julia S Gerke
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, 80337 Munich, Germany
| | - Sakina Zaidi
- INSERM Unit 830 "Genetics and Biology of Cancers," Institut Curie Research Center, 75005 Paris, France
| | - Javier Alonso
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras, Instituto de Salud Carlos III, 28029 Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CB06/07/1009, CIBERER-ISCIII), 28029 Madrid, Spain
| | - Ana Sastre
- Unidad Hemato-oncología Pediátrica, Hospital Infantil Universitario La Paz, 28029 Madrid, Spain
| | - Sylvain Baulande
- Institut Curie Genomics of Excellence (ICGex) Platform, Institut Curie Research Center, 75005 Paris, France
| | - Martin Sill
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neuro-Oncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Florencia Cidre-Aranaz
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Shunya Ohmura
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Thomas Kirchner
- Institute of Pathology, Faculty of Medicine, LMU Munich, 80337 Munich, Germany; German Cancer Consortium (DKTK), Partner Site Munich, 80337 Munich, Germany; German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Stefanie M Hauck
- Research Unit Protein Science and Metabolomics and Proteomics Core, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Eva Reischl
- Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Melissa Gymrek
- Division of Genetics, Department of Medicine, University of California, San Diego, San Diego, CA 92093, USA; Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA 92093, USA
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neuro-Oncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Department of Pediatric Hematology & Oncology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Konstantin Strauch
- Institute of Medical Biometry, Epidemiology, and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany; Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany; Institute for Medical Information Processing, Biometry, and Epidemiology (IBE), Faculty of Medicine, LMU Munich, 81377 Munich, Germany
| | - Jan Koster
- Department of Oncogenomics, Amsterdam University Medical Centers (AUMC), 1105 Amsterdam, the Netherlands
| | - Olivier Delattre
- INSERM Unit 830 "Genetics and Biology of Cancers," Institut Curie Research Center, 75005 Paris, France
| | - Thomas G P Grünewald
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, 80337 Munich, Germany; Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Institute of Pathology, Heidelberg University Hospital, 69120 Heidelberg, Germany.
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14
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Regulation of Metastasis in Ewing Sarcoma. Cancers (Basel) 2022; 14:cancers14194902. [PMID: 36230825 PMCID: PMC9563756 DOI: 10.3390/cancers14194902] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/01/2022] [Accepted: 10/04/2022] [Indexed: 11/17/2022] Open
Abstract
Ewing sarcoma (EwS) is a type of bone and soft tissue tumor in children and adolescents. Over 85% of cases are caused by the expression of fusion protein EWSR1-FLI1 generated by chromosome translocation. Acting as a potent chimeric oncoprotein, EWSR1-FLI1 binds to chromatin, changes the epigenetic states, and thus alters the expression of a large set of genes. Several studies have revealed that the expression level of EWSR1-FLI1 is variable and dynamic within and across different EwS cell lines and primary tumors, leading to tumoral heterogeneity. Cells with high EWSR1-FLI1 expression (EWSR1-FLI1-high) proliferate in an exponential manner, whereas cells with low EWSR1-FLI1 expression (EWSR1-FLI1-low) tend to have a strong propensity to migrate, invade, and metastasize. Metastasis is the leading cause of cancer-related deaths. The continuous evolution of EwS research has revealed some of the molecular underpinnings of this dissemination process. In this review, we discuss the molecular signatures that contribute to metastasis.
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15
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Molnar C, Reina J, Herrero A, Heinen JP, Méndiz V, Bonnal S, Irimia M, Sánchez-Jiménez M, Sánchez-Molina S, Mora J, Gonzalez C. Human EWS-FLI protein recapitulates in Drosophila the neomorphic functions that induce Ewing sarcoma tumorigenesis. PNAS NEXUS 2022; 1:pgac222. [PMID: 36714878 PMCID: PMC9802468 DOI: 10.1093/pnasnexus/pgac222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022]
Abstract
Ewing sarcoma (EwS) is a human malignant tumor typically driven by the Ewing sarcoma-Friend leukemia integration (EWS-FLI) fusion protein. A paucity of genetically modified animal models, partially owed to the high toxicity of EWS-FLI, hinders research on EwS. Here, we report a spontaneous mutant variant, EWS-FLI1FS, that circumvents the toxicity issue in Drosophila. Through proteomic and genomic analyses, we show that human EWS-FLI1FS interacts with the Drosophila homologues of EWS-FLI human protein partners, including core subunits of chromatin remodeling complexes, the transcription machinery, and the spliceosome; brings about a massive dysregulation of transcription that affects a significant fraction of known targets of EWS-FLI in human cells; and modulates splicing. We also show that EWS-FLI1FS performs in Drosophila the two major neomorphic activities that it is known to have in human cells: activation of transcription from GGAA microsatellites and out competition of ETS transcription factors. We conclude that EWS-FLI1FS reproduces in Drosophila the known oncogenic activities of EWS-FLI that drive EwS tumorigenesis in humans. These results open up an unprecedented opportunity to investigate EWS-FLI's oncogenic pathways in vivo in a genetically tractable organism.
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Affiliation(s)
- Cristina Molnar
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Carrer Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Jose Reina
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Carrer Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Anastasia Herrero
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Carrer Baldiri Reixac 10, 08028 Barcelona, Spain,Developmental Tumor Biology Laboratory, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat 08950 Barcelona, Spain
| | - Jan Peter Heinen
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Carrer Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Victoria Méndiz
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Carrer Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Sophie Bonnal
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain,Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain,Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Pg Lluis Companys 23, 08010 Barcelona, Spain
| | - María Sánchez-Jiménez
- Developmental Tumor Biology Laboratory, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat 08950 Barcelona, Spain,Pediatric Cancer Center Barcelona (PCCB), Hospital Sant Joan de Déu, Esplugues de Llobregat, 08950 Barcelona, Spain
| | - Sara Sánchez-Molina
- Developmental Tumor Biology Laboratory, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat 08950 Barcelona, Spain,Pediatric Cancer Center Barcelona (PCCB), Hospital Sant Joan de Déu, Esplugues de Llobregat, 08950 Barcelona, Spain
| | - Jaume Mora
- To whom correspondence should be addressed:
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16
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Kitagawa T, Kobayashi D, Baron B, Okita H, Miyamoto T, Takai R, Paudel D, Ohta T, Asaoka Y, Tokunaga M, Nakagawa K, Furutani-Seiki M, Araki N, Kuramitsu Y, Kobayashi M. AT-hook DNA-binding motif-containing protein one knockdown downregulates EWS-FLI1 transcriptional activity in Ewing's sarcoma cells. PLoS One 2022; 17:e0269077. [PMID: 36194562 PMCID: PMC9531837 DOI: 10.1371/journal.pone.0269077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/06/2022] [Indexed: 11/18/2022] Open
Abstract
Ewing's sarcoma is the second most common bone malignancy in children or young adults and is caused by an oncogenic transcription factor by a chromosomal translocation between the EWSR1 gene and the ETS transcription factor family. However, the transcriptional mechanism of EWS-ETS fusion proteins is still unclear. To identify the transcriptional complexes of EWS-ETS fusion transcription factors, we applied a proximal labeling system called BioID in Ewing's sarcoma cells. We identified AHDC1 as a proximal protein of EWS-ETS fusion proteins. AHDC1 knockdown showed a reduced cell growth and transcriptional activity of EWS-FLI1. AHDC1 knockdown also reduced BRD4 and BRG1 protein levels, both known as interacting proteins of EWS-FLI1. Our results suggest that AHDC1 supports cell growth through EWS-FLI1.
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Affiliation(s)
- Takao Kitagawa
- Advanced Research Promotion Center, Health Sciences University of Hokkaido, Kanazawa, Ishikari-Tobetsu, Hokkaido, Japan
- * E-mail:
| | - Daiki Kobayashi
- Department of Omics and Systems Biology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
- Department of Tumor Genetics and Biology, Faculty of Life Sciences, Kumamoto University, Kumamoto-Shi, Kumamoto, Japan
| | - Byron Baron
- Center for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Hajime Okita
- Division of Diagnostic Pathology, Keio University School of Medicine, Shinano, Shinjuku-ku, Tokyo, Japan
| | - Tatsuo Miyamoto
- Department of Molecular and Cellular Physiology, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Rie Takai
- Advanced Research Promotion Center, Health Sciences University of Hokkaido, Kanazawa, Ishikari-Tobetsu, Hokkaido, Japan
| | - Durga Paudel
- Advanced Research Promotion Center, Health Sciences University of Hokkaido, Kanazawa, Ishikari-Tobetsu, Hokkaido, Japan
| | - Tohru Ohta
- Advanced Research Promotion Center, Health Sciences University of Hokkaido, Kanazawa, Ishikari-Tobetsu, Hokkaido, Japan
| | - Yoichi Asaoka
- Department of Systems Biochemistry in Pathology and Regeneration, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Masayuki Tokunaga
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Koji Nakagawa
- Advanced Research Promotion Center, Health Sciences University of Hokkaido, Kanazawa, Ishikari-Tobetsu, Hokkaido, Japan
| | - Makoto Furutani-Seiki
- Department of Systems Biochemistry in Pathology and Regeneration, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Norie Araki
- Department of Tumor Genetics and Biology, Faculty of Life Sciences, Kumamoto University, Kumamoto-Shi, Kumamoto, Japan
| | - Yasuhiro Kuramitsu
- Advanced Research Promotion Center, Health Sciences University of Hokkaido, Kanazawa, Ishikari-Tobetsu, Hokkaido, Japan
| | - Masanobu Kobayashi
- Advanced Research Promotion Center, Health Sciences University of Hokkaido, Kanazawa, Ishikari-Tobetsu, Hokkaido, Japan
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17
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Liu C, Pu M, Ma Y, Wang C, Kong L, Zhang S, Zhao X, Lian X. Intra-tumor heterogeneity and prognostic risk signature for hepatocellular carcinoma based on single-cell analysis. Exp Biol Med (Maywood) 2022; 247:1741-1751. [PMID: 36330895 PMCID: PMC9638959 DOI: 10.1177/15353702221110659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Intra-tumor heterogeneity poses a serious challenge in the treatment of cancer, including hepatocellular carcinoma (HCC). Recent developments in single-cell RNA sequencing (scRNA-seq) make it possible to examine the heterogeneity of tumor cells. The Gene Expression Omnibus (GEO) database was retrieved to obtain scRNA-seq data of 13 HCC and 8 para cancer samples, and the cells were clustered using FindNeighbors and FindClusters functions. Cell subsets were defined using the "Enricher" function of the clusterProfiler package. Monocle was used to predict cell developmental trajectory. The LIMMA package included in the R program was utilized to detect differentially expressed genes (DEGs) between HCC and paracancerous tissues. Univariate Cox analysis and Least Absolute and Selection Operator (Lasso) Cox regression analysis were conducted to establish a risk assessment model. Thirteen cell subpopulations were identified from the sequencing data of 64,634 single cells. Four cell subgroups (dendritic cells, hepatocytes, liver bud hepatic cells, and liver progenitor cells) in tumor tissues were highly enriched. Between HCC and para cancer tissues, 3024 DEGs were identified, and 641 were specific markers of four cell subgroups. To develop a prognostic risk model, 9 genes among the 641 genes were selected. In the training and validation sets, the model demonstrated a higher 5-year AUC and independently served as a prognostic marker as confirmed by multivariate and univariate Cox analyses. This study revealed the characteristics of different cell subpopulations of immune cells and tumor cells from the HCC microenvironment. We established a novel nine-gene prognostic model to determine the death risk of HCC patients. The discoveries in this research improved the current knowledge of HCC heterogeneity and may inspire future research.
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Affiliation(s)
- Chengli Liu
- Department of Hepatobiliary Surgery, Air Force Medical Center, Air Force Clinical College (Air Force Medical Center) of Anhui Medical University, Beijing 100142, China,Chengli Liu.
| | - Meng Pu
- Department of Hepatobiliary Surgery, Air Force Medical Center, Beijing 100142, China
| | - Yingbo Ma
- Department of Hepatobiliary Surgery, Standardized Residency Training Base, Air Force Medical Center, Beijing 100142, China
| | - Cheng Wang
- Department of Hepatobiliary Surgery, Air Force Medical Center, Beijing 100142, China
| | - Linghong Kong
- Department of Hepatobiliary Surgery, Air Force Medical Center, Beijing 100142, China
| | - Shuhan Zhang
- Department of Hepatobiliary Surgery, Air Force Medical Center, Beijing 100142, China
| | - Xuying Zhao
- Department of Hepatobiliary Surgery, Standardized General Surgery Specialists Training Base, Air Force Medical Center, Beijing 100142, China
| | - Xiaopeng Lian
- Department of Hepatobiliary Surgery, Standardized General Surgery Specialists Training Base, Air Force Medical Center, Beijing 100142, China
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18
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Showpnil IA, Selich-Anderson J, Taslim C, Boone MA, Crow JC, Theisen ER, Lessnick SL. EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma. Nucleic Acids Res 2022; 50:9814-9837. [PMID: 36124657 PMCID: PMC9508825 DOI: 10.1093/nar/gkac747] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 08/10/2022] [Accepted: 08/23/2022] [Indexed: 12/13/2022] Open
Abstract
Ewing sarcoma is a prototypical fusion transcription factor-associated pediatric cancer that expresses EWS/FLI or a highly related FET/ETS chimera. EWS/FLI dysregulates transcription to induce and maintain sarcomagenesis, but the mechanisms utilized are not fully understood. We therefore sought to define the global effects of EWS/FLI on chromatin conformation and transcription in Ewing sarcoma cells using a well-validated ‘knock-down/rescue’ model of EWS/FLI function in combination with next generation sequencing assays to evaluate how the chromatin landscape changes with loss, and recovery, of EWS/FLI expression. We found that EWS/FLI (and EWS/ERG) genomic localization is largely conserved across multiple patient-derived Ewing sarcoma cell lines. This EWS/FLI binding signature is associated with establishment of topologically-associated domain (TAD) boundaries, compartment activation, enhancer-promoter looping that involve both intra- and inter-TAD interactions, and gene activation. In addition, EWS/FLI co-localizes with the loop-extrusion factor cohesin to promote chromatin loops and TAD boundaries. Importantly, local chromatin features provide the basis for transcriptional heterogeneity in regulation of direct EWS/FLI target genes across different Ewing sarcoma cell lines. These data demonstrate a key role of EWS/FLI in mediating genome-wide changes in chromatin configuration and support the notion that fusion transcription factors serve as master regulators of three-dimensional reprogramming of chromatin.
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Affiliation(s)
- Iftekhar A Showpnil
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA.,Molecular, Cellular, and Developmental Biology Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Julia Selich-Anderson
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Cenny Taslim
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Megann A Boone
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA.,Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Jesse C Crow
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Emily R Theisen
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA.,Molecular, Cellular, and Developmental Biology Graduate Program, The Ohio State University, Columbus, OH 43210, USA.,Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH 43210, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Stephen L Lessnick
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA.,Molecular, Cellular, and Developmental Biology Graduate Program, The Ohio State University, Columbus, OH 43210, USA.,Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH 43210, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA.,Division of Pediatric Heme/Onc/BMT, The Ohio State University College of Medicine, Columbus, OH 43210, USA
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19
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Wu X, Wang Y, Yang M, Wang Y, Wang X, Zhang L, Liao L, Li N, Mao M, Guan J, Ye F. Exploring prognostic value and regulation network of PPP1R1A in hepatocellular carcinoma. Hum Cell 2022; 35:1856-1868. [PMID: 36018458 DOI: 10.1007/s13577-022-00771-9] [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: 04/07/2022] [Accepted: 08/15/2022] [Indexed: 12/24/2022]
Abstract
Novel and accurate biomarkers are needed for early detection and progression evaluation of hepatocellular carcinoma (HCC). Protein phosphatase 1 regulatory subunit 1A (PPP1R1A) has been studied in cancer biology; however, the expression pattern and biological function of PPP1R1A in HCC are unclear. The differentially expressed genes (DEGs) in HCC were screened by The Cancer Genome Atlas (TCGA) database. Real-time PCR and immunohistochemistry (IHC) assay were used to detect the expression of PPP1R1A in BALB/c mice, human normal tissues and corresponding tumor tissues, especially HCC. Then, Kaplan-Meier analysis of patients with HCC was performed to evaluate the relationship between PPP1R1A expression and prognosis. The transcriptional regulatory network of PPP1R1A was constructed based on the differentially expressed mRNAs, microRNAs and transcription factors (TFs). To explore the downstream regulation of PPP1R1A, the Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis and immune infiltration score were performed. A total of 4 DEGs were screened out. PPP1R1A was differentially distributed and expressed in BALB/c mice and human tissues. PPP1R1A expression was higher in normal tissues than that in tumor tissues, and patients with higher PPP1R1A expression had better clinical outcome in HCC. In addition, we constructed miR-21-3p/TAL1/PPP1R1A transcriptional network. Furthermore, PPP1R1A may modulate the activation of PI3K-Akt pathway, cell cycle, glycogen metabolism and the recruitment of M2 macrophage in HCC. This study may help to clarify the function and mechanism of PPP1R1A in HCC and provide a potential biomarker for tumor prevention and treatment.
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Affiliation(s)
- Xixi Wu
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Department of Radiation Oncology, Guangxi Zhuang Autonomous Region People's Hospital, Nanning, Guangxi, China
| | - Yin Wang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Mi Yang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yingqiao Wang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiaoqing Wang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Longshan Zhang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Liwei Liao
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Nan Li
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Mengyuan Mao
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jian Guan
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
| | - Feng Ye
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
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20
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Thind AS, Ashford B, Strbenac D, Mitchell J, Lee J, Mueller SA, Minaei E, Perry JR, Ch’ng S, Iyer NG, Clark JR, Gupta R, Ranson M. Whole genome analysis reveals the genomic complexity in metastatic cutaneous squamous cell carcinoma. Front Oncol 2022; 12:919118. [PMID: 35982973 PMCID: PMC9379253 DOI: 10.3389/fonc.2022.919118] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/27/2022] [Indexed: 12/13/2022] Open
Abstract
Metastatic cutaneous squamous cell carcinoma (CSCC) is a highly morbid disease requiring radical surgery and adjuvant therapy, which is associated with a poor prognosis. Yet, compared to other advanced malignancies, relatively little is known of the genomic landscape of metastatic CSCC. We have previously reported the mutational signatures and mutational patterns of CCCTC-binding factor (CTCF) regions in metastatic CSCC. However, many other genomic components (indel signatures, non-coding drivers, and structural variants) of metastatic CSCC have not been reported. To this end, we performed whole genome sequencing on lymph node metastases and blood DNA from 25 CSCC patients with regional metastases of the head and neck. We designed a multifaceted computational analysis at the whole genome level to provide a more comprehensive perspective of the genomic landscape of metastatic CSCC. In the non-coding genome, 3′ untranslated region (3′UTR) regions of EVC (48% of specimens), PPP1R1A (48% of specimens), and ABCA4 (20% of specimens) along with the tumor-suppressing long non-coding RNA (lncRNA) LINC01003 (64% of specimens) were significantly functionally altered (Q-value < 0.05) and represent potential non-coding biomarkers of CSCC. Recurrent copy number loss in the tumor suppressor gene PTPRD was observed. Gene amplification was much less frequent, and few genes were recurrently amplified. Single nucleotide variants driver analyses from three tools confirmed TP53 and CDKN2A as recurrently mutated genes but also identified C9 as a potential novel driver in this disease. Furthermore, indel signature analysis highlighted the dominance of ID signature 13 (ID13) followed by ID8 and ID9. ID9 has previously been shown to have no association with skin melanoma, unlike ID13 and ID8, suggesting a novel pattern of indel variation in metastatic CSCC. The enrichment analysis of various genetically altered candidates shows enrichment of “TGF-beta regulation of extracellular matrix” and “cell cycle G1 to S check points.” These enriched terms are associated with genetic instability, cell proliferation, and migration as mechanisms of genomic drivers of metastatic CSCC.
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Affiliation(s)
- Amarinder Singh Thind
- School of Medicine, University of Wollongong, Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Bruce Ashford
- School of Medicine, University of Wollongong, Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- Illawarra Shoalhaven Local Health District, Wollongong, NSW, Australia
- *Correspondence: Bruce Ashford,
| | - Dario Strbenac
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, NSW, Australia
| | - Jenny Mitchell
- Illawarra Shoalhaven Local Health District, Wollongong, NSW, Australia
| | - Jenny Lee
- Sydney Head and Neck Cancer Institute, Chris O’Brien Lifehouse, Sydney, NSW, Australia
- Department of Clinical Medicine, Macquarie University, Sydney, NSW, Australia
| | - Simon A. Mueller
- Sydney Head and Neck Cancer Institute, Chris O’Brien Lifehouse, Sydney, NSW, Australia
- Department of Otorhinolaryngology, Head and Neck Surgery, Zurich University Hospital and University of Zurich, Zurich, Switzerland
| | - Elahe Minaei
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Jay R. Perry
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Sydney Ch’ng
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, NSW, Australia
- Sydney Head and Neck Cancer Institute, Chris O’Brien Lifehouse, Sydney, NSW, Australia
| | - N. Gopalakrishna Iyer
- Department of Head and Neck Surgery, National Cancer Center, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Jonathan R. Clark
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, NSW, Australia
- Sydney Head and Neck Cancer Institute, Chris O’Brien Lifehouse, Sydney, NSW, Australia
- Royal Prince Alfred Institute of Academic Surgery, Sydney Local Health District, Sydney, NSW, Australia
| | - Ruta Gupta
- Anatomical Pathology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Marie Ranson
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
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21
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Karlina I, Schroeder BA, Kirgizov K, Romantsova O, Istranov AL, Nedorubov A, Timashev P, Ulasov I. Latest developments in the pathobiology of Ewing sarcoma. J Bone Oncol 2022; 35:100440. [PMID: 35855933 PMCID: PMC9287185 DOI: 10.1016/j.jbo.2022.100440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 06/20/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
- Irina Karlina
- Group of Experimental Biotherapy and Diagnostics, Institute for Regenerative Medicine, World-Class Research Centre “Digital Biodesign and Personalized Healthcare”, I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Brett A. Schroeder
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - Kirill Kirgizov
- Research Institute of Pediatric Oncology and Hematology at N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health of Russia Moscow, 115478, Russia
| | - Olga Romantsova
- Research Institute of Pediatric Oncology and Hematology at N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health of Russia Moscow, 115478, Russia
| | - Andrey L. Istranov
- Department of Oncology, radiation therapy and plastic surgery, I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - Andrey Nedorubov
- Center for Preclinical Research, Institute of Translational Medicine and Biotechnology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Peter Timashev
- World-Class Research Centre “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Ilya Ulasov
- Group of Experimental Biotherapy and Diagnostics, Institute for Regenerative Medicine, World-Class Research Centre “Digital Biodesign and Personalized Healthcare”, I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
- Corresponding author at: Group of Experimental Biotherapy and Diagnostics, Institute for Regenerative Medicine, World-Class Research Centre “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, Moscow 119991, Russia.
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22
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Flores G, Grohar PJ. One oncogene, several vulnerabilities: EWS/FLI targeted therapies for Ewing sarcoma. J Bone Oncol 2021; 31:100404. [PMID: 34976713 PMCID: PMC8686064 DOI: 10.1016/j.jbo.2021.100404] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/18/2021] [Accepted: 11/23/2021] [Indexed: 12/23/2022] Open
Abstract
EWS/FLI is the defining mutation of Ewing sarcoma. This oncogene drives malignant transformation and progression and occurs in a genetic background characterized by few other recurrent cooperating mutations. In addition, the tumor is absolutely dependent on the continued expression of EWS/FLI to maintain the malignant phenotype. However, EWS/FLI is a transcription factor and therefore a challenging drug target. The difficulty of directly targeting EWS/FLI stems from unique features of this fusion protein as well as the network of interacting proteins required to execute the transcriptional program. This network includes interacting proteins as well as upstream and downstream effectors that together reprogram the epigenome and transcriptome. While the vast number of proteins involved in this process challenge the development of a highly specific inhibitors, they also yield numerous therapeutic opportunities. In this report, we will review how this vast EWS-FLI transcriptional network has been exploited over the last two decades to identify compounds that directly target EWS/FLI and/or associated vulnerabilities.
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Affiliation(s)
- Guillermo Flores
- Van Andel Research Institute, Grand Rapids, MI, USA
- Michigan State University, College of Human Medicine, USA
| | - Patrick J Grohar
- Children's Hospital of Philadelphia, University of Pennsylvania, Perelman School of Medicine, 3501 Civic Center Blvd., Philadelphia, PA, USA
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23
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Wang J, Zhang Q, Shi F, Yadav DK, Hong Z, Wang J, Liang T, Bai X. A Seven-Gene Signature to Predict Prognosis of Patients With Hepatocellular Carcinoma. Front Genet 2021; 12:728476. [PMID: 34603388 PMCID: PMC8481951 DOI: 10.3389/fgene.2021.728476] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/13/2021] [Indexed: 01/27/2023] Open
Abstract
Purpose: Hepatocellular carcinoma (HCC) is one of the most prevalent malignant diseases worldwide and has a poor prognosis. Gene-based prognostic models have been reported to predict the overall survival of patients with HCC. Unfortunately, most of the genes used in earlier prognostic models lack prospective validation and, thus, cannot be used in clinical practice. Methods: Candidate genes were selected from GEPIA (Gene Expression Profiling Interactive Analysis), and their associations with patients’ survival were confirmed by RT-PCR using cDNA tissue microarrays established from patients with HCC after radical resection. A multivariate Cox proportion model was used to calculate the coefficient of corresponding gene. The expression of seven genes of interest (MKI67, AR, PLG, DNASE1L3, PTTG1, PPP1R1A, and TTR) with two reference genes was defined to calculate a risk score which determined groups of different risks. Results: Our risk scoring efficiently classified patients (n = 129) with HCC into a low-, intermediate-, and high-risk group. The three groups showed meaningful distinction of 3-year overall survival rate, i.e., 88.9, 74.5, and 20.6% for the low-, intermediate-, and high-risk group, respectively. The prognostic prediction model of risk scores was subsequently verified using an independent prospective cohort (n = 77) and showed high accuracy. Conclusion: Our seven-gene signature model performed excellent long-term prediction power and provided crucially guiding therapy for patients who are not a candidate for surgery.
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Affiliation(s)
- Junli Wang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qi Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China.,Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, China
| | - Fukang Shi
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Dipesh Kumar Yadav
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhengtao Hong
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianing Wang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China.,Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, China
| | - Xueli Bai
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China.,Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, China
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24
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Matos B, Howl J, Jerónimo C, Fardilha M. Modulation of serine/threonine-protein phosphatase 1 (PP1) complexes: A promising approach in cancer treatment. Drug Discov Today 2021; 26:2680-2698. [PMID: 34390863 DOI: 10.1016/j.drudis.2021.08.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/23/2021] [Accepted: 08/05/2021] [Indexed: 01/21/2023]
Abstract
Cancer is the second leading cause of death worldwide. Despite the availability of numerous therapeutic options, tumor heterogeneity and chemoresistance have limited the success of these treatments, and the development of effective anticancer therapies remains a major focus in oncology research. The serine/threonine-protein phosphatase 1 (PP1) and its complexes have been recognized as potential drug targets. Research on the modulation of PP1 complexes is currently at an early stage, but has immense potential. Chemically diverse compounds have been developed to disrupt or stabilize different PP1 complexes in various cancer types, with the objective of inhibiting disease progression. Beneficial results obtained in vitro now require further pre-clinical and clinical validation. In conclusion, the modulation of PP1 complexes seems to be a promising, albeit challenging, therapeutic strategy for cancer.
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Affiliation(s)
- Bárbara Matos
- Laboratory of Signal Transduction, Department of Medical Sciences, Institute of Biomedicine-iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal; Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Institute of Oncology of Porto (IPO Porto), 4200-072 Porto, Portugal
| | - John Howl
- Molecular Pharmacology Group, Research Institute in Healthcare Science, University of Wolverhampton, Wolverhampton WV1 1LY, UK
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Institute of Oncology of Porto (IPO Porto), 4200-072 Porto, Portugal; Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), 4050-513 Porto, Portugal
| | - Margarida Fardilha
- Laboratory of Signal Transduction, Department of Medical Sciences, Institute of Biomedicine-iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal.
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25
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Comprehensive Genomic and Transcriptomic Analysis of Three Synchronous Primary Tumours and a Recurrence from a Head and Neck Cancer Patient. Int J Mol Sci 2021; 22:ijms22147583. [PMID: 34299215 PMCID: PMC8305204 DOI: 10.3390/ijms22147583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/29/2021] [Accepted: 07/01/2021] [Indexed: 11/17/2022] Open
Abstract
Synchronous primary malignancies occur in a small proportion of head and neck squamous cell carcinoma (HNSCC) patients. Here, we analysed three synchronous primaries and a recurrence from one patient by comparing the genomic and transcriptomic profiles among the tumour samples and determining the recurrence origin. We found remarkable levels of heterogeneity among the primary tumours, and through the patterns of shared mutations, we traced the origin of the recurrence. Interestingly, the patient carried germline variants that might have predisposed him to carcinogenesis, together with a history of alcohol and tobacco consumption. The mutational signature analysis confirmed the impact of alcohol exposure, with Signature 16 present in all tumour samples. Characterisation of immune cell infiltration highlighted an immunosuppressive environment in all samples, which exceeded the potential activity of T cells. Studies such as the one described here have important clinical value and contribute to personalised treatment decisions for patients with synchronous primaries and matched recurrences.
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26
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Ogura K, Somwar R, Hmeljak J, Magnan H, Benayed R, Momeni Boroujeni A, Bowman AS, Mattar MS, Khodos I, de Stanchina E, Jungbluth A, Asher M, Odintsov I, Hartono AB, LaQuaglia MP, Slotkin E, Pratilas CA, Lee SB, Spraggon L, Ladanyi M. Therapeutic Potential of NTRK3 Inhibition in Desmoplastic Small Round Cell Tumor. Clin Cancer Res 2020; 27:1184-1194. [PMID: 33229458 DOI: 10.1158/1078-0432.ccr-20-2585] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/27/2020] [Accepted: 11/18/2020] [Indexed: 12/12/2022]
Abstract
PURPOSE Desmoplastic small round cell tumor (DSRCT) is a highly lethal intra-abdominal sarcoma of adolescents and young adults. DSRCT harbors a t(11;22)(p13:q12) that generates the EWSR1-WT1 chimeric transcription factor, the key oncogenic driver of DSRCT. EWSR1-WT1 rewires global gene expression networks and activates aberrant expression of targets that together mediate oncogenesis. EWSR1-WT1 also activates a neural gene expression program. EXPERIMENTAL DESIGN Among these neural markers, we found prominent expression of neurotrophic tyrosine kinase receptor 3 (NTRK3), a druggable receptor tyrosine kinase. We investigated the regulation of NTRK3 by EWSR1-WT1 and its potential as a therapeutic target in vitro and in vivo, the latter using novel patient-derived models of DSRCT. RESULTS We found that EWSR1-WT1 binds upstream of NTRK3 and activates its transcription. NTRK3 mRNA is highly expressed in DSRCT compared with other major chimeric transcription factor-driven sarcomas and most DSRCTs are strongly immunoreactive for NTRK3 protein. Remarkably, expression of NTRK3 kinase domain mRNA in DSRCT is also higher than in cancers with NTRK3 fusions. Abrogation of NTRK3 expression by RNAi silencing reduces growth of DSRCT cells and pharmacologic targeting of NTRK3 with entrectinib is effective in both in vitro and in vivo models of DSRCT. CONCLUSIONS Our results indicate that EWSR1-WT1 directly activates NTRK3 expression in DSRCT cells, which are dependent on its expression and activity for growth. Pharmacologic inhibition of NTRK3 by entrectinib significantly reduces growth of DSRCT cells both in vitro and in vivo, providing a rationale for clinical evaluation of NTRK3 as a therapeutic target in DSRCT.
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Affiliation(s)
- Koichi Ogura
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Romel Somwar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Julija Hmeljak
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Heather Magnan
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Anita S Bowman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marissa S Mattar
- Anti-tumor Assessment Core Facility, Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Inna Khodos
- Anti-tumor Assessment Core Facility, Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elisa de Stanchina
- Anti-tumor Assessment Core Facility, Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Achim Jungbluth
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marina Asher
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Igor Odintsov
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alifiani B Hartono
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Michael P LaQuaglia
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Emily Slotkin
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christine A Pratilas
- Division of Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | - Sean Bong Lee
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Lee Spraggon
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York. .,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
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McCann TS, Parrish JK, Hsieh J, Sechler M, Sobral LM, Self C, Jones KL, Goodspeed A, Costello JC, Jedlicka P. KDM5A and PHF2 positively control expression of pro-metastatic genes repressed by EWS/Fli1, and promote growth and metastatic properties in Ewing sarcoma. Oncotarget 2020; 11:3818-3831. [PMID: 33196691 PMCID: PMC7597412 DOI: 10.18632/oncotarget.27737] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 08/24/2020] [Indexed: 02/07/2023] Open
Abstract
Ewing sarcoma is an aggressive malignant neoplasm with high propensity for metastasis and poor clinical outcomes. The EWS/Fli1 oncofusion is the disease driver in > 90% of cases, but presents a difficult therapeutic target. Moreover, EWS/Fli1 plays a complex role in disease progression, with inhibitory effects on critical steps of metastasis. Like many other pediatric cancers, Ewing sarcoma is a disease marked by epigenetic dysregulation. Epigenetic mechanisms present alternative targeting opportunities, but their contributions to Ewing sarcoma metastasis and disease progression remain poorly understood. Here, we show that the epigenetic regulators KDM5A and PHF2 promote growth and metastatic properties in Ewing sarcoma, and, strikingly, activate expression many pro-metastatic genes repressed by EWS/Fli1. These genes include L1CAM, which is associated with adverse outcomes in Ewing sarcoma, and promotes migratory and invasive properties. KDM5A and PHF2 retain their growth promoting effects in more metastatically potent EWS/Fli1low cells, and PHF2 promotes both invasion and L1CAM expression in this cell population. Furthermore, KDM5A and PHF2 each contribute to the increased metastatic potency of EWS/Fli1low cells in vivo. Together, these studies identify KDM5A and PHF2 as novel disease-promoting factors, and potential new targets, in Ewing sarcoma, including the more metastatically potent EWS/Fli1low cell population.
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Affiliation(s)
- Tyler S McCann
- Department of Pathology, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Janet K Parrish
- Department of Pathology, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Joseph Hsieh
- Department of Pathology, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA.,Medical Scientist Training Program, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA.,Cancer Biology Graduate Program, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Marybeth Sechler
- Department of Pathology, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA.,Cancer Biology Graduate Program, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Lays M Sobral
- Department of Pathology, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Chelsea Self
- Department of Pediatrics, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Kenneth L Jones
- Department of Pediatrics, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA.,Bioinformatics Shared Resource, University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO, USA
| | - Andrew Goodspeed
- Department of Pharmacology, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA.,Bioinformatics Shared Resource, University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO, USA
| | - James C Costello
- Department of Pharmacology, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA.,Bioinformatics Shared Resource, University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO, USA
| | - Paul Jedlicka
- Department of Pathology, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA.,Medical Scientist Training Program, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA.,Cancer Biology Graduate Program, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
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28
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Casamayor A, Ariño J. Controlling Ser/Thr protein phosphatase PP1 activity and function through interaction with regulatory subunits. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 122:231-288. [PMID: 32951813 DOI: 10.1016/bs.apcsb.2020.06.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein phosphatase 1 is a major Ser/Thr protein phosphatase activity in eukaryotic cells. It is composed of a catalytic polypeptide (PP1C), with little substrate specificity, that interacts with a large variety of proteins of diverse structure (regulatory subunits). The diversity of holoenzymes that can be formed explain the multiplicity of cellular functions under the control of this phosphatase. In quite a few cases, regulatory subunits have an inhibitory role, downregulating the activity of the phosphatase. In this chapter we shall introduce PP1C and review the most relevant families of PP1C regulatory subunits, with particular emphasis in describing the structural basis for their interaction.
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Affiliation(s)
- Antonio Casamayor
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola, del Vallès, Spain
| | - Joaquín Ariño
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola, del Vallès, Spain
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29
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Pietropaolo V, Prezioso C, Moens U. Merkel Cell Polyomavirus and Merkel Cell Carcinoma. Cancers (Basel) 2020; 12:E1774. [PMID: 32635198 PMCID: PMC7407210 DOI: 10.3390/cancers12071774] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 06/26/2020] [Accepted: 06/28/2020] [Indexed: 12/12/2022] Open
Abstract
Viruses are the cause of approximately 15% of all human cancers. Both RNA and DNA human tumor viruses have been identified, with Merkel cell polyomavirus being the most recent one to be linked to cancer. This virus is associated with about 80% of Merkel cell carcinomas, a rare, but aggressive cutaneous malignancy. Despite its name, the cells of origin of this tumor may not be Merkel cells. This review provides an update on the structure and life cycle, cell tropism and epidemiology of the virus and its oncogenic properties. Putative strategies to prevent viral infection or treat virus-positive Merkel cell carcinoma patients are discussed.
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Affiliation(s)
- Valeria Pietropaolo
- Department of Public Health and Infectious Diseases, “Sapienza” University, 00185 Rome, Italy; (V.P.); (C.P.)
| | - Carla Prezioso
- Department of Public Health and Infectious Diseases, “Sapienza” University, 00185 Rome, Italy; (V.P.); (C.P.)
- IRCSS San Raffaele Pisana, Microbiology of Chronic Neuro-Degenerative Pathologies, 00166 Rome, Italy
| | - Ugo Moens
- Molecular Inflammation Research Group, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø—The Arctic University of Norway, 9037 Tromsø, Norway
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30
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Luo W, Xu C, Phillips S, Gardenswartz A, Rosenblum JM, Ayello J, Lessnick SL, Hao HX, Cairo MS. Protein phosphatase 1 regulatory subunit 1A regulates cell cycle progression in Ewing sarcoma. Oncotarget 2020; 11:1691-1704. [PMID: 32477459 PMCID: PMC7233808 DOI: 10.18632/oncotarget.27571] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/10/2020] [Indexed: 12/02/2022] Open
Abstract
Ewing sarcoma (ES) is a malignant pediatric bone and soft tissue tumor. Patients with metastatic ES have a dismal outcome which has not been improved in decades. The major challenge in the treatment of metastatic ES is the lack of specific targets and rational combinatorial therapy. We recently found that protein phosphatase 1 regulatory subunit 1A (PPP1R1A) is specifically highly expressed in ES and promotes tumor growth and metastasis in ES. In the current investigation, we show that PPP1R1A regulates ES cell cycle progression in G1/S phase by down-regulating cell cycle inhibitors p21Cip1 and p27Kip1, which leads to retinoblastoma (Rb) protein hyperphosphorylation. In addition, we show that PPP1R1A promotes normal transcription of histone genes during cell cycle progression. Importantly, we demonstrate a synergistic/additive effect of the combinatorial therapy of PPP1R1A and insulin-like growth factor 1 receptor (IGF-1R) inhibition on decreasing ES cell proliferation and migration in vitro and limiting xenograft tumor growth and metastasis in vivo. Taken together, our findings suggest a role of PPP1R1A as an ES specific cell cycle modulator and that simultaneous targeting of PPP1R1A and IGF-1R pathways is a promising specific and effective strategy to treat both primary and metastatic ES.
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Affiliation(s)
- Wen Luo
- Department of Pediatrics, New York Medical College, Valhalla, NY, USA.,Department of Pathology, New York Medical College, Valhalla, NY, USA
| | - Changxin Xu
- James J. Peters Veterans Affairs Medical Center, Bronx, NY, USA
| | - Sarah Phillips
- Department of Medicine, New York Medical College, Valhalla, NY, USA
| | | | | | - Janet Ayello
- Department of Pediatrics, New York Medical College, Valhalla, NY, USA
| | | | - Huai-Xiang Hao
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Mitchell S Cairo
- Department of Pediatrics, New York Medical College, Valhalla, NY, USA.,Department of Pathology, New York Medical College, Valhalla, NY, USA.,Department of Medicine, New York Medical College, Valhalla, NY, USA.,Department of Immunology and Microbiology, New York Medical College, Valhalla, NY, USA.,Department of Cell Biology and Anatomy, New York Medical College, Valhalla, NY, USA
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31
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Chicón-Bosch M, Tirado OM. Exosomes in Bone Sarcomas: Key Players in Metastasis. Cells 2020; 9:cells9010241. [PMID: 31963599 PMCID: PMC7016778 DOI: 10.3390/cells9010241] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/11/2020] [Accepted: 01/15/2020] [Indexed: 12/12/2022] Open
Abstract
Bone sarcomas are rare cancers which often present with metastatic disease and are still associated with poor survival rates. Studies in the last decade have identified that exosomes, a type of extracellular vesicle released by cells, play an important role in tumour progression and dissemination. Through the transfer of their cargo (RNAs, proteins, and lipids) across cells, they are involved in cellular cross-talk and can induce changes in cellular behaviour. Exosomes have been shown to be important in metastasis organotropism, induction of angiogenesis and vascular permeability, the education of cells towards a pro-metastatic phenotype or the interaction between stromal and tumour cells. Due to the importance exosomes have in disease progression and the high incidence of metastasis in bone sarcomas, recent studies have evaluated the implications of these extracellular vesicles in bone sarcomas. In this review, we discuss the studies that evaluate the role of exosomes in osteosarcoma, Ewing sarcoma, and preliminary data on chondrosarcoma.
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Affiliation(s)
- Mariona Chicón-Bosch
- Sarcoma Research Group, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- Correspondence: (M.C.-B.); (O.M.T.); Tel.: +34-9326-0742 (M.C.-B.); +34-932-603-823 (O.M.T.)
| | - Oscar M. Tirado
- Sarcoma Research Group, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- CIBERONC, Carlos III Institute of Health (ISCIII), 28029 Madrid, Spain
- Institut Català d’Oncologia (ICO), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- Correspondence: (M.C.-B.); (O.M.T.); Tel.: +34-9326-0742 (M.C.-B.); +34-932-603-823 (O.M.T.)
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32
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Shi SH, Jiang J, Zhang W, Sun L, Li XJ, Li C, Ge QD, Zhuang ZG. A Novel lncRNA HOXC-AS3 Acts as a miR-3922-5p Sponge to Promote Breast Cancer Metastasis. Cancer Invest 2019; 38:1-12. [PMID: 31797701 DOI: 10.1080/07357907.2019.1695816] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Purpose: The function of long noncoding RNAs (lncRNA) in breast cancer metastasis remains largely unknown. In this work, the role of HOXC-AS3 in breast cancer progression was investigated.Methods: By using Cancer Genome Atlas (TCGA) Database, we investigated the expression of HOXC-AS3 in breast cancer and explored the association between HOXC-AS3 expression and prognosis. Then, we studied the biological function of HOXC-AS3 in cell migration and invasion both in vitro and in vivo. Furthermore, the target miRNA of HOXC-AS3, and the target mRNA of miR-3922-5p were proved.Results: HOXC-AS3 is aberrantly overexpressed in breast cancers especially the HER2+ type. Moreover, high expression of HOXC-AS3 has a relationship with poor clinical outcomes of breast cancer. In addition, HOXC-AS3 regulates cell Invasion and migration both in vitro and in vivo. Our results demonstrated that miR-3922-5p was a direct target of HOXC-AS3, and PPP1R1A was a target of miR-3922-5p in breast cancer.Conclusions: The novel lncRNA HOXC-AS3 acts as a miR-3922-5p sponge to upregulate PPP1R1A protein expression, and thus results in promoting breast cancer metastasis. HOXC-AS3 could be a novel therapeutic target for breast cancer therapeutics.
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Affiliation(s)
- Sheng-Hong Shi
- Department of Breast Disease, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, P.R. China.,Department of Breast Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, P.R. China
| | - Jing Jiang
- Department of Breast Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, P.R. China
| | - Wei Zhang
- Department of Breast Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, P.R. China
| | - Long Sun
- Department of Breast Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, P.R. China
| | - Xu-Jun Li
- Department of Breast Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, P.R. China
| | - Chao Li
- Department of Breast Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, P.R. China
| | - Qi-Dong Ge
- Department of Breast Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, P.R. China
| | - Zhi-Gang Zhuang
- Department of Breast Disease, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, P.R. China
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33
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Romswinkel A, Infanger M, Dietz C, Strube F, Kraus A. The Role of C-X-C Chemokine Receptor Type 4 (CXCR4) in Cell Adherence and Spheroid Formation of Human Ewing's Sarcoma Cells under Simulated Microgravity. Int J Mol Sci 2019; 20:ijms20236073. [PMID: 31810195 PMCID: PMC6929163 DOI: 10.3390/ijms20236073] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 11/29/2019] [Indexed: 12/17/2022] Open
Abstract
We studied the behavior of Ewing's Sarcoma cells of the line A673 under simulated microgravity (s-µg). These cells express two prominent markers-the oncogene EWS/FLI1 and the chemokine receptor CXCR4, which is used as a target of treatment in several types of cancer. The cells were exposed to s-µg in a random-positioning machine (RPM) for 24 h in the absence and presence of the CXCR4 inhibitor AMD3100. Then, their morphology and cytoskeleton were examined. The expression of selected mutually interacting genes was measured by qRT-PCR and protein accumulation was determined by western blotting. After 24 h incubation on the RPM, a splitting of the A673 cell population in adherent and spheroid cells was observed. Compared to 1 g control cells, EWS/FLI1 was significantly upregulated in the adherent cells and in the spheroids, while CXCR4 and CD44 expression were significantly enhanced in spheroids only. Transcription of CAV-1 was upregulated and DKK2 and VEGF-A were down-regulated in both, adherent in spheroid cells, respectively. Regarding, protein accumulation EWS/FLI1 was enhanced in adherent cells only, but CD44 decreased in spheroids and adherent cells. Inhibition of CXCR4 did not change spheroid count, or structure. Under s-µg, the tumor marker EWS/FLI1 is intensified, while targeting CXCR4, which influences adhesion proteins, did not affect spheroid formation.
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Affiliation(s)
| | | | | | | | - Armin Kraus
- Correspondence: ; Tel.: +49-391-67-15599; Fax: +49-391-67-15588
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34
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Inhibition of protein phosphatase 1 stimulates noncanonical ER stress eIF2α activation to enhance fisetin-induced chemosensitivity in HDAC inhibitor-resistant hepatocellular carcinoma cells. Cancers (Basel) 2019; 11:cancers11070918. [PMID: 31261976 PMCID: PMC6678694 DOI: 10.3390/cancers11070918] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 06/14/2019] [Accepted: 06/28/2019] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a common fatal type of malignant tumor that has highly metastatic and recurrent properties. Fisetin is a natural flavonoid found in various vegetables and fruits which exhibits anti-cancer and anti-inflammatory properties, as well as other effects. Thus, we hypothesized that fisetin can act as an adjuvant therapy in cancer or drug-resistant cancer cells, and further investigated the molecular mechanisms underlying the development of drug-resistance in HCC cells. We found that fisetin effectively inhibited the cell viability of not only parental cells but also histone deacetylase inhibitors-resistant (HDACis-R) cells and enhanced the chemosensitivity of HCC cells. Interestingly, fisetin did not induce cell apoptosis through the activation of the endoplasmic reticulum (ER) stress sensor of protein kinase R (PKR)-like endoplasmic reticulum kinase, but rather through the non-canonical pathway of the protein phosphatase 1 (PP1)-mediated suppression of eIF2α phosphorylation. Moreover, fisetin-induced cell apoptosis was reversed by treatment with PP1 activator or eIF2α siRNA in HCC cells. Based on these observations, we suggest that PP1-eIF2α pathways are significantly involved in the effect of fisetin on HCC apoptosis. Thus, fisetin may act as a novel anticancer drug and new chemotherapy adjuvant which can improve the efficacy of chemotherapeutic agents and diminish their side-effects.
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35
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Bowlt Blacklock KL, Birand Z, Selmic LE, Nelissen P, Murphy S, Blackwood L, Bass J, McKay J, Fox R, Beaver S, Starkey M. Genome-wide analysis of canine oral malignant melanoma metastasis-associated gene expression. Sci Rep 2019; 9:6511. [PMID: 31019223 PMCID: PMC6482147 DOI: 10.1038/s41598-019-42839-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 04/04/2019] [Indexed: 12/12/2022] Open
Abstract
Oral malignant melanoma (OMM) is the most common canine melanocytic neoplasm. Overlap between the somatic mutation profiles of canine OMM and human mucosal melanomas suggest a shared UV-independent molecular aetiology. In common with human mucosal melanomas, most canine OMM metastasise. There is no reliable means of predicting canine OMM metastasis, and systemic therapies for metastatic disease are largely palliative. Herein, we employed exon microarrays for comparative expression profiling of FFPE biopsies of 18 primary canine OMM that metastasised and 10 primary OMM that did not metastasise. Genes displaying metastasis-associated expression may be targets for anti-metastasis treatments, and biomarkers of OMM metastasis. Reduced expression of CXCL12 in the metastasising OMMs implies that the CXCR4/CXCL12 axis may be involved in OMM metastasis. Increased expression of APOBEC3A in the metastasising OMMs may indicate APOBEC3A-induced double-strand DNA breaks and pro-metastatic hypermutation. DNA double strand breakage triggers the DNA damage response network and two Fanconi anaemia DNA repair pathway members showed elevated expression in the metastasising OMMs. Cross-validation was employed to test a Linear Discriminant Analysis classifier based upon the RT-qPCR-measured expression levels of CXCL12, APOBEC3A and RPL29. Classification accuracies of 94% (metastasising OMMs) and 86% (non-metastasising OMMs) were estimated.
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Affiliation(s)
| | - Z Birand
- Animal Health Trust, Newmarket, Suffolk, UK
| | - L E Selmic
- Department of Veterinary Clinical Sciences, The Ohio State University, Columbus, Ohio, USA
| | - P Nelissen
- Dick White Referrals, Newmarket, Suffolk, UK
| | - S Murphy
- Animal Health Trust, Newmarket, Suffolk, UK
- The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - L Blackwood
- Institute of Veterinary Science, University of Liverpool, Liverpool, UK
| | - J Bass
- Animal Health Trust, Newmarket, Suffolk, UK
- Finn Pathologists, Harleston, UK
| | - J McKay
- IDEXX Laboratories, Ltd, Wetherby, UK
| | - R Fox
- Finn Pathologists, Harleston, UK
| | - S Beaver
- Nationwide Laboratory Services, Poulton-le-Fylde, UK
| | - M Starkey
- Animal Health Trust, Newmarket, Suffolk, UK.
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36
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IPP-1 controls Akt/CREB phosphorylation extension in A 2a adenosine receptor signaling cascade in MIN6 pancreatic β-cell line. Eur J Pharmacol 2019; 850:88-96. [PMID: 30772395 DOI: 10.1016/j.ejphar.2019.02.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 02/12/2019] [Accepted: 02/13/2019] [Indexed: 11/23/2022]
Abstract
Signaling through A2a adenosine receptor specifically prevent pancreatic β-cells (PBCs) loses under diabetogenic conditions. However, signaling mediators of this receptor in PBCs remained unidentified. Thus, we aimed to investigate the possible involvement of PKA/Akt/IPP-1/CREB pathway in MIN6 β-cells. In addition, we investigated IPP-1 role in A2a receptor signaling pathway. The expression of A2a receptor in MIN6 cell line was evaluated by RT-PCR and its functionality confirmed by quantification of cAMP in response to the CGS 21680, an A2a receptor agonist. MTT and Brdu assays were used to evaluate cell viability and proliferation, respectively. PKA activity and insulin release were evaluated using ELISA methods. P-Akt/Akt, p-IPP-1/IPP-1, and p-CREB/CREB levels were assessed using western blotting. IPP-1 knock down assessments was performed using specific siRNA. Our result revealed that MIN6 cells express A2a receptor which actively increased cAMP levels (with EC50 = 2.41 µM) and PKA activity. Activation of this receptor increased cell viability, proliferation and insulin release. Moreover, we mentioned A2a receptor stimulation increased p-Akt, p-IPP-1, and p-CREB levels in dose (max at 10 µM of CGS 21680) and time (max at 30 min after CGS 21680 treatment) dependent manner. Interestingly, herein, we found in IPP-1 knocked down cells, A2a receptor failed to activate Akt and CREB. Altogether, we mentioned that in MIN6 cells A2a receptor increase cell viability, proliferation and insulin release through PKA/Akt/IPP-1/CREB signaling pathway. In addition, we conclude A2a receptor signaling through this pathway is dependent to activation of IPP-1.
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37
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Xie XP, Xie YF, Liu YT, Wang HQ. Adaptively capturing the heterogeneity of expression for cancer biomarker identification. BMC Bioinformatics 2018; 19:401. [PMID: 30390627 PMCID: PMC6215657 DOI: 10.1186/s12859-018-2437-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 10/15/2018] [Indexed: 11/25/2022] Open
Abstract
Background Identifying cancer biomarkers from transcriptomics data is of importance to cancer research. However, transcriptomics data are often complex and heterogeneous, which complicates the identification of cancer biomarkers in practice. Currently, the heterogeneity still remains a challenge for detecting subtle but consistent changes of gene expression in cancer cells. Results In this paper, we propose to adaptively capture the heterogeneity of expression across samples in a gene regulation space instead of in a gene expression space. Specifically, we transform gene expression profiles into gene regulation profiles and mathematically formulate gene regulation probabilities (GRPs)-based statistics for characterizing differential expression of genes between tumor and normal tissues. Finally, an unbiased estimator (aGRP) of GRPs is devised that can interrogate and adaptively capture the heterogeneity of gene expression. We also derived an asymptotical significance analysis procedure for the new statistic. Since no parameter needs to be preset, aGRP is easy and friendly to use for researchers without computer programming background. We evaluated the proposed method on both simulated data and real-world data and compared with previous methods. Experimental results demonstrated the superior performance of the proposed method in exploring the heterogeneity of expression for capturing subtle but consistent alterations of gene expression in cancer. Conclusions Expression heterogeneity largely influences the performance of cancer biomarker identification from transcriptomics data. Models are needed that efficiently deal with the expression heterogeneity. The proposed method can be a standalone tool due to its capacity of adaptively capturing the sample heterogeneity and the simplicity in use. Software availability The source code of aGRP can be downloaded from https://github.com/hqwang126/aGRP. Electronic supplementary material The online version of this article (10.1186/s12859-018-2437-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xin-Ping Xie
- School of Mathematics and Physics, Anhui Jianzhu University, Hefei, 230022, Anhui, China
| | - Yu-Feng Xie
- School of Mathematics and Physics, Anhui Jianzhu University, Hefei, 230022, Anhui, China.,Institute of Intelligent Machines, Hefei Institutes of Physical Science, CAS, 350 Shushanhu Road, P.O.Box 1130, Hefei, 230031, Anhui, China.,Present Address: School of Electronics and Information, Northwestern Polytechnical University, Xi'an, 710100, China
| | - Yi-Tong Liu
- School of Mathematics and Physics, Anhui Jianzhu University, Hefei, 230022, Anhui, China.,Institute of Intelligent Machines, Hefei Institutes of Physical Science, CAS, 350 Shushanhu Road, P.O.Box 1130, Hefei, 230031, Anhui, China
| | - Hong-Qiang Wang
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, CAS, 350 Shushanhu Road, P.O.Box 1130, Hefei, 230031, Anhui, China.
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