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Deng EZ, Marino GB, Clarke DJB, Diamant I, Resnick AC, Ma W, Wang P, Ma'ayan A. Multiomics2Targets identifies targets from cancer cohorts profiled with transcriptomics, proteomics, and phosphoproteomics. CELL REPORTS METHODS 2024; 4:100839. [PMID: 39127042 DOI: 10.1016/j.crmeth.2024.100839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 06/06/2024] [Accepted: 07/19/2024] [Indexed: 08/12/2024]
Abstract
The availability of data from profiling of cancer patients with multiomics is rapidly increasing. However, integrative analysis of such data for personalized target identification is not trivial. Multiomics2Targets is a platform that enables users to upload transcriptomics, proteomics, and phosphoproteomics data matrices collected from the same cohort of cancer patients. After uploading the data, Multiomics2Targets produces a report that resembles a research publication. The uploaded matrices are processed, analyzed, and visualized using the tools Enrichr, KEA3, ChEA3, Expression2Kinases, and TargetRanger to identify and prioritize proteins, genes, and transcripts as potential targets. Figures and tables, as well as descriptions of the methods and results, are automatically generated. Reports include an abstract, introduction, methods, results, discussion, conclusions, and references and are exportable as citable PDFs and Jupyter Notebooks. Multiomics2Targets is applied to analyze version 3 of the Clinical Proteomic Tumor Analysis Consortium (CPTAC3) pan-cancer cohort, identifying potential targets for each CPTAC3 cancer subtype. Multiomics2Targets is available from https://multiomics2targets.maayanlab.cloud/.
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Affiliation(s)
- Eden Z Deng
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA
| | - Giacomo B Marino
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA
| | - Daniel J B Clarke
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA
| | - Ido Diamant
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA
| | - Adam C Resnick
- Center for Data Driven Discovery in Biomedicine, Division of Neurosurgery, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Weiping Ma
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY 10029, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY 10029, USA
| | - Avi Ma'ayan
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA.
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Brandt N, Köper F, Hausmann J, Bräuer AU. Spotlight on plasticity-related genes: Current insights in health and disease. Pharmacol Ther 2024; 260:108687. [PMID: 38969308 DOI: 10.1016/j.pharmthera.2024.108687] [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: 02/08/2024] [Revised: 06/07/2024] [Accepted: 07/02/2024] [Indexed: 07/07/2024]
Abstract
The development of the central nervous system is highly complex, involving numerous developmental processes that must take place with high spatial and temporal precision. This requires a series of complex and well-coordinated molecular processes that are tighly controlled and regulated by, for example, a variety of proteins and lipids. Deregulations in these processes, including genetic mutations, can lead to the most severe maldevelopments. The present review provides an overview of the protein family Plasticity-related genes (PRG1-5), including their role during neuronal differentiation, their molecular interactions, and their participation in various diseases. As these proteins can modulate the function of bioactive lipids, they are able to influence various cellular processes. Furthermore, they are dynamically regulated during development, thus playing an important role in the development and function of synapses. First studies, conducted not only in mouse experiments but also in humans, revealed that mutations or dysregulations of these proteins lead to changes in lipid metabolism, resulting in severe neurological deficits. In recent years, as more and more studies have shown their involvement in a broad range of diseases, the complexity and broad spectrum of known and as yet unknown interactions between PRGs, lipids, and proteins make them a promising and interesting group of potential novel therapeutic targets.
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Affiliation(s)
- Nicola Brandt
- Research Group Anatomy, Department of Human Medicine, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Franziska Köper
- Research Group Anatomy, Department of Human Medicine, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Jens Hausmann
- Research Group Anatomy, Department of Human Medicine, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Anja U Bräuer
- Research Group Anatomy, Department of Human Medicine, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany; Research Center for Neurosensory Science, Carl von Ossietzky University Oldenburg, Oldenburg, Germany.
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Pathania AS, Chava H, Chaturvedi NK, Chava S, Byrareddy SN, Coulter DW, Challagundla KB. The miR-29 family facilitates the activation of NK-cell immune responses by targeting the B7-H3 immune checkpoint in neuroblastoma. Cell Death Dis 2024; 15:428. [PMID: 38890285 PMCID: PMC11189583 DOI: 10.1038/s41419-024-06791-7] [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: 11/20/2023] [Revised: 05/22/2024] [Accepted: 05/29/2024] [Indexed: 06/20/2024]
Abstract
Neuroblastoma (NB) is a highly aggressive pediatric cancer that originates from immature nerve cells, presenting significant treatment challenges due to therapy resistance. Despite intensive treatment, approximately 50% of high-risk NB cases exhibit therapy resistance or experience relapse, resulting in poor outcomes often associated with tumor immune evasion. B7-H3 is an immune checkpoint protein known to inhibit immune responses. MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional gene regulation. Our study aims to explore the impact of miRNAs on B7-H3 regulation, the anti-tumor immune response, and tumorigenicity in NB. Analysis of NB patients and patient-derived xenograft tumors revealed a correlation between higher B7-H3 expression and poorer patient survival. Notably, deceased patients exhibited a depletion of miR-29 family members (miR-29a, miR-29b, and miR-29c), which displayed an inverse association with B7-H3 expression in NB patients. Overexpression and knockdown experiments demonstrated that these miRNAs degrade B7-H3 mRNA, resulting in enhanced NK cell activation and cytotoxicity. In vivo, experiments provided further evidence that miR-29 family members reduce tumorigenicity, macrophage infiltration, and microvessel density, promote infiltration and activation of NK cells, and induce tumor cell apoptosis. These findings offer a rationale for developing more effective combination treatments that leverage miRNAs to target B7-H3 in NB patients.
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Affiliation(s)
- Anup S Pathania
- Department of Biochemistry and Molecular Biology & The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Haritha Chava
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Nagendra K Chaturvedi
- Department of Pediatrics, Division of Hematology/Oncology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Srinivas Chava
- Department of Biochemistry and Molecular Biology & The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Siddappa N Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Don W Coulter
- Department of Pediatrics, Division of Hematology/Oncology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Kishore B Challagundla
- Department of Biochemistry and Molecular Biology & The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
- The Child Health Research Institute, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
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Morel VJ, Rössler J, Bernasconi M. Targeted immunotherapy and nanomedicine for rhabdomyosarcoma: The way of the future. Med Res Rev 2024. [PMID: 38885148 DOI: 10.1002/med.22059] [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: 06/29/2023] [Revised: 04/17/2024] [Accepted: 05/20/2024] [Indexed: 06/20/2024]
Abstract
Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma of childhood. Histology separates two main subtypes: embryonal RMS (eRMS; 60%-70%) and alveolar RMS (aRMS; 20%-30%). The aggressive aRMS carry one of two characteristic chromosomal translocations that result in the expression of a PAX3::FOXO1 or PAX7::FOXO1 fusion transcription factor; therefore, aRMS are now classified as fusion-positive (FP) RMS. Embryonal RMS have a better prognosis and are clinically indistinguishable from fusion-negative (FN) RMS. Next to histology and molecular characteristics, RMS risk groupings are now available defining low risk tumors with excellent outcomes and advanced stage disease with poor prognosis, with an overall survival of about only 20% despite intensified multimodal treatment. Therefore, development of novel effective targeted strategies to increase survival and to decrease long-term side effects is urgently needed. Recently, immunotherapies and nanomedicine have been emerging for potent and effective tumor treatments with minimal side effects, raising hopes for effective and safe cures for RMS patients. This review aims to describe the most relevant preclinical and clinical studies in immunotherapy and targeted nanomedicine performed so far in RMS and to provide an insight in future developments.
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Affiliation(s)
- Victoria Judith Morel
- Department of Pediatric Hematology and Oncology, Inselspital, Bern University Hospital, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Jochen Rössler
- Department of Pediatric Hematology and Oncology, Inselspital, Bern University Hospital, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Michele Bernasconi
- Department of Pediatric Hematology and Oncology, Inselspital, Bern University Hospital, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
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Dabiri H, Habibi-Anbouhi M, Ziaei V, Moghadasi Z, Sadeghizadeh M, Hajizadeh-Saffar E. Candidate Biomarkers for Targeting in Type 1 Diabetes; A Bioinformatic Analysis of Pancreatic Cell Surface Antigens. CELL JOURNAL 2024; 26:51-61. [PMID: 38351729 PMCID: PMC10864774 DOI: 10.22074/cellj.2023.1996297.1262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 08/27/2023] [Accepted: 10/24/2023] [Indexed: 02/18/2024]
Abstract
OBJECTIVE Type 1 diabetes (T1Ds) is an autoimmune disease in which the immune system invades and destroys insulin-producing cells. Nevertheless, at the time of diagnosis, about 30-40% of pancreatic beta cells are healthy and capable of producing insulin. Bi-specific antibodies, chimeric antigen receptor regulatory T cells (CAR-Treg cells), and labeled antibodies could be a new emerging option for the treatment or diagnosis of type I diabetic patients. The aim of the study is to choose appropriate cell surface antigens in the pancreas tissue for generating an antibody for type I diabetic patients. MATERIALS AND METHODS In this bioinformatics study, we extracted pancreas-specific proteins from two large databases; the Human Protein Atlas (HPA) and Genotype-Tissue Expression (GTEx) Portal. Pancreatic-enriched genes were chosen and narrowed down by Protter software for the investigation of accessible extracellular domains. The immunohistochemistry (IHC) data of the protein atlas database were used to evaluate the protein expression of selected antigens. We explored the function of candidate antigens by using the GeneCards database to evaluate the potential dysfunction or activation/hyperactivation of antigens after antibody binding. RESULTS The results showed 429 genes are highly expressed in the pancreas tissue. Also, eighteen genes encoded plasma membrane proteins that have high expression in the microarray (GEO) dataset. Our results introduced four structural proteins, including NPHS1, KIRREL2, GP2, and CUZD1, among all seventeen candidate proteins. CONCLUSION The presented antigens can potentially be used to produce specific pancreatic antibodies that guide CARTreg, bi-specific, or labeling molecules to the pancreas for treatment, detection, or other molecular targeted therapy scopes for type I diabetes.
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Affiliation(s)
- Hamed Dabiri
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | | | - Vahab Ziaei
- National Cell Bank of Iran, Pasteur Institute of Iran, Tehran, Iran
| | - Zahra Moghadasi
- National Cell Bank of Iran, Pasteur Institute of Iran, Tehran, Iran
| | - Majid Sadeghizadeh
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Ensiyeh Hajizadeh-Saffar
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
- Advanced Therapy Medicinal Product Technology Development Center (ATMP-TDC), Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
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Vieira LS, Zhang Y, López Quiñones AJ, Hu T, Singh DK, Stevens J, Prasad B, Park JR, Wang J. The Plasma Membrane Monoamine Transporter is Highly Expressed in Neuroblastoma and Functions as an mIBG Transporter. J Pharmacol Exp Ther 2023; 387:239-248. [PMID: 37541765 PMCID: PMC10658915 DOI: 10.1124/jpet.123.001672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/27/2023] [Accepted: 07/06/2023] [Indexed: 08/06/2023] Open
Abstract
Neuroblastoma (NB) is a pediatric cancer with low survival rates in high-risk patients. 131I-mIBG has emerged as a promising therapy for high-risk NB and kills tumor cells by radiation. Consequently, 131I-mIBG tumor uptake and retention are major determinants for its therapeutic efficacy. mIBG enters NB cells through the norepinephrine transporter (NET), and accumulates in mitochondria through unknown mechanisms. Here we evaluated the expression of monoamine and organic cation transporters in high-risk NB tumors and explored their relationship with MYCN amplification and patient survival. We found that NB mainly expresses NET, the plasma membrane monoamine transporter (PMAT), and the vesicular membrane monoamine transporter 1/2 (VMAT1/2), and that the expression of these transporters is significantly reduced in MYCN-amplified tumor samples. PMAT expression is the highest and correlates with overall survival in high-risk NB patients without MYCN amplification. Immunostaining showed that PMAT resides intracellularly in NB cells and co-localizes with mitochondria. Using cells expressing PMAT, mIBG was identified as a PMAT substrate. In mitochondria isolated from NB cell lines, mIBG uptake was reduced by ∼50% by a PMAT inhibitor. Together, our data suggest that PMAT is a previously unrecognized transporter highly expressed in NB and could impact intracellular transport and therapeutic response to 131I-mIBG. SIGNIFICANCE STATEMENT: This study identified that plasma membrane monoamine transporter (PMAT) is a novel transporter highly expressed in neuroblastoma and its expression level is associated with overall survival rate in high-risk patients without MYCN amplification. PMAT is expressed intracellularly in neuroblastoma cells, transports meta-iodobenzylguanidine (mIBG) and thus could impact tumor retention and response to 131I-mIBG therapy. These findings have important clinical implications as PMAT could represent a novel molecular marker to help inform disease prognosis and predict response to 131I-mIBG therapy.
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Affiliation(s)
- Letícia Salvador Vieira
- Department of Pharmaceutics, University of Washington, Seattle, Washington (L.S.V., Y.Z., A.J.L.Q., T.H., J.W.); Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington (D.K.S., B.P.); and Seattle Children's Hospital, Seattle, Washington (J.S., J.R.P.)
| | - Yuchen Zhang
- Department of Pharmaceutics, University of Washington, Seattle, Washington (L.S.V., Y.Z., A.J.L.Q., T.H., J.W.); Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington (D.K.S., B.P.); and Seattle Children's Hospital, Seattle, Washington (J.S., J.R.P.)
| | - Antonio J López Quiñones
- Department of Pharmaceutics, University of Washington, Seattle, Washington (L.S.V., Y.Z., A.J.L.Q., T.H., J.W.); Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington (D.K.S., B.P.); and Seattle Children's Hospital, Seattle, Washington (J.S., J.R.P.)
| | - Tao Hu
- Department of Pharmaceutics, University of Washington, Seattle, Washington (L.S.V., Y.Z., A.J.L.Q., T.H., J.W.); Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington (D.K.S., B.P.); and Seattle Children's Hospital, Seattle, Washington (J.S., J.R.P.)
| | - Dilip Kumar Singh
- Department of Pharmaceutics, University of Washington, Seattle, Washington (L.S.V., Y.Z., A.J.L.Q., T.H., J.W.); Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington (D.K.S., B.P.); and Seattle Children's Hospital, Seattle, Washington (J.S., J.R.P.)
| | - Jeffrey Stevens
- Department of Pharmaceutics, University of Washington, Seattle, Washington (L.S.V., Y.Z., A.J.L.Q., T.H., J.W.); Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington (D.K.S., B.P.); and Seattle Children's Hospital, Seattle, Washington (J.S., J.R.P.)
| | - Bhagwat Prasad
- Department of Pharmaceutics, University of Washington, Seattle, Washington (L.S.V., Y.Z., A.J.L.Q., T.H., J.W.); Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington (D.K.S., B.P.); and Seattle Children's Hospital, Seattle, Washington (J.S., J.R.P.)
| | - Julie R Park
- Department of Pharmaceutics, University of Washington, Seattle, Washington (L.S.V., Y.Z., A.J.L.Q., T.H., J.W.); Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington (D.K.S., B.P.); and Seattle Children's Hospital, Seattle, Washington (J.S., J.R.P.)
| | - Joanne Wang
- Department of Pharmaceutics, University of Washington, Seattle, Washington (L.S.V., Y.Z., A.J.L.Q., T.H., J.W.); Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington (D.K.S., B.P.); and Seattle Children's Hospital, Seattle, Washington (J.S., J.R.P.)
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Zappa E, Vitali A, Anders K, Molenaar JJ, Wienke J, Künkele A. Adoptive cell therapy in paediatric extracranial solid tumours: current approaches and future challenges. Eur J Cancer 2023; 194:113347. [PMID: 37832507 PMCID: PMC10695178 DOI: 10.1016/j.ejca.2023.113347] [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: 07/17/2023] [Revised: 09/03/2023] [Accepted: 09/09/2023] [Indexed: 10/15/2023]
Abstract
Immunotherapy has ignited hope to cure paediatric solid tumours that resist traditional therapies. Among the most promising methods is adoptive cell therapy (ACT). Particularly, ACT using T cells equipped with chimeric antigen receptors (CARs) has moved into the spotlight in clinical studies. However, the efficacy of ACT is challenged by ACT-intrinsic factors, like lack of activation or T cell exhaustion, as well as immune evasion strategies of paediatric solid tumours, such as their highly immunosuppressive microenvironment. Novel strategies, including ACT using innate-like lymphocytes, innovative cell engineering techniques, and ACT combination therapies, are being developed and will be crucial to overcome these challenges. Here, we discuss the main classes of ACT for the treatment of paediatric extracranial solid tumours, reflect on the available preclinical and clinical evidence supporting promising strategies, and address the challenges that ACT is still facing. Ultimately, we highlight state-of-the-art developments and opportunities for new therapeutic options, which hold great potential for improving outcomes in this challenging patient population.
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Affiliation(s)
- Elisa Zappa
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Alice Vitali
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany.
| | - Kathleen Anders
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jan J Molenaar
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Department of Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Judith Wienke
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Annette Künkele
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
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Wang J, Yu W, D'Anna R, Przybyla A, Wilson M, Sung M, Bullen J, Hurt E, D'Angelo G, Sidders B, Lai Z, Zhong W. Pan-Cancer Proteomics Analysis to Identify Tumor-Enriched and Highly Expressed Cell Surface Antigens as Potential Targets for Cancer Therapeutics. Mol Cell Proteomics 2023; 22:100626. [PMID: 37517589 PMCID: PMC10494184 DOI: 10.1016/j.mcpro.2023.100626] [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: 01/23/2023] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 08/01/2023] Open
Abstract
The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) provides unique opportunities for cancer target discovery using protein expression. Proteomics data from CPTAC tumor types have been primarily generated using a multiplex tandem mass tag (TMT) approach, which is designed to provide protein quantification relative to reference samples. However, relative protein expression data are suboptimal for prioritization of targets within a tissue type, which requires additional reprocessing of the original proteomics data to derive absolute quantitation estimation. We evaluated the feasibility of using differential protein analysis coupled with intensity-based absolute quantification (iBAQ) to identify tumor-enriched and highly expressed cell surface antigens, employing tandem mass tag (TMT) proteomics data from CPTAC. Absolute quantification derived from TMT proteomics data was highly correlated with that of label-free proteomics data from the CPTAC colon adenocarcinoma cohort, which contains proteomics data measured by both approaches. We validated the TMT-iBAQ approach by comparing the iBAQ value to the receptor density value of HER2 and TROP2 measured by flow cytometry in about 30 selected breast and lung cancer cell lines from the Cancer Cell Line Encyclopedia. Collections of these tumor-enriched and highly expressed cell surface antigens could serve as a valuable resource for the development of cancer therapeutics, including antibody-drug conjugates and immunotherapeutic agents.
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Affiliation(s)
- Jixin Wang
- Oncology Data Science, AstraZeneca, Gaithersburg, Maryland, USA
| | - Wen Yu
- Data Science and AI, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland, USA
| | - Rachel D'Anna
- Oncology Data Science, AstraZeneca, Gaithersburg, Maryland, USA
| | | | - Matt Wilson
- Early TDE Discovery, AstraZeneca, Cambridge, UK
| | | | - John Bullen
- Early TTD Discovery, AstraZeneca, Cambridge, UK
| | - Elaine Hurt
- Early TTD Discovery, AstraZeneca, Cambridge, UK
| | - Gina D'Angelo
- Late Oncology Statistics, Oncology R&D, AstraZeneca, Gaithersburg, Maryland, USA
| | - Ben Sidders
- Oncology Data Science, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Zhongwu Lai
- Oncology Data Science, Oncology R&D, AstraZeneca, Waltham, Massachusetts, USA
| | - Wenyan Zhong
- Oncology Data Science, Oncology R&D, AstraZeneca, New York, New York, USA.
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Penco-Campillo M, Pages G, Martial S. Angiogenesis and Lymphangiogenesis in Medulloblastoma Development. BIOLOGY 2023; 12:1028. [PMID: 37508458 PMCID: PMC10376362 DOI: 10.3390/biology12071028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023]
Abstract
Medulloblastoma (MB) is the most prevalent brain tumor in children. Although the current cure rate stands at approximately 70%, the existing treatments that involve a combination of radio- and chemotherapy are highly detrimental to the patients' quality of life. These aggressive therapies often result in a significant reduction in the overall well-being of the patients. Moreover, the most aggressive forms of MB frequently relapse, leading to a fatal outcome in a majority of cases. However, MB is highly vascularized, and both angiogenesis and lymphangiogenesis are believed to play crucial roles in tumor development and spread. In this context, our objective is to provide a comprehensive overview of the current research progress in elucidating the functions of these two pathways.
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Affiliation(s)
- Manon Penco-Campillo
- Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, CNRS UMR 7284 and INSERM U1081, 33 Avenue de Valombrose, 06107 Nice, France
| | - Gilles Pages
- Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, CNRS UMR 7284 and INSERM U1081, 33 Avenue de Valombrose, 06107 Nice, France
| | - Sonia Martial
- Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, CNRS UMR 7284 and INSERM U1081, 33 Avenue de Valombrose, 06107 Nice, France
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10
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Vilen Z, Joeh E, Lee E, Huang ML. Surfaceome Profiling Identifies Basigin-Chaperoned Protein Clients. Chembiochem 2023; 24:e202300073. [PMID: 36973167 PMCID: PMC10424708 DOI: 10.1002/cbic.202300073] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/21/2023] [Accepted: 03/25/2023] [Indexed: 03/29/2023]
Abstract
The surface proteome or "surfaceome" is a critical mediator of cellular biology, facilitating cell-to-cell interactions and communication with extracellular biomolecules. Constituents of the surfaceome can serve as biomarkers for changing cell states and as targets for pharmacological intervention. While some pathways of cell surface trafficking are well characterized to allow prediction of surface localization, some non-canonical trafficking mechanisms do not. Basigin (Bsg), a cell surface glycoprotein, has been shown to chaperone protein clients to the cell surface. However, understanding which proteins are served by Bsg is not always straightforward. To accelerate such identification, we applied a surfaceome proximity labeling method that is integrated with quantitative mass spectrometry-based proteomics to discern changes in the surfaceome of hepatic stellate cells that occur in response to the genetic loss of Bsg. Using this strategy, we observed that the loss of Bsg leads to corresponding reductions in the cell surface expression of monocarboxylate transporters MCT1 and MCT4. We also found that these relationships were unique to Bsg and not found in neuroplastin (Nptn), a related family member. These results establish the utility of the surfaceome proximity labeling method to determine clients of cell surface chaperone proteins.
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Affiliation(s)
- Zak Vilen
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
- Department of Molecular Medicine, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Eugene Joeh
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
- Department of Molecular Medicine, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Elizabeth Lee
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
- Department of Molecular Medicine, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Mia L. Huang
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
- Department of Molecular Medicine, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
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11
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Marino G, Ngai M, Clarke DB, Fleishman R, Deng E, Xie Z, Ahmed N, Ma’ayan A. GeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discovery. Nucleic Acids Res 2023; 51:W213-W224. [PMID: 37166966 PMCID: PMC10320068 DOI: 10.1093/nar/gkad399] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/23/2023] [Accepted: 05/02/2023] [Indexed: 05/12/2023] Open
Abstract
Several atlasing efforts aim to profile human gene and protein expression across tissues, cell types and cell lines in normal physiology, development and disease. One utility of these resources is to examine the expression of a single gene across all cell types, tissues and cell lines in each atlas. However, there is currently no centralized place that integrates data from several atlases to provide this type of data in a uniform format for visualization, analysis and download, and via an application programming interface. To address this need, GeneRanger is a web server that provides access to processed data about gene and protein expression across normal human cell types, tissues and cell lines from several atlases. At the same time, TargetRanger is a related web server that takes as input RNA-seq data from profiled human cells and tissues, and then compares the uploaded input data to expression levels across the atlases to identify genes that are highly expressed in the input and lowly expressed across normal human cell types and tissues. Identified targets can be filtered by transmembrane or secreted proteins. The results from GeneRanger and TargetRanger are visualized as box and scatter plots, and as interactive tables. GeneRanger and TargetRanger are available from https://generanger.maayanlab.cloud and https://targetranger.maayanlab.cloud, respectively.
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Affiliation(s)
- Giacomo B Marino
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael Ngai
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Daniel J B Clarke
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Reid H Fleishman
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eden Z Deng
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zhuorui Xie
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nasheath Ahmed
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Avi Ma’ayan
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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12
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Karthik N, Lee JJH, Soon JLJ, Chiu HY, Loh AHP, Ong DST, Tam WL, Taneja R. Histone variant H3.3 promotes metastasis in alveolar rhabdomyosarcoma. J Pathol 2023; 259:342-356. [PMID: 36573560 DOI: 10.1002/path.6048] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022]
Abstract
The relatively quiet mutational landscape of rhabdomyosarcoma (RMS) suggests that epigenetic deregulation could be central to oncogenesis and tumour aggressiveness. Histone variants have long been recognised as important epigenetic regulators of gene expression. However, the role of histone variants in RMS has not been studied hitherto. In this study, we show that histone variant H3.3 is overexpressed in alveolar RMS (ARMS), an aggressive subtype of RMS. Functionally, knockdown of H3F3A, which encodes for H3.3, significantly impairs the ability of ARMS cells to undertake migration and invasion and reduces Rho activation. In addition, a striking reduction in metastatic tumour burden and improved survival is apparent in vivo. Using RNA-sequencing and ChIP-sequencing analyses, we identified melanoma cell adhesion molecule (MCAM/CD146) as a direct downstream target of H3.3. Loss of H3.3 resulted in a reduction in the presence of active marks and an increase in the occupancy of H1 at the MCAM promoter. Cell migration and invasion were rescued in H3F3A-depleted cells through MCAM overexpression. Moreover, we identified G9a, a lysine methyltransferase encoded by EHMT2, as an upstream regulator of H3F3A. Therefore, this study identifies a novel H3.3 dependent axis involved in ARMS metastasis. These findings establish the potential of MCAM as a therapeutic target for high-risk ARMS patients. © 2022 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Nandini Karthik
- Department of Physiology, Healthy Longevity and NUS Cancer Centre for Cancer Research Translation Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jane Jia Hui Lee
- Genome Institute of Singapore (GIS), Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | - Joshua Ling Jun Soon
- Department of Physiology, Healthy Longevity and NUS Cancer Centre for Cancer Research Translation Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Hsin Yao Chiu
- Department of Physiology, Healthy Longevity and NUS Cancer Centre for Cancer Research Translation Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Amos Hong Pheng Loh
- VIVA-KKH Paediatric Brain and Solid Tumour Programme, KK Women's and Children's Hospital, Singapore, Singapore
| | - Derrick Sek Tong Ong
- Department of Physiology and NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Wai Leong Tam
- Genome Institute of Singapore (GIS), Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | - Reshma Taneja
- Department of Physiology, Healthy Longevity and NUS Cancer Centre for Cancer Research Translation Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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13
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Surfaceome Profiling of Cell Lines and Patient-Derived Xenografts Confirm FGFR4, NCAM1, CD276, and Highlight AGRL2, JAM3, and L1CAM as Surface Targets for Rhabdomyosarcoma. Int J Mol Sci 2023; 24:ijms24032601. [PMID: 36768928 PMCID: PMC9917031 DOI: 10.3390/ijms24032601] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/17/2023] [Accepted: 01/27/2023] [Indexed: 02/03/2023] Open
Abstract
Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children. The prognosis for patients with high-grade and metastatic disease is still very poor, and survivors are burdened with long-lasting side effects. Therefore, more effective and less toxic therapies are needed. Surface proteins are ideal targets for antibody-based therapies, like bispecific antibodies, antibody-drug conjugates, or chimeric antigen receptor (CAR) T-cells. Specific surface targets for RMS are scarce. Here, we performed a surfaceome profiling based on differential centrifugation enrichment of surface/membrane proteins and detection by LC-MS on six fusion-positive (FP) RMS cell lines, five fusion-negative (FN) RMS cell lines, and three RMS patient-derived xenografts (PDXs). A total of 699 proteins were detected in the three RMS groups. Ranking based on expression levels and comparison to expression in normal MRC-5 fibroblasts and myoblasts, followed by statistical analysis, highlighted known RMS targets such as FGFR4, NCAM1, and CD276/B7-H3, and revealed AGRL2, JAM3, MEGF10, GPC4, CADM2, as potential targets for immunotherapies of RMS. L1CAM expression was investigated in RMS tissues, and strong L1CAM expression was observed in more than 80% of alveolar RMS tumors, making it a practicable target for antibody-based therapies of alveolar RMS.
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14
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Altered Extracellular Matrix as an Alternative Risk Factor for Epileptogenicity in Brain Tumors. Biomedicines 2022; 10:biomedicines10102475. [PMID: 36289737 PMCID: PMC9599244 DOI: 10.3390/biomedicines10102475] [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: 07/29/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022] Open
Abstract
Seizures are one of the most common symptoms of brain tumors. The incidence of seizures differs among brain tumor type, grade, location and size, but paediatric-type diffuse low-grade gliomas/glioneuronal tumors are often highly epileptogenic. The extracellular matrix (ECM) is known to play a role in epileptogenesis and tumorigenesis because it is involved in the (re)modelling of neuronal connections and cell-cell signaling. In this review, we discuss the epileptogenicity of brain tumors with a focus on tumor type, location, genetics and the role of the extracellular matrix. In addition to functional problems, epileptogenic tumors can lead to increased morbidity and mortality, stigmatization and life-long care. The health advantages can be major if the epileptogenic properties of brain tumors are better understood. Surgical resection is the most common treatment of epilepsy-associated tumors, but post-surgery seizure-freedom is not always achieved. Therefore, we also discuss potential novel therapies aiming to restore ECM function.
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15
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Fuchs J, Bareesel S, Kroon C, Polyzou A, Eickholt BJ, Leondaritis G. Plasma membrane phospholipid phosphatase-related proteins as pleiotropic regulators of neuron growth and excitability. Front Mol Neurosci 2022; 15:984655. [PMID: 36187351 PMCID: PMC9520309 DOI: 10.3389/fnmol.2022.984655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/23/2022] [Indexed: 11/22/2022] Open
Abstract
Neuronal plasma membrane proteins are essential for integrating cell extrinsic and cell intrinsic signals to orchestrate neuronal differentiation, growth and plasticity in the developing and adult nervous system. Here, we shed light on the family of plasma membrane proteins phospholipid phosphatase-related proteins (PLPPRs) (alternative name, PRGs; plasticity-related genes) that fine-tune neuronal growth and synaptic transmission in the central nervous system. Several studies uncovered essential functions of PLPPRs in filopodia formation, axon guidance and branching during nervous system development and regeneration, as well as in the control of dendritic spine number and excitability. Loss of PLPPR expression in knockout mice increases susceptibility to seizures, and results in defects in sensory information processing, development of psychiatric disorders, stress-related behaviors and abnormal social interaction. However, the exact function of PLPPRs in the context of neurological diseases is largely unclear. Although initially described as active lysophosphatidic acid (LPA) ecto-phosphatases that regulate the levels of this extracellular bioactive lipid, PLPPRs lack catalytic activity against LPA. Nevertheless, they emerge as atypical LPA modulators, by regulating LPA mediated signaling processes. In this review, we summarize the effects of this protein family on cellular morphology, generation and maintenance of cellular protrusions as well as highlight their known neuronal functions and phenotypes of KO mice. We discuss the molecular mechanisms of PLPPRs including the deployment of phospholipids, actin-cytoskeleton and small GTPase signaling pathways, with a focus on identifying gaps in our knowledge to stimulate interest in this understudied protein family.
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Affiliation(s)
- Joachim Fuchs
- Institute of Molecular Biology and Biochemistry, Charité – Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Shannon Bareesel
- Institute of Molecular Biology and Biochemistry, Charité – Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Cristina Kroon
- Institute of Molecular Biology and Biochemistry, Charité – Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Alexandra Polyzou
- Department of Pharmacology, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Britta J. Eickholt
- Institute of Molecular Biology and Biochemistry, Charité – Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- *Correspondence: Britta J. Eickholt,
| | - George Leondaritis
- Department of Pharmacology, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece
- Institute of Biosciences, University Research Center Ioannina, University of Ioannina, Ioannina, Greece
- George Leondaritis,
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16
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Tian M, Cheuk AT, Wei JS, Abdelmaksoud A, Chou HC, Milewski D, Kelly MC, Song YK, Dower CM, Li N, Qin H, Kim YY, Wu JT, Wen X, Benzaoui M, Masih KE, Wu X, Zhang Z, Badr S, Taylor N, Croix BS, Ho M, Khan J. An optimized bicistronic chimeric antigen receptor against GPC2 or CD276 overcomes heterogeneous expression in neuroblastoma. J Clin Invest 2022; 132:155621. [PMID: 35852863 PMCID: PMC9374382 DOI: 10.1172/jci155621] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 06/28/2022] [Indexed: 11/17/2022] Open
Affiliation(s)
- Meijie Tian
- Genetics Branch, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Adam T. Cheuk
- Genetics Branch, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Jun S. Wei
- Genetics Branch, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Abdalla Abdelmaksoud
- Genetics Branch, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Hsien-Chao Chou
- Genetics Branch, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - David Milewski
- Genetics Branch, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Michael C. Kelly
- Single Cell Analysis Facility, Center for Cancer Research, NIH, Bethesda, Maryland, USA
| | - Young K. Song
- Genetics Branch, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Christopher M. Dower
- Mouse Cancer Genetics Program, Center for Cancer Research, NCI, Frederick, Maryland, USA
| | - Nan Li
- Laboratory of Molecular Biology, Center for Cancer Research and
| | - Haiying Qin
- Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Yong Yean Kim
- Genetics Branch, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Jerry T. Wu
- Genetics Branch, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Xinyu Wen
- Genetics Branch, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Mehdi Benzaoui
- Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Katherine E. Masih
- Genetics Branch, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Xiaolin Wu
- Cancer Research Technology Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Zhongmei Zhang
- Experimental Immunology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Sherif Badr
- Experimental Immunology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Naomi Taylor
- Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Brad St. Croix
- Mouse Cancer Genetics Program, Center for Cancer Research, NCI, Frederick, Maryland, USA
| | - Mitchell Ho
- Laboratory of Molecular Biology, Center for Cancer Research and
| | - Javed Khan
- Genetics Branch, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
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17
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Lv M, Liu Y, Liu W, Xing Y, Zhang S. Immunotherapy for Pediatric Acute Lymphoblastic Leukemia: Recent Advances and Future Perspectives. Front Immunol 2022; 13:921894. [PMID: 35769486 PMCID: PMC9234114 DOI: 10.3389/fimmu.2022.921894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Pediatric acute lymphoblastic leukemia (ALL) is the most common subtype of childhood leukemia, which is characterized by the abnormal proliferation and accumulation of immature lymphoid cell in the bone marrow. Although the long-term survival rate for pediatric ALL has made significant progress over years with the development of contemporary therapeutic regimens, patients are still suffered from relapse, leading to an unsatisfactory outcome. Since the immune system played an important role in the progression and relapse of ALL, immunotherapy including bispecific T-cell engagers and chimeric antigen receptor T cells has been demonstrated to be capable of enhancing the immune response in pediatric patients with refractory or relapsed B-cell ALL, and improving the cure rate of the disease and patients’ quality of life, thus receiving the authorization for market. Nevertheless, the resistance and toxicities associated with the current immunotherapy remains a huge challenge. Novel therapeutic options to overcome the above disadvantages should be further explored. In this review, we will thoroughly discuss the emerging immunotherapeutics for the treatment of pediatric ALL, as well as side-effects and new development.
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Affiliation(s)
- Meng Lv
- Department of Pharmacy, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Yan Liu
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wei Liu
- Department of Hematology Oncology, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Yabing Xing
- Department of Pharmacy, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
- *Correspondence: Yabing Xing, ; Shengnan Zhang,
| | - Shengnan Zhang
- Department of Pharmacy, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
- *Correspondence: Yabing Xing, ; Shengnan Zhang,
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18
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Chen G, Luo D, Zhong N, Li D, Zheng J, Liao H, Li Z, Lin X, Chen Q, Zhang C, Lu Y, Chan YT, Ren Q, Wang N, Feng Y. GPC2 Is a Potential Diagnostic, Immunological, and Prognostic Biomarker in Pan-Cancer. Front Immunol 2022; 13:857308. [PMID: 35345673 PMCID: PMC8957202 DOI: 10.3389/fimmu.2022.857308] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/01/2022] [Indexed: 11/17/2022] Open
Abstract
Background Glypican 2 (GPC2), a member of glypican (GPC) family genes, produces proteoglycan with a glycosylphosphatidylinositol anchor. It has shown its ascending significance in multiple cancers such as neuroblastoma, malignant brain tumor, and small-cell lung cancer. However, no systematic pan-cancer analysis has been conducted to explore its function in diagnosis, prognosis, and immunological prediction. Methods By comprehensive use of datasets from The Cancer Genome Atlas (TCGA), Cancer Cell Line Encyclopedia (CCLE), Genotype-Tissue Expression Project (GTEx), cBioPortal, Human Protein Atlas (HPA), UALCAN, StarBase, and Comparative Toxicogenomics Database (CTD), we adopted bioinformatics methods to excavate the potential carcinogenesis of GPC2, including dissecting the correlation between GPC2 and prognosis, gene mutation, immune cell infiltration, and DNA methylation of different tumors, and constructed the competing endogenous RNA (ceRNA) networks of GPC2 as well as explored the interaction of GPC2 with chemicals and genes. Results The results indicated that GPC2 was highly expressed in most cancers, except in pancreatic adenocarcinoma, which presented at a quite low level. Furthermore, GPC2 showed the early diagnostic value in 16 kinds of tumors and was positively or negatively associated with the prognosis of different tumors. It also verified that GPC2 was a gene associated with most immune-infiltrating cells in pan-cancer, especially in thymoma. Moreover, the correlation with GPC2 expression varied depending on the type of immune-related genes. Additionally, GPC2 gene expression has a correlation with DNA methylation in 20 types of cancers. Conclusion Through pan-cancer analysis, we discovered and verified that GPC2 might be useful in cancer detection for the first time. The expression level of GPC2 in a variety of tumors is significantly different from that of normal tissues. In addition, the performance of GPC2 in tumorigenesis and tumor immunity also confirms our conjecture. At the same time, it has high specificity and sensitivity in the detection of cancers. Therefore, GPC2 can be used as an auxiliary indicator for early tumor diagnosis and a prognostic marker for many types of tumors.
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Affiliation(s)
- Guoming Chen
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Dongqiang Luo
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Nan Zhong
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Danyun Li
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jiyuan Zheng
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Hui Liao
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhuoyao Li
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaoxiao Lin
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qiqi Chen
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Cheng Zhang
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Yuanjun Lu
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Yau-Tuen Chan
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Qing Ren
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ning Wang
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Yibin Feng
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
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19
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Vilen Z, Reeves AE, O’Leary TR, Joeh E, Kamasawa N, Huang ML. Cell Surface Engineering Enables Surfaceome Profiling. ACS Chem Biol 2022; 18:701-710. [PMID: 35443134 PMCID: PMC9901301 DOI: 10.1021/acschembio.1c00865] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Cell surface proteins (CSPs) are vital molecular mediators for cells and their extracellular environment. Thus, understanding which CSPs are displayed on cells, especially in different cell states, remains an important endeavor in cell biology. Here, we describe the integration of cell surface engineering with radical-mediated protein biotinylation to profile CSPs. This method relies on the prefunctionalization of cells with cholesterol lipid groups, followed by sortase-catalyzed conjugation with an APEX2 ascorbate peroxidase enzyme. In the presence of biotin-phenol and H2O2, APEX2 catalyzes the formation of highly reactive biotinyl radicals that covalently tag electron-rich residues within CSPs for subsequent streptavidin-based enrichment and analysis by quantitative mass spectrometry. While APEX2 is traditionally used to capture proximity-based interactomes, we envisioned using it in a "baitless" manner on cell surfaces to capture CSPs. We evaluate this strategy in light of another CSP labeling method that relies on the presence of cell surface sialic acid. Using the APEX2 strategy, we describe the CSPs found in three mammalian cell lines and compare CSPs in adherent versus three-dimensional pancreatic adenocarcinoma cells.
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Affiliation(s)
- Zak Vilen
- Department of Molecular Medicine, Scripps Research, 120 Scripps Way, Jupiter, FL 33458-5284,Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, CA 92037,Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, CA 92037
| | - Abigail E. Reeves
- Department of Molecular Medicine, Scripps Research, 120 Scripps Way, Jupiter, FL 33458-5284,Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, CA 92037,Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, CA 92037
| | - Timothy R. O’Leary
- Department of Molecular Medicine, Scripps Research, 120 Scripps Way, Jupiter, FL 33458-5284
| | - Eugene Joeh
- Department of Molecular Medicine, Scripps Research, 120 Scripps Way, Jupiter, FL 33458-5284,Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, CA 92037,Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, CA 92037
| | - Naomi Kamasawa
- The Imaging Center and Electron Microscopy Core Facility, Max Planck Florida Institute for Neuroscience, 1 Max Planck Way, Jupiter, FL, 33458
| | - Mia L. Huang
- Department of Molecular Medicine, Scripps Research, 120 Scripps Way, Jupiter, FL 33458-5284,Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, CA 92037,Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, CA 92037,Corresponding author:
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20
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Finding New Ways How to Control BACE1. J Membr Biol 2022; 255:293-318. [PMID: 35305135 DOI: 10.1007/s00232-022-00225-1] [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: 02/02/2022] [Accepted: 02/24/2022] [Indexed: 01/18/2023]
Abstract
Recently, all applications of BACE1 inhibitors failed as therapeutical targets for Alzheimer´s disease (AD) due to severe side effects. Therefore, alternative ways for treatment development are a hot research topic. The present analysis investigates BACE1 protein-protein interaction networks and attempts to solve the absence of complete knowledge about pathways involving BACE1. A bioinformatics analysis matched the functions of the non-substrate interaction network with Voltage-gated potassium channels, which also appear as top priority protein nodes. Targeting BACE1 interactions with PS1 and GGA-s, blocking of BACE1 access to APP by BRI3 and RTN-s, activation of Wnt signaling and upregulation of β-catenin, and brain delivery of the extracellular domain of p75NTR, are the main alternatives to the use of BACE 1 inhibitors highlighted by the analysis. The pathway enrichment analysis also emphasized substrates and substrate candidates with essential biological functions, which cleavage must remain controlled. They include ephrin receptors, ROBO1, ROBO2, CNTN-s, CASPR-s, CD147, CypB, TTR, APLP1/APLP2, NRXN-s, and PTPR-s. The analysis of the interaction subnetwork of BACE1 functionally related to inflammation identified a connection to three cardiomyopathies, which supports the hypothesis of the common molecular mechanisms with AD. A lot of potential shows the regulation of BACE1 activity through post-translational modifications. The interaction network of BACE1 and its phosphorylation enzyme CSNK1D functionally match the Circadian clock, p53, and Hedgehog signaling pathways. The regulation of BACE1 glycosylation could be achieved through N-acetylglucosamine transferases, α-(1→6)-fucosyltransferase, β-galactoside α-(2→6)-sialyltransferases, galactosyltransferases, and mannosidases suggested by the interaction network analysis of BACE1-MGAT3. The present analysis proposes possibilities for the alternative control of AD pathology.
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21
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Lopez Quiñones AJ, Vieira LS, Wang J. Clinical Applications and the Roles of Transporters in Disposition, Tumor Targeting, and Tissue Toxicity of meta-Iodobenzylguanidine (mIBG). Drug Metab Dispos 2022; 50:DMD-MR-2021-000707. [PMID: 35197314 PMCID: PMC9488973 DOI: 10.1124/dmd.121.000707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 02/01/2022] [Accepted: 02/17/2022] [Indexed: 11/22/2022] Open
Abstract
Transporters on the plasma membrane of tumor cells are promising molecular "Trojan horses" to deliver drugs and imaging agents into cancer cells. Radioiodine-labeled meta-iodobenzylguanidine (mIBG) is used as a diagnostic agent (123I-mIBG) and a targeted radiotherapy (131I-mIBG) for neuroendocrine cancers. mIBG enters cancer cells through the norepinephrine transporter (NET) where the radioactive decay of 131I causes DNA damage, cell death, and tumor necrosis. mIBG is predominantly eliminated unchanged by the kidney. Despite its selective uptake by neuroendocrine tumors, mIBG accumulates in several normal tissues and leads to tissue-specific radiation toxicities. Emerging evidences suggest that the polyspecific organic cation transporters play important roles in systemic disposition and tissue-specific uptake of mIBG. In particular, human organic cation transporter 2 (hOCT2) and toxin extrusion proteins 1 and 2-K (hMATE1/2-K) likely mediate renal secretion of mIBG whereas hOCT1 and hOCT3 may contribute to mIBG uptake into normal tissues such as the liver, salivary glands, and heart. This mini-review focuses on the clinical applications of mIBG in neuroendocrine cancers and the differential roles of NET, OCT and MATE transporters in mIBG disposition, response and toxicity. Understanding the molecular mechanisms governing mIBG transport in cancer and normal cells is a critical step for developing strategies to optimize the efficacy of 131I-mIBG while minimizing toxicity in normal tissues. Significance Statement Radiolabeled mIBG has been used as a diagnostic tool and as radiotherapy for neuroendocrine cancers and other diseases. NET, OCT and MATE transporters play differential roles in mIBG tumor targeting, systemic elimination, and accumulation in normal tissues. The clinical use of mIBG as a radiopharmaceutical in cancer diagnosis and treatment can be further improved by taking a holistic approach considering mIBG transporters in both cancer and normal tissues.
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Affiliation(s)
| | | | - Joanne Wang
- Dept. of Pharmaceutics, University of Washington, United States
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22
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Li N, Nguyen R, Thiele CJ, Ho M. Preclinical testing of chimeric antigen receptor T cells in neuroblastoma mouse models. STAR Protoc 2021; 2:100942. [PMID: 34825213 PMCID: PMC8603305 DOI: 10.1016/j.xpro.2021.100942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The translation of chimeric antigen receptor (CAR) T cell therapy for pediatric solid tumors is limited by the lack of preclinical models that fully recapitulate solid tumor biology. We describe steps to implement neuroblastoma metastatic and orthotopic mouse models. We delineate an analysis pipeline to quantify the efficacy and determine the immunological characteristics of both CAR T and tumor cells in these models. Both mouse models can be applied to evaluate other experimental therapies for neuroblastoma. For complete details on the use and execution of this protocol, please refer to Li et al. (2021).
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Affiliation(s)
- Nan Li
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rosa Nguyen
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Carol J Thiele
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mitchell Ho
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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23
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Schreiner P, Velasquez MP, Gottschalk S, Zhang J, Fan Y. Unifying heterogeneous expression data to predict targets for CAR-T cell therapy. Oncoimmunology 2021; 10:2000109. [PMID: 34858726 PMCID: PMC8632331 DOI: 10.1080/2162402x.2021.2000109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 10/08/2021] [Accepted: 10/26/2021] [Indexed: 10/29/2022] Open
Abstract
Chimeric antigen receptor (CAR) T-cell therapy combines antigen-specific properties of monoclonal antibodies with the lytic capacity of T cells. An effective and safe CAR-T cell therapy strategy relies on identifying an antigen that has high expression and is tumor specific. This strategy has been successfully used to treat patients with CD19+ B-cell acute lymphoblastic leukemia (B-ALL). Finding a suitable target antigen for other cancers such as acute myeloid leukemia (AML) has proven challenging, as the majority of currently targeted AML antigens are also expressed on hematopoietic progenitor cells (HPCs) or mature myeloid cells. Herein, we developed a computational method to perform a data transformation to enable the comparison of publicly available gene expression data across different datasets or assay platforms. The resulting transformed expression values (TEVs) were used in our antigen prediction algorithm to assess suitable tumor-associated antigens (TAAs) that could be targeted with CAR-T cells. We validated this method by identifying B-ALL antigens with known clinical effectiveness, such as CD19 and CD22. Our algorithm predicted TAAs being currently explored preclinically and in clinical CAR-T AML therapy trials, as well as novel TAAs in pediatric megakaryoblastic AML. Thus, this analytical approach presents a promising new strategy to mine diverse datasets for identifying TAAs suitable for immunotherapy.
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Affiliation(s)
- Patrick Schreiner
- The Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Mireya Paulina Velasquez
- Department of Bone Marrow Transplantation and Cell Therapy, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Stephen Gottschalk
- Department of Bone Marrow Transplantation and Cell Therapy, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Yiping Fan
- The Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN, USA
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24
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Giannikopoulos P, Parham DM. Rhabdomyosarcoma: How Advanced Molecular Methods Are Shaping the Diagnostic and Therapeutic Paradigm. Pediatr Dev Pathol 2021; 24:395-404. [PMID: 34107813 DOI: 10.1177/10935266211013621] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
For the past 40 years, progress in rhabdomyosarcoma (RMS) has been focused on understanding its molecular basis and characterizing the mutations that drive its tumorigenesis and progression. Genetic predisposition to RMS has allowed discovery of key genetic pathways and driver mutations. Subclassification of RMS into embryonal (ERMS) and alveolar (ARMS) subtypes has shifted from histology to PAX-FOXO1 fusion status, and new driver mutations have been found in spindle cell RMS. Comprehensive molecular profiling leveraging genome-scale next-generation sequencing (NGS) indicates that the RAS/RAF/PI3K axis is mutated in the majority of ERMS and modulated by downstream effects of PAX-FOXO1 fusions in ARMS. Because of the continued poor outcome of high-risk RMS, a variety of molecular targets have been or are now being tested in current or recent therapy trials. New techniques such as single cell sequencing, spatial multi-omics, and CRISPR/Cas9 genome editing offer potential for further discovery, but a need for clinically annotated specimens persists.
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Affiliation(s)
- Petros Giannikopoulos
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - David M Parham
- Children's Hospital Los Angeles, University of Southern California Keck School of Medicine, Los Angeles, CA, USA (retired)
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25
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Obu S, Umeda K, Ueno H, Sonoda M, Tasaka K, Ogata H, Kouzuki K, Nodomi S, Saida S, Kato I, Hiramatsu H, Okamoto T, Ogawa E, Okajima H, Morita K, Kamikubo Y, Kawaguchi K, Watanabe K, Iwafuchi H, Yagyu S, Iehara T, Hosoi H, Nakahata T, Adachi S, Uemoto S, Heike T, Takita J. CD146 is a potential immunotarget for neuroblastoma. Cancer Sci 2021; 112:4617-4626. [PMID: 34464480 PMCID: PMC8586675 DOI: 10.1111/cas.15124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/13/2021] [Accepted: 08/26/2021] [Indexed: 11/28/2022] Open
Abstract
Neuroblastoma, the most common extracranial solid tumor of childhood, is thought to arise from neural crest‐derived immature cells. The prognosis of patients with high‐risk or recurrent/refractory neuroblastoma remains quite poor despite intensive multimodality therapy; therefore, novel therapeutic interventions are required. We examined the expression of a cell adhesion molecule CD146 (melanoma cell adhesion molecule [MCAM]) by neuroblastoma cell lines and in clinical samples and investigated the anti‐tumor effects of CD146‐targeting treatment for neuroblastoma cells both in vitro and in vivo. CD146 is expressed by 4 cell lines and by most of primary tumors at any stage. Short hairpin RNA‐mediated knockdown of CD146, or treatment with an anti‐CD146 polyclonal antibody, effectively inhibited growth of neuroblastoma cells both in vitro and in vivo, principally due to increased apoptosis via the focal adhesion kinase and/or nuclear factor‐kappa B signaling pathway. Furthermore, the anti‐CD146 polyclonal antibody markedly inhibited tumor growth in immunodeficient mice inoculated with primary neuroblastoma cells. In conclusion, CD146 represents a promising therapeutic target for neuroblastoma.
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Affiliation(s)
- Satoshi Obu
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Katsutsugu Umeda
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroo Ueno
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Mari Sonoda
- Department of Pediatric Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Keiji Tasaka
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hideto Ogata
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kagehiro Kouzuki
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Seishiro Nodomi
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Satoshi Saida
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Itaru Kato
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hidefumi Hiramatsu
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tatsuya Okamoto
- Department of Pediatric Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Eri Ogawa
- Department of Pediatric Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hideaki Okajima
- Department of Pediatric Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Department of Pediatric Surgery, Kanazawa Medical University, Ishikawa, Japan
| | - Ken Morita
- Department of Human Health Science, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasuhiko Kamikubo
- Department of Human Health Science, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koji Kawaguchi
- Department of Hematology and Oncology, Shizuoka Children's Hospital, Shizuoka, Japan
| | - Kenichiro Watanabe
- Department of Hematology and Oncology, Shizuoka Children's Hospital, Shizuoka, Japan
| | - Hideto Iwafuchi
- Department of Pathology, Shizuoka Children's Hospital, Shizuoka, Japan
| | - Shigeki Yagyu
- Department of Pediatrics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tomoko Iehara
- Department of Pediatrics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hajime Hosoi
- Department of Pediatrics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tatsutoshi Nakahata
- Drug Discovery Technology Development Office, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Souichi Adachi
- Department of Human Health Science, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shinji Uemoto
- Department of Pediatric Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Toshio Heike
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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26
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Ali Akbari Ghavimi S, Gehret PM, Aronson MR, Schipani R, Smith KW, Borek RC, Germiller JA, Jacobs IN, Zur KB, Gottardi R. Drug delivery to the pediatric upper airway. Adv Drug Deliv Rev 2021; 174:168-189. [PMID: 33845038 DOI: 10.1016/j.addr.2021.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 03/22/2021] [Accepted: 04/06/2021] [Indexed: 11/25/2022]
Abstract
Pediatric upper airway disorders are frequently life-threatening and require precise assessment and intervention. Targeting these pathologies remains a challenge for clinicians due to the high complexity of pediatric upper airway anatomy and numerous potential etiologies; the most common treatments include systemic delivery of high dose steroids and antibiotics or complex and invasive surgeries. Furthermore, the majority of innovative airway management technologies are only designed and tested for adults, limiting their widespread implementation in the pediatric population. Here, we provide a comprehensive review of the most recent challenges of managing common pediatric upper airway disorders, describe the limitations of current clinical treatments, and elaborate on how to circumvent those limitations via local controlled drug delivery. Furthermore, we propose future advancements in the field of drug-eluting technologies to improve pediatric upper airway management outcomes.
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27
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Li N, Torres MB, Spetz MR, Wang R, Peng L, Tian M, Dower CM, Nguyen R, Sun M, Tai CH, de Val N, Cachau R, Wu X, Hewitt SM, Kaplan RN, Khan J, St Croix B, Thiele CJ, Ho M. CAR T cells targeting tumor-associated exons of glypican 2 regress neuroblastoma in mice. Cell Rep Med 2021; 2:100297. [PMID: 34195677 PMCID: PMC8233664 DOI: 10.1016/j.xcrm.2021.100297] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/21/2021] [Accepted: 05/10/2021] [Indexed: 01/05/2023]
Abstract
Targeting solid tumors must overcome several major obstacles, in particular, the identification of elusive tumor-specific antigens. Here, we devise a strategy to help identify tumor-specific epitopes. Glypican 2 (GPC2) is overexpressed in neuroblastoma. Using RNA sequencing (RNA-seq) analysis, we show that exon 3 and exons 7-10 of GPC2 are expressed in cancer but are minimally expressed in normal tissues. Accordingly, we discover a monoclonal antibody (CT3) that binds exons 3 and 10 and visualize the complex structure of CT3 and GPC2 by electron microscopy. The potential of this approach is exemplified by designing CT3-derived chimeric antigen receptor (CAR) T cells that regress neuroblastoma in mice. Genomic sequencing of T cells recovered from mice reveals the CAR integration sites that may contribute to CAR T cell proliferation and persistence. These studies demonstrate how RNA-seq data can be exploited to help identify tumor-associated exons that can be targeted by CAR T cell therapies.
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MESH Headings
- Animals
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/genetics
- Antibodies, Monoclonal/metabolism
- Antibodies, Monoclonal/pharmacology
- Cell Line, Tumor
- Cell Proliferation
- Exons
- Female
- Gene Expression
- Glypicans/antagonists & inhibitors
- Glypicans/chemistry
- Glypicans/genetics
- Glypicans/immunology
- Humans
- Immunotherapy, Adoptive/methods
- Mice
- Mice, Nude
- Models, Molecular
- Nervous System Neoplasms/genetics
- Nervous System Neoplasms/mortality
- Nervous System Neoplasms/pathology
- Nervous System Neoplasms/therapy
- Neuroblastoma/genetics
- Neuroblastoma/mortality
- Neuroblastoma/pathology
- Neuroblastoma/therapy
- Protein Binding
- Protein Conformation
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Chimeric Antigen/genetics
- Receptors, Chimeric Antigen/immunology
- Sequence Analysis, RNA
- Survival Analysis
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- Tumor Burden
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Nan Li
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Madeline B. Torres
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Madeline R. Spetz
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ruixue Wang
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Luyi Peng
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Meijie Tian
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christopher M. Dower
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Rosa Nguyen
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ming Sun
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chin-Hsien Tai
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Natalia de Val
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Raul Cachau
- Data Science and Information Technology Program, Leidos Biomedical Research, Frederick, MD 21702, USA
| | - Xiaolin Wu
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Stephen M. Hewitt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rosandra N. Kaplan
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Javed Khan
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Brad St Croix
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Carol J. Thiele
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mitchell Ho
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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28
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Advances in immunotherapeutic targets for childhood cancers: A focus on glypican-2 and B7-H3. Pharmacol Ther 2021; 223:107892. [PMID: 33992682 DOI: 10.1016/j.pharmthera.2021.107892] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/05/2021] [Accepted: 05/10/2021] [Indexed: 12/16/2022]
Abstract
Cancer immunotherapies have revolutionized how we can treat adult malignancies and are being translated to pediatric oncology. Chimeric antigen receptor T-cell therapy and bispecific antibodies targeting CD19 have shown success for the treatment of pediatric patients with B-cell acute lymphoblastic leukemia. Anti-GD2 monoclonal antibody has demonstrated efficacy in neuroblastoma. In this review, we summarize the immunotherapeutic agents that have been approved for treating childhood cancers and provide an updated review of molecules expressed by pediatric cancers that are under study or are emerging candidates for future immunotherapies. Advances in our knowledge of tumor immunology and in genome profiling of cancers has led to the identification of new tumor-specific/associated antigens. While cell surface antigens are normally targeted in a major histocompatibility complex (MHC)-independent manner using antibody-based therapies, intracellular antigens are normally targeted with MHC-dependent T cell therapies. Glypican 2 (GPC2) and B7-H3 (CD276) are two cell surface antigens that are expressed by a variety of pediatric tumors such as neuroblastoma and potentially can have a positive impact on the treatment of pediatric cancers in the clinic.
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29
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Koo B, Rhee JK. Prediction of tumor purity from gene expression data using machine learning. Brief Bioinform 2021; 22:6265216. [PMID: 33954576 DOI: 10.1093/bib/bbab163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 01/11/2023] Open
Abstract
MOTIVATION Bulk tumor samples used for high-throughput molecular profiling are often an admixture of cancer cells and non-cancerous cells, which include immune and stromal cells. The mixed composition can confound the analysis and affect the biological interpretation of the results, and thus, accurate prediction of tumor purity is critical. Although several methods have been proposed to predict tumor purity using high-throughput molecular data, there has been no comprehensive study on machine learning-based methods for the estimation of tumor purity. RESULTS We applied various machine learning models to estimate tumor purity. Overall, the models predicted the tumor purity accurately and showed a high correlation with well-established gold standard methods. In addition, we identified a small group of genes and demonstrated that they could predict tumor purity well. Finally, we confirmed that these genes were mainly involved in the immune system. AVAILABILITY The machine learning models constructed for this study are available at https://github.com/BonilKoo/ML_purity.
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Affiliation(s)
- Bonil Koo
- School of Systems Biomedical Science, Soongsil University, Seoul, Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Korea
| | - Je-Keun Rhee
- School of Systems Biomedical Science, Soongsil University, Seoul, Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Korea
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30
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Wang JY, Wang XK, Zhu GZ, Zhou X, Yao J, Ma XP, Wang B, Peng T. Distinct diagnostic and prognostic values of Glypicans gene expression in patients with hepatocellular carcinoma. BMC Cancer 2021; 21:462. [PMID: 33902495 PMCID: PMC8073913 DOI: 10.1186/s12885-021-08104-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 03/25/2021] [Indexed: 12/11/2022] Open
Abstract
Backgroud In our current work, we aimed to investigate the expressions of glypican (GPC) family genes at the mRNA level and assess their prognostic significances in patients with hepatocellular carcinoma (HCC). Methods The pathological roles of GPC family genes were examined using bioinformatics analysis. The diagnostic values of GPC genes were explored with the Gene Expression Profiling Interactive Analysis. Moreover, the mRNA expression and prognostic values of GPC genes were assessed via the KM plotter database. Results Our data showed that the expression of GPC-3 was dramatically increased in the liver tumor tissue. Moreover, the expressions of the other five GPC family members were not significantly different between the tumor and normal liver tissues (P > 0.05). Furthermore, the up-regulation of GPC-1 at the mRNA level was dramatically correlated to the reduced overall survival (OS) for all HCC patients (hazard ratio = 2.03, 95% confidence intervals =1.44–2.87, P = 4.1e-05) compared with its low-expression group. Besides, the prognosis of the Caucasians was related to most GPC family genes, while the prognosis of the Asian race was only related to the expression of GPC-2. Besides, for pathological factors, including stage, grade, AJCC, and vascular invasion, the higher the pathological grade and vascular invasiveness, the lower the expression levels of GPC family genes (P < 0.05). Finally, the expression levels of GPC-1, 2, and 3 in the hepatitis group were related to the poor prognosis of HCC in the risk factor (alcohol consumption and hepatitis) subgroup (P < 0.05). Conclusions Our findings indicated that GPC-3 was dysregulated in HCC compared with paracancerous tissues. The expression of GPC-1 could be used as a potent predictive index for the general prognosis of HCC. The pathology, patients, and risk factors might affect the prognostic value of GPC family genes in HCC. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08104-z.
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Affiliation(s)
- Jian-Yao Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Shuang Yong Road 6#, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.,Department of General Surgery, Shenzhen Children's Hospital, Yi Tian Road 7019#, Shenzhen, 518026, Guangdong Province, People's Republic of China
| | - Xiang-Kun Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Shuang Yong Road 6#, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Guang-Zhi Zhu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Shuang Yong Road 6#, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Xin Zhou
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Shuang Yong Road 6#, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Jun Yao
- Department of Gastroenterology, Jinan University of Second Clinical Medical Sciences, Shenzhen Municipal People's Hospital, Dong Men Bei Road 1017#, Shenzhen, 518020, Guangdong Province, People's Republic of China.
| | - Xiao-Peng Ma
- Department of General Surgery, Shenzhen Children's Hospital, Yi Tian Road 7019#, Shenzhen, 518026, Guangdong Province, People's Republic of China.
| | - Bin Wang
- Department of General Surgery, Shenzhen Children's Hospital, Yi Tian Road 7019#, Shenzhen, 518026, Guangdong Province, People's Republic of China.
| | - Tao Peng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Shuang Yong Road 6#, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.
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31
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Liu Z, Chen X, Roberts R, Huang R, Mikailov M, Tong W. Unraveling Gene Fusions for Drug Repositioning in High-Risk Neuroblastoma. Front Pharmacol 2021; 12:608778. [PMID: 33967751 PMCID: PMC8105087 DOI: 10.3389/fphar.2021.608778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 03/23/2021] [Indexed: 11/13/2022] Open
Abstract
High-risk neuroblastoma (NB) remains a significant therapeutic challenge facing current pediatric oncology patients. Structural variants such as gene fusions have shown an initial promise in enhancing mechanistic understanding of NB and improving survival rates. In this study, we performed a comprehensive in silico investigation on the translational ability of gene fusions for patient stratification and treatment development for high-risk NB patients. Specifically, three state-of-the-art gene fusion detection algorithms, including ChimeraScan, SOAPfuse, and TopHat-Fusion, were employed to identify the fusion transcripts in a RNA-seq data set of 498 neuroblastoma patients. Then, the 176 high-risk patients were further stratified into four different subgroups based on gene fusion profiles. Furthermore, Kaplan-Meier survival analysis was performed, and differentially expressed genes (DEGs) for the redefined high-risk group were extracted and functionally analyzed. Finally, repositioning candidates were enriched in each patient subgroup with drug transcriptomic profiles from the LINCS L1000 Connectivity Map. We found the number of identified gene fusions was increased from clinical the low-risk stage to the high-risk stage. Although the technical concordance of fusion detection algorithms was suboptimal, they have a similar biological relevance concerning perturbed pathways and regulated DEGs. The gene fusion profiles could be utilized to redefine high-risk patient subgroups with significant onset age of NB, which yielded the improved survival curves (Log-rank p value ≤ 0.05). Out of 48 enriched repositioning candidates, 45 (93.8%) have antitumor potency, and 24 (50%) were confirmed with either on-going clinical trials or literature reports. The gene fusion profiles have a discrimination power for redefining patient subgroups in high-risk NB and facilitate precision medicine-based drug repositioning implementation.
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Affiliation(s)
- Zhichao Liu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, United States
| | - Xi Chen
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, United States
| | - Ruth Roberts
- ApconiX, BioHub at Alderley Park, Alderley Edge, United Kingdom.,University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Mike Mikailov
- Office of Science and Engineering Labs, Center for Devices and Radiological Health, US Food and Drug Administration, Silver Spring, MD, United States
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, United States
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Teneurins: Role in Cancer and Potential Role as Diagnostic Biomarkers and Targets for Therapy. Int J Mol Sci 2021; 22:ijms22052321. [PMID: 33652578 PMCID: PMC7956758 DOI: 10.3390/ijms22052321] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 02/06/2023] Open
Abstract
Teneurins have been identified in vertebrates as four different genes (TENM1-4), coding for membrane proteins that are mainly involved in embryonic and neuronal development. Genetic studies have correlated them with various diseases, including developmental problems, neurological disorders and congenital general anosmia. There is some evidence to suggest their possible involvement in cancer initiation and progression, and drug resistance. Indeed, mutations, chromosomal alterations and the deregulation of teneurins expression have been associated with several tumor types and patient survival. However, the role of teneurins in cancer-related regulatory networks is not fully understood, as both a tumor-suppressor role and pro-tumoral functions have been proposed, depending on tumor histotype. Here, we summarize and discuss the literature data on teneurins expression and their potential role in different tumor types, while highlighting the possibility of using teneurins as novel molecular diagnostic and prognostic biomarkers and as targets for cancer treatments, such as immunotherapy, in some tumors.
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Wagner J, Wickman E, DeRenzo C, Gottschalk S. CAR T Cell Therapy for Solid Tumors: Bright Future or Dark Reality? Mol Ther 2020; 28:2320-2339. [PMID: 32979309 DOI: 10.1016/j.ymthe.2020.09.015] [Citation(s) in RCA: 196] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/08/2020] [Accepted: 09/11/2020] [Indexed: 01/07/2023] Open
Abstract
Chimeric antigen receptor (CAR) T cell therapy has garnered significant excitement due to its success for hematological malignancies in clinical studies leading to the US Food and Drug Administration (FDA) approval of three CD19-targeted CAR T cell products. In contrast, the clinical experience with CAR T cell therapy for solid tumors and brain tumors has been less encouraging, with only a few patients achieving complete responses. Clinical and preclinical studies have identified multiple "roadblocks," including (1) a limited array of targetable antigens and heterogeneous antigen expression, (2) limited T cell fitness and survival before reaching tumor sites, (3) an inability of T cells to efficiently traffic to tumor sites and penetrate physical barriers, and (4) an immunosuppressive tumor microenvironment. Herein, we review these challenges and discuss strategies that investigators have taken to improve the effector function of CAR T cells for the adoptive immunotherapy of solid tumors.
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Affiliation(s)
- Jessica Wagner
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Elizabeth Wickman
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Christopher DeRenzo
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Stephen Gottschalk
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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Liu KX, Joshi S. "Re-educating" Tumor Associated Macrophages as a Novel Immunotherapy Strategy for Neuroblastoma. Front Immunol 2020; 11:1947. [PMID: 32983125 PMCID: PMC7493646 DOI: 10.3389/fimmu.2020.01947] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/20/2020] [Indexed: 12/14/2022] Open
Abstract
Neuroblastoma is the most common extracranial pediatric tumor and often presents with metastatic disease, and patients with high-risk neuroblastoma have survival rates of ~50%. Neuroblastoma tumorigenesis is associated with the infiltration of various types of immune cells, including myeloid derived suppressor cells, tumor associated macrophages (TAMs), and regulatory T cells, which foster tumor growth and harbor immunosuppressive functions. In particular, TAMs predict poor clinical outcomes in neuroblastoma, and among these immune cells, TAMs with an M2 phenotype comprise an immune cell population that promotes tumor metastasis, contributes to immunosuppression, and leads to failure of radiation or checkpoint inhibitor therapy. This review article summarizes the role of macrophages in tumor angiogenesis, metastasis, and immunosuppression in neuroblastoma and discusses the recent advances in "macrophage-targeting strategies" in neuroblastoma with a focus on three aspects: (1) inhibition of macrophage recruitment, (2) targeting macrophage survival, and (3) reprogramming of macrophages into an immunostimulatory phenotype.
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Affiliation(s)
- Kevin X. Liu
- Department of Radiation Oncology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
| | - Shweta Joshi
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, UCSD Rady's Children's Hospital, University of California, San Diego, La Jolla, CA, United States
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Yang W, Song A, Ao M, Xu Y, Zhang H. Large-scale site-specific mapping of the O-GalNAc glycoproteome. Nat Protoc 2020; 15:2589-2610. [PMID: 32681153 PMCID: PMC8620167 DOI: 10.1038/s41596-020-0345-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 04/21/2020] [Indexed: 01/20/2023]
Abstract
Protein glycosylation is one of the most common protein modifications. A major type of protein glycosylation is O-GalNAcylation, in which GalNAc-type glycans are attached to protein Ser or Thr residues via an O-linked glycosidic bond. O-GalNAcylation is thought to play roles in protein folding, stability, trafficking and protein interactions, and identification of the site-specific O-GalNAc glycoproteome is a crucial step toward understanding the biological significance of the modification. However, lack of suitable methodology, absence of consensus sequon of O-GalNAcylation sites and complex O-GalNAc glycan structures pose analytical challenges. We recently developed a mass spectrometry-based method called extraction of O-linked glycopeptides (EXoO) that enables large-scale mapping of site-specific mucin-type O-GalNAcylation sites. Here we provide a detailed protocol for EXoO, which includes seven stages of: (1) extraction and proteolytic digestion of proteins to peptides, (2) sequential guanidination and de-salting of peptides, (3) enrichment of glycopeptides, (4) solid-phase peptide conjugation and release of O-GalNAc glycopeptides using the OpeRATOR protease, (5) liquid chromatography with tandem mass spectrometry analysis of O-GalNAc glycopeptides, (6) identification of O-GalNAc glycopeptides by database search and (7) quantification of O-GalNAc glycopeptides. Using this protocol, thousands of O-GalNAcylation sites from hundreds of glycoproteins with information regarding site-specific O-GalNAc glycan can be identified and quantified from complex samples. The protocol can be performed by a researcher with basic proteomics skills and takes about 4 d to complete.
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Affiliation(s)
- Weiming Yang
- Corresponding Author: Address: Department of Pathology, Johns Hopkins University School of Medicine, 400 North Broadway, Room 4001A, Baltimore, Maryland, United States.
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Abstract
Glypicans are a family of heparan sulfate proteoglycans that are attached to the cell membrane via a glycosylphosphatidylinositol anchor. Glypicans interact with multiple ligands, including morphogens, growth factors, chemokines, ligands, receptors, and components of the extracellular matrix through their heparan sulfate chains and core protein. Therefore, glypicans can function as coreceptors to regulate cell proliferation, cell motility, and morphogenesis. In addition, some glypicans are abnormally expressed in cancers, possibly involved in tumorigenesis, and have the potential to be cancer-specific biomarkers. Here, we provide a brief review focusing on the expression of glypicans in various cancers and their potential to be targets for cancer therapy.
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Affiliation(s)
- Nan Li
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Madeline R Spetz
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Mitchell Ho
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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Loktev A, Shipley JM. Desmoplastic small round cell tumor (DSRCT): emerging therapeutic targets and future directions for potential therapies. Expert Opin Ther Targets 2020; 24:281-285. [PMID: 32125905 DOI: 10.1080/14728222.2020.1738392] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Anastasia Loktev
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Janet M Shipley
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, UK
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Bosse KR, Majzner RG, Mackall CL, Maris JM. Immune-Based Approaches for the Treatment of Pediatric Malignancies. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2020; 4:353-370. [PMID: 34113750 PMCID: PMC8189419 DOI: 10.1146/annurev-cancerbio-030419-033436] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Immune-based therapies have now been credentialed for pediatric cancers with the robust efficacy of chimeric antigen receptor (CAR) T cells for pediatric B cell acute lymphocytic leukemia (ALL), offering a chance of a cure for children with previously lethal disease and a potentially more targeted therapy to limit treatment-related morbidities. The developmental origins of most pediatric cancers make them ideal targets for immune-based therapies that capitalize on the differential expression of lineage-specific cell surface molecules such as antibodies, antibody-drug conjugates, or CAR T cells, while the efficacy of other therapies that depend on tumor immunogenicity such as immune checkpoint inhibitors has been limited to date. Here we review the current status of immune-based therapies for childhood cancers, discuss challenges to developing immunotherapeutics for these diseases, and outline future directions of pediatric immunotherapy discovery and development.
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Affiliation(s)
- Kristopher R Bosse
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Robbie G Majzner
- Department of Pediatrics and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Crystal L Mackall
- Department of Pediatrics and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California 94305, USA
| | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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SLAM family member 8 is expressed in and enhances the growth of anaplastic large cell lymphoma. Sci Rep 2020; 10:2505. [PMID: 32054954 PMCID: PMC7018816 DOI: 10.1038/s41598-020-59530-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 01/30/2020] [Indexed: 12/03/2022] Open
Abstract
Signaling lymphocytic activation molecule family member 8 (SLAMF8) / B-lymphocyte activator macrophage expressed/CD353 is a member of the CD2 family. SLAMF8 suppresses macrophage function but enhances the growth of neoplastic mast cells via SHP-2. In this study, we found that some anaplastic large cell lymphoma (ALCL) samples were immunohistochemically positive for SLAMF8. However, we found no significant differences between SLAMF8-positive and SLAMF8-negative ALCL samples with respect to age, gender, site, or prognosis. We also identified SLAMF8 expression in ALCL cell lines, Karpas299, and SU-DHL-1. SLAMF8 knockdown decreased the activation of SHP-2 and the growth of these cell lines, and increased the apoptosis of these cell lines. In addition, we observed the interaction between SLAMF8 and SHP-2 in these cell lines using the DuoLink in situ kit. Taken together, these results suggest that SLAMF8 may enhance the growth of ALCL via SHP-2 interaction.
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40
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Sobral LM, Sechler M, Parrish JK, McCann TS, Jones KL, Black JC, Jedlicka P. KDM3A/Ets1/MCAM axis promotes growth and metastatic properties in Rhabdomyosarcoma. Genes Cancer 2020; 11:53-65. [PMID: 32577157 PMCID: PMC7289905 DOI: 10.18632/genesandcancer.200] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Rhabdomyosarcoma (RMS) is the most common soft tissue malignancy of childhood. RMS exists as two major disease subtypes, with oncofusion-positive RMS (FP-RMS) typically carrying a worse prognosis than oncofusion-negative RMS (FN-RMS), in part due to higher propensity for metastasis. Epigenetic mechanisms have recently emerged as critical players in the pathogenesis of pediatric cancers, as well as potential new therapeutic vulnerabilities. Herein, we show that the epigenetic regulator KDM3A, a member of the Jumonji-domain histone demethylase (JHDM) family, is overexpressed, potently promotes colony formation and transendothelial invasion, and activates the expression of genes involved in cell growth, migration and metastasis, in both FN-RMS and FP-RMS. In mechanistic studies, we demonstrate that both RMS subtypes utilize a KDM3A/Ets1/MCAM disease-promoting axis recently discovered in Ewing Sarcoma, another aggressive pediatric cancer of distinct cellular and molecular origin. We further show that KDM3A depletion in FP-RMS cells inhibits both tumor growth and metastasis in vivo, and that RMS cells are highly sensitive to colony growth inhibition by the pan-JHDM inhibitor JIB-04. Together, our studies reveal an important role for the KDM3A/Ets1/MCAM axis in pediatric sarcomas of distinct cellular and molecular ontogeny, and identify new targetable vulnerabilities in RMS.
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Affiliation(s)
- Lays Martin Sobral
- Department of Pathology, 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
| | - Janet K Parrish
- Department of Pathology, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Tyler S McCann
- Department of Pathology, 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
| | - Joshua C Black
- Department of Pharmacology, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Paul Jedlicka
- 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
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41
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Chen C, Dorado Garcia H, Scheer M, Henssen AG. Current and Future Treatment Strategies for Rhabdomyosarcoma. Front Oncol 2019; 9:1458. [PMID: 31921698 PMCID: PMC6933601 DOI: 10.3389/fonc.2019.01458] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/05/2019] [Indexed: 12/31/2022] Open
Abstract
Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children, and can be subcategorized histologically and/or based on PAX-FOXO1 fusion gene status. Over the last four decades, there have been no significant improvements in clinical outcomes for advanced and metastatic RMS patients, underscoring a need for new treatment options for these groups. Despite significant advancements in our understanding of the genomic landscape and underlying biological mechanisms governing RMS that have informed the identification of novel therapeutic targets, development of these therapies in clinical trials has lagged far behind. In this review, we summarize the current frontline multi-modality therapy for RMS according to pediatric protocols, highlight emerging targeted therapies and immunotherapies identified by preclinical studies, and discuss early clinical trial data and the implications they hold for future clinical development.
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Affiliation(s)
- Celine Chen
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Heathcliff Dorado Garcia
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Monika Scheer
- Pediatrics 5, Klinikum Stuttgart, Olgahospital, Stuttgart, Germany
| | - Anton G. Henssen
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
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42
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Shukla GS, Sun YJ, Pero SC, Krag DN. A cocktail of polyclonal affinity enriched antibodies against melanoma mutations increases binding and inhibits tumor growth. J Immunol Methods 2019; 478:112720. [PMID: 31812660 DOI: 10.1016/j.jim.2019.112720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/02/2019] [Accepted: 12/04/2019] [Indexed: 12/25/2022]
Abstract
BACKGROUND Antibodies that target a single tumor antigen fail to cure stage IV cancer patients due to tumor heterogeneity and variable expression of antigen. Tumor cells with insufficient binding of antibody will not undergo antibody induced cytotoxicity. We describe targeting multiple tumor-specific antigens that resulted in homogeneous dense binding to mouse melanoma cells and significant tumor growth inhibition. METHODS Surface-related tumor-specific mutations on B16-F10 cells were identified. Peptides containing the single amino acid mutation were synthesized for 9 different neoantigens. Rabbits were vaccinated with each of these peptides and high affinity polyclonal antibodies to each peptide were obtained. The 9 antibodies were combined as a cocktail and mice with implanted B16-F10 cells were treated with and without PD1 inhibitor. RESULTS Even a single dose of the antibody cocktail inhibited tumor growth and prolonged survival. PD1 inhibitor alone had little effect on tumor growth. The antibody cocktail plus PD1 inhibition increased tumor response and 4 doses of the cocktail completely prevented tumor growth in 50% of the mice. Complete responses were durable. The complete responders were highly resistant to tumor re-challenge at 6 months. No adverse events were identified in the antibody treated mice. CONCLUSIONS Multiple tumor-specific cell surface-related neoantigens were abundant in B16-F10 cells. Antibodies to 9 of these neoantigens had variable binding but when combined had dense homogeneous binding. Even one dose of this cocktail of 9 antibodies improved survival and when multiple doses were combined with PD1 inhibition 50% of the mice were rendered permanently tumor free.
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Affiliation(s)
- Girja S Shukla
- Department of Surgery, University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT, USA.
| | - Yu-Jing Sun
- Department of Surgery, University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT, USA.
| | - Stephanie C Pero
- Department of Surgery, University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT, USA.
| | - David N Krag
- Department of Surgery, University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT, USA.
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Role of glypicans in regulation of the tumor microenvironment and cancer progression. Biochem Pharmacol 2019; 168:108-118. [PMID: 31251939 DOI: 10.1016/j.bcp.2019.06.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 06/20/2019] [Indexed: 12/28/2022]
Abstract
Glypicans are evolutionary conserved, cell surface heparan sulfate (HS) proteoglycans that are attached to the cell membrane via a glycosylphosphatidylinositol (GPI) anchor. Glypicans interact with a broad class of soluble and insoluble ligands, such as morphogens, growth factors, chemokines, receptors and components of the extracellular matrix (ECM). Such versatility comes from their ability to interact through both their HS chains and core protein. Glypicans are involved in cellular and tissue development, morphogenesis and cell motility. They exhibit differential expression in several cancers, acting as both tumor promoters and inhibitors in a cancer type-specific manner. They also influence tumor stroma by facilitating angiogenesis, ECM remodeling and alteration of immune cell functions. Glypicans have emerged as a new therapeutic moiety, whose functions can be exploited in the field of targeted therapies and precision medicine in cancer. This is demonstrated by the emergence of several anti-glypican antibody-based immunologics that have been recently developed and are being evaluated in clinical trials. This review will focus on glypican structure and function with an emphasis on their expression in various cancers. Discussion will also center on the potential of glypicans to be therapeutic targets for inhibition of cancer cell growth.
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44
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Expressions of HLA Class II Genes in Cutaneous Melanoma Were Associated with Clinical Outcome: Bioinformatics Approaches and Systematic Analysis of Public Microarray and RNA-Seq Datasets. Diagnostics (Basel) 2019; 9:diagnostics9020059. [PMID: 31212865 PMCID: PMC6628136 DOI: 10.3390/diagnostics9020059] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/06/2019] [Accepted: 06/10/2019] [Indexed: 12/24/2022] Open
Abstract
Major histocompatibility complex (MHC) class II molecules, encoded by human leukocyte antigen (HLA) class II genes, play important roles in antigen presentation and initiation of immune responses. However, the correlation between HLA class II gene expression level and patient survival and disease progression in cutaneous melanoma is still under investigation. In the present study, we analyzed microarray and RNA-Seq data of cutaneous melanoma from The Cancer Genome Atlas (TCGA) using different bioinformatics tools. Survival analysis revealed higher expression level of HLA class II genes in cutaneous melanoma, especially HLA-DP and -DR, was significantly associated with better overall survival. Furthermore, the expressions of HLA class II genes were most closely associated with survival in cutaneous melanoma as compared with other cancer types. The expression of HLA class II co-expressed genes, which were found to associate with antigen processing, immune response, and inflammatory response, was also positively associated with overall survival in cutaneous melanoma. Therefore, the results indicated that increased HLA class II expression may contribute to enhanced anti-tumor immunity and related inflammatory response via presenting tumor antigens to the immune system. The expression pattern of HLA class II genes may serve as a prognostic biomarker and therapeutic targets in cutaneous melanoma.
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Carrero I, Liu HC, Sikora AG, Milosavljevic A. Histoepigenetic analysis of HPV- and tobacco-associated head and neck cancer identifies both subtype-specific and common therapeutic targets despite divergent microenvironments. Oncogene 2019; 38:3551-3568. [PMID: 30655605 PMCID: PMC6756123 DOI: 10.1038/s41388-018-0659-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 12/07/2018] [Accepted: 12/11/2018] [Indexed: 01/30/2023]
Abstract
Although head and neck squamous cell carcinoma (HNSCC) has in the past been largely associated with tobacco use, human papillomavirus (HPV+) oropharynx cancer has in recent years emerged as the fastest growing type of HNSCC. Patients with HPV+ HNSCC have a better prognosis; however, the 5-year survival for both HPV+ and HPV- subtypes with recurrent or metastatic disease is poor. To gain insights into the tumor microenvironments of both HNSCC subtypes and identify potential therapeutic targets, we performed epigenomic deconvolution on 580 HNSCC samples from the TCGA dataset. Deconvolution revealed distinct molecular and histoepigenetic profiles of the two tumor subtypes, including their cellular composition, epigenomic profiles and gene expression for constituent cell types, and potential cancer cell-specific targets. Our analyses show that high abundance of both CD8 T-cells and B-cells explains better prognosis in HPV+ HNSCC. Deconvolution of gene expression profiles revealed higher expression of the immunotherapy target PD-1 in HPV+ immune cells compared to HPV- cells, suggesting that HPV+ tumors may preferentially benefit from PD-1 targeted therapy. Further analyses identified HPV+ and HPV- cancer cell surface proteins that can also serve as potential targets for therapy. Specifically, Wnt pathway receptor ROR2 is preferentially overexpressed in HPV+ subtypes, suggesting opportunities for development of targeted therapy based on HPV status. In summary, the comprehensive molecular and histoepigenetic analysis of tumor microenvironments by epigenomic deconvolution reveals potential novel biomarkers and targets for precision therapy of HNSCC.
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Affiliation(s)
- Ivenise Carrero
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
| | - Hsuan-Chen Liu
- Translational Biology and Molecular Medicine Program, Baylor College of Medicine, Houston, TX, USA
- Department of Otolaryngology-Head and Neck Surgery, Baylor College of Medicine, Houston, TX, USA
| | - Andrew G Sikora
- Department of Otolaryngology-Head and Neck Surgery, Baylor College of Medicine, Houston, TX, USA.
| | - Aleksandar Milosavljevic
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA.
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA.
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA.
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He L, Li Z. B7-H3 and its role in bone cancers. Pathol Res Pract 2019; 215:152420. [PMID: 31060912 DOI: 10.1016/j.prp.2019.04.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 04/02/2019] [Accepted: 04/16/2019] [Indexed: 11/18/2022]
Abstract
Most bone cancers have a high risk of metastasis, recurrence, and poor prognosis. Although conventional treatments are still the most important therapy, disadvantages still exist. Therefore, there is an unmet need to develop effective strategies. Immunotherapy is a promising therapy. Immunotherapies targeting checkpoints have proven to be successful, but B7-H3 (CD276, clusters of differentiation protein 276), a member of the B7-family of co-stimulatory molecules, is not being widely studied in bone cancers. This review summarized the studies on B7-H3 in bone cancers. 4 studies investigated B7-H3 expression in osteosarcoma, but there is no study on B7-H3 expression in chondrosarcoma. Two studies investigated the possibility to treat Ewing`s sarcoma through targeting the B7-H3 CAR (chimeric antigen receptors) T-cells or using anti-B7-H3 antibody. A study observed the growth of myeloma in B7-H3-deficient mice and the therapeutic effect of B7-H3 antibody and a study invested B7-H3 expression in myeloma patients. One study reported B7-H3 expression in osteoclastomas and one study investigated B7-H3 expression in chordoma tumor tissues. Two clinical trials are conducting on the therapy of osteosarcoma and myeloma using B7-H3 as a target. In conclusion, B7-H3 could be a target of bone cancers.
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Affiliation(s)
- Lile He
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Zhihong Li
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China.
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Riegler LL, Jones GP, Lee DW. Current approaches in the grading and management of cytokine release syndrome after chimeric antigen receptor T-cell therapy. Ther Clin Risk Manag 2019; 15:323-335. [PMID: 30880998 PMCID: PMC6400118 DOI: 10.2147/tcrm.s150524] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
With immunotherapy innovations for cancer treatment, in particular chimeric antigen receptor (CAR) T cells, becoming more successful and prevalent, strategies to mitigate and manage their toxicities are required. Anti-CD19 CAR T-cell therapy has revolutionized the treatment of relapsed/refractory pediatric and adult acute lymphoblastic leukemia and refractory adult non-Hodgkin lymphoma, resulting in the expanded use of CAR T cells in multicenter trials and as US FDA-approved products. Cytokine release syndrome (CRS) and CAR-associated neurotoxicity, which can occur independently or concurrently with CRS, are two potentially life-threatening toxicities of CAR T-cell therapy. In this review, we will focus on describing the pathophysiology behind CRS, the proposed definitions of and grading systems for CRS, and innovative options for treating this potentially lethal systemic inflammatory condition.
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Affiliation(s)
- Lara L Riegler
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Virginia, Charlottesville, VA, USA,
| | - Gavin P Jones
- School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Daniel W Lee
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Virginia, Charlottesville, VA, USA,
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DeRenzo C, Gottschalk S. Genetic Modification Strategies to Enhance CAR T Cell Persistence for Patients With Solid Tumors. Front Immunol 2019; 10:218. [PMID: 30828333 PMCID: PMC6384227 DOI: 10.3389/fimmu.2019.00218] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Accepted: 01/25/2019] [Indexed: 01/19/2023] Open
Abstract
Immunotherapy with chimeric antigen receptor (CAR) T cells offers a promising method to improve cure rates and decrease morbidities for patients with cancer. In this regard, CD19-specific CAR T cell therapies have achieved dramatic objective responses for a high percent of patients with CD19-positive leukemia or lymphoma. Most patients with solid tumors however, have experienced transient or no benefit from CAR T cell therapies. Novel strategies are therefore needed to improve CAR T cell function for patients with solid tumors. One obstacle for the field is limited CAR T cell persistence after infusion into patients. In this review we highlight genetic engineering strategies to improve CAR T cell persistence for enhancing antitumor activity for patients with solid tumors.
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Affiliation(s)
- Christopher DeRenzo
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Stephen Gottschalk
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, United States
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Li N, Gao W, Zhang YF, Ho M. Glypicans as Cancer Therapeutic Targets. Trends Cancer 2018; 4:741-754. [PMID: 30352677 PMCID: PMC6209326 DOI: 10.1016/j.trecan.2018.09.004] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/29/2018] [Accepted: 09/06/2018] [Indexed: 12/14/2022]
Abstract
Glypicans are a group of cell-surface glycoproteins in which heparan sulfate (HS) glycosaminoglycan chains are covalently linked to a protein core. The glypican gene family is broadly conserved across animal species and plays important roles in biological processes. Glypicans can function as coreceptors for multiple signaling molecules known for regulating cell growth, motility, and differentiation. Some members of the glypican family, including glypican 2 (GPC2) and glypican 3 (GPC3), are expressed in childhood cancers and liver cancers, respectively. Antibody-based therapies targeting glypicans are being investigated in preclinical and clinical studies, with the goal of treating solid tumors that do not respond to standard therapies. These studies may establish glypicans as a new class of therapeutic targets for treating cancer.
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Affiliation(s)
- Nan Li
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wei Gao
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Department of Cell Biology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 211166, China
| | - Yi-Fan Zhang
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD 21201, USA
| | - Mitchell Ho
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Richards RM, Sotillo E, Majzner RG. CAR T Cell Therapy for Neuroblastoma. Front Immunol 2018; 9:2380. [PMID: 30459759 PMCID: PMC6232778 DOI: 10.3389/fimmu.2018.02380] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 09/25/2018] [Indexed: 12/11/2022] Open
Abstract
Patients with high risk neuroblastoma have a poor prognosis and survivors are often left with debilitating long term sequelae from treatment. Even after integration of anti-GD2 monoclonal antibody therapy into standard, upftont protocols, 5-year overall survival rates are only about 50%. The success of anti-GD2 therapy has proven that immunotherapy can be effective in neuroblastoma. Adoptive transfer of chimeric antigen receptor (CAR) T cells has the potential to build on this success. In early phase clinical trials, CAR T cell therapy for neuroblastoma has proven safe and feasible, but significant barriers to efficacy remain. These include lack of T cell persistence and potency, difficulty in target identification, and an immunosuppressive tumor microenvironment. With recent advances in CAR T cell engineering, many of these issues are being addressed in the laboratory. In this review, we summarize the clinical trials that have been completed or are underway for CAR T cell therapy in neuroblastoma, discuss the conclusions and open questions derived from these trials, and consider potential strategies to improve CAR T cell therapy for patients with neuroblastoma.
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Affiliation(s)
- Rebecca M. Richards
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States
| | - Elena Sotillo
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, United States
| | - Robbie G. Majzner
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States
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