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1
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He F, Bandyopadhyay AM, Klesse LJ, Rogojina A, Chun SH, Butler E, Hartshorne T, Holland T, Garcia D, Weldon K, Prado LNP, Langevin AM, Grimes AC, Sugalski A, Shah S, Assanasen C, Lai Z, Zou Y, Kurmashev D, Xu L, Xie Y, Chen Y, Wang X, Tomlinson GE, Skapek SX, Houghton PJ, Kurmasheva RT, Zheng S. Genomic profiling of subcutaneous patient-derived xenografts reveals immune constraints on tumor evolution in childhood solid cancer. Nat Commun 2023; 14:7600. [PMID: 37990009 PMCID: PMC10663468 DOI: 10.1038/s41467-023-43373-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 11/07/2023] [Indexed: 11/23/2023] Open
Abstract
Subcutaneous patient-derived xenografts (PDXs) are an important tool for childhood cancer research. Here, we describe a resource of 68 early passage PDXs established from 65 pediatric solid tumor patients. Through genomic profiling of paired PDXs and patient tumors (PTs), we observe low mutational similarity in about 30% of the PT/PDX pairs. Clonal analysis in these pairs show an aggressive PT minor subclone seeds the major clone in the PDX. We show evidence that this subclone is more immunogenic and is likely suppressed by immune responses in the PT. These results suggest interplay between intratumoral heterogeneity and antitumor immunity may underlie the genetic disparity between PTs and PDXs. We further show that PDXs generally recapitulate PTs in copy number and transcriptomic profiles. Finally, we report a gene fusion LRPAP1-PDGFRA. In summary, we report a childhood cancer PDX resource and our study highlights the role of immune constraints on tumor evolution.
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Affiliation(s)
- Funan He
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
- Department of Population Health Sciences, University of Texas Health Science Center, San Antonio, TX, USA
| | - Abhik M Bandyopadhyay
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
| | - Laura J Klesse
- Department of Pediatrics, Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Gill Center for Cancer and Blood Disorders, Children's Health Children's Medical Center, Dallas, TX, USA
| | - Anna Rogojina
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
| | - Sang H Chun
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, USA
| | - Erin Butler
- Department of Pediatrics, Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Gill Center for Cancer and Blood Disorders, Children's Health Children's Medical Center, Dallas, TX, USA
| | - Taylor Hartshorne
- Department of Pediatrics, Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Trevor Holland
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
| | - Dawn Garcia
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
| | - Korri Weldon
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
| | - Luz-Nereida Perez Prado
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
| | - Anne-Marie Langevin
- Department of Pediatrics, University of Texas Health Science Center, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA
| | - Allison C Grimes
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
- Department of Pediatrics, University of Texas Health Science Center, San Antonio, TX, USA
| | - Aaron Sugalski
- Department of Pediatrics, University of Texas Health Science Center, San Antonio, TX, USA
| | - Shafqat Shah
- Department of Pediatrics, University of Texas Health Science Center, San Antonio, TX, USA
| | - Chatchawin Assanasen
- Department of Pediatrics, University of Texas Health Science Center, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA
| | - Zhao Lai
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Yi Zou
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
| | - Dias Kurmashev
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
| | - Lin Xu
- Department of Pediatrics, Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yang Xie
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yidong Chen
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
- Department of Population Health Sciences, University of Texas Health Science Center, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA
| | - Xiaojing Wang
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
- Department of Population Health Sciences, University of Texas Health Science Center, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA
| | - Gail E Tomlinson
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
- Department of Pediatrics, University of Texas Health Science Center, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA
| | - Stephen X Skapek
- Department of Pediatrics, Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Gill Center for Cancer and Blood Disorders, Children's Health Children's Medical Center, Dallas, TX, USA
| | - Peter J Houghton
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Raushan T Kurmasheva
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA.
- Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA.
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA.
| | - Siyuan Zheng
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA.
- Department of Population Health Sciences, University of Texas Health Science Center, San Antonio, TX, USA.
- Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA.
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Rogojina A, Klesse LJ, Butler E, Kim J, Zhang H, Xiao X, Guo L, Zhou Q, Hartshorne T, Garcia D, Weldon K, Holland T, Bandyopadhyay A, Prado LP, Wang S, Yang DM, Langevan AM, Zou Y, Grimes AC, Assanasen C, Gidvani-Diaz V, Zheng S, Lai Z, Chen Y, Xie Y, Tomlinson GE, Skapek SX, Kurmasheva RT, Houghton PJ, Xu L. Comprehensive characterization of patient-derived xenograft models of pediatric leukemia. iScience 2023; 26:108171. [PMID: 37915590 PMCID: PMC10616347 DOI: 10.1016/j.isci.2023.108171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/25/2023] [Accepted: 10/06/2023] [Indexed: 11/03/2023] Open
Abstract
Patient-derived xenografts (PDX) remain valuable models for understanding the biology and for developing novel therapeutics. To expand current PDX models of childhood leukemia, we have developed new PDX models from Hispanic patients, a subgroup with a poorer overall outcome. Of 117 primary leukemia samples obtained, successful engraftment and serial passage in mice were achieved in 82 samples (70%). Hispanic patient samples engrafted at a rate (51/73, 70%) that was similar to non-Hispanic patient samples (31/45, 70%). With a new algorithm to remove mouse contamination in multi-omics datasets including methylation data, we found PDX models faithfully reflected somatic mutations, copy-number alterations, RNA expression, gene fusions, whole-genome methylation patterns, and immunophenotypes found in primary tumor (PT) samples in the first 50 reported here. This cohort of characterized PDX childhood leukemias represents a valuable resource in that germline DNA sequencing has allowed the unambiguous determination of somatic mutations in both PT and PDX.
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Affiliation(s)
- Anna Rogojina
- Greehey Children’s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Laura J. Klesse
- Department of Pediatrics, Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Gill Center for Cancer and Blood Disorders, Children’s Health Children’s Medical Center, Dallas, TX, USA
| | - Erin Butler
- Department of Pediatrics, Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Gill Center for Cancer and Blood Disorders, Children’s Health Children’s Medical Center, Dallas, TX, USA
| | - Jiwoong Kim
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - He Zhang
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xue Xiao
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lei Guo
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Qinbo Zhou
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Taylor Hartshorne
- Department of Pediatrics, Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Dawn Garcia
- Greehey Children’s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Korri Weldon
- Greehey Children’s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Trevor Holland
- Greehey Children’s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Abhik Bandyopadhyay
- Greehey Children’s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Luz Perez Prado
- Greehey Children’s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Shidan Wang
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Donghan M. Yang
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Anne-Marie Langevan
- Department of Pediatrics, Division of Pediatric Hematology Oncology, University of Texas Health San Antonio, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Yi Zou
- Greehey Children’s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Allison C. Grimes
- Greehey Children’s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, USA
- Department of Pediatrics, Division of Pediatric Hematology Oncology, University of Texas Health San Antonio, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Chatchawin Assanasen
- Department of Pediatrics, Division of Pediatric Hematology Oncology, University of Texas Health San Antonio, San Antonio, TX, USA
| | | | - Siyuan Zheng
- Greehey Children’s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, TX, USA
- Department of Population Health Sciences, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Zhao Lai
- Greehey Children’s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, TX, USA
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Yidong Chen
- Greehey Children’s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, TX, USA
- Department of Population Health Sciences, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Yang Xie
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Gail E. Tomlinson
- Greehey Children’s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, USA
- Department of Pediatrics, Division of Pediatric Hematology Oncology, University of Texas Health San Antonio, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Stephen X. Skapek
- Department of Pediatrics, Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Gill Center for Cancer and Blood Disorders, Children’s Health Children’s Medical Center, Dallas, TX, USA
| | - Raushan T. Kurmasheva
- Greehey Children’s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Peter J. Houghton
- Greehey Children’s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Lin Xu
- Department of Pediatrics, Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, USA
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Failli M, Demir S, Del Río-Álvarez Á, Carrillo-Reixach J, Royo L, Domingo-Sàbat M, Childs M, Maibach R, Alaggio R, Czauderna P, Morland B, Branchereau S, Cairo S, Kappler R, Armengol C, di Bernardo D. Computational drug prediction in hepatoblastoma by integrating pan-cancer transcriptomics with pharmacological response. Hepatology 2023:01515467-990000000-00573. [PMID: 37729391 DOI: 10.1097/hep.0000000000000601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/11/2023] [Indexed: 09/22/2023]
Abstract
BACKGROUND AND AIMS Hepatoblastoma (HB) is the predominant form of pediatric liver cancer, though it remains exceptionally rare. While treatment outcomes for children with HB have improved, patients with advanced tumors face limited therapeutic choices. Additionally, survivors often suffer from long-term adverse effects due to treatment, including ototoxicity, cardiotoxicity, delayed growth, and secondary tumors. Consequently, there is a pressing need to identify new and effective therapeutic strategies for patients with HB. Computational methods to predict drug sensitivity from a tumor's transcriptome have been successfully applied for some common adult malignancies, but specific efforts in pediatric cancers are lacking because of the paucity of data. APPROACH AND RESULTS In this study, we used DrugSense to assess drug efficacy in patients with HB, particularly those with the aggressive C2 subtype associated with poor clinical outcomes. Our method relied on publicly available collections of pan-cancer transcriptional profiles and drug responses across 36 tumor types and 495 compounds. The drugs predicted to be most effective were experimentally validated using patient-derived xenograft models of HB grown in vitro and in vivo. We thus identified 2 cyclin-dependent kinase 9 inhibitors, alvocidib and dinaciclib as potent HB growth inhibitors for the high-risk C2 molecular subtype. We also found that in a cohort of 46 patients with HB, high cyclin-dependent kinase 9 tumor expression was significantly associated with poor prognosis. CONCLUSIONS Our work proves the usefulness of computational methods trained on pan-cancer data sets to reposition drugs in rare pediatric cancers such as HB, and to help clinicians in choosing the best treatment options for their patients.
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Affiliation(s)
- Mario Failli
- Telethon Institute of Genetics and Medicine, Pozzuoli, Naples, Italy
- Department of Chemical, Materials and Industrial Production Engineering, University of Naples "Federico II", Naples, Italy
| | - Salih Demir
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Germany
| | - Álvaro Del Río-Álvarez
- Childhood Liver Oncology Group (c-LOG), Health Sciences Research Institute Germans Trias i Pujol (IGTP), Badalona, Catalonia, Spain
| | - Juan Carrillo-Reixach
- Childhood Liver Oncology Group (c-LOG), Health Sciences Research Institute Germans Trias i Pujol (IGTP), Badalona, Catalonia, Spain
- Nottingham Clinical Trials Unit, Nottingham, United Kingdom
| | - Laura Royo
- Childhood Liver Oncology Group (c-LOG), Health Sciences Research Institute Germans Trias i Pujol (IGTP), Badalona, Catalonia, Spain
| | - Montserrat Domingo-Sàbat
- Childhood Liver Oncology Group (c-LOG), Health Sciences Research Institute Germans Trias i Pujol (IGTP), Badalona, Catalonia, Spain
| | | | - Rudolf Maibach
- International Breast Cancer Study Group Coordinating Center, Bern, Switzerland
| | - Rita Alaggio
- Pathology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Piotr Czauderna
- Department of Surgery and Urology for Children and Adolescents, Medical University of Gdansk, Gdansk, Poland
| | - Bruce Morland
- Department of Oncology, Birmingham Women's and Children's Hospital, Birmingham, United Kingdom
| | | | - Stefano Cairo
- XenTech, Evry, France
- Champions Oncology, Rockville, Maryland, USA
| | - Roland Kappler
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Germany
| | - Carolina Armengol
- Childhood Liver Oncology Group (c-LOG), Health Sciences Research Institute Germans Trias i Pujol (IGTP), Badalona, Catalonia, Spain
- Liver and Digestive Diseases Networking Biomedical Research Centre (CIBEREHD), Madrid, Spain
| | - Diego di Bernardo
- Telethon Institute of Genetics and Medicine, Pozzuoli, Naples, Italy
- Department of Chemical, Materials and Industrial Production Engineering, University of Naples "Federico II", Naples, Italy
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You S, Wang MJ, Hou ZY, Wang WD, Du TT, Xue NN, Ji M, Chen XG. Chlorogenic Acid Induced Neuroblastoma Cells Differentiation via the ACAT1-TPK1-PDH Pathway. Pharmaceuticals (Basel) 2023; 16:877. [PMID: 37375824 DOI: 10.3390/ph16060877] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/02/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Chlorogenic acid (CHA) has been shown to have substantial biological activities, including anti-inflammatory, antioxidant, and antitumor effects. However, the pharmacological role of CHA in neuroblastoma has not yet been assessed. Neuroblastoma is a type of cancer that develops in undifferentiated sympathetic ganglion cells. This study aims to assess the antitumor activity of CHA against neuroblastoma and reveal its mechanism of action in cell differentiation. METHODS Be(2)-M17 and SH-SY5Y neuroblastoma cells were used to confirm the differentiation phenotype. Subcutaneous and orthotopic xenograft mouse models were also used to evaluate the antitumor activity of CHA. Seahorse assays and metabolomic analyses were further performed to investigate the roles of CHA and its target ACAT1 in mitochondrial metabolism. RESULTS CHA induced the differentiation of Be(2)-M17 and SH-SY5Y neuroblastoma cells in vivo and in vitro. The knockdown of mitochondrial ACAT1, which was inhibited by CHA, also resulted in differentiation characteristics in vivo and in vitro. A metabolomic analysis revealed that thiamine metabolism was involved in the differentiation of neuroblastoma cells. CONCLUSIONS These results provide evidence that CHA shows good antitumor activity against neuroblastoma via the induction of differentiation, by which the ACAT1-TPK1-PDH pathway is involved. CHA is a potential drug candidate for neuroblastoma therapy.
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Affiliation(s)
- Shen You
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Ming-Jin Wang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Zhen-Yan Hou
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Wei-Da Wang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Ting-Ting Du
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Ni-Na Xue
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Ming Ji
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- Key Laboratory of Small Molecule Immuno-Oncology Drug Discovery, Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Xiao-Guang Chen
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
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5
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Pandya PH, Jannu AJ, Bijangi-Vishehsaraei K, Dobrota E, Bailey BJ, Barghi F, Shannon HE, Riyahi N, Damayanti NP, Young C, Malko R, Justice R, Albright E, Sandusky GE, Wurtz LD, Collier CD, Marshall MS, Gallagher RI, Wulfkuhle JD, Petricoin EF, Coy K, Trowbridge M, Sinn AL, Renbarger JL, Ferguson MJ, Huang K, Zhang J, Saadatzadeh MR, Pollok KE. Integrative Multi-OMICs Identifies Therapeutic Response Biomarkers and Confirms Fidelity of Clinically Annotated, Serially Passaged Patient-Derived Xenografts Established from Primary and Metastatic Pediatric and AYA Solid Tumors. Cancers (Basel) 2022; 15:259. [PMID: 36612255 PMCID: PMC9818438 DOI: 10.3390/cancers15010259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 01/04/2023] Open
Abstract
Establishment of clinically annotated, molecularly characterized, patient-derived xenografts (PDXs) from treatment-naïve and pretreated patients provides a platform to test precision genomics-guided therapies. An integrated multi-OMICS pipeline was developed to identify cancer-associated pathways and evaluate stability of molecular signatures in a panel of pediatric and AYA PDXs following serial passaging in mice. Original solid tumor samples and their corresponding PDXs were evaluated by whole-genome sequencing, RNA-seq, immunoblotting, pathway enrichment analyses, and the drug−gene interaction database to identify as well as cross-validate actionable targets in patients with sarcomas or Wilms tumors. While some divergence between original tumor and the respective PDX was evident, majority of alterations were not functionally impactful, and oncogenic pathway activation was maintained following serial passaging. CDK4/6 and BETs were prioritized as biomarkers of therapeutic response in osteosarcoma PDXs with pertinent molecular signatures. Inhibition of CDK4/6 or BETs decreased osteosarcoma PDX growth (two-way ANOVA, p < 0.05) confirming mechanistic involvement in growth. Linking patient treatment history with molecular and efficacy data in PDX will provide a strong rationale for targeted therapy and improve our understanding of which therapy is most beneficial in patients at diagnosis and in those already exposed to therapy.
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Affiliation(s)
- Pankita H. Pandya
- Department of Pediatrics, Hematology/Oncology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Asha Jacob Jannu
- Department of Biostatistics & Health Data Science Indiana, University School of Medicine, Indianapolis, IN 46202, USA
| | - Khadijeh Bijangi-Vishehsaraei
- Department of Pediatrics, Hematology/Oncology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Erika Dobrota
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Barbara J. Bailey
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Farinaz Barghi
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Harlan E. Shannon
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Niknam Riyahi
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Nur P. Damayanti
- Department of Neurological Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Courtney Young
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Rada Malko
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Ryli Justice
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Eric Albright
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - George E. Sandusky
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - L. Daniel Wurtz
- Department of Orthopedics Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Christopher D. Collier
- Department of Orthopedics Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Mark S. Marshall
- Department of Pediatrics, Hematology/Oncology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Rosa I. Gallagher
- Center for Applied Proteomics and Molecular Medicine, Institute for Biomedical Innovation, George Mason University, Manassas, VA 20110, USA
| | - Julia D. Wulfkuhle
- Center for Applied Proteomics and Molecular Medicine, Institute for Biomedical Innovation, George Mason University, Manassas, VA 20110, USA
| | - Emanuel F. Petricoin
- Center for Applied Proteomics and Molecular Medicine, Institute for Biomedical Innovation, George Mason University, Manassas, VA 20110, USA
| | - Kathy Coy
- Preclinical Modeling and Therapeutics Core, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Melissa Trowbridge
- Preclinical Modeling and Therapeutics Core, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Anthony L. Sinn
- Preclinical Modeling and Therapeutics Core, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Jamie L. Renbarger
- Department of Pediatrics, Hematology/Oncology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Michael J. Ferguson
- Department of Pediatrics, Hematology/Oncology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Kun Huang
- Department of Biostatistics & Health Data Science Indiana, University School of Medicine, Indianapolis, IN 46202, USA
| | - Jie Zhang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - M. Reza Saadatzadeh
- Department of Pediatrics, Hematology/Oncology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Karen E. Pollok
- Department of Pediatrics, Hematology/Oncology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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6
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Yadav P, Subbarayalu P, Medina D, Nirzhor S, Timilsina S, Rajamanickam S, Eedunuri VK, Gupta Y, Zheng S, Abdelfattah N, Huang Y, Vadlamudi R, Hromas R, Meltzer P, Houghton P, Chen Y, Rao MK. M6A RNA Methylation Regulates Histone Ubiquitination to Support Cancer Growth and Progression. Cancer Res 2022; 82:1872-1889. [PMID: 35303054 DOI: 10.1158/0008-5472.can-21-2106] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 02/04/2022] [Accepted: 03/16/2022] [Indexed: 11/16/2022]
Abstract
Osteosarcoma is the most common malignancy of the bone, yet the survival for osteosarcoma patients is virtually unchanged over the past 30 years. This is principally because development of new therapies is hampered by a lack of recurrent mutations that can be targeted in osteosarcoma. Here, we report that epigenetic changes via mRNA methylation holds great promise to better understand the mechanisms of osteosarcoma growth and to develop targeted therapeutics. In osteosarcoma patients, the RNA demethylase ALKBH5 was amplified and higher expression correlated with copy number changes. ALKBH5 was critical for promoting osteosarcoma growth and metastasis, yet it was dispensable for normal cell survival. Me-RIP-seq analysis and functional studies showed that ALKBH5 mediates its pro-tumorigenic function by regulating m6A levels of histone deubiquitinase USP22 and the ubiquitin ligase RNF40. ALKBH5-mediated m6A deficiency in osteosarcoma led to increased expression of USP22 and RNF40 that resulted in inhibition of histone H2A monoubiquitination and induction of key pro-tumorigenic genes, consequently driving unchecked cell cycle progression, incessant replication and DNA repair. RNF40, which is historically known to ubiquitinate H2B, inhibited H2A ubiquitination in cancer by interacting with and affecting the stability of DDB1-CUL4-based ubiquitin E3 ligase complex. Taken together, this study directly links increased activity of ALKBH5 with dysregulation of USP22/RNF40 and histone ubiquitination in cancers. More broadly, these results suggest that m6A RNA methylation works in concert with other epigenetic mechanisms to control cancer growth.
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Affiliation(s)
- Pooja Yadav
- Greehey Children's Cancer Research Institute, United States
| | | | - Daisy Medina
- The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Saif Nirzhor
- The University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States
| | - Santosh Timilsina
- The University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States
| | - Subapriya Rajamanickam
- The University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States
| | | | - Yogesh Gupta
- UT Health Science Center at San Antonio, San Antonio, TX, United States
| | - Siyuan Zheng
- The University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States
| | | | - Yufei Huang
- The University of Texas at San Antonio, San Antonio, Texas, United States
| | - Ratna Vadlamudi
- The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Robert Hromas
- The University of Texas Health Science Center at San Antonio, United States
| | - Paul Meltzer
- National Cancer Institute, Bethesda, MD, United States
| | - Peter Houghton
- The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Yidong Chen
- The University of Texas Health Science Center at San Antonio, San Antonio, United States
| | - Manjeet K Rao
- The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
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7
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Jia L, Yao W, Jiang Y, Li Y, Wang Z, Li H, Huang F, Li J, Chen T, Zhang H. Development of interactive biological web applications with R/Shiny. Brief Bioinform 2021; 23:6387320. [PMID: 34642739 DOI: 10.1093/bib/bbab415] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/09/2021] [Accepted: 09/12/2021] [Indexed: 12/13/2022] Open
Abstract
Development of interactive web applications to deposit, visualize and analyze biological datasets is a major subject of bioinformatics. R is a programming language for data science, which is also one of the most popular languages used in biological data analysis and bioinformatics. However, building interactive web applications was a great challenge for R users before the Shiny package was developed by the RStudio company in 2012. By compiling R code into HTML, CSS and JavaScript code, Shiny has made it incredibly easy to build web applications for the large R community in bioinformatics and for even non-programmers. Over 470 biological web applications have been developed with R/Shiny up to now. To further promote the utilization of R/Shiny, we reviewed the development of biological web applications with R/Shiny, including eminent biological web applications built with R/Shiny, basic steps to build an R/Shiny application, commonly used R packages to build the interface and server of R/Shiny applications, deployment of R/Shiny applications in the cloud and online resources for R/Shiny.
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Affiliation(s)
- Lihua Jia
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China.,College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Wen Yao
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Yingru Jiang
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Yang Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhizhan Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Haoran Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Fangfang Huang
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Jiaming Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Tiantian Chen
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Huiyong Zhang
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
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