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Banaszek N, Kurpiewska D, Kozak K, Rutkowski P, Sobczuk P. Hedgehog pathway in sarcoma: from preclinical mechanism to clinical application. J Cancer Res Clin Oncol 2023; 149:17635-17649. [PMID: 37815662 PMCID: PMC10657326 DOI: 10.1007/s00432-023-05441-3] [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: 07/27/2023] [Accepted: 09/20/2023] [Indexed: 10/11/2023]
Abstract
Sarcomas are a diverse group of malignant neoplasms of mesenchymal origin. They develop rarely, but due to poor prognosis, they are a challenging and significant clinical problem. Currently, available therapeutic options have very limited activity. A better understating of sarcomas' pathogenesis may help develop more effective therapies in the future. The Sonic hedgehog (Shh) signaling pathway is involved in both embryonic development and mature tissue repair and carcinogenesis. Shh pathway inhibitors are presently used in the treatment of basal cell carcinoma. Its increased activity has been demonstrated in many sarcomas, including osteosarcoma, Ewing sarcoma, chondrosarcoma, rhabdomyosarcoma, leiomyosarcoma, and malignant rhabdoid tumor. In vitro studies have demonstrated the effectiveness of inhibitors of the Hedgehog pathway in inhibiting proliferation in those sarcomas in which the components of the pathway are overexpressed. These results were confirmed by in vivo studies, which additionally proved the influence of Shh pathway inhibitors on limiting the metastatic potential of sarcoma cells. However, until now, the efficacy of sarcomas treatment with Shh pathway inhibitors has not been established in clinical trials. The reason for that may be the non-canonical activation of the pathway or interactions with other signaling pathways, such as Wnt or Notch. In this review, we present the Shh signaling pathway's role in the pathogenesis of sarcomas, including both canonical and non-canonical signaling. We also propose how this knowledge could be potentially translated into clinics.
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Affiliation(s)
- Natalia Banaszek
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Skłodowska-Curie National Research Institute of Oncology in Warsaw, Warsaw, Poland
- Faculty of Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Dominika Kurpiewska
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Skłodowska-Curie National Research Institute of Oncology in Warsaw, Warsaw, Poland
- Faculty of Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Katarzyna Kozak
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Skłodowska-Curie National Research Institute of Oncology in Warsaw, Warsaw, Poland
| | - Piotr Rutkowski
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Skłodowska-Curie National Research Institute of Oncology in Warsaw, Warsaw, Poland
| | - Paweł Sobczuk
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Skłodowska-Curie National Research Institute of Oncology in Warsaw, Warsaw, Poland.
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Iqbal H, Kim GL, Kim JH, Ghosh P, Shah M, Lee W, Rhee DK. Pneumococcal pep27-mutant inhibits Wnt5a expression via the regulation of T helper cells to attenuate colitis. Int Immunopharmacol 2022; 109:108927. [PMID: 35691272 DOI: 10.1016/j.intimp.2022.108927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 06/02/2022] [Accepted: 06/05/2022] [Indexed: 01/04/2023]
Abstract
Inflammatory bowel disease (IBD) is a chronic gut inflammatory disease characterized by extensive colitis and remission of the symptoms. The incidence rate and prevalence of IBD are increasing worldwide; IBD affects millions of people, has poorly defined etiology, and often results in a failure of pharmacological interventions. Regardless of the cause, mucosal healing is indispensable for the regeneration of inflamed mucosa to ensure intestinal homeostasis. Intranasal immunization with the pneumococcal pep27 mutant (Δpep27) has been reported as an avirulent and live vaccine that has been proposed to suppress immune-regulated disorders, eliciting long-lasting immunity. The dose-dependent activity of Δpep27 in the lungs was measured by transcriptome analysis to investigate the long-lasting immunogenic response against IBD. Novel therapeutic targets based on the modulation of Wnt signaling and T regulatory cells interconnected with other signaling cascades in the context of IBD were investigated by qPCR and immunoblotting. M1/M2 macrophages were quantified by FACS analysis. Dextran sulfate sodium-induced colitis induced significant upregulation of Th2 and Th17 as well as noncanonical Wnt5, which subsequently inhibited regulatory T (Treg) expression. In contrast, Δpep27 immunization significantly attenuated the levels of Wnt5, proinflammatory cytokines, oxidative stress parameters, and infiltration of inflammatory cells and enhanced barrier integrity via T helper cell homeostasis and upregulation of M2 macrophages. The data of the present study suggested that Δpep27-elicited Tregs were able to repress Wnt5a expression, assisting with the restoration of immunological tolerance and providing a robust regenerative and antioxidant milieu.
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Affiliation(s)
- Hamid Iqbal
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, South Korea
| | - Gyu-Lee Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, South Korea
| | - Ji-Hoon Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, South Korea
| | - Prachetash Ghosh
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, South Korea
| | - Masaud Shah
- Department of Physiology, Ajou University, Suwon 16499, South Korea
| | - Wonsik Lee
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, South Korea
| | - Dong-Kwon Rhee
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, South Korea; DNBIO Pharm. Inc., Research Center, Suwon 16419, South Korea.
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Gu HY, Qu WQ, Peng HH, Yu YF, Jiang ZZ, Qi BW, Yu AX. Stemness Subtypes and Scoring System Predict Prognosis and Efficacy of Immunotherapy in Soft Tissue Sarcoma. Front Immunol 2022; 13:796606. [PMID: 35464409 PMCID: PMC9022121 DOI: 10.3389/fimmu.2022.796606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 03/07/2022] [Indexed: 11/29/2022] Open
Abstract
Tumor stemness has been reported to play important roles in cancers. However, a comprehensive analysis of tumor stemness remains to be performed to investigate the specific mechanisms and practical values of stemness in soft tissue sarcomas (STS). Here, we applied machine learning to muti-omic data of patients from TCGA-SARC and GSE21050 cohorts to reveal important roles of stemness in STS. We demonstrated limited roles of existing mRNAsi in clinical application. Therefore, based on stemness-related signatures (SRSs), we identified three stemness subtypes with distinct stemness, immune, and metabolic characteristics using consensus clustering. The low-stemness subtype had better prognosis, activated innate and adaptive immunity (e.g., infiltrating B, DC, Th1, CD8+ T, activated NK, gamma delta T cells, and M1 macrophages), more enrichment of metabolic pathways, more sites with higher methylation level, higher gene mutations, CNA burdens, and immunogenicity indicators. Furthermore, the 16 SRS-based stemness prognostic index (SPi) was developed, and we found that low-SPi patients with low stemness had better prognosis and other characteristics similar to those in the low-stemness subtype. Besides, low-stemness subtype and low-SPi patients could benefit from immunotherapy. The predictive value of SPi in immunotherapy was more accurate after the addition of MSI into SPi. MSIlowSPilow patients might be more sensitive to immunotherapy. In conclusion, we highlighted mechanisms and practical values of the stemness in STS. We also recommended the combination of MSI and SPi which is a promising tool to predict prognosis and achieve precise treatments of immunotherapy in STS.
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Affiliation(s)
- Hui-Yun Gu
- Department of Orthopedics Trauma and Microsurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Wen-Qiang Qu
- Department of Orthopedics Trauma and Microsurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hai-Heng Peng
- Department of Orthopedics Trauma and Microsurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yi-Feng Yu
- Department of Orthopedics Trauma and Microsurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhe-Zhen Jiang
- Department of Orthopedics Trauma and Microsurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Bai-Wen Qi
- Department of Orthopedics Trauma and Microsurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ai-Xi Yu
- Department of Orthopedics Trauma and Microsurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
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Krausert S, Brabetz S, Mack NL, Schmitt-Hoffner F, Schwalm B, Peterziel H, Mangang A, Holland-Letz T, Sieber L, Korshunov A, Oehme I, Jäger N, Witt O, Pfister SM, Kool M. Predictive modeling of resistance to SMO-inhibition in a patient-derived orthotopic xenograft model of SHH medulloblastoma. Neurooncol Adv 2022; 4:vdac026. [PMID: 35475274 PMCID: PMC9034118 DOI: 10.1093/noajnl/vdac026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Background Inhibition of the sonic hedgehog (SHH) pathway with Smoothened (SMO) inhibitors is a promising treatment strategy in SHH-activated medulloblastoma, especially in adult patients. However, the problem is that tumors frequently acquire resistance to the treatment. To understand the underlying resistance mechanisms and to find ways to overcome the resistance, preclinical models that became resistant to SMO inhibition are needed. Methods To induce SMO inhibitor resistant tumors, we have treated a patient-derived xenograft (PDX) model of SHH medulloblastoma, sensitive to SMO inhibition, with 20 mg/kg Sonidegib using an intermitted treatment schedule. Vehicle-treated and resistant models were subjected to whole-genome and RNA sequencing for molecular characterization and target engagement. In vitro drug screens (76 drugs) were performed using Sonidegib-sensitive and -resistant lines to find other drugs to target the resistant lines. One of the top hits was then validated in vivo. Results Nine independent Sonidegib-resistant PDX lines were generated. Molecular characterization of the resistant models showed that eight models developed missense mutations in SMO and one gained an inactivating point mutation in MEGF8, which acts downstream of SMO as a repressor in the SHH pathway. The in vitro drug screen with Sonidegib-sensitive and -resistant lines identified good efficacy for Selinexor in the resistant line. Indeed, in vivo treatment with Selinexor revealed that it is more effective in resistant than in sensitive models. Conclusions We report the first human SMO inhibitor resistant medulloblastoma PDX models, which can be used for further preclinical experiments to develop the best strategies to overcome the resistance to SMO inhibitors in patients.
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Affiliation(s)
- Sonja Krausert
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Germany
| | - Sebastian Brabetz
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Germany
| | - Norman L Mack
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Felix Schmitt-Hoffner
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Germany
| | - Benjamin Schwalm
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Heike Peterziel
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), German Cancer Research Consortium (DKTK), Heidelberg, Germany
| | - Aileen Mangang
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), German Cancer Research Consortium (DKTK), Heidelberg, Germany
| | - Tim Holland-Letz
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Laura Sieber
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Andrey Korshunov
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg and Clinical Cooperation Unit Neuropathology, German Cancer Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ina Oehme
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), German Cancer Research Consortium (DKTK), Heidelberg, Germany
| | - Natalie Jäger
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Olaf Witt
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), German Cancer Research Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
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Jit BP, Pradhan B, Dash R, Bhuyan PP, Behera C, Behera RK, Sharma A, Alcaraz M, Jena M. Phytochemicals: Potential Therapeutic Modulators of Radiation Induced Signaling Pathways. Antioxidants (Basel) 2021; 11:antiox11010049. [PMID: 35052553 PMCID: PMC8773162 DOI: 10.3390/antiox11010049] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/22/2021] [Accepted: 12/24/2021] [Indexed: 02/06/2023] Open
Abstract
Ionizing radiation results in extensive damage to biological systems. The massive amount of ionizing radiation from nuclear accidents, radiation therapy (RT), space exploration, and the nuclear battlefield leads to damage to biological systems. Radiation injuries, such as inflammation, fibrosis, and atrophy, are characterized by genomic instability, apoptosis, necrosis, and oncogenic transformation, mediated by the activation or inhibition of specific signaling pathways. Exposure of tumors or normal cells to different doses of ionizing radiation could lead to the generation of free radical species, which can release signal mediators and lead to harmful effects. Although previous FDA-approved agents effectively mitigate radiation-associated toxicities, their use is limited due to their high cellular toxicities. Preclinical and clinical findings reveal that phytochemicals derived from plants that exhibit potent antioxidant activities efficiently target several signaling pathways. This review examined the prospective roles played by some phytochemicals in altering signal pathways associated with radiation response.
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Affiliation(s)
- Bimal Prasad Jit
- School of Life Sciences, Sambalpur University, Jyoti Vihar, Burla 768019, India; (B.P.J.); (R.D.); (R.K.B.)
- Department of Biochemistry, AIIMS, Ansari Nagar, New Delhi 110029, India;
| | - Biswajita Pradhan
- Algal Biotechnology and Molecular Systematic Laboratory, Post Graduate Department of Botany, Berhampur University, Bhanja Bihar, Berhampur 760007, India; (B.P.); (C.B.)
- Department of Biotechnology, Sangmyung University, Seoul 03016, Korea
| | - Rutumbara Dash
- School of Life Sciences, Sambalpur University, Jyoti Vihar, Burla 768019, India; (B.P.J.); (R.D.); (R.K.B.)
| | - Prajna Paramita Bhuyan
- Department of Botany, Maharaja Sriram Chandra Bhanja Deo University, Baripada 757003, India;
| | - Chhandashree Behera
- Algal Biotechnology and Molecular Systematic Laboratory, Post Graduate Department of Botany, Berhampur University, Bhanja Bihar, Berhampur 760007, India; (B.P.); (C.B.)
| | - Rajendra Kumar Behera
- School of Life Sciences, Sambalpur University, Jyoti Vihar, Burla 768019, India; (B.P.J.); (R.D.); (R.K.B.)
| | - Ashok Sharma
- Department of Biochemistry, AIIMS, Ansari Nagar, New Delhi 110029, India;
| | - Miguel Alcaraz
- Radiology and Physical Medicine Department, School of Medicine, Campus de Excelencia Internacional de Ámbito Regional (CEIR)-Campus Mare Nostrum (CMN), Universidad de Murcia, 30100 Murcia, Spain
- Correspondence: (M.A.); (M.J.); Tel.: +34-868883601 (M.A.); +91-7978478950 (M.J.)
| | - Mrutyunjay Jena
- Algal Biotechnology and Molecular Systematic Laboratory, Post Graduate Department of Botany, Berhampur University, Bhanja Bihar, Berhampur 760007, India; (B.P.); (C.B.)
- Correspondence: (M.A.); (M.J.); Tel.: +34-868883601 (M.A.); +91-7978478950 (M.J.)
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Patel TN, Dhanyamraju PK. Role of aberrant Sonic hedgehog signaling pathway in cancers and developmental anomalies. J Biomed Res 2021; 36:1-9. [PMID: 34963676 PMCID: PMC8894283 DOI: 10.7555/jbr.35.20210139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Development is a sophisticated process maintained by various signal transduction pathways, including the Hedgehog (Hh) pathway. Several important functions are executed by the Hh signaling cascade such as organogenesis, tissue regeneration, and tissue homeostasis, among various others. Considering the multiple functions carried out by this pathway, any mutation causing aberrant Hh signaling may lead to myriad developmental abnormalities besides cancers. In the present review article, we explored a wide range of diseases caused by aberrant Hh signaling, including developmental defects and cancers. Finally, we concluded this mini-review with various treatment strategies for Hh-induced diseases.
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Affiliation(s)
- Trupti N Patel
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore Campus, Vellore, Tamil Nadu 632014, India
| | - Pavan Kumar Dhanyamraju
- Department of Pharmacology, Penn State University College of Medicine, Hershey, PA 17033, USA.,Penn State Cancer Institute, Hershey, PA 17033, USA
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The Sarcoma Immune Landscape: Emerging Challenges, Prognostic Significance and Prospective Impact for Immunotherapy Approaches. Cancers (Basel) 2021; 13:cancers13030363. [PMID: 33498238 PMCID: PMC7863949 DOI: 10.3390/cancers13030363] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/19/2021] [Accepted: 01/19/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Sarcomas are a rare disease with high rates of recurrence and poor prognosis. Important discoveries about the biology of sarcomas have been done during the last decades, without a substantial improvement of systemic treatments. With the agnostic effectivity of immuno-oncological agents in different cancer indications, it is expected that sarcomas can also benefit from these treatments. This article gathers the available data on the specific immune tumor microenvironment of sarcoma and the immunotherapeutic strategies currently under investigation. Abstract Despite significant advances in multidisciplinary treatment strategies including surgery, radiotherapy, targeted therapy and chemotherapy there are yet no substantial improvements in the clinical benefit of patients with sarcomas. Current understanding of the underlying cellular and molecular pathways which govern the dynamic interactions between the tumor stroma, tumor cells and immune infiltrates in sarcoma tissues, led to the clinical development of new therapeutic options based on immunotherapies. Moreover, progress of the treatment of sarcomas also depends on the identification of biomarkers with prognostic and predictive values for selecting patients most likely to benefit from these new therapeutic treatments and also serving as potent therapeutic targets. Novel combinations with radiotherapy, chemotherapy, targeted therapy, vaccines, CAR-T cells and treatments targeting other immune components of the tumor microenvironment are underway aiming to bypass known resistance mechanisms. This review focuses on the role of tumor microenvironment in sarcoma, prognosis and response to novel immunotherapies.
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Dasgupta A, Sierra L, Tsang SV, Kurenbekova L, Patel T, Rajapakse K, Shuck RL, Rainusso N, Landesman Y, Unger T, Coarfa C, Yustein JT. Targeting PAK4 Inhibits Ras-Mediated Signaling and Multiple Oncogenic Pathways in High-Risk Rhabdomyosarcoma. Cancer Res 2021; 81:199-212. [PMID: 33168646 PMCID: PMC7878415 DOI: 10.1158/0008-5472.can-20-0854] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 09/15/2020] [Accepted: 11/04/2020] [Indexed: 11/16/2022]
Abstract
Rhabdomyosarcoma (RMS) is the most prevalent pediatric soft-tissue sarcoma. Multimodal treatment, including surgery and traditional chemotherapy with radiotherapy, has contributed to improvements in overall survival rates. However, patients with recurrent or metastatic disease have 5-year survival rates of less than 30%. One reason for the lack of therapeutic advancement is identification and targeting of critical signaling nodes. p21-activated kinases (PAK) are a family of serine/threonine kinases downstream of multiple critical tumorigenic receptor tyrosine kinase receptors and oncogenic regulators, including IGFR and RAS signaling, that significantly contribute to aggressive malignant phenotypes. Here, we report that RMS cell lines and tumors exhibit enhanced PAK4 expression levels and activity, which are further activated by growth factors involved in RMS development. Molecular perturbation of PAK4 in multiple RMS models in vitro and in vivo resulted in inhibition of RMS development and progression. Fusion-positive and -negative RMS models were sensitive to two PAK4 small-molecule inhibitors, PF-3758309 and KPT-9274, which elicited significant antitumor and antimetastatic potential in several primary and metastatic in vivo models, including a relapsed RMS patient-derived xenograft model. Transcriptomic analysis of PAK4-targeted tumors revealed inhibition of the RAS-GTPase, Hedgehog, and Notch pathways, along with evidence of activation of antitumor immune response signatures. This PAK4-targeting gene signature showed prognostic significance for patients with sarcoma. Overall, our results show for the first time that PAK4 is a novel and viable therapeutic target for the treatment of high-risk RMS. SIGNIFICANCE: These data demonstrate a novel oncogenic role for PAK4 in rhabdomyosarcoma and show that targeting PAK4 activity is a promising viable therapeutic option for advanced rhabdomyosarcoma.
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Affiliation(s)
- Atreyi Dasgupta
- Texas Children's Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of Medicine, Houston, Texas
| | - Laura Sierra
- Texas Children's Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of Medicine, Houston, Texas
| | - Susan V Tsang
- Integrative Molecular and Biological Sciences Program, Baylor College of Medicine, Houston, Texas
| | - Lyazat Kurenbekova
- Texas Children's Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of Medicine, Houston, Texas
| | - Tajhal Patel
- Texas Children's Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of Medicine, Houston, Texas
| | - Kimal Rajapakse
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Comprehensive Center, Baylor College of Medicine, Houston, Texas
| | - Ryan L Shuck
- Texas Children's Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of Medicine, Houston, Texas
| | - Nino Rainusso
- Texas Children's Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of Medicine, Houston, Texas
| | | | | | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Comprehensive Center, Baylor College of Medicine, Houston, Texas
| | - Jason T Yustein
- Texas Children's Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of Medicine, Houston, Texas.
- Integrative Molecular and Biological Sciences Program, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Comprehensive Center, Baylor College of Medicine, Houston, Texas
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Establishment and Characterization of a Sclerosing Spindle Cell Rhabdomyosarcoma Cell Line with a Complex Genomic Profile. Cells 2020; 9:cells9122668. [PMID: 33322555 PMCID: PMC7763666 DOI: 10.3390/cells9122668] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/29/2020] [Accepted: 12/05/2020] [Indexed: 02/07/2023] Open
Abstract
Sclerosing spindle cell rhabdomyosarcoma (SSRMS) is a rare rhabdomyosarcomas (RMS) subtype. Especially cases bearing a myogenic differentiation 1 (MYOD1) mutation are characterized by a high recurrence and metastasis rate, often leading to a fatal outcome. SSRMS cell lines are valuable in vitro models for studying disease mechanisms and for the preclinical evaluation of new therapeutic approaches. In this study, a cell line established from a primary SSRMS tumor of a 24-year-old female after multimodal chemotherapeutic pretreatment has been characterized in detail, including immunohistochemistry, growth characteristics, cytogenetic analysis, mutation analysis, evaluation of stem cell marker expression, differentiation potential, and tumorigenicity in mice. The cell line which was designated SRH exhibited a complex genomic profile, including several translocations and deletions. Array-comparative genomic hybridization (CGH) revealed an overall predominating loss of gene loci. The mesenchymal tumor origin was underlined by the expression of mesenchymal markers and potential to undergo adipogenic and osteogenic differentiation. Despite myogenic marker expression, terminal myogenic differentiation was inhibited, which might be elicited by the MYOD1 hotspot mutation. In vivo tumorigenicity could be confirmed after subcutaneous injection into NOD/SCID/γcnull mice. Summarized, the SRH cell line is the first adult SSRMS cell line available for preclinical research on this rare RMS subtype.
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10
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Cancer Stem Cells in Soft-Tissue Sarcomas. Cells 2020; 9:cells9061449. [PMID: 32532153 PMCID: PMC7349510 DOI: 10.3390/cells9061449] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/06/2020] [Accepted: 06/08/2020] [Indexed: 02/06/2023] Open
Abstract
Soft tissue sarcomas (STS) are a rare group of mesenchymal solid tumors with heterogeneous genetic profiles and clinical features. Systemic chemotherapy is the backbone treatment for advanced STS; however, STS frequently acquire resistance to standard therapies, which highlights the need to improve treatments and identify novel therapeutic targets. Increases in the knowledge of the molecular pathways that drive sarcomas have brought to light different molecular alterations that cause tumor initiation and progression. These findings have triggered a breakthrough of targeted therapies that are being assessed in clinical trials. Cancer stem cells (CSCs) exhibit mesenchymal stem cell (MSC) features and represent a subpopulation of tumor cells that play an important role in tumor progression, chemotherapy resistance, recurrence and metastasis. In fact, CSCs phenotypes have been identified in sarcomas, allied to drug resistance and tumorigenesis. Herein, we will review the published evidence of CSCs in STS, discussing the molecular characteristic of CSCs, the commonly used isolation techniques and the new possibilities of targeting CSCs as a way to improve STS treatment and consequently patient outcome.
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Abstract
Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children and represents a high-grade neoplasm of skeletal myoblast-like cells. Decades of clinical and basic research have gradually improved our understanding of the pathophysiology of RMS and helped to optimize clinical care. The two major subtypes of RMS, originally characterized on the basis of light microscopic features, are driven by fundamentally different molecular mechanisms and pose distinct clinical challenges. Curative therapy depends on control of the primary tumour, which can arise at many distinct anatomical sites, as well as controlling disseminated disease that is known or assumed to be present in every case. Sophisticated risk stratification for children with RMS incorporates various clinical, pathological and molecular features, and that information is used to guide the application of multifaceted therapy. Such therapy has historically included cytotoxic chemotherapy as well as surgery, ionizing radiation or both. This Primer describes our current understanding of RMS epidemiology, disease susceptibility factors, disease mechanisms and elements of clinical care, including diagnostics, risk-based care of newly diagnosed and relapsed disease and the prevention and management of late effects in survivors. We also outline potential opportunities to further translate new biological insights into improved clinical outcomes.
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Affiliation(s)
- Stephen X Skapek
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Andrea Ferrari
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Abha A Gupta
- Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Philip J Lupo
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Erin Butler
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Janet Shipley
- Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, Belmont, UK
| | - Frederic G Barr
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Douglas S Hawkins
- Seattle Children's Hospital, University of Washington, and Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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Genadry KC, Pietrobono S, Rota R, Linardic CM. Soft Tissue Sarcoma Cancer Stem Cells: An Overview. Front Oncol 2018; 8:475. [PMID: 30416982 PMCID: PMC6212576 DOI: 10.3389/fonc.2018.00475] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 10/05/2018] [Indexed: 12/18/2022] Open
Abstract
Soft tissue sarcomas (STSs) are an uncommon group of solid tumors that can arise throughout the human lifespan. Despite their commonality as non-bony cancers that develop from mesenchymal cell precursors, they are heterogeneous in their genetic profiles, histology, and clinical features. This has made it difficult to identify a single target or therapy specific to STSs. And while there is no one cell of origin ascribed to all STSs, the cancer stem cell (CSC) principle—that a subpopulation of tumor cells possesses stem cell-like properties underlying tumor initiation, therapeutic resistance, disease recurrence, and metastasis—predicts that ultimately it should be possible to identify a feature common to all STSs that could function as a therapeutic Achilles' heel. Here we review the published evidence for CSCs in each of the most common STSs, then focus on the methods used to study CSCs, the developmental signaling pathways usurped by CSCs, and the epigenetic alterations critical for CSC identity that may be useful for further study of STS biology. We conclude with discussion of some challenges to the field and future directions.
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Affiliation(s)
- Katia C Genadry
- Division of Hematology-Oncology, Department of Pediatrics, Duke University Medical Center, Durham, NC, United States
| | - Silvia Pietrobono
- Department of Hematology-Oncology, Bambino Gesù Pediatric Hospital, IRCCS, Rome, Italy
| | - Rossella Rota
- Department of Hematology-Oncology, Bambino Gesù Pediatric Hospital, IRCCS, Rome, Italy
| | - Corinne M Linardic
- Division of Hematology-Oncology, Department of Pediatrics, Duke University Medical Center, Durham, NC, United States.,Department of Pharmacology & Cancer Biology, Duke University Medical Center, Durham, NC, United States
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Diao Y, Azatyan A, Rahman MFU, Zhao C, Zhu J, Dahlman-Wright K, Zaphiropoulos PG. Blockade of the Hedgehog pathway downregulates estrogen receptor alpha signaling in breast cancer cells. Oncotarget 2018; 7:71580-71593. [PMID: 27689403 PMCID: PMC5342103 DOI: 10.18632/oncotarget.12259] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 09/19/2016] [Indexed: 02/07/2023] Open
Abstract
Anti-estrogen treatment, exemplified by tamoxifen, is a well-established adjuvant therapy for estrogen receptor alpha (ERα)-positive breast cancer. However, the effectiveness of this drug is limited due to the development of resistance. The Hedgehog (HH) signaling pathway is critical in embryonic development, and aberrant activation of this transduction cascade is linked to various malignancies. However, it remains unclear whether HH signaling is activated in human breast cancer and related to tamoxifen resistance. Deciphering how this pathway may be involved in breast cancer is a crucial step towards the establishment of targeted combinatorial treatments for this disease. Here, we show that the expression of the HH signaling effector protein GLI1 is higher in tamoxifen resistant compared to sensitive cells. Tamoxifen resistant cells have stronger ERα transcriptional activity relative to sensitive cells, even though the ERα expression is similar in both cell types. Knockdown of GLI1 attenuates cell proliferation and reduces ERα transcriptional activity in both sensitive and resistant cells, irrespective of estrogen stimulation. Combinatorial treatment of tamoxifen and the GLI antagonist GANT61 further suppresses the growth of sensitive and resistant cells relative to administration of only tamoxifen, and this was irrespective of estrogen stimulation. Moreover, a positive correlation between GLI1 and ERα expression was identified in breast cancer samples. Additionally, high GLI1 expression predicted worse distant metastasis-free survival in breast cancer patients. These data suggest that the HH pathway may be a new candidate for therapeutic targeting and prognosis in ERα-positive breast cancer.
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Affiliation(s)
- Yumei Diao
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Ani Azatyan
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | | | - Chunyan Zhao
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Jian Zhu
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Karin Dahlman-Wright
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
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Xiao Q, Chen Z, Jin X, Mao R, Chen Z. The many postures of noncanonical Wnt signaling in development and diseases. Biomed Pharmacother 2017. [PMID: 28651237 DOI: 10.1016/j.biopha.2017.06.061] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Wnt signaling regulates many aspects of vertebrate development. Its dysregulation causes developmental defects and diseases including cancer. The signaling can be categorized in two pathways: canonical and noncanonical. Canonical pathway plays a key role in regulating proliferation and differentiation of cells whilst noncanonical Wnt signaling mainly controls cellular polarity and motility. During development, noncanonical Wnt signaling is required for tissue formation. Recent studies have shown that noncanonical Wnt signaling is involved in adult tissue development and cancer progression. In this review, we try to describe and discuss the mechanisms behind the biological effects of noncanonical Wnt signaling, diseases caused by its dysregulation, and implications in adult tissue development biology.
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Affiliation(s)
- Qian Xiao
- Senior Research Scientist, Department of Pharmacology, School of Medicine, Yale University, New Haven, USA
| | - Zhengxi Chen
- PhD, Department of Orthodontics, Ninth People's Hospital, School of Stomatology, Shanghai Key Laboratory of Stomatology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaozhuang Jin
- PhD, Faculty of Dentistry, The University of Hong Kong, Hong Kong
| | - Runyi Mao
- MDS student, Department of Oral and Maxillofacial Surgery, Ninth People's Hospital, School of Stomatology, Shanghai Key Laboratory of Stomatology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhenqi Chen
- Professor, Department of Orthodontics, Ninth People's Hospital, School of Stomatology, Shanghai Key Laboratory of Stomatology, Shanghai Jiao Tong University, Shanghai, China
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Hedgehog Pathway Inhibition Hampers Sphere and Holoclone Formation in Rhabdomyosarcoma. Stem Cells Int 2017; 2017:7507380. [PMID: 28243259 PMCID: PMC5294584 DOI: 10.1155/2017/7507380] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 12/02/2016] [Accepted: 12/28/2016] [Indexed: 01/06/2023] Open
Abstract
Rhabdomyosarcoma (RMS) is the most common type of soft tissue sarcoma in children and can be divided into two main subtypes: embryonal (eRMS) and alveolar (aRMS). Among the cellular heterogeneity of tumors, the existence of a small fraction of cells called cancer stem cells (CSC), thought to be responsible for the onset and propagation of cancer, has been demonstrated in some neoplasia. Although the existence of CSC has been reported for eRMS, their existence in aRMS, the most malignant subtype, has not been demonstrated to date. Given the lack of suitable markers to identify this subpopulation in aRMS, we used cancer stem cell-enriched supracellular structures (spheres and holoclones) to study this subpopulation. This strategy allowed us to demonstrate the capacity of both aRMS and eRMS cells to form these structures and retain self-renewal capacity. Furthermore, cells contained in spheres and holoclones showed significant Hedgehog pathway induction, the inhibition of which (pharmacologic or genetic) impairs the formation of both holoclones and spheres. Our findings point to a crucial role of this pathway in the maintenance of these structures and suggest that Hedgehog pathway targeting in CSC may have great potential in preventing local relapses and metastases.
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Liu X, Shen Q, Yu T, Huang H, Zhang Z, Ding J, Tang Y, Xu N, Yue S. Small GTPase Arl6 controls RH30 rhabdomyosarcoma cell growth through ciliogenesis and Hedgehog signaling. Cell Biosci 2016; 6:61. [PMID: 27999656 PMCID: PMC5154108 DOI: 10.1186/s13578-016-0126-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 11/28/2016] [Indexed: 12/04/2022] Open
Abstract
Background Rhabdomyosarcoma (RMS) originates from skeletal muscle precursors that fail to differentiate. Hedgehog (Hh) signaling and primary cilia contribute to the pathobiology of RMS. Results Here we showed ADP ribosylation factor like GTPase 6 (ARL6) localizes at the base of primary cilium, controls ciliogenesis and Hh signaling. The transcription of Arl6 is dynamic during the differentiation of myoblasts, companying with the growth and elimination of primary cilia. Arl6 expression is significantly up regulated in cilia-dependent RMS cells and tissues. Knockdown of Arl6 inhibits proliferation and promotes apoptosis of RMS RH30 cells through defected ciliogenesis and reduced Hh activity. Conclusions Taken together, the functions of Arl6 in ciliogenesis and Hh signaling suggest it as a potential RMS drug target. Electronic supplementary material The online version of this article (doi:10.1186/s13578-016-0126-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaotong Liu
- Department of Developmental Genetics, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166 Jiangsu People's Republic of China
| | - Qiuhong Shen
- Department of Developmental Genetics, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166 Jiangsu People's Republic of China
| | - Tingting Yu
- Department of Developmental Genetics, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166 Jiangsu People's Republic of China
| | - Huijie Huang
- Department of Developmental Genetics, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166 Jiangsu People's Republic of China
| | - Ziyu Zhang
- Department of Developmental Genetics, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166 Jiangsu People's Republic of China
| | - Jie Ding
- Department of Developmental Genetics, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166 Jiangsu People's Republic of China
| | - Ying Tang
- Department of Developmental Genetics, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166 Jiangsu People's Republic of China.,Central Laboratory, The First People's Hospital of Wujiang District, Suzhou, 215200 People's Republic of China
| | - Ning Xu
- Department of Pathology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166 Jiangsu People's Republic of China
| | - Shen Yue
- Department of Developmental Genetics, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166 Jiangsu People's Republic of China
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Dezaki ES, Yaghoobi MM, Taheri E, Almani PG, Tohidi F, Gottstein B, Harandi MF. Differential Expression of Hox and Notch Genes in Larval and Adult Stages of Echinococcus granulosus. THE KOREAN JOURNAL OF PARASITOLOGY 2016; 54:653-658. [PMID: 27853123 PMCID: PMC5127546 DOI: 10.3347/kjp.2016.54.5.653] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 05/10/2016] [Accepted: 05/13/2016] [Indexed: 12/20/2022]
Abstract
This investigation aimed to evaluate the differential expression of HoxB7 and notch genes in different developmental stages of Echinococcus granulosus sensu stricto. The expression of HoxB7 gene was observed at all developmental stages. Nevertheless, significant fold differences in the expression level was documented in the juvenile worm with 3 or more proglottids, the germinal layer from infected sheep, and the adult worm from an experimentally infected dog. The notch gene was expressed at all developmental stages of E. granulosus; however, the fold difference was significantly increased at the microcysts in monophasic culture medium and the germinal layer of infected sheep in comparison with other stages. The findings demonstrated that the 2 aforementioned genes evaluated in the present study were differentially expressed at different developmental stages of the parasite and may contribute to some important biological processes of E. granulosus.
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Affiliation(s)
- Ebrahim Saedi Dezaki
- Research Center for Hydatid Disease in Iran, School of Medicine, Kerman University of Medical Sciences, Kerman 7615614115, Iran
| | - Mohammad Mehdi Yaghoobi
- Research Department of Biotechnology, Institute of Sciences and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Elham Taheri
- Department of Pathology, School of Medicine, Kerman University of Medical Sciences, Kerman 7615614115, Iran
| | - Pooya Ghaseminejad Almani
- Research Center for Hydatid Disease in Iran, School of Medicine, Kerman University of Medical Sciences, Kerman 7615614115, Iran
| | - Farideh Tohidi
- Research Center for Hydatid Disease in Iran, School of Medicine, Kerman University of Medical Sciences, Kerman 7615614115, Iran
| | - Bruno Gottstein
- Institute of Parasitology, Faculty of Medicine and Vetsuisse Faculty of the University of Bern, Bern, Switzerland
| | - Majid Fasihi Harandi
- Research Center for Hydatid Disease in Iran, School of Medicine, Kerman University of Medical Sciences, Kerman 7615614115, Iran
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Skowron MA, Niegisch G, Fritz G, Arent T, van Roermund JGH, Romano A, Albers P, Schulz WA, Hoffmann MJ. Phenotype plasticity rather than repopulation from CD90/CK14+ cancer stem cells leads to cisplatin resistance of urothelial carcinoma cell lines. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2015; 34:144. [PMID: 26606927 PMCID: PMC4660687 DOI: 10.1186/s13046-015-0259-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 11/14/2015] [Indexed: 02/12/2023]
Abstract
BACKGROUND Tumour heterogeneity and resistance to systemic treatment in urothelial carcinoma (UC) may arise from cancer stem cells (CSC). A recent model describes cellular differentiation states within UC based on corresponding expression of surface markers (CD) and cytokeratins (CK) with CD90 and CK14 positive cells representing the least differentiated and most tumourigenic population. Based on the fact that this population is postulated to constitute CSCs and the origin of cisplatin resistance, we enriched urothelial carcinoma cell lines (UCCs) for CD90 and studied the tumour-initiating potential of these separated cells in vitro. METHODS Magnetic- and fluorescence-activated- cell sorting were used for separation of CD90(+) and CD90(-) UCCs. Distribution of cell surface markers CD90, CD44, and CD49f and cytokeratins CK14, CK5, and CK20 as well as the effects of short- and long-term treatment with cisplatin were assessed in vitro and measured by qRT-PCR, immunocytochemistry, reporter assay and flow cytometry in 11 UCCs. RESULTS We observed cell populations with surface markers according to those reported in tumour xenografts. However, expression of cytokeratins did not concord regularly with that of the surface markers. In particular, expression of CD90 and CK14 diverged during enrichment of CD90(+) cells by immunomagnetic sorting or following cisplatin treatment. Enriched CD90(+) cells did not exhibit CSC-like characteristics like enhanced clonogenicity and cisplatin resistance. Moreover, selection of cisplatin-resistant sublines by long-term drug treatment did not result in enrichment of CD90(+) cells. Rather, these sublines displayed significant phenotypic plasticity expressing EMT markers, an altered pattern of CKs, and WNT-pathway target genes. CONCLUSIONS Our findings indicate that the correspondence between CD surface markers and cytokeratins reported in xenografts is not maintained in commonly used UCCs and that CD90 may not be a stable marker of CSC in UC. Moreover, UCCs cells are capable of substantial phenotypic plasticity that may significantly contribute to the emergence of cisplatin resistance.
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Affiliation(s)
- Margaretha A Skowron
- Department of Urology, Medical Faculty, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225, Düsseldorf, Germany.
| | - Günter Niegisch
- Department of Urology, Medical Faculty, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225, Düsseldorf, Germany.
| | - Gerhard Fritz
- Institute of Toxicology, Medical Faculty, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225, Düsseldorf, Germany.
| | - Tanja Arent
- Department of Forensic Medicine, Medical Faculty, Heinrich-Heine-University Duesseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany.
| | - Joep G H van Roermund
- Department of Urology, Maastricht University Medical Centre, P. Debyelaan 25, 6202, AZ, Maastricht, The Netherlands.
| | - Andrea Romano
- Department of Obstetrics and Gynaecology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Centre, P. Debyelaan 25, 6202, AZ, Maastricht, The Netherlands.
| | - Peter Albers
- Department of Urology, Medical Faculty, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225, Düsseldorf, Germany.
| | - Wolfgang A Schulz
- Department of Urology, Medical Faculty, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225, Düsseldorf, Germany.
| | - Michèle J Hoffmann
- Department of Urology, Medical Faculty, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225, Düsseldorf, Germany.
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Takebe N, Miele L, Harris PJ, Jeong W, Bando H, Kahn M, Yang SX, Ivy SP. Targeting Notch, Hedgehog, and Wnt pathways in cancer stem cells: clinical update. Nat Rev Clin Oncol 2015; 12:445-64. [PMID: 25850553 PMCID: PMC4520755 DOI: 10.1038/nrclinonc.2015.61] [Citation(s) in RCA: 920] [Impact Index Per Article: 102.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
During the past decade, cancer stem cells (CSCs) have been increasingly identified in many malignancies. Although the origin and plasticity of these cells remain controversial, tumour heterogeneity and the presence of small populations of cells with stem-like characteristics is established in most malignancies. CSCs display many features of embryonic or tissue stem cells, and typically demonstrate persistent activation of one or more highly conserved signal transduction pathways involved in development and tissue homeostasis, including the Notch, Hedgehog (HH), and Wnt pathways. CSCs generally have slow growth rates and are resistant to chemotherapy and/or radiotherapy. Thus, new treatment strategies targeting these pathways to control stem-cell replication, survival and differentiation are under development. Herein, we provide an update on the latest advances in the clinical development of such approaches, and discuss strategies for overcoming CSC-associated primary or acquired resistance to cancer treatment. Given the crosstalk between the different embryonic developmental signalling pathways, as well as other pathways, designing clinical trials that target CSCs with rational combinations of agents to inhibit possible compensatory escape mechanisms could be of particular importance. We also share our views on the future directions for targeting CSCs to advance the clinical development of these classes of agents.
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Affiliation(s)
- Naoko Takebe
- Investigational Drug Branch, Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institute of Health, 9609 Medical Center Drive MSC9739, Bethesda, MD 20852, USA (N.T., P.J.H., S.P.I.). Stanley Scott Cancer Center, Louisiana State University Health Sciences Center and Louisiana Cancer Research Consortium, USA (L.M.). Cancer Therapy and Research Center, University of Texas, USA (W.J.). Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Japan (H.B.). Norris Comprehensive Cancer Research Center, University of Southern California, USA (M.K.). National Clinical Target Validation Laboratory, Division of Cancer Treatment and Diagnosis, National Cancer Institute, USA (S.X.Y.)
| | - Lucio Miele
- Investigational Drug Branch, Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institute of Health, 9609 Medical Center Drive MSC9739, Bethesda, MD 20852, USA (N.T., P.J.H., S.P.I.). Stanley Scott Cancer Center, Louisiana State University Health Sciences Center and Louisiana Cancer Research Consortium, USA (L.M.). Cancer Therapy and Research Center, University of Texas, USA (W.J.). Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Japan (H.B.). Norris Comprehensive Cancer Research Center, University of Southern California, USA (M.K.). National Clinical Target Validation Laboratory, Division of Cancer Treatment and Diagnosis, National Cancer Institute, USA (S.X.Y.)
| | - Pamela Jo Harris
- Investigational Drug Branch, Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institute of Health, 9609 Medical Center Drive MSC9739, Bethesda, MD 20852, USA (N.T., P.J.H., S.P.I.). Stanley Scott Cancer Center, Louisiana State University Health Sciences Center and Louisiana Cancer Research Consortium, USA (L.M.). Cancer Therapy and Research Center, University of Texas, USA (W.J.). Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Japan (H.B.). Norris Comprehensive Cancer Research Center, University of Southern California, USA (M.K.). National Clinical Target Validation Laboratory, Division of Cancer Treatment and Diagnosis, National Cancer Institute, USA (S.X.Y.)
| | - Woondong Jeong
- Investigational Drug Branch, Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institute of Health, 9609 Medical Center Drive MSC9739, Bethesda, MD 20852, USA (N.T., P.J.H., S.P.I.). Stanley Scott Cancer Center, Louisiana State University Health Sciences Center and Louisiana Cancer Research Consortium, USA (L.M.). Cancer Therapy and Research Center, University of Texas, USA (W.J.). Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Japan (H.B.). Norris Comprehensive Cancer Research Center, University of Southern California, USA (M.K.). National Clinical Target Validation Laboratory, Division of Cancer Treatment and Diagnosis, National Cancer Institute, USA (S.X.Y.)
| | - Hideaki Bando
- Investigational Drug Branch, Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institute of Health, 9609 Medical Center Drive MSC9739, Bethesda, MD 20852, USA (N.T., P.J.H., S.P.I.). Stanley Scott Cancer Center, Louisiana State University Health Sciences Center and Louisiana Cancer Research Consortium, USA (L.M.). Cancer Therapy and Research Center, University of Texas, USA (W.J.). Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Japan (H.B.). Norris Comprehensive Cancer Research Center, University of Southern California, USA (M.K.). National Clinical Target Validation Laboratory, Division of Cancer Treatment and Diagnosis, National Cancer Institute, USA (S.X.Y.)
| | - Michael Kahn
- Investigational Drug Branch, Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institute of Health, 9609 Medical Center Drive MSC9739, Bethesda, MD 20852, USA (N.T., P.J.H., S.P.I.). Stanley Scott Cancer Center, Louisiana State University Health Sciences Center and Louisiana Cancer Research Consortium, USA (L.M.). Cancer Therapy and Research Center, University of Texas, USA (W.J.). Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Japan (H.B.). Norris Comprehensive Cancer Research Center, University of Southern California, USA (M.K.). National Clinical Target Validation Laboratory, Division of Cancer Treatment and Diagnosis, National Cancer Institute, USA (S.X.Y.)
| | - Sherry X. Yang
- Investigational Drug Branch, Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institute of Health, 9609 Medical Center Drive MSC9739, Bethesda, MD 20852, USA (N.T., P.J.H., S.P.I.). Stanley Scott Cancer Center, Louisiana State University Health Sciences Center and Louisiana Cancer Research Consortium, USA (L.M.). Cancer Therapy and Research Center, University of Texas, USA (W.J.). Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Japan (H.B.). Norris Comprehensive Cancer Research Center, University of Southern California, USA (M.K.). National Clinical Target Validation Laboratory, Division of Cancer Treatment and Diagnosis, National Cancer Institute, USA (S.X.Y.)
| | - S. Percy Ivy
- Investigational Drug Branch, Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institute of Health, 9609 Medical Center Drive MSC9739, Bethesda, MD 20852, USA (N.T., P.J.H., S.P.I.). Stanley Scott Cancer Center, Louisiana State University Health Sciences Center and Louisiana Cancer Research Consortium, USA (L.M.). Cancer Therapy and Research Center, University of Texas, USA (W.J.). Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Japan (H.B.). Norris Comprehensive Cancer Research Center, University of Southern California, USA (M.K.). National Clinical Target Validation Laboratory, Division of Cancer Treatment and Diagnosis, National Cancer Institute, USA (S.X.Y.)
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Abstract
Embryonal rhabdomyosarcoma is one of the major defined histologic variants of rhabdomyosarcoma that is mainly reported in children. The histologic appearance of this neoplastic entity recapitulates normal myogenesis. The tumor cells variably exhibit the different cellular phases of myogenesis ranging from undifferentiated mesenchymal cells to elongated myoblasts, multinucleated myotubes and differentiated muscle fibers. The carefully orchestrated embryonic signaling pathways that are involved in myogenesis, conceivably also result in the genesis of rhabdomyosarcoma; albeit as a corollary to an imbalance. We have attempted to review the pathogenesis of embryonal rhabdomyosarcoma in an endeavor to understand better, how closely it is linked to normal myogenesis in terms of its molecular dynamics and histologic presentation.
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Petrova R, Joyner AL. Roles for Hedgehog signaling in adult organ homeostasis and repair. Development 2014; 141:3445-57. [PMID: 25183867 DOI: 10.1242/dev.083691] [Citation(s) in RCA: 286] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The hedgehog (HH) pathway is well known for its mitogenic and morphogenic functions during development, and HH signaling continues in discrete populations of cells within many adult mammalian tissues. Growing evidence indicates that HH regulates diverse quiescent stem cell populations, but the exact roles that HH signaling plays in adult organ homeostasis and regeneration remain poorly understood. Here, we review recently identified functions of HH in modulating the behavior of tissue-specific adult stem and progenitor cells during homeostasis, regeneration and disease. We conclude that HH signaling is a key factor in the regulation of adult tissue homeostasis and repair, acting via multiple different routes to regulate distinct cellular outcomes, including maintenance of plasticity, in a context-dependent manner.
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Affiliation(s)
- Ralitsa Petrova
- Developmental Biology Program, Sloan-Kettering Institute, 1275 York Avenue, New York, NY 10065, USA BCMB Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Alexandra L Joyner
- Developmental Biology Program, Sloan-Kettering Institute, 1275 York Avenue, New York, NY 10065, USA BCMB Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
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HES1 as an Independent Prognostic Marker in Esophageal Squamous Cell Carcinoma. J Gastrointest Cancer 2014; 45:466-71. [DOI: 10.1007/s12029-014-9648-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Primary cilia control hedgehog signaling during muscle differentiation and are deregulated in rhabdomyosarcoma. Proc Natl Acad Sci U S A 2014; 111:9151-6. [PMID: 24927541 DOI: 10.1073/pnas.1323265111] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The primary cilium acts as a cellular antenna, transducing diverse signaling pathways, and recent evidence suggests that primary cilia are important in development and cancer. However, a role for cilia in normal muscle development and rhabdomyosarcoma (RMS) has not been explored. Here we implicate primary cilia in proliferation, hedgehog (Hh) signaling, and differentiation of skeletal muscle cells. Cilia and Hh signaling are highly dynamic during the differentiation of myoblasts. We show that cilia are assembled during the initial stages of myogenic differentiation but disappear as cells progress through myogenesis, concomitant with the destruction of proteins critical for cilia assembly and shortly after the Hh effector, Gli3, leaves the cilium. Importantly, we show that ablation of primary cilia strongly suppresses Hh signaling and myogenic differentiation while enhancing proliferation. Interestingly, our data further indicate that both cilia assembly and Hh signaling are deregulated in RMS, and cilia respond to Hh ligand in certain subsets of RMS cells but not others. Together, these findings provide evidence for an essential role for both primary cilia assembly and disassembly in the control of Hh signaling and early differentiation in muscle cells. We suggest that the temporally orchestrated destruction of centrosomal and ciliary proteins is a necessary antecedent for removal of the primary cilium and cessation of Hh signaling during myogenic differentiation. Additionally, our results further stratify RMS populations and highlight cilia assembly and disassembly as potential RMS drug targets.
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Cieśla M, Dulak J, Józkowicz A. MicroRNAs and epigenetic mechanisms of rhabdomyosarcoma development. Int J Biochem Cell Biol 2014; 53:482-92. [PMID: 24831881 DOI: 10.1016/j.biocel.2014.05.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 05/04/2014] [Accepted: 05/05/2014] [Indexed: 01/10/2023]
Abstract
Rhabdomyosarcoma is the most common type of soft tissue sarcoma in children. Two main subtypes of rhabdomyosarcoma with different molecular pattern and distinct clinical behaviour may be identified - embryonal and alveolar rhabdomyosarcoma. All types of rhabdomyosarcoma are believed to be of myogenic origin as they express high levels of myogenesis-related factors. They all, however, fail to undergo a terminal differentiation which results in tumour formation. In the aberrant regulation of myogenesis in rhabdomyosarcoma, microRNAs and epigenetic factors are particularly involved. Indeed, these mediators seem to be even more significant for the development of rhabdomyosarcoma than canonical myogenic transcription factors like MyoD, a master regulatory switch for myogenesis. Therefore, in this review we focus on the regulation of rhabdomyosarcoma progression by microRNAs, and especially on microRNAs of the myo-miRNAs family (miR-1, -133a/b and -206), other well-known myogenic regulators like miR-29, and on microRNAs recently recognized to play a role in the differentiation of rhabdomyosarcoma, such as miR-450b-5p or miR-203. We also review changes in epigenetic modifiers associated with rhabdomyosarcoma, namely histone deacetylases and methyltransferases, especially from the Polycomp Group, like Yin Yang1 and Enhancer of Zeste Homolog2. Finally, we summarize how the functioning of these molecules can be affected by oxidative stress and how antioxidative enzymes can influence the development of this tumour. This article is part of a Directed Issue entitled: Rare Cancers.
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Affiliation(s)
- Maciej Cieśla
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Gronostajowa 7, 30-387 Krakow, Poland
| | - Józef Dulak
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Gronostajowa 7, 30-387 Krakow, Poland.
| | - Alicja Józkowicz
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Gronostajowa 7, 30-387 Krakow, Poland.
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Mbodj A, Junion G, Brun C, Furlong EEM, Thieffry D. Logical modelling of Drosophila signalling pathways. MOLECULAR BIOSYSTEMS 2014; 9:2248-58. [PMID: 23868318 DOI: 10.1039/c3mb70187e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A limited number of signalling pathways are involved in the specification of cell fate during the development of all animals. Several of these pathways were originally identified in Drosophila. To clarify their roles, and possible cross-talk, we have built a logical model for the nine key signalling pathways recurrently used in metazoan development. In each case, we considered the associated ligands, receptors, signal transducers, modulators, and transcription factors reported in the literature. Implemented using the logical modelling software GINsim, the resulting models qualitatively recapitulate the main characteristics of each pathway, in wild type as well as in various mutant situations (e.g. loss-of-function or gain-of-function). These models constitute pluggable modules that can be used to assemble comprehensive models of complex developmental processes. Moreover, these models of Drosophila pathways could serve as scaffolds for more complicated models of orthologous mammalian pathways. Comprehensive model annotations and GINsim files are provided for each of the nine considered pathways.
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Affiliation(s)
- Abibatou Mbodj
- Technological Advances for Genomics and Clinics (TAGC), INSERM UMR_S 1090, Aix-Marseille Université, Marseille, France.
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Radaelli S, Stacchiotti S, Casali PG, Gronchi A. Emerging therapies for adult soft tissue sarcoma. Expert Rev Anticancer Ther 2014; 14:689-704. [DOI: 10.1586/14737140.2014.885840] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Characterization of Wnt/β-catenin signaling in rhabdomyosarcoma. J Transl Med 2013; 93:1090-9. [PMID: 23999248 DOI: 10.1038/labinvest.2013.97] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Revised: 07/06/2013] [Accepted: 07/07/2013] [Indexed: 11/09/2022] Open
Abstract
Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children and accounts for about 5% of all malignant paediatric tumours. β-Catenin, a multifunctional nuclear transcription factor in the canonical Wnt signaling pathway, is active in myogenesis and embryonal somite patterning. Dysregulation of Wnt signaling facilitates tumour invasion and metastasis. This study characterizes Wnt/β-catenin signaling and functional activity in paediatric embryonal and alveolar RMS. Immunohistochemical assessment of paraffin-embedded tissues from 44 RMS showed β-catenin expression in 26 cases with cytoplasmic/membranous expression in 9/14 cases of alveolar RMS, and 15/30 cases of embryonal RMS, whereas nuclear expression was only seen in 2 cases of embryonal RMS. The potential functional significance of β-catenin expression was tested in four RMS cell lines, two derived from embryonal (RD and RD18) RMS and two from alveolar (Rh4 and Rh30) RMS. Western blot analysis demonstrated the expression of Wnt-associated proteins including β-catenin, glycogen synthase kinase-3β, disheveled, axin-1, naked, LRP-6 and cadherins in all cell lines. Cell fractionation and immunofluorescence studies of the cell lines (after stimulation by human recombinant Wnt3a) showed reduced phosphorylation of β-catenin, stabilization of the active cytosolic form and nuclear translocation of β-catenin. Reporter gene assay demonstrated a T-cell factor/lymphoid-enhancing factor-mediated transactivation in these cells. In response to human recombinant Wnt3a, the alveolar RMS cells showed a significant decrease in proliferation rate and induction of myogenic differentiation (myogenin, MyoD1 and myf5). These data indicate that the central regulatory components of canonical Wnt/β-catenin signaling are expressed and that this pathway is functionally active in a significant subset of RMS tumours and might represent a novel therapeutic target.
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Xie L, Ng C, Ali T, Valencia R, Ferreira BL, Xue V, Tanweer M, Zhou D, Haddad GG, Bourne PE, Xie L. Multiscale modeling of the causal functional roles of nsSNPs in a genome-wide association study: application to hypoxia. BMC Genomics 2013; 14 Suppl 3:S9. [PMID: 23819581 PMCID: PMC3665574 DOI: 10.1186/1471-2164-14-s3-s9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND It is a great challenge of modern biology to determine the functional roles of non-synonymous Single Nucleotide Polymorphisms (nsSNPs) on complex phenotypes. Statistical and machine learning techniques establish correlations between genotype and phenotype, but may fail to infer the biologically relevant mechanisms. The emerging paradigm of Network-based Association Studies aims to address this problem of statistical analysis. However, a mechanistic understanding of how individual molecular components work together in a system requires knowledge of molecular structures, and their interactions. RESULTS To address the challenge of understanding the genetic, molecular, and cellular basis of complex phenotypes, we have, for the first time, developed a structural systems biology approach for genome-wide multiscale modeling of nsSNPs--from the atomic details of molecular interactions to the emergent properties of biological networks. We apply our approach to determine the functional roles of nsSNPs associated with hypoxia tolerance in Drosophila melanogaster. The integrated view of the functional roles of nsSNP at both molecular and network levels allows us to identify driver mutations and their interactions (epistasis) in H, Rad51D, Ulp1, Wnt5, HDAC4, Sol, Dys, GalNAc-T2, and CG33714 genes, all of which are involved in the up-regulation of Notch and Gurken/EGFR signaling pathways. Moreover, we find that a large fraction of the driver mutations are neither located in conserved functional sites, nor responsible for structural stability, but rather regulate protein activity through allosteric transitions, protein-protein interactions, or protein-nucleic acid interactions. This finding should impact future Genome-Wide Association Studies. CONCLUSIONS Our studies demonstrate that the consolidation of statistical, structural, and network views of biomolecules and their interactions can provide new insight into the functional role of nsSNPs in Genome-Wide Association Studies, in a way that neither the knowledge of molecular structures nor biological networks alone could achieve. Thus, multiscale modeling of nsSNPs may prove to be a powerful tool for establishing the functional roles of sequence variants in a wide array of applications.
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Affiliation(s)
- Li Xie
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
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