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Wang C, Liang C. Dysregulation of Locus-Specific Repetitive Elements in TCGA Pan-Cancers. Genes (Basel) 2025; 16:528. [PMID: 40428352 DOI: 10.3390/genes16050528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2025] [Revised: 04/24/2025] [Accepted: 04/27/2025] [Indexed: 05/29/2025] Open
Abstract
Background: Understanding the role of repetitive elements (REs) in cancer development is crucial for identifying novel biomarkers and therapeutic targets. Methods: This study investigated the locus-specific dysregulation of REs, including the differential expression and methylation of REs, across 12 TCGA cancer types stratified by their genomic context (i.e., genic and intergenic REs). Results: We found uniquely dysregulated genic REs co-regulated with their corresponding transcripts and associated with distinct biological functions in different cancer types. Uniquely dysregulated intergenic REs were identified in each cancer type and used to cluster different sample types. Recurrently dysregulated REs were identified in several cancer types, with genes associated with up-regulated genic REs involved in cell cycle processes and those associated with down-regulated REs involved in the extracellular matrix. Interestingly, four out of five REs consistently down-regulated in all 12 cancer types were located in the intronic region of the TMEM252, a recently discovered tumor suppressor gene. TMEM252 expression was also down-regulated in 10 of 12 cancer types, suggesting its potential importance across a wide range of cancer types. With the corresponding DNA methylation array data, we found a higher prevalence of hypo-methylated REs in most cancer types (10 out of 12). Despite the slight overlaps between differentially expressed REs and differentially methylated REs, we showed that the methylation of locus-specific REs negatively correlates with their expression in some of these 12 cancer types. Conclusions: Our findings highlight the cancer-specific and recurrent deregulation of REs, their functional associations, and the potential role of TMEM252 as a pan-cancer tumor suppressor, providing new insights into biomarker discovery and therapeutic development.
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Affiliation(s)
- Chao Wang
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Chun Liang
- Department of Biology, Miami University, Oxford, OH 45056, USA
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Anderson CJ, Yang H, Parsons J, Ahrens WA, Jagosky MH, Hsu JH, Patt JC, Kneisl JS, Steuerwald NM. Can a Liquid Biopsy Detect Circulating Tumor DNA With Low-passage Whole-genome Sequencing in Patients With a Sarcoma? A Pilot Evaluation. Clin Orthop Relat Res 2025; 483:39-48. [PMID: 38905450 PMCID: PMC11658723 DOI: 10.1097/corr.0000000000003161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 05/30/2024] [Indexed: 06/23/2024]
Abstract
BACKGROUND A liquid biopsy is a test that evaluates the status of a disease by analyzing a sample of bodily fluid, most commonly blood. In recent years, there has been progress in the development and clinical application of liquid biopsy methods to identify blood-based, tumor-specific biomarkers for many cancer types. However, the implementation of these technologies to aid in the treatment of patients who have a sarcoma remains behind other fields of cancer medicine. For this study, we chose to evaluate a sarcoma liquid biopsy based on circulating tumor DNA (ctDNA). All human beings have normal cell-free DNA (cfDNA) circulating in the blood. In contrast with cfDNA, ctDNA is genetic material present in the blood stream that is derived from a tumor. ctDNA carries the unique genomic fingerprint of the tumor with changes that are not present in normal circulating cfDNA. A successful ctDNA liquid biopsy must be able to target these tumor-specific genetic alterations. For instance, epidermal growth factor receptor (EGFR) mutations are common in lung cancers, and ctDNA liquid biopsies are currently in clinical use to evaluate the status of disease in patients who have a lung cancer by detecting EGFR mutations in the blood. As opposed to many carcinomas, sarcomas do not have common recurrent mutations that could serve as the foundation to a ctDNA liquid biopsy. However, many sarcomas have structural changes to their chromosomes, including gains and losses of portions or entire chromosomes, known as copy number alterations (CNAs), that could serve as a target for a ctDNA liquid biopsy. Murine double minute 2 (MDM2) amplification in select lipomatous tumors or parosteal osteosarcoma is an example of a CNA due to the presence of extra copies of a segment of the long arm of chromosome 12. Since a majority of sarcomas demonstrate a complex karyotype with numerous CNAs, a blood-based liquid biopsy strategy that searches for these CNAs may be able to detect the presence of sarcoma ctDNA. Whole-genome sequencing (WGS) is a next-generation sequencing technique that evaluates the entire genome. The depth of coverage of WGS refers to how detailed the sequencing is, like higher versus lower power on a microscope. WGS can be performed with high-depth sequencing (that is, > 60×), which can detect individual point mutations, or low-depth sequencing (that is, 0.1× to 5×), referred to as low-passage whole-genome sequencing (LP-WGS), which may not detect individual mutations but can detect structural chromosomal changes including gains and losses (that is, CNAs). While similar strategies have shown favorable early results for specific sarcoma subtypes, LP-WGS has not been evaluated for applicability to the broader population of patients who have a sarcoma. QUESTIONS/PURPOSES Does an LP-WGS liquid biopsy evaluating for CNAs detect ctDNA in plasma samples from patients who have sarcomas representing a variety of histologic subtypes? METHODS This was a retrospective study conducted at a community-based, tertiary referral center. Nine paired (plasma and formalin-fixed paraffin-embedded [FFPE] tissue) and four unpaired (plasma) specimens from patients who had a sarcoma were obtained from a commercial biospecimen bank. Three control specimens from individuals who did not have cancer were also obtained. The paired and unpaired specimens from patients who had a sarcoma represented a variety of sarcoma histologic subtypes. cfDNA was extracted, amplified, and quantified. Libraries were prepared, and LP-WGS was performed using a NextSeq 500 next-generation sequencing machine at a low depth of sequencing coverage (∼1×). The ichorCNA bioinformatics algorithm, which was designed to detect CNAs from low-depth genomic sequencing data, was used to analyze the data. In contrast with the gold standard for diagnosis in the form of histopathologic analysis of a tissue sample, this test does not discriminate between sarcoma subtypes but detects the presence of tumor-derived CNAs within the ctDNA in the blood that should not be present in a patient who does not have cancer. The liquid biopsy was positive for the detection of cancer if the ichorCNA algorithm detected the presence of ctDNA. The algorithm was also used to quantitatively estimate the percent ctDNA within the cfDNA. The concentration of ctDNA was then calculated from the percent ctDNA relative to the total concentration of cfDNA. The CNAs of the paired FFPE tissue and plasma samples were graphically visualized using aCNViewer software. RESULTS This LP-WGS liquid biopsy detected ctDNA in 9 of 13 of the plasma specimens from patients with a sarcoma. The other four samples from patients with a sarcoma and all serum specimens from patients without cancer had no detectable ctDNA. Of those 9 patients with positive liquid biopsy results, the percent ctDNA ranged from 6% to 11%, and calculated ctDNA quantities were 0.04 to 5.6 ng/mL, which are levels to be expected when ctDNA is detectable. CONCLUSION In this small pilot study, we were able to detect sarcoma ctDNA with an LP-WGS liquid biopsy searching for CNAs in the plasma of most patients who had a sarcoma representing a variety of histologic subtypes. CLINICAL RELEVANCE These results suggest that an LP-WGS liquid biopsy evaluating for CNAs to identify ctDNA may be more broadly applicable to the population of patients who have a sarcoma than previously reported in studies focusing on specific subtypes. Large prospective clinical trials that gather samples at multiple time points during the process of diagnosis, treatment, and surveillance will be needed to further assess whether this technique can be clinically useful. At our institution, we are in the process of developing a large prospective clinical trial for this purpose.
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Affiliation(s)
- Colin J. Anderson
- Musculoskeletal Institute, Atrium Health Wake Forest Baptist, Charlotte, NC, USA
- Levine Cancer Institute, Atrium Health Wake Forest Baptist, Charlotte, NC, USA
| | - HsihTe Yang
- Levine Cancer Institute, Atrium Health Wake Forest Baptist, Charlotte, NC, USA
| | - Judy Parsons
- Levine Cancer Institute, Atrium Health Wake Forest Baptist, Charlotte, NC, USA
| | - Will A. Ahrens
- Carolina Pathology Group, Atrium Health Wake Forest Baptist, Charlotte, NC, USA
| | - Megan H. Jagosky
- Levine Cancer Institute, Atrium Health Wake Forest Baptist, Charlotte, NC, USA
| | - Johann H. Hsu
- Levine Cancer Institute, Atrium Health Wake Forest Baptist, Charlotte, NC, USA
| | - Joshua C. Patt
- Musculoskeletal Institute, Atrium Health Wake Forest Baptist, Charlotte, NC, USA
- Levine Cancer Institute, Atrium Health Wake Forest Baptist, Charlotte, NC, USA
| | - Jeffrey S. Kneisl
- Musculoskeletal Institute, Atrium Health Wake Forest Baptist, Charlotte, NC, USA
- Levine Cancer Institute, Atrium Health Wake Forest Baptist, Charlotte, NC, USA
| | - Nury M. Steuerwald
- Levine Cancer Institute, Atrium Health Wake Forest Baptist, Charlotte, NC, USA
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3
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Kaseb H, Tan C, Townsend JP, Costa J, Laskin WB. Genomic Landscape of Osteosarcoma of Bone in an Older-Aged Patient Population and Analysis of Possible Etiologies Based on Molecular Signature. Genet Test Mol Biomarkers 2024; 28:351-359. [PMID: 39052504 DOI: 10.1089/gtmb.2024.0080] [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] [Indexed: 07/27/2024] Open
Abstract
Background: Osteosarcoma (OS), the most common primary malignant bone tumor, occurs mostly in the pediatric and adolescent (P/A) population where it has been subject to intense study whereas OS arising in the older-aged adult population has undergone less scrutiny. Materials and Methods: In this study, we assess the molecular aberrations detected in eight older adult patients (>59 years of age) with OS of bone by whole-exome sequencing (WES) on formalin-fixed, paraffin-embedded tissue and quantified the contributions of endogenous and exogenous mutational processes to tumor mutational burden and to tumorigenesis through computational analysis. Results: We identified 86 clinically significant somatic mutations. TP53 mutations occurred in OSs of three patients and one patient harbored a pathogenic germline mutation of TP53. Loss-of-heterozygosity of DNA-damage repair genes occurred in all six tumors evaluated. Computational analysis of single nucleotide variants within each tumor detected eight distinct mutagenic processes of which age-associated mutational processes, thiopurine chemotherapy, and defective homologous DNA recombination repair contributed the most to both tumor mutation burden and tumor pathogenesis. Conclusion: The genomic landscape of our older OS patients deciphered by WES is extremely diverse with only 15% of mutated somatic genes uncovered in our study previously described in P/A-enriched OS studies. Endogenous age-related mutagenic processes, defective DNA homologous recombination repair, and exogenous effects of chemotherapy are mainly responsible for pathogenic mutations in OS occurring in our cohort.
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Affiliation(s)
- Hatem Kaseb
- Department of Clinical Sciences Pathology, University of Central Florida College of Medicine, Orlando, Florida, USA
- Department of Pathology, University of Central Florida Lake Nona Hospital, Orlando, Florida, USA
| | - Chichun Tan
- Department of Biostatistics, School of Public Health, Brown University, Providence, Rhode Island, USA
| | - Jeffrey P Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | - Jose Costa
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
| | - William B Laskin
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
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Ma M, Zhu Y, Xiao C, Li R, Cao X, Kang R, Wang X, Li E. Novel insights into RB1 in prostate cancer lineage plasticity and drug resistance. TUMORI JOURNAL 2024; 110:252-263. [PMID: 38316605 DOI: 10.1177/03008916231225576] [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] [Indexed: 02/07/2024]
Abstract
Prostate cancer is the second most common malignancy among men in the world, posing a serious threat to men's health and lives. RB1 is the first human tumor suppressor gene to be described, and it is closely associated with the development, progression, and suppression of a variety of tumors. It was found that the loss of RB1 is an early event in prostate cancer development and is closely related to prostate cancer development, progression and treatment resistance. This paper reviews the current status of research on the relationship between RB1 and prostate cancer from three aspects: RB1 and prostate cell lineage plasticity; biological behavior; and therapeutic resistance. Providing a novel perspective for developing new therapeutic strategies for RB1-loss prostate cancer.
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Affiliation(s)
- Min Ma
- Institute of Translational Medicine, School of Basic Medical, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Yazhi Zhu
- Institute of Translational Medicine, School of Basic Medical, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Changkai Xiao
- Department of Urology, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Ruidong Li
- Department of Urology, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Xingyu Cao
- Institute of Translational Medicine, School of Basic Medical, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Ran Kang
- Department of Urology, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Xiaolan Wang
- Department of Reproductive Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Ermao Li
- Institute of Translational Medicine, School of Basic Medical, Hengyang Medical School, University of South China, Hengyang, Hunan, China
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5
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Yang S, Zhao Y, Tan Y, Zheng C. Identification of microtubule-associated biomarker using machine learning methods in osteonecrosis of the femoral head and osteosarcoma. Heliyon 2024; 10:e31853. [PMID: 38868049 PMCID: PMC11168324 DOI: 10.1016/j.heliyon.2024.e31853] [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: 08/04/2023] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 06/14/2024] Open
Abstract
Background This study aims to explore the microtubule-associated gene signatures and molecular processes shared by osteonecrosis of the femoral head (ONFH) and osteosarcoma (OS). Methods Datasets from the TARGET and GEO databases were subjected to bioinformatics analysis, including the functional enrichment analysis of genes shared by ONFH and OS. Prognostic genes were identified using univariate and multivariate Cox regression analyses to develop a risk score model for predicting overall survival and immune characteristics. Furthermore, LASSO and SVM-RFE algorithms identified biomarkers for ONFH, which were validated in OS. Function prediction, ceRNA network analysis, and gene-drug interaction network construction were subsequently conducted. Biomarker expression was then validated on clinical samples by using qPCR. Results A total of 14 microtubule-associated disease genes were detected in ONFH and OS. Subsequently, risk score model based on four genes was then created, revealing that patients with low-risk exhibited superior survival outcomes compared with those with high-risk. Notably, ONFH with low-risk profiles may manifest an antitumor immune microenvironment. Moreover, by utilizing LASSO and SVM-RFE algorithms, four diagnostic biomarkers were pinpointed, enabling effective discrimination between patients with ONFH and healthy individuals as well as between OS and normal tissues. Additionally, 21 drugs targeting these biomarkers were predicted, and a comprehensive ceRNA network comprising four mRNAs, 71 miRNAs, and 98 lncRNAs was established. The validation of biomarker expression in clinical samples through qPCR affirmed consistency with the results of bioinformatics analysis. Conclusion Microtubule-associated genes may play pivotal roles in OS and ONFH. Additionally, a prognostic model was constructed, and four genes were identified as potential biomarkers and therapeutic targets for both diseases.
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Affiliation(s)
- Sha Yang
- Guizhou University Medical College, Guiyang, 550025, Guizhou Province, PR China
| | - Ying Zhao
- Department of Orthopedics, GuiQian International General Hospital, GuiYang, PR China
| | - Ying Tan
- Department of Neurosurgery, Guizhou Provincial People's Hospital, Guiyang, PR China
| | - Chao Zheng
- Department of Orthopaedics, Children's Hospital of Chongqing Medical University, Chongqing, PR China
- Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing Engineering Research Center of Stem Cell Therapy, Children S Hospital of Chongqing Medical University, Chongqing, PR China
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6
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Zhao S, Wang T, Huang F, Zhao Q, Gong D, Liu J, Yi C, Liang S, Bian E, Tian D, Jing J. A Novel Defined Necroptosis-Related Genes Prognostic Signature for Predicting Prognosis and Treatment of Osteosarcoma. Biochem Genet 2024; 62:831-852. [PMID: 37460861 DOI: 10.1007/s10528-023-10446-1] [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: 03/15/2023] [Accepted: 06/29/2023] [Indexed: 04/20/2024]
Abstract
Osteosarcoma (OS) is a frequent primary malignant bone tumor, with a poor prognosis. Necroptosis is strongly correlated with OS and may be an influential target for treating OS. This study's objective was to establish a necroptosis-related gene (NRG) prognostic signature that could predict OS prognosis and guide OS treatment. First, we identified 20 NRGs associated with OS survival based on the TARGET database. We then derived a 7 NRG prognostic signature. Our findings revealed that the 7 NRG prognostic signature performed well in predicting the survival of OS patients. We next analyzed differences in immunological status and immune cell infiltration. In addition, we examined the relationship between chemo/immunotherapeutic response and the 7-NRG prognostic signature. In addition, to probe the mechanisms underlying the NRG prognostic signature, we performed functional enrichment assays including GO and KEGG. Finally, CHMP4C was selected for functional experiments. Silencing CHMP4C prevented OS cells from proliferating, migrating, and invading. This 7-NRG prognostic signature seems to be an excellent predictor that can provide a fresh direction for OS treatment.
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Affiliation(s)
- Shibing Zhao
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
| | - Tao Wang
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
| | - Fei Huang
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
| | - Qingzhong Zhao
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
| | - Deliang Gong
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
| | - Jun Liu
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
| | - Chengfeng Yi
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
| | - Shuai Liang
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
| | - Erbao Bian
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China.
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China.
| | - Dasheng Tian
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China.
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China.
| | - Juehua Jing
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China.
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China.
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Wang Z, Xia Y, Mills L, Nikolakopoulos AN, Maeser N, Dehm SM, Sheltzer JM, Sun R. Evolving copy number gains promote tumor expansion and bolster mutational diversification. Nat Commun 2024; 15:2025. [PMID: 38448455 PMCID: PMC10918155 DOI: 10.1038/s41467-024-46414-5] [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: 06/06/2023] [Accepted: 02/20/2024] [Indexed: 03/08/2024] Open
Abstract
The timing and fitness effect of somatic copy number alterations (SCNA) in cancer evolution remains poorly understood. Here we present a framework to determine the timing of a clonal SCNA that encompasses multiple gains. This involves calculating the proportion of time from its last gain to the onset of population expansion (lead time) as well as the proportion of time prior to its first gain (initiation time). Our method capitalizes on the observation that a genomic segment, while in a specific copy number (CN) state, accumulates point mutations proportionally to its CN. Analyzing 184 whole genome sequenced samples from 75 patients across five tumor types, we commonly observe late gains following early initiating events, occurring just before the clonal expansion relevant to the sampling. These include gains acquired after genome doubling in more than 60% of cases. Notably, mathematical modeling suggests that late clonal gains may contain final-expansion drivers. Lastly, SCNAs bolster mutational diversification between subpopulations, exacerbating the circle of proliferation and increasing heterogeneity.
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Affiliation(s)
- Zicheng Wang
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- School of Data Science, The Chinese University of Hong Kong (CUHK-Shenzhen), Shenzhen, China
| | - Yunong Xia
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Lauren Mills
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Athanasios N Nikolakopoulos
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Nicole Maeser
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Scott M Dehm
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Department of Urology, University of Minnesota, Minneapolis, MN, USA
| | | | - Ruping Sun
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA.
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.
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Schott CR, Koehne AL, Sayles LC, Young EP, Luck C, Yu K, Lee AG, Breese MR, Leung SG, Xu H, Shah AT, Liu HY, Spillinger A, Behroozfard IH, Marini KD, Dinh PT, Pons Ventura MV, Vanderboon EN, Hazard FK, Cho SJ, Avedian RS, Mohler DG, Zimel M, Wustrack R, Curtis C, Sirota M, Sweet-Cordero EA. Osteosarcoma PDX-Derived Cell Line Models for Preclinical Drug Evaluation Demonstrate Metastasis Inhibition by Dinaciclib through a Genome-Targeted Approach. Clin Cancer Res 2024; 30:849-864. [PMID: 37703185 PMCID: PMC10870121 DOI: 10.1158/1078-0432.ccr-23-0873] [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: 03/21/2023] [Revised: 03/26/2023] [Accepted: 08/08/2023] [Indexed: 09/15/2023]
Abstract
PURPOSE Models to study metastatic disease in rare cancers are needed to advance preclinical therapeutics and to gain insight into disease biology. Osteosarcoma is a rare cancer with a complex genomic landscape in which outcomes for patients with metastatic disease are poor. As osteosarcoma genomes are highly heterogeneous, multiple models are needed to fully elucidate key aspects of disease biology and to recapitulate clinically relevant phenotypes. EXPERIMENTAL DESIGN Matched patient samples, patient-derived xenografts (PDX), and PDX-derived cell lines were comprehensively evaluated using whole-genome sequencing and RNA sequencing. The in vivo metastatic phenotype of the PDX-derived cell lines was characterized in both an intravenous and an orthotopic murine model. As a proof-of-concept study, we tested the preclinical effectiveness of a cyclin-dependent kinase inhibitor on the growth of metastatic tumors in an orthotopic amputation model. RESULTS PDXs and PDX-derived cell lines largely maintained the expression profiles of the patient from which they were derived despite the emergence of whole-genome duplication in a subset of cell lines. The cell lines were heterogeneous in their metastatic capacity, and heterogeneous tissue tropism was observed in both intravenous and orthotopic models. Single-agent dinaciclib was effective at dramatically reducing the metastatic burden. CONCLUSIONS The variation in metastasis predilection sites between osteosarcoma PDX-derived cell lines demonstrates their ability to recapitulate the spectrum of the disease observed in patients. We describe here a panel of new osteosarcoma PDX-derived cell lines that we believe will be of wide use to the osteosarcoma research community.
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Affiliation(s)
- Courtney R. Schott
- Department of Pediatrics, University of California San Francisco, San Francisco, California
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Amanda L. Koehne
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Leanne C. Sayles
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Elizabeth P. Young
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Cuyler Luck
- Department of Pediatrics, University of California San Francisco, San Francisco, California
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, California
| | - Katherine Yu
- Department of Pediatrics, University of California San Francisco, San Francisco, California
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, California
| | - Alex G. Lee
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Marcus R. Breese
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Stanley G. Leung
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Hang Xu
- Departments of Genetics and Medicine, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Avanthi Tayi Shah
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Heng-Yi Liu
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Aviv Spillinger
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Inge H. Behroozfard
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Kieren D. Marini
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Phuong T. Dinh
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - María V. Pons Ventura
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Emma N. Vanderboon
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Florette K. Hazard
- Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Soo-Jin Cho
- Department of Pathology, University of California San Francisco, San Francisco, California
| | - Raffi S. Avedian
- Department of Orthopedic Surgery, Stanford University School of Medicine, Stanford University, Stanford, California
| | - David G. Mohler
- Department of Orthopedic Surgery, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Melissa Zimel
- Department of Orthopedic Surgery, University of California San Francisco, San Francisco, California
| | - Rosanna Wustrack
- Department of Orthopedic Surgery, University of California San Francisco, San Francisco, California
| | - Christina Curtis
- Departments of Genetics and Medicine, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Marina Sirota
- Department of Pediatrics, University of California San Francisco, San Francisco, California
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, California
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9
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Saba KH, Difilippo V, Kovac M, Cornmark L, Magnusson L, Nilsson J, van den Bos H, Spierings DC, Bidgoli M, Jonson T, Sumathi VP, Brosjö O, Staaf J, Foijer F, Styring E, Nathrath M, Baumhoer D, Nord KH. Disruption of the TP53 locus in osteosarcoma leads to TP53 promoter gene fusions and restoration of parts of the TP53 signalling pathway. J Pathol 2024; 262:147-160. [PMID: 38010733 DOI: 10.1002/path.6219] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/24/2023] [Accepted: 09/19/2023] [Indexed: 11/29/2023]
Abstract
TP53 is the most frequently mutated gene in human cancer. This gene shows not only loss-of-function mutations but also recurrent missense mutations with gain-of-function activity. We have studied the primary bone malignancy osteosarcoma, which harbours one of the most rearranged genomes of all cancers. This is odd since it primarily affects children and adolescents who have not lived the long life thought necessary to accumulate massive numbers of mutations. In osteosarcoma, TP53 is often disrupted by structural variants. Here, we show through combined whole-genome and transcriptome analyses of 148 osteosarcomas that TP53 structural variants commonly result in loss of coding parts of the gene while simultaneously preserving and relocating the promoter region. The transferred TP53 promoter region is fused to genes previously implicated in cancer development. Paradoxically, these erroneously upregulated genes are significantly associated with the TP53 signalling pathway itself. This suggests that while the classical tumour suppressor activities of TP53 are lost, certain parts of the TP53 signalling pathway that are necessary for cancer cell survival and proliferation are retained. In line with this, our data suggest that transposition of the TP53 promoter is an early event that allows for a new normal state of genome-wide rearrangements in osteosarcoma. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Karim H Saba
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Valeria Difilippo
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Michal Kovac
- Bone Tumour Reference Centre at the Institute of Pathology, University Hospital and University of Basel, Basel, Switzerland
- Faculty of Informatics and Information Technologies, Slovak University of Technology, Bratislava, Slovakia
| | - Louise Cornmark
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Linda Magnusson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Jenny Nilsson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Hilda van den Bos
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Diana Cj Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Mahtab Bidgoli
- Department of Clinical Genetics and Pathology, Laboratory Medicine, Medical Services, Skåne University Hospital, Lund, Sweden
| | - Tord Jonson
- Department of Clinical Genetics and Pathology, Laboratory Medicine, Medical Services, Skåne University Hospital, Lund, Sweden
| | - Vaiyapuri P Sumathi
- Department of Musculoskeletal Pathology, Royal Orthopaedic Hospital, Birmingham, UK
| | - Otte Brosjö
- Department of Orthopedics, Karolinska University Hospital, Stockholm, Sweden
| | - Johan Staaf
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Emelie Styring
- Department of Orthopedics, Lund University, Skåne University Hospital, Lund, Sweden
| | - Michaela Nathrath
- Children's Cancer Research Centre and Department of Pediatrics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Department of Pediatric Oncology, Klinikum Kassel, Kassel, Germany
| | - Daniel Baumhoer
- Bone Tumour Reference Centre at the Institute of Pathology, University Hospital and University of Basel, Basel, Switzerland
| | - Karolin H Nord
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
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10
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Difilippo V, Saba KH, Styring E, Magnusson L, Nilsson J, Nathrath M, Baumhoer D, Nord KH. Osteosarcomas With Few Chromosomal Alterations or Adult Onset Are Genetically Heterogeneous. J Transl Med 2024; 104:100283. [PMID: 37931683 DOI: 10.1016/j.labinv.2023.100283] [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: 06/22/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/08/2023] Open
Abstract
Osteosarcoma is the most common primary bone malignancy, often detected in children and adolescents and commonly associated with TP53 alterations along with a high number of chromosomal rearrangements. However, osteosarcoma can affect patients of any age, and some tumors display less genetic complexity. Besides TP53 variants, data on key driving mutations are lacking for many osteosarcomas, particularly those affecting adults. To detect osteosarcoma-specific alterations, we screened transcriptomic and genomic sequencing and copy number data from 150 bone tumors originally diagnosed as osteosarcomas. To increase the precision in gene fusion detection, we developed a bioinformatic tool denoted as NAFuse, which extracts gene fusions that are verified at both the genomic and transcriptomic levels. Apart from the already reported genetic subgroups of osteosarcoma with TP53 structural variants, or MDM2 and/or CDK4 amplification, we did not identify any recurrent genetic driver that signifies the remaining cases. Among the plethora of mutations identified, we found genetic alterations characteristic of, or similar to, those of other bone and soft tissue tumors in 8 cases. These mutations were found in tumors with relatively few other genetic alterations or in adults. Due to the lack of clinical context and available tissue, we can question the diagnosis only on a genetic basis. However, our findings support the notion that osteosarcomas with few chromosomal alterations or adult onset seem genetically distinct from conventional osteosarcomas of children and adolescents.
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Affiliation(s)
- Valeria Difilippo
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Karim H Saba
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Emelie Styring
- Department of Orthopedics, Lund University, Skåne University Hospital, Lund, Sweden
| | - Linda Magnusson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Jenny Nilsson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Michaela Nathrath
- Children's Cancer Research Centre and Department of Pediatrics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany; Department of Pediatric Oncology, Klinikum Kassel, Kassel, Germany
| | - Daniel Baumhoer
- Bone Tumour Reference Centre at the Institute of Pathology, University Hospital and University of Basel, Basel, Switzerland
| | - Karolin H Nord
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden.
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11
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Kinnaman MD, Zaccaria S, Makohon-Moore A, Arnold B, Levine MF, Gundem G, Arango Ossa JE, Glodzik D, Rodríguez-Sánchez MI, Bouvier N, Li S, Stockfisch E, Dunigan M, Cobbs C, Bhanot UK, You D, Mullen K, Melchor JP, Ortiz MV, O'Donohue TJ, Slotkin EK, Wexler LH, Dela Cruz FS, Hameed MR, Glade Bender JL, Tap WD, Meyers PA, Papaemmanuil E, Kung AL, Iacobuzio-Donahue CA. Subclonal Somatic Copy-Number Alterations Emerge and Dominate in Recurrent Osteosarcoma. Cancer Res 2023; 83:3796-3812. [PMID: 37812025 PMCID: PMC10646480 DOI: 10.1158/0008-5472.can-23-0385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 07/14/2023] [Accepted: 09/01/2023] [Indexed: 10/10/2023]
Abstract
Multiple large-scale genomic profiling efforts have been undertaken in osteosarcoma to define the genomic drivers of tumorigenesis, therapeutic response, and disease recurrence. The spatial and temporal intratumor heterogeneity could also play a role in promoting tumor growth and treatment resistance. We conducted longitudinal whole-genome sequencing of 37 tumor samples from 8 patients with relapsed or refractory osteosarcoma. Each patient had at least one sample from a primary site and a metastatic or relapse site. Subclonal copy-number alterations were identified in all patients except one. In 5 patients, subclones from the primary tumor emerged and dominated at subsequent relapses. MYC gain/amplification was enriched in the treatment-resistant clones in 6 of 7 patients with multiple clones. Amplifications in other potential driver genes, such as CCNE1, RAD21, VEGFA, and IGF1R, were also observed in the resistant copy-number clones. A chromosomal duplication timing analysis revealed that complex genomic rearrangements typically occurred prior to diagnosis, supporting a macroevolutionary model of evolution, where a large number of genomic aberrations are acquired over a short period of time followed by clonal selection, as opposed to ongoing evolution. A mutational signature analysis of recurrent tumors revealed that homologous repair deficiency (HRD)-related SBS3 increases at each time point in patients with recurrent disease, suggesting that HRD continues to be an active mutagenic process after diagnosis. Overall, by examining the clonal relationships between temporally and spatially separated samples from patients with relapsed/refractory osteosarcoma, this study sheds light on the intratumor heterogeneity and potential drivers of treatment resistance in this disease. SIGNIFICANCE The chemoresistant population in recurrent osteosarcoma is subclonal at diagnosis, emerges at the time of primary resection due to selective pressure from neoadjuvant chemotherapy, and is characterized by unique oncogenic amplifications.
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Affiliation(s)
- Michael D. Kinnaman
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York
| | - Simone Zaccaria
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, United Kingdom
| | - Alvin Makohon-Moore
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Brian Arnold
- Department of Computer Science, Princeton University, Princeton, New Jersey
- Center for Statistics and Machine Learning, Princeton University, Princeton, New Jersey
| | - Max F. Levine
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gunes Gundem
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Juan E. Arango Ossa
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dominik Glodzik
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Nancy Bouvier
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Shanita Li
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Emily Stockfisch
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marisa Dunigan
- Integrated Genomics Operation Core, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Cassidy Cobbs
- Integrated Genomics Operation Core, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Umesh K. Bhanot
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
- Precision Pathology Biobanking Center, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daoqi You
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Katelyn Mullen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, New York
| | - Jerry P. Melchor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael V. Ortiz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Tara J. O'Donohue
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Emily K. Slotkin
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Leonard H. Wexler
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Filemon S. Dela Cruz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Meera R. Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Julia L. Glade Bender
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - William D. Tap
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paul A. Meyers
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elli Papaemmanuil
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrew L. Kung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christine A. Iacobuzio-Donahue
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
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12
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Chen J, Baxi K, Lipsitt AE, Hensch NR, Wang L, Sreenivas P, Modi P, Zhao XR, Baudin A, Robledo DG, Bandyopadhyay A, Sugalski A, Challa AK, Kurmashev D, Gilbert AR, Tomlinson GE, Houghton P, Chen Y, Hayes MN, Chen EY, Libich DS, Ignatius MS. Defining function of wild-type and three patient-specific TP53 mutations in a zebrafish model of embryonal rhabdomyosarcoma. eLife 2023; 12:e68221. [PMID: 37266578 PMCID: PMC10322150 DOI: 10.7554/elife.68221] [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: 03/09/2021] [Accepted: 06/01/2023] [Indexed: 06/03/2023] Open
Abstract
In embryonal rhabdomyosarcoma (ERMS) and generally in sarcomas, the role of wild-type and loss- or gain-of-function TP53 mutations remains largely undefined. Eliminating mutant or restoring wild-type p53 is challenging; nevertheless, understanding p53 variant effects on tumorigenesis remains central to realizing better treatment outcomes. In ERMS, >70% of patients retain wild-type TP53, yet mutations when present are associated with worse prognosis. Employing a kRASG12D-driven ERMS tumor model and tp53 null (tp53-/-) zebrafish, we define wild-type and patient-specific TP53 mutant effects on tumorigenesis. We demonstrate that tp53 is a major suppressor of tumorigenesis, where tp53 loss expands tumor initiation from <35% to >97% of animals. Characterizing three patient-specific alleles reveals that TP53C176F partially retains wild-type p53 apoptotic activity that can be exploited, whereas TP53P153Δ and TP53Y220C encode two structurally related proteins with gain-of-function effects that predispose to head musculature ERMS. TP53P153Δ unexpectedly also predisposes to hedgehog-expressing medulloblastomas in the kRASG12D-driven ERMS-model.
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Affiliation(s)
- Jiangfei Chen
- Institute of Environmental Safety and Human Health, Wenzhou Medical UniversityWenzhouChina
- Greehey Children's Cancer Research Institute (GCCRI), UT Health Sciences CenterSan AntonioUnited States
| | - Kunal Baxi
- Greehey Children's Cancer Research Institute (GCCRI), UT Health Sciences CenterSan AntonioUnited States
- Department of Molecular Medicine, UT Health Sciences CenterSan AntonioUnited States
| | - Amanda E Lipsitt
- Greehey Children's Cancer Research Institute (GCCRI), UT Health Sciences CenterSan AntonioUnited States
- Department of Pediatrics, Division of Hematology Oncology, UT Health Sciences CenterSan AntonioUnited States
| | - Nicole Rae Hensch
- Greehey Children's Cancer Research Institute (GCCRI), UT Health Sciences CenterSan AntonioUnited States
- Department of Molecular Medicine, UT Health Sciences CenterSan AntonioUnited States
| | - Long Wang
- Greehey Children's Cancer Research Institute (GCCRI), UT Health Sciences CenterSan AntonioUnited States
- Department of Molecular Medicine, UT Health Sciences CenterSan AntonioUnited States
| | - Prethish Sreenivas
- Greehey Children's Cancer Research Institute (GCCRI), UT Health Sciences CenterSan AntonioUnited States
- Department of Molecular Medicine, UT Health Sciences CenterSan AntonioUnited States
| | - Paulomi Modi
- Greehey Children's Cancer Research Institute (GCCRI), UT Health Sciences CenterSan AntonioUnited States
- Department of Molecular Medicine, UT Health Sciences CenterSan AntonioUnited States
| | - Xiang Ru Zhao
- Greehey Children's Cancer Research Institute (GCCRI), UT Health Sciences CenterSan AntonioUnited States
- Department of Molecular Medicine, UT Health Sciences CenterSan AntonioUnited States
| | - Antoine Baudin
- Greehey Children's Cancer Research Institute (GCCRI), UT Health Sciences CenterSan AntonioUnited States
- Department of Biochemistry and Structural Biology, UT Health Sciences CenterSan AntonioUnited States
| | - Daniel G Robledo
- Greehey Children's Cancer Research Institute (GCCRI), UT Health Sciences CenterSan AntonioUnited States
| | - Abhik Bandyopadhyay
- Greehey Children's Cancer Research Institute (GCCRI), UT Health Sciences CenterSan AntonioUnited States
| | - Aaron Sugalski
- Department of Pediatrics, Division of Hematology Oncology, UT Health Sciences CenterSan AntonioUnited States
| | - Anil K Challa
- Greehey Children's Cancer Research Institute (GCCRI), UT Health Sciences CenterSan AntonioUnited States
- Department of Biology, University of Alabama at BirminghamBirminghamUnited States
| | - Dias Kurmashev
- Greehey Children's Cancer Research Institute (GCCRI), UT Health Sciences CenterSan AntonioUnited States
| | - Andrea R Gilbert
- Department of Pathology and Laboratory Medicine, UT Health Sciences CenterSan AntonioUnited States
| | - Gail E Tomlinson
- Greehey Children's Cancer Research Institute (GCCRI), UT Health Sciences CenterSan AntonioUnited States
- Department of Pediatrics, Division of Hematology Oncology, UT Health Sciences CenterSan AntonioUnited States
| | - Peter Houghton
- Greehey Children's Cancer Research Institute (GCCRI), UT Health Sciences CenterSan AntonioUnited States
- Department of Molecular Medicine, UT Health Sciences CenterSan AntonioUnited States
| | - Yidong Chen
- Department of Population Health Sciences, UT Health Sciences CenterSan AntonioUnited States
| | - Madeline N Hayes
- Developmental and Stem Cell Biology, Hospital for Sick ChildrenTorontoCanada
| | - Eleanor Y Chen
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | - David S Libich
- Greehey Children's Cancer Research Institute (GCCRI), UT Health Sciences CenterSan AntonioUnited States
- Department of Biochemistry and Structural Biology, UT Health Sciences CenterSan AntonioUnited States
| | - Myron S Ignatius
- Greehey Children's Cancer Research Institute (GCCRI), UT Health Sciences CenterSan AntonioUnited States
- Department of Molecular Medicine, UT Health Sciences CenterSan AntonioUnited States
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13
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Xie L, Cai Z, Lu H, Meng F, Zhang X, Luo K, Su X, Lei Y, Xu J, Lou J, Wang H, Du Z, Wang Y, Li Y, Ren T, Xu J, Sun X, Tang X, Guo W. Distinct genomic features between osteosarcomas firstly metastasing to bone and to lung. Heliyon 2023; 9:e15527. [PMID: 37205995 PMCID: PMC10189180 DOI: 10.1016/j.heliyon.2023.e15527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 03/26/2023] [Accepted: 04/12/2023] [Indexed: 05/21/2023] Open
Abstract
Background Osteosarcoma initially metastasing to bone only shows distinct biological features compared to osteosarcoma that firstly metastasizes to the lung, which suggests us underlying different genomic pathogenetic mechanism. Methods We analyzed whole-exome sequencing (WES) data for 38 osteosarcoma with paired samples in different relapse patterns. We also sought to redefine disease subclassifications for osteosarcoma based on genetic alterations and correlate these genetic profiles with clinical treatment courses to elucidate potential evolving cladograms. Results We investigated WES of 12/38 patients with high-grade osteosarcoma (31.6%) with initial bone metastasis (group A) and 26/38 (68.4%) with initial pulmonary metastasis (group B), of whom 15/38 (39.5%) had paired samples of primary lesions and metastatic lesions. We found that osteosarcoma in group A mainly carries single-nucleotide variations displaying higher tumor mutation burden and neoantigen load and more tertiary lymphoid structures, while those in group B mainly exhibits structural variants. High conservation of reported genetic sequencing over time in their evolving cladograms. Conclusions Osteosarcoma with mainly single-nucleotide variations other than structural variants might exhibit biological behavior predisposing toward bone metastases as well as better immunogenicity in tumor microenvironment.
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Affiliation(s)
- Lu Xie
- Musculoskeletal Tumor Center, Peking University People's Hospital, No. 11 Xizhimen South Street, Xicheng District, Beijing 100044, China
| | - Zhenyu Cai
- Musculoskeletal Tumor Center, Peking University People's Hospital, No. 11 Xizhimen South Street, Xicheng District, Beijing 100044, China
| | - Hezhe Lu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, No. A3 Datun Road, Chaoyang District, Beijing 100101, China
| | - Fanfei Meng
- Shanghai OrigiMed Co., Ltd, Shanghai, No. 3576 Zhaolou Road, Minhang District, Shanghai, 201112, China
| | - Xin Zhang
- Shanghai OrigiMed Co., Ltd, Shanghai, No. 3576 Zhaolou Road, Minhang District, Shanghai, 201112, China
| | - Kun Luo
- Shanghai OrigiMed Co., Ltd, Shanghai, No. 3576 Zhaolou Road, Minhang District, Shanghai, 201112, China
| | - Xiaoxing Su
- Berry Oncology Corporation, Fuzhou, 350200, China
| | - Yan Lei
- Berry Oncology Corporation, Fuzhou, 350200, China
| | - Jiuhui Xu
- Musculoskeletal Tumor Center, Peking University People's Hospital, No. 11 Xizhimen South Street, Xicheng District, Beijing 100044, China
| | - Jingbing Lou
- Musculoskeletal Tumor Center, Peking University People's Hospital, No. 11 Xizhimen South Street, Xicheng District, Beijing 100044, China
| | - Han Wang
- Musculoskeletal Tumor Center, Peking University People's Hospital, No. 11 Xizhimen South Street, Xicheng District, Beijing 100044, China
| | - Zhiye Du
- Musculoskeletal Tumor Center, Peking University People's Hospital, No. 11 Xizhimen South Street, Xicheng District, Beijing 100044, China
| | - Yunfan Wang
- Pathology Department, Peking University Shougang Hospital, No. 9 Jinyuanzhuang Road, Shijingshan District, Beijing, 100144, China
| | - Yuan Li
- Radiology Department & Nuclear Medicine Department, Peking University People's Hospital, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Tingting Ren
- Musculoskeletal Tumor Center, Peking University People's Hospital, No. 11 Xizhimen South Street, Xicheng District, Beijing 100044, China
| | - Jie Xu
- Musculoskeletal Tumor Center, Peking University People's Hospital, No. 11 Xizhimen South Street, Xicheng District, Beijing 100044, China
| | - Xin Sun
- Musculoskeletal Tumor Center, Peking University People's Hospital, No. 11 Xizhimen South Street, Xicheng District, Beijing 100044, China
| | - Xiaodong Tang
- Musculoskeletal Tumor Center, Peking University People's Hospital, No. 11 Xizhimen South Street, Xicheng District, Beijing 100044, China
- Corresponding author.
| | - Wei Guo
- Musculoskeletal Tumor Center, Peking University People's Hospital, No. 11 Xizhimen South Street, Xicheng District, Beijing 100044, China
- Corresponding author.
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14
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Rajan S, Zaccaria S, Cannon MV, Cam M, Gross AC, Raphael BJ, Roberts RD. Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time. CANCER RESEARCH COMMUNICATIONS 2023; 3:564-575. [PMID: 37066022 PMCID: PMC10093779 DOI: 10.1158/2767-9764.crc-22-0348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/18/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023]
Abstract
Osteosarcoma is an aggressive malignancy characterized by high genomic complexity. Identification of few recurrent mutations in protein coding genes suggests that somatic copy-number aberrations (SCNA) are the genetic drivers of disease. Models around genomic instability conflict-it is unclear whether osteosarcomas result from pervasive ongoing clonal evolution with continuous optimization of the fitness landscape or an early catastrophic event followed by stable maintenance of an abnormal genome. We address this question by investigating SCNAs in >12,000 tumor cells obtained from human osteosarcomas using single-cell DNA sequencing, with a degree of precision and accuracy not possible when inferring single-cell states using bulk sequencing. Using the CHISEL algorithm, we inferred allele- and haplotype-specific SCNAs from this whole-genome single-cell DNA sequencing data. Surprisingly, despite extensive structural complexity, these tumors exhibit a high degree of cell-cell homogeneity with little subclonal diversification. Longitudinal analysis of patient samples obtained at distant therapeutic timepoints (diagnosis, relapse) demonstrated remarkable conservation of SCNA profiles over tumor evolution. Phylogenetic analysis suggests that the majority of SCNAs were acquired early in the oncogenic process, with relatively few structure-altering events arising in response to therapy or during adaptation to growth in metastatic tissues. These data further support the emerging hypothesis that early catastrophic events, rather than sustained genomic instability, give rise to structural complexity, which is then preserved over long periods of tumor developmental time. Significance Chromosomally complex tumors are often described as genomically unstable. However, determining whether complexity arises from remote time-limited events that give rise to structural alterations or a progressive accumulation of structural events in persistently unstable tumors has implications for diagnosis, biomarker assessment, mechanisms of treatment resistance, and represents a conceptual advance in our understanding of intratumoral heterogeneity and tumor evolution.
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Affiliation(s)
- Sanjana Rajan
- Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, Ohio
- Center for Childhood Cancers and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Simone Zaccaria
- Department of Computer Science, Princeton University, Princeton, New Jersey
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, United Kingdom
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
| | - Matthew V. Cannon
- Center for Childhood Cancers and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Maren Cam
- Center for Childhood Cancers and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Amy C. Gross
- Center for Childhood Cancers and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Benjamin J. Raphael
- Department of Computer Science, Princeton University, Princeton, New Jersey
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Ryan D. Roberts
- Center for Childhood Cancers and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
- The Ohio State University James Comprehensive Cancer Center, Columbus, Ohio
- Division of Pediatric Hematology, Oncology, and BMT, Nationwide Children's Hospital, Columbus, Ohio
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15
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Li Z, Jin C, Lu X, Zhang Y, Zhang Y, Wen J, Liu Y, Liu X, Li J. Studying the mechanism underlying lipid metabolism in osteosarcoma based on transcriptomic RNA sequencing and single-cell data. J Gene Med 2023:e3491. [PMID: 36847293 DOI: 10.1002/jgm.3491] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/03/2023] [Accepted: 02/16/2023] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND We aimed to provide a new typing method for osteosarcoma (OS) based on single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data from the perspective of lipid metabolism and examine its potential mechanisms in the onset and progression of OS. METHODS Scores for six lipid metabolic pathways were calculated by single-sample gene set enrichment analysis (ssGSEA) based on a scRNA-seq dataset and three microarray expression profiles. Subsequently, cluster typing was conducted using unsupervised consistency clustering. Furthermore, single-cell clustering and dimensionality-reduction analyses identified cell subtypes. Finally, an analysis of cellular receptors was performed using CellphoneDB to identify cellular communication. RESULTS OS was classified into three subtypes based on lipid metabolic pathways. Among them, patients in clust3 showed poor prognoses, whereas those in clust1 and clust2 exhibited good prognoses. In addition, ssGSEA analysis showed that patients in clust3 had lower immune cell scores. Moreover, the Th17 cell differentiation pathway was significantly differentially enriched between clust2 and clust3, with lower enrichment scores for metabolic pathways in the former relative to clust1 and clust2. In total, 24 genes were upregulated between clust1 and clust2, whereas 20 were downregulated in clust3. These observations were validated by single-cell data analysis. Finally, through scRNA-seq data analysis, we identified nine ligand-receptor pairs particularly critical for communication between normal and malignant cells. CONCLUSIONS Three clusters were identified and the single-cell analysis revealed that malignant cells dominated lipid metabolism patterns in tumors, thereby influencing the tumor microenvironment.
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Affiliation(s)
- Zhe Li
- Orthopaedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Chi Jin
- Orthopaedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xinchang Lu
- Orthopaedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yan Zhang
- Orthopaedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yi Zhang
- Orthopaedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jia Wen
- Orthopaedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yongkui Liu
- Orthopaedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xiaoting Liu
- Orthopaedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jiazhen Li
- Orthopaedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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Candido MF, Medeiros M, Veronez LC, Bastos D, Oliveira KL, Pezuk JA, Valera ET, Brassesco MS. Drugging Hijacked Kinase Pathways in Pediatric Oncology: Opportunities and Current Scenario. Pharmaceutics 2023; 15:pharmaceutics15020664. [PMID: 36839989 PMCID: PMC9966033 DOI: 10.3390/pharmaceutics15020664] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/18/2023] Open
Abstract
Childhood cancer is considered rare, corresponding to ~3% of all malignant neoplasms in the human population. The World Health Organization (WHO) reports a universal occurrence of more than 15 cases per 100,000 inhabitants around the globe, and despite improvements in diagnosis, treatment and supportive care, one child dies of cancer every 3 min. Consequently, more efficient, selective and affordable therapeutics are still needed in order to improve outcomes and avoid long-term sequelae. Alterations in kinases' functionality is a trademark of cancer and the concept of exploiting them as drug targets has burgeoned in academia and in the pharmaceutical industry of the 21st century. Consequently, an increasing plethora of inhibitors has emerged. In the present study, the expression patterns of a selected group of kinases (including tyrosine receptors, members of the PI3K/AKT/mTOR and MAPK pathways, coordinators of cell cycle progression, and chromosome segregation) and their correlation with clinical outcomes in pediatric solid tumors were accessed through the R2: Genomics Analysis and Visualization Platform and by a thorough search of published literature. To further illustrate the importance of kinase dysregulation in the pathophysiology of pediatric cancer, we analyzed the vulnerability of different cancer cell lines against their inhibition through the Cancer Dependency Map portal, and performed a search for kinase-targeted compounds with approval and clinical applicability through the CanSAR knowledgebase. Finally, we provide a detailed literature review of a considerable set of small molecules that mitigate kinase activity under experimental testing and clinical trials for the treatment of pediatric tumors, while discuss critical challenges that must be overcome before translation into clinical options, including the absence of compounds designed specifically for childhood tumors which often show differential mutational burdens, intrinsic and acquired resistance, lack of selectivity and adverse effects on a growing organism.
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Affiliation(s)
- Marina Ferreira Candido
- Department of Cell Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil
| | - Mariana Medeiros
- Regional Blood Center, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil
| | - Luciana Chain Veronez
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil
| | - David Bastos
- Department of Biology, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-901, SP, Brazil
| | - Karla Laissa Oliveira
- Department of Biology, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-901, SP, Brazil
| | - Julia Alejandra Pezuk
- Departament of Biotechnology and Innovation, Anhanguera University of São Paulo, UNIAN/SP, São Paulo 04119-001, SP, Brazil
| | - Elvis Terci Valera
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil
| | - María Sol Brassesco
- Departament of Biotechnology and Innovation, Anhanguera University of São Paulo, UNIAN/SP, São Paulo 04119-001, SP, Brazil
- Correspondence: ; Tel.: +55-16-3315-9144; Fax: +55-16-3315-4886
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17
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Schott CR, Koehne AL, Sayles LC, Young EP, Luck C, Yu K, Lee AG, Breese MR, Leung SG, Xu H, Shah AT, Liu HY, Spillinger A, Behroozfard IH, Marini KD, Dinh PT, Pons Ventura MAV, Vanderboon EN, Hazard FK, Cho SJ, Avedian RS, Mohler DG, Zimel M, Wustrack R, Curtis C, Sirota M, Sweet-Cordero EA. Development and characterization of new patient-derived xenograft (PDX) models of osteosarcoma with distinct metastatic capacities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.19.524562. [PMID: 36711882 PMCID: PMC9882347 DOI: 10.1101/2023.01.19.524562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Models to study metastatic disease in rare cancers are needed to advance preclinical therapeutics and to gain insight into disease biology, especially for highly aggressive cancers with a propensity for metastatic spread. Osteosarcoma is a rare cancer with a complex genomic landscape in which outcomes for patients with metastatic disease are poor. As osteosarcoma genomes are highly heterogeneous, a large panel of models is needed to fully elucidate key aspects of disease biology and to recapitulate clinically-relevant phenotypes. We describe the development and characterization of osteosarcoma patient-derived xenografts (PDXs) and a panel of PDX-derived cell lines. Matched patient samples, PDXs, and PDX-derived cell lines were comprehensively evaluated using whole genome sequencing and RNA sequencing. PDXs and PDX-derived cell lines largely maintained the expression profiles of the patient from which they were derived despite the emergence of whole-genome duplication (WGD) in a subset of cell lines. These cell line models were heterogeneous in their metastatic capacity and their tissue tropism as observed in both intravenous and orthotopic models. As proof-of-concept study, we used one of these models to test the preclinical effectiveness of a CDK inhibitor on the growth of metastatic tumors in an orthotopic amputation model. Single-agent dinaciclib was effective at dramatically reducing the metastatic burden in this model.
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18
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Zhang W, Lyu P, Andreev D, Jia Y, Zhang F, Bozec A. Hypoxia-immune-related microenvironment prognostic signature for osteosarcoma. Front Cell Dev Biol 2022; 10:974851. [PMID: 36578780 PMCID: PMC9791087 DOI: 10.3389/fcell.2022.974851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/25/2022] [Indexed: 12/14/2022] Open
Abstract
Introduction: Increasing evidences have shown that hypoxia and the immune microenvironment play vital roles in the development of osteosarcoma. However, reliable gene signatures based on the combination of hypoxia and the immune status for prognostic prediction of osteosarcoma have so far not been identified. Methods: The individual hypoxia and immune status of osteosarcoma patients were identified with transcriptomic profiles of a training cohort from the TARGET database using ssGSEA and ESTIMATE algorithms, respectively. Lasso regression and stepwise Cox regression were performed to develop a hypoxia-immune-based gene signature. An independent cohort from the GEO database was used for external validation. Finally, a nomogram was constructed based on the gene signature and clinical features to improve the risk stratification and to quantify the risk assessment for individual patients. Results: Hypoxia and the immune status were significantly associated with the prognosis of osteosarcoma patients. Seven hypoxia- and immune-related genes (BNIP3, SLC38A5, SLC5A3, CKMT2, S100A3, CXCL11 and PGM1) were identified to be involved in our prognostic signature. In the training cohort, the prognostic signature discriminated high-risk patients with osteosarcoma. The hypoxia-immune-based gene signature proved to be a stable and predictive method as determined in different datasets and subgroups of patients. Furthermore, a nomogram based on the prognostic signature was generated to optimize the risk stratification and to quantify the risk assessment. Similar results were validated in an independent GEO cohort, confirming the stability and reliability of the prognostic signature. Conclusion: The hypoxia-immune-based prognostic signature might contribute to the optimization of risk stratification for survival and personalized management of osteosarcoma patients.
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19
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Xie X, Bian Y, Li H, Yin J, Tian L, Jiang R, Zeng Z, Shi X, Lei Z, Hou C, Qu Y, Wang L, Shen J. A Comprehensive Understanding of the Genomic Bone Tumor Landscape: A Multicenter Prospective Study. Front Oncol 2022; 12:835004. [PMID: 35756627 PMCID: PMC9213736 DOI: 10.3389/fonc.2022.835004] [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: 12/14/2021] [Accepted: 05/09/2022] [Indexed: 11/25/2022] Open
Abstract
Complexity and heterogeneity increases the difficulty of diagnosis and treatment of bone tumors. We aimed to identify the mutational characterization and potential biomarkers of bone tumors. In this study, a total of 357 bone tumor patients were recruited and the next generation sequencing (NGS)-based YuanSu450 panel, that includes both DNA and RNA sequencing, was performed for genomic alteration identification. The most common mutated genes in bone tumors included TP53, NCOR1, VEGFA, RB1, CCND3, CDKN2A, GID4, CCNE1, TERT, and MAP2K4. The amplification of genes such as NCOR1, VEGFA, and CCND3 mainly occurred in osteosarcoma. Germline mutation analysis reveal a high frequency of HRD related mutations (46.4%, 13/28) in this cohort. With the assistance of RNA sequencing, 16.8% (19/113) gene fusions were independently detected in 20% (16/79) of patients. Nearly 34.2% of patients harbored actionable targeted mutations, of which the most common mutation is CDKN2A deletion. The different mutational characterizations between juvenile patients and adult patients indicated the potential effect of age in bone tumor treatment. According to the genomic alterations, the diagnosis of 26 (7.28%) bone tumors were corrected. The most easily misdiagnosed bone tumor included malignant giant cell tumors of bone (2.8%, 10/357) and fibrous dysplasia of bone (1.7%, 6/357). Meanwhile, we found that the mutations of MUC16 may be a potential biomarker for the diagnosis of mesenchymal chondrosarcomas. Our results indicated that RNA sequencing effectively complements DNA sequencing and increased the detection rate of gene fusions, supporting that NGS technology can effectively assist the diagnosis of bone tumors.
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Affiliation(s)
- Xianbiao Xie
- Department of Musculoskeletal Oncology Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yiying Bian
- Department of Musculoskeletal Oncology Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Haomiao Li
- Department of Musculoskeletal Oncology, Center for Orthopaedic Surgery, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Junqiang Yin
- Department of Musculoskeletal Oncology Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Lantian Tian
- Department of Hepatobiliary Surgery, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Renbing Jiang
- Department of Bone and Soft Tissue, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, China
| | - Ziliang Zeng
- Department of Musculoskeletal Oncology Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaoliang Shi
- Department of Medicine, Shanghai OrigiMed Co., Ltd, Shanghai, China
| | - Zixiong Lei
- Department of Musculoskeletal Oncology, Center for Orthopaedic Surgery, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Changhe Hou
- Department of Musculoskeletal Oncology, Center for Orthopaedic Surgery, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Yueting Qu
- Department of Medicine, Shanghai OrigiMed Co., Ltd, Shanghai, China
| | - Liwei Wang
- Department of Medicine, Shanghai OrigiMed Co., Ltd, Shanghai, China
| | - Jingnan Shen
- Department of Musculoskeletal Oncology Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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20
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Wang C, Liang C. The insertion and dysregulation of transposable elements in osteosarcoma and their association with patient event-free survival. Sci Rep 2022; 12:377. [PMID: 35013466 PMCID: PMC8748539 DOI: 10.1038/s41598-021-04208-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/23/2021] [Indexed: 12/11/2022] Open
Abstract
The dysregulation of transposable elements (TEs) has been explored in a variety of cancers. However, TE activities in osteosarcoma (OS) have not been extensively studied yet. By integrative analysis of RNA-seq, whole-genome sequencing (WGS), and methylation data, we showed aberrant TE activities associated with dysregulations of TEs in OS tumors. Specifically, expression levels of LINE-1 and Alu of different evolutionary ages, as well as subfamilies of SVA and HERV-K, were significantly up-regulated in OS tumors, accompanied by enhanced DNA repair responses. We verified the characteristics of LINE-1 mediated TE insertions, including target site duplication (TSD) length (centered around 15 bp) and preferential insertions into intergenic and AT-rich regions as well as intronic regions of longer genes. By filtering polymorphic TE insertions reported in 1000 genome project (1KGP), besides 148 tumor-specific somatic TE insertions, we found most OS patient-specific TE insertions (3175 out of 3326) are germline insertions, which are associated with genes involved in neuronal processes or with transcription factors important for cancer development. In addition to 68 TE-affected cancer genes, we found recurrent germline TE insertions in 72 non-cancer genes with high frequencies among patients. We also found that +/− 500 bps flanking regions of transcription start sites (TSS) of LINE-1 (young) and Alu showed lower methylation levels in OS tumor samples than controls. Interestingly, by incorporating patient clinical data and focusing on TE activities in OS tumors, our data analysis suggested that higher TE insertions in OS tumors are associated with a longer event-free survival time.
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Affiliation(s)
- Chao Wang
- Department of Biology, Miami University, Oxford, Ohio, 45056, USA.
| | - Chun Liang
- Department of Biology, Miami University, Oxford, Ohio, 45056, USA.
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21
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Zoumpoulidou G, Alvarez-Mendoza C, Mancusi C, Ahmed RM, Denman M, Steele CD, Tarabichi M, Roy E, Davies LR, Manji J, Cristalli C, Scotlandi K, Pillay N, Strauss SJ, Mittnacht S. Therapeutic vulnerability to PARP1,2 inhibition in RB1-mutant osteosarcoma. Nat Commun 2021; 12:7064. [PMID: 34862364 PMCID: PMC8642453 DOI: 10.1038/s41467-021-27291-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 11/11/2021] [Indexed: 11/09/2022] Open
Abstract
Loss-of-function mutations in the RB1 tumour suppressor are key drivers in cancer, including osteosarcoma. RB1 loss-of-function compromises genome-maintenance and hence could yield vulnerability to therapeutics targeting such processes. Here we demonstrate selective hypersensitivity to clinically-approved inhibitors of Poly-ADP-Polymerase1,2 inhibitors (PARPi) in RB1-defective cancer cells, including an extended panel of osteosarcoma-derived lines. PARPi treatment results in extensive cell death in RB1-defective backgrounds and prolongs survival of mice carrying human RB1-defective osteosarcoma grafts. PARPi sensitivity is not associated with canonical homologous recombination defect (HRd) signatures that predict PARPi sensitivity in cancers with BRCA1,2 loss, but is accompanied by rapid activation of DNA replication checkpoint signalling, and active DNA replication is a prerequisite for sensitivity. Importantly, sensitivity in backgrounds with natural or engineered RB1 loss surpasses that seen in BRCA-mutated backgrounds where PARPi have established clinical benefit. Our work provides evidence that PARPi sensitivity extends beyond cancers identifiable by HRd and advocates PARP1,2 inhibition as a personalised strategy for RB1-mutated osteosarcoma and other cancers.
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Affiliation(s)
| | | | | | | | - Milly Denman
- UCL Cancer Institute, University College London, London, UK
| | | | - Maxime Tarabichi
- The Francis Crick Institute, London, UK.,Institute for Interdisciplinary Research, Université Libre de Bruxelles, Brussels, Belgium
| | - Errin Roy
- UCL Cancer Institute, University College London, London, UK
| | | | - Jiten Manji
- UCL Cancer Institute, University College London, London, UK
| | - Camilla Cristalli
- Experimental Oncology Laboratory, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Katia Scotlandi
- Experimental Oncology Laboratory, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Nischalan Pillay
- UCL Cancer Institute, University College London, London, UK.,Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, London, UK
| | - Sandra J Strauss
- UCL Cancer Institute, University College London, London, UK.,London Sarcoma Service, University College London Hospitals Foundation Trust, London, UK
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22
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Barenboim M, Kovac M, Ameline B, Jones DTW, Witt O, Bielack S, Burdach S, Baumhoer D, Nathrath M. DNA methylation-based classifier and gene expression signatures detect BRCAness in osteosarcoma. PLoS Comput Biol 2021; 17:e1009562. [PMID: 34762643 PMCID: PMC8584788 DOI: 10.1371/journal.pcbi.1009562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 10/14/2021] [Indexed: 11/29/2022] Open
Abstract
Although osteosarcoma (OS) is a rare cancer, it is the most common primary malignant bone tumor in children and adolescents. BRCAness is a phenotypical trait in tumors with a defect in homologous recombination repair, resembling tumors with inactivation of BRCA1/2, rendering these tumors sensitive to poly (ADP)-ribose polymerase inhibitors (PARPi). Recently, OS was shown to exhibit molecular features of BRCAness. Our goal was to develop a method complementing existing genomic methods to aid clinical decision making on administering PARPi in OS patients. OS samples with DNA-methylation data were divided to BRCAness-positive and negative groups based on the degree of their genomic instability (n = 41). Methylation probes were ranked according to decreasing variance difference between two groups. The top 2000 probes were selected for training and cross-validation of the random forest algorithm. Two-thirds of available OS RNA-Seq samples (n = 17) from the top and bottom of the sample list ranked according to genome instability score were subjected to differential expression and, subsequently, to gene set enrichment analysis (GSEA). The combined accuracy of trained random forest was 85% and the average area under the ROC curve (AUC) was 0.95. There were 449 upregulated and 1,079 downregulated genes in the BRCAness-positive group (fdr < 0.05). GSEA of upregulated genes detected enrichment of DNA replication and mismatch repair and homologous recombination signatures (FWER < 0.05). Validation of the BRCAness classifier with an independent OS set (n = 20) collected later in the course of study showed AUC of 0.87 with an accuracy of 90%. GSEA signatures computed for this test set were matching the ones observed in the training set enrichment analysis. In conclusion, we developed a new classifier based on DNA-methylation patterns that detects BRCAness in OS samples with high accuracy. GSEA identified genome instability signatures. Machine-learning and gene expression approaches add new epigenomic and transcriptomic aspects to already established genomic methods for evaluation of BRCAness in osteosarcoma and can be extended to cancers characterized by genome instability. Osteosarcoma (OS) is the most common primary malignant tumor of bone in children and young adults with poor prognosis for patients with refractory or metastatic disease. A common feature, so-called BRCAness, exists in multiple cancers including OS and is characterized by homologous recombination deficiency. Tumors exhibiting BRCAness have been shown to respond to therapy with PARP inhibitors. Currently, BRCAness is mostly assessed by the genomic instability score. This method based on the DNA sequencing requires normal tissue DNA as control and is vulnerable to subjective interpretation of "genomic scarring" events. In this study, we implemented a classifier based on DNA methylation patterns. It is capable of detecting BRCAness in OS samples and does not require control tissue DNA. Therefore, it has the potential to support clinical decision making on administering PARPi in OS patients. We further corroborated the presence of BRCAness in OS by detecting homologous recombination signatures through gene expression analysis.
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Affiliation(s)
- Maxim Barenboim
- Department of Pediatrics and Children’s Cancer Research Center, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- * E-mail: (MB); (MN)
| | - Michal Kovac
- University Hospital Basel and University of Basel, Bone Tumour Reference Centre at the Institute of Pathology, Basel, Switzerland
- Faculty of Informatics and Information Technologies, Slovak University of Technology, Bratislava, Slovakia
| | - Baptiste Ameline
- University Hospital Basel and University of Basel, Bone Tumour Reference Centre at the Institute of Pathology, Basel, Switzerland
| | - David T. W. Jones
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Olaf Witt
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- University Hospital Heidelberg, Hematology and Immunology at the Department of Pediatric Oncology, Heidelberg, Germany
| | - Stefan Bielack
- Klinikum Stuttgart–Olgahospital, Stuttgart Cancer Center, Pediatrics 5 (Oncology, Hematology, Immunology), Stuttgart, Germany
| | - Stefan Burdach
- Department of Pediatrics and Children’s Cancer Research Center, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- CCC München—Comprehensive Cancer Center, DKTK German Cancer Consortium, Munich, Germany
| | - Daniel Baumhoer
- University Hospital Basel and University of Basel, Bone Tumour Reference Centre at the Institute of Pathology, Basel, Switzerland
| | - Michaela Nathrath
- Department of Pediatrics and Children’s Cancer Research Center, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- Klinikum Kassel, Department of Pediatric Oncology, Kassel, Germany
- * E-mail: (MB); (MN)
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23
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Chi X, Ji T, Li J, Xu J, Tang X, Xie L, Meng F, Guo W. Genomic Analysis Revealed Mutational Traits Associated with Clinical Outcomes in Osteosarcoma. Cancer Manag Res 2021; 13:5101-5111. [PMID: 34234554 PMCID: PMC8254031 DOI: 10.2147/cmar.s317809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/17/2021] [Indexed: 12/01/2022] Open
Abstract
Objective The limited understanding of correlation between genomic features and biological behaviors has impeded the therapeutic breakthrough in osteosarcoma (OS). This study aimed to reveal the correlation of mutational and evolutionary traits with clinical outcomes. Methods We applied a case-based targeted and whole exome sequencing of eleven matched primary, recurrent and metastatic samples from three OS patients characterized by different clinical behaviors in local recurrence or systematic progression pattern. Results Extensive OS-associated driver genes were detected including TP53, RB1, NF1, PTEN, SPEN, CDKN2A. Oncogenic signaling pathways including cell cycle, TP53, MYC, Notch, WNT, RTK-RAS and PI3K were determined. MYC amplification was observed in the patient with shortest disease-free interval. Linear, branched or mixed evolutionary models were constructed in the three OS cases. A branched evolution with limited root mutation was detected in patient with shorter survival interval. ADAM17 mutation and HEY1 amplification were identified in OS happening dedifferentiation. Signatures 21 associated with microsatellite instability (MSI) was identified in OS patient with extra-pulmonary metastases. Conclusion OS was characterized by complex genomic alterations. MYC aberration, limited root mutations, and a branched evolutionary model were observed in OS patient with relatively aggressive course. Extra-pulmonary metastases of OS might attribute to distinct mutational process pertaining to MSI. Further research in a larger number of people is needed to confirm these findings.
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Affiliation(s)
- Xiying Chi
- Musculoskeletal Tumor Center, Peking University, People's Hospital, Beijing, 100044, People's Republic of China
| | - Tao Ji
- Musculoskeletal Tumor Center, Peking University, People's Hospital, Beijing, 100044, People's Republic of China
| | - Junying Li
- Department of Medicine, OrigiMed, Shanghai, 201114, People's Republic of China
| | - Jie Xu
- Musculoskeletal Tumor Center, Peking University, People's Hospital, Beijing, 100044, People's Republic of China
| | - Xiaodong Tang
- Musculoskeletal Tumor Center, Peking University, People's Hospital, Beijing, 100044, People's Republic of China
| | - Lu Xie
- Musculoskeletal Tumor Center, Peking University, People's Hospital, Beijing, 100044, People's Republic of China
| | - Fanfei Meng
- Department of Medicine, OrigiMed, Shanghai, 201114, People's Republic of China
| | - Wei Guo
- Musculoskeletal Tumor Center, Peking University, People's Hospital, Beijing, 100044, People's Republic of China
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24
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Zhang GZ, Wu ZL, Li CY, Ren EH, Yuan WH, Deng YJ, Xie QQ. Development of a Machine Learning-Based Autophagy-Related lncRNA Signature to Improve Prognosis Prediction in Osteosarcoma Patients. Front Mol Biosci 2021; 8:615084. [PMID: 34095215 PMCID: PMC8176230 DOI: 10.3389/fmolb.2021.615084] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/29/2021] [Indexed: 12/15/2022] Open
Abstract
Background Osteosarcoma is a frequent bone malignancy in children and young adults. Despite the availability of some prognostic biomarkers, most of them fail to accurately predict prognosis in osteosarcoma patients. In this study, we used bioinformatics tools and machine learning algorithms to establish an autophagy-related long non-coding RNA (lncRNA) signature to predict the prognosis of osteosarcoma patients. Methods We obtained expression and clinical data from osteosarcoma patients in the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) and Gene Expression Omnibus (GEO) databases. We acquired an autophagy gene list from the Human Autophagy Database (HADb) and identified autophagy-related lncRNAs by co-expression analyses. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of the autophagy-related lncRNAs were conducted. Univariate and multivariate Cox regression analyses were performed to assess the prognostic value of the autophagy-related lncRNA signature and validate the relationship between the signature and osteosarcoma patient survival in an independent cohort. We also investigated the relationship between the signature and immune cell infiltration. Results We initially identified 69 autophagy-related lncRNAs, 13 of which were significant predictors of overall survival in osteosarcoma patients. Kaplan-Meier analyses revealed that the 13 autophagy-related lncRNAs could stratify patients based on their outcomes. Receiver operating characteristic curve analyses confirmed the superior prognostic value of the lncRNA signature compared to clinically used prognostic biomarkers. Importantly, the autophagy-related lncRNA signature predicted patient prognosis independently of clinicopathological characteristics. Furthermore, we found that the expression levels of the autophagy-related lncRNA signature were significantly associated with the infiltration levels of different immune cell subsets, including T cells, NK cells, and dendritic cells. Conclusion The autophagy-related lncRNA signature established here is an independent and robust predictor of osteosarcoma patient survival. Our findings also suggest that the expression of these 13 autophagy-related lncRNAs may promote osteosarcoma progression by regulating immune cell infiltration in the tumor microenvironment.
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Affiliation(s)
- Guang-Zhi Zhang
- The Second Clinical Medical College, Lanzhou University, Lanzhou, China.,Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou, China.,Lintao County Traditional Chinese Medicine Hospital of Gansu Province, Lintao, China
| | - Zuo-Long Wu
- The Second Clinical Medical College, Lanzhou University, Lanzhou, China.,Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou, China
| | - Chun-Ying Li
- The Fourth People's Hospital of Qinghai Province, Xining, China
| | - En-Hui Ren
- The Second Clinical Medical College, Lanzhou University, Lanzhou, China.,Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou, China.,Department of Orthopaedics, Xining First People's Hospital, Xining, China
| | - Wen-Hua Yuan
- The Second Clinical Medical College, Lanzhou University, Lanzhou, China.,Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou, China
| | - Ya-Jun Deng
- The Second Clinical Medical College, Lanzhou University, Lanzhou, China.,Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou, China
| | - Qi-Qi Xie
- Affiliated Hospital of Qinghai University, Xining, China.,Affiliated Cancer Hospital of Qinghai University, Xining, China.,Breast Disease Diagnosis and Treatment Center, Affiliated Hospital of Qinghai University & Affiliated Cancer Hospital of Qinghai University, Xining, China
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25
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Chen Y, Liu R, Wang W, Wang C, Zhang N, Shao X, He Q, Ying M. Advances in targeted therapy for osteosarcoma based on molecular classification. Pharmacol Res 2021; 169:105684. [PMID: 34022396 DOI: 10.1016/j.phrs.2021.105684] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 05/03/2021] [Accepted: 05/15/2021] [Indexed: 02/08/2023]
Abstract
Osteosarcoma, a highly malignant tumor, is characterized by widespread and recurrent chromosomal and genetic abnormalities. In recent years, a number of elaborated sequencing analyses have made it possible to cluster the osteosarcoma based on the identification of candidate driver genes and develop targeted therapy. Here, we reviewed recent next-generation genome sequencing studies and advances in targeted therapies for osteosarcoma based on molecular classification. First, we stratified osteosarcomas into ten molecular subtypes based on genetic changes. And we analyzed potential targeted therapies for osteosarcoma based on the identified molecular subtypes. Finally, the development of targeted therapies for osteosarcoma investigated in clinical trials were further summarized and discussed. Therefore, we indicated the importance of molecular classification on the targeted therapy for osteosarcoma. And the stratification of patients based on the genetic characteristics of osteosarcoma will help to obtain a better therapeutic response to targeted therapies, bringing us closer to the era of personalized medicine.
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Affiliation(s)
- Yingqian Chen
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Runzhi Liu
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Wei Wang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Chen Wang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Ning Zhang
- Department of Orthopedics, The Second Affiliated Hospital of Zhejiang University, Zhejiang University, Hangzhou, China
| | - Xuejing Shao
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.
| | - Qiaojun He
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.
| | - Meidan Ying
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China; Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China; Institute of Pharmacology & Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
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26
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Qian H, Lei T, Hu Y, Lei P. Expression of Lipid-Metabolism Genes Is Correlated With Immune Microenvironment and Predicts Prognosis in Osteosarcoma. Front Cell Dev Biol 2021; 9:673827. [PMID: 33937273 PMCID: PMC8085431 DOI: 10.3389/fcell.2021.673827] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 03/30/2021] [Indexed: 12/29/2022] Open
Abstract
Objectives Osteosarcoma was the most popular primary malignant tumor in children and adolescent, and the 5-year survival of osteosarcoma patients gained no substantial improvement over the past 35 years. This study aims to explore the role of lipid metabolism in the development and diagnosis of osteosarcoma. Methods Clinical information and corresponding RNA data of osteosarcoma patients were downloaded from TRGET and GEO databases. Consensus clustering was performed to identify new molecular subgroups. ESTIMATE, TIMER and ssGSEA analyses were applied to determinate the tumor immune microenvironment (TIME) and immune status of the identified subgroups. Functional analyses including GO, KEGG, GSVA and GSEA analyses were conducted to elucidate the underlying mechanisms. Prognostic risk model was constructed using LASSO algorithm and multivariate Cox regression analysis. Results Two molecular subgroups with significantly different survival were identified. Better prognosis was associated with high immune score, low tumor purity, high abundance of immune infiltrating cells and relatively high immune status. GO and KEGG analyses revealed that the DEGs between the two subgroups were mainly enriched in immune- and bone remodeling-associated pathways. GSVA and GSEA analyses indicated that, lipid catabolism downregulation and lipid hydroxylation upregulation may impede the bone remodeling and development of immune system. Risk model based on lipid metabolism related genes (LMRGs) showed potent potential for survival prediction in osteosarcoma. Nomogram integrating risk model and clinical characteristics could predict the prognosis of osteosarcoma patients accurately. Conclusion Expression of lipid-metabolism genes is correlated with immune microenvironment of osteosarcoma patients and could be applied to predict the prognosis of in osteosarcoma accurately.
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Affiliation(s)
- Hu Qian
- Department of Orthopeadic Surgery, Xiangya Hospital Central South University, Changsha, China
| | - Ting Lei
- Department of Orthopeadic Surgery, Xiangya Hospital Central South University, Changsha, China
| | - Yihe Hu
- Department of Orthopeadic Surgery, Xiangya Hospital Central South University, Changsha, China.,Hunan Engineering Research Center of Biomedical Metal and Ceramic Implants, Changsha, China.,Department of Sports Medicine, Xiangya Hospital Central South University, Changsha, China
| | - Pengfei Lei
- Department of Orthopeadic Surgery, Xiangya Hospital Central South University, Changsha, China.,Hunan Engineering Research Center of Biomedical Metal and Ceramic Implants, Changsha, China
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27
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Roessner A, Lohmann C, Jechorek D. Translational cell biology of highly malignant osteosarcoma. Pathol Int 2021; 71:291-303. [PMID: 33631032 DOI: 10.1111/pin.13080] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 01/31/2021] [Indexed: 12/19/2022]
Abstract
Highly malignant osteosarcoma (HMO) is the most frequent malignant bone tumor preferentially occurring in adolescents and children with a second more flat peak in patients over the age of 60. The younger patients benefit from combined neoadjuvant chemotherapy with 65-70% 5-year survival rate. In patients with metastatic HMO the 5-year survival rate is consistently poor with approximately 30%. In the last several years strategies for target therapies have been developed by using next generation sequencing (NGS) for defining targetable molecular factors. However, it has so far been challenging to establish an effective target therapy for so-called 'orphan tumors' without recognizable driver mutations, including HMO. The molecular genetic studies using NGS have shown that HMOs are genomically unstable tumors with highly complex chaotic karyotypes. Before the background of this genetic complexity more investigations should be performed in the future for defining targetable biological factors. As the prognosis could not be improved for 40 years one may expect improvements for patients only by gaining a deeper understanding of the cell and molecular biology of HMO. The cell of origin of HMO is being clarified now. The majority of studies indicate that an osteoblastic progenitor cell is probably the cell of origin of HMO and not an undifferentiated mesenchymal stem cell. This means that the established histopathological definition of HMO through verification of osteoid production by the osteoblastic cells is well justified and will probably be the cornerstone for a precise differential diagnosis of HMO also in the years to come.
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Affiliation(s)
- Albert Roessner
- Department of Pathology, Otto-von-Guericke University, Magdeburg, Germany
| | - Christoph Lohmann
- Department of Orthopedics, Otto-von-Guericke University, Magdeburg, Germany
| | - Doerthe Jechorek
- Department of Pathology, Otto-von-Guericke University, Magdeburg, Germany
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28
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Englisch A, Altvater B, Kailayangiri S, Hartmann W, Rossig C. VEGFR2 as a target for CAR T cell therapy of Ewing sarcoma. Pediatr Blood Cancer 2020; 67:e28313. [PMID: 32729251 DOI: 10.1002/pbc.28313] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 02/28/2020] [Accepted: 03/23/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND T cells engineered to express chimeric antigen receptors (CARs) are a novel modality to treat refractory cancers. The development of CAR T cells against Ewing sarcoma (EwS) is limited by a lack of targetable surface antigens. We investigated vascular endothelial growth factor receptor 2 (VEGFR2) expressed on tumor-associated blood vessels as potential CAR target in this cancer. METHODS Expression of VEGFR2 was studied by immunohistochemistry in human EwS biopsies and in murine xenografts and by flow cytometry in EwS cell lines. CARs with short, medium, and long hinge domains against either human or murine VEGFR2 were generated and expressed in human T cells by retroviral gene transfer. The capacity of the individual CARs to activate T cells in response to VEGFR2-expressing cells was compared in vitro. RESULTS Tumor-associated endothelial cells in human EwS biopsies and in xenografts expressed VEGFR2. Tumor cells in the majority of EwS biopsies were also VEGFR2-positive. Following modification with anti-mouse or anti-human VEGFR2-specific CAR genes, T cells specifically lysed VEGFR2-expressing target cells of the respective species. CAR T cells with short-length or medium-length hinge domains were functionally superior over those with the long hinge region by in vitro parameters, including antigen-specific degranulation responses, lysis of tumor spheroids, tumor necrosis factor α secretion, sequential killing, and proliferation. CONCLUSIONS VEGFR2 is consistently expressed on endothelial cells of the tumor stroma in EwS and thus is a candidate target for CAR T cells in this cancer. Among various VEGFR2-specific CARs, a construct with a short hinge domain was chosen to be further developed toward clinical translation.
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Affiliation(s)
- Alexander Englisch
- Department of Pediatric Hematology and Oncology, University Children's Hospital Muenster, Muenster, Germany
| | - Bianca Altvater
- Department of Pediatric Hematology and Oncology, University Children's Hospital Muenster, Muenster, Germany
| | - Sareetha Kailayangiri
- Department of Pediatric Hematology and Oncology, University Children's Hospital Muenster, Muenster, Germany
| | - Wolfgang Hartmann
- Division of Translational Pathology, Gerhard-Domagk Institute for Pathology, University of Muenster, Muenster, Germany
| | - Claudia Rossig
- Department of Pediatric Hematology and Oncology, University Children's Hospital Muenster, Muenster, Germany.,Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Muenster, Muenster, Germany
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29
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PD-L1 and IDO1 expression and tumor-infiltrating lymphocytes in osteosarcoma patients: comparative study of primary and metastatic lesions. J Cancer Res Clin Oncol 2020; 146:2607-2620. [PMID: 32388585 DOI: 10.1007/s00432-020-03242-6] [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: 02/17/2020] [Accepted: 05/01/2020] [Indexed: 12/12/2022]
Abstract
PURPOSE Programmed death ligand 1 (PD-L1) and indoleamine 2,3-dioxygenase 1 (IDO1) are immunosuppressive proteins known to be associated with poor prognosis in various cancers. However, their expression and clinical relevance in osteosarcoma remain unknown. In this study, the relationships of PD-L1 and IDO1 expression with clinicopathological features and prognosis were explored. METHODS The expression of PD-L1, IDO1, CD3, CD4, and CD8 in 112 formalin-fixed, paraffin-embedded tumor tissues collected by biopsy or surgical resection from 56 osteosarcoma patients was evaluated immunohistochemically. Moreover, four osteosarcoma cell lines were evaluated for the effects of IFNγ on PD-L1 and IDO1 mRNA expression by real-time reverse-transcription polymerase chain reaction. RESULTS In pre-neoadjuvant chemotherapy (NAC) primary specimens, 10 cases (17%) showed PD-L1 expression and 12 (21%) showed IDO1 expression. Six of ten cases (60%) with PD-L1 positivity co-expressed IDO1. In post-NAC metastatic lesions, the frequency of immunoexpression of PD-L1 and IDO1 was increased compared with that in pre-NAC specimens. PD-L1 and/or IDO1 expression was not associated with poor prognosis. PD-L1 immunoexpression was significantly associated with the infiltration of CD3+ T cells, CD4+ T cells, and CD8+ T cells; while, IDO1 immunoexpression was significantly associated with the infiltration of CD3+ T cells and CD4+ T cells. In all osteosarcoma cell lines, PD-L1 and IDO1 expression was upregulated by stimulation with IFNγ. CONCLUSION Our results suggest that the PD-L1 and IDO1 immune checkpoint inhibitors may provide clinical benefit in osteosarcoma patients with metastatic lesions after conventional chemotherapy.
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30
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Genomics and Therapeutic Vulnerabilities of Primary Bone Tumors. Cells 2020; 9:cells9040968. [PMID: 32295254 PMCID: PMC7227002 DOI: 10.3390/cells9040968] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/08/2020] [Accepted: 04/10/2020] [Indexed: 12/17/2022] Open
Abstract
Osteosarcoma, Ewing sarcoma and chondrosarcoma are rare diseases but the most common primary tumors of bone. The genes directly involved in the sarcomagenesis, tumor progression and treatment responsiveness are not completely defined for these tumors, and the powerful discovery of genetic analysis is highly warranted in the view of improving the therapy and cure of patients. The review summarizes recent advances concerning the molecular and genetic background of these three neoplasms and, of their most common variants, highlights the putative therapeutic targets and the clinical trials that are presently active, and notes the fundamental issues that remain unanswered. In the era of personalized medicine, the rarity of sarcomas may not be the major obstacle, provided that each patient is studied extensively according to a road map that combines emerging genomic and functional approaches toward the selection of novel therapeutic strategies.
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31
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Zhao J, Dean DC, Hornicek FJ, Yu X, Duan Z. Emerging next-generation sequencing-based discoveries for targeted osteosarcoma therapy. Cancer Lett 2020; 474:158-167. [PMID: 31987920 DOI: 10.1016/j.canlet.2020.01.020] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/18/2020] [Accepted: 01/20/2020] [Indexed: 12/28/2022]
Abstract
Osteosarcoma (OS) is the most common primary bone malignancy and is frequently lethal via metastasis to the lung. While surgical techniques and adjuvant chemotherapies have emerged to combat this deadly cancer, the 5-year survival rate has plateaued over the past four decades. Therapeutic progress has been notably poor because past technologies have not been able to reveal obscured OS biomarkers and targets. With the advent and implementation of large-scale next-generation sequencing (NGS) studies, various somatic mutations and copy number changes involved in OS progression and metastasis have surfaced. These findings have significantly expanded the amount of genome-informed pathways and candidate genes suitable for targeting in pre-clinical models. Furthermore, NGS analyses comparing primary and matched pulmonary metastatic tumor tissues have catalogued previously unknown prognostic biomarkers in OS. In this review, we delineate the most recent findings in NGS for OS therapy and how this technology has advanced personalized therapy.
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Affiliation(s)
- Jie Zhao
- First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, 250355, China; Department of Orthopaedic Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA; Department of Orthopaedic Surgery, The 960th Hospital of the PLA Joint Logistics Support Force, Jinan, Shandong, 250031, China.
| | - Dylan C Dean
- Department of Orthopaedic Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA.
| | - Francis J Hornicek
- Department of Orthopaedic Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA.
| | - Xiuchun Yu
- Department of Orthopaedic Surgery, The 960th Hospital of the PLA Joint Logistics Support Force, Jinan, Shandong, 250031, China.
| | - Zhenfeng Duan
- Department of Orthopaedic Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA.
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32
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Schott C, Shah AT, Sweet-Cordero EA. Genomic Complexity of Osteosarcoma and Its Implication for Preclinical and Clinical Targeted Therapies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1258:1-19. [PMID: 32767231 DOI: 10.1007/978-3-030-43085-6_1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Osteosarcoma is a genomically complex disease characterized by few recurrent single-nucleotide mutations or in-frame fusions. In contrast, structural alterations, including copy number changes, chromothripsis, kataegis, loss of heterozygosity (LOH), and other large-scale genomic alterations, are frequent and widespread across the osteosarcoma genome. These observed structural alterations lead to activation of oncogenes and loss of tumor suppressors which together contribute to oncogenesis. To date, few targeted therapies for osteosarcoma have been identified. It is likely that effectiveness of targeted therapies will vary greatly in subsets of tumors with distinct key driver events. Model systems which can recapitulate the genetic heterogeneity of this disease are needed to test this hypothesis. One possible approach is to use patient-derived xenograft (PDX) models characterized with regards to their similarity to the human tumor samples from which they were derived. Here we review evidence pointing to the genomic complexity of osteosarcoma and how this is reflected in available model systems. We also review the current state of preclinical testing for targeted therapies using these models.
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Affiliation(s)
- Courtney Schott
- Department of Pediatrics, Division of Hematology and Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Avanthi Tayi Shah
- Department of Pediatrics, Division of Hematology and Oncology, University of California San Francisco, San Francisco, CA, USA
| | - E Alejandro Sweet-Cordero
- Department of Pediatrics, Division of Hematology and Oncology, University of California San Francisco, San Francisco, CA, USA.
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33
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The Fas/FasL Signaling Pathway: Its Role in the Metastatic Process and as a Target for Treating Osteosarcoma Lung Metastases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1258:177-187. [PMID: 32767242 DOI: 10.1007/978-3-030-43085-6_12] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Understanding how the tumor microenvironment participates in inhibiting or supporting tumor growth is critical for the development of novel therapies. Osteosarcoma (OS) metastasizes almost exclusively to the lung, an organ where Fas ligand (FasL) is constitutively expressed. This chapter focuses on our studies dedicated to the interaction of OS cells with the lung microenvironment. We will summarize our studies conducted over the past 20 years showing the importance of the Fas/FasL signaling pathway to the establishment and progression of OS metastases in the lung. We demonstrated that the FasL+ lung microenvironment eliminates Fas-positive (Fas+) OS cells that metastasize to the lungs, through apoptosis induced by Fas signaling following interaction of Fas on the tumor cell surface with FasL on the lung epithelial cells. Expression of the Fas receptor on OS cells inversely correlated with the ability of OS cells to form lung metastases. Blocking this pathway interferes with this process, allowing Fas+ cells to grow in the lung. By contrast, upregulation of Fas on Fas- OS cells inhibited their ability to metastasize to the lung. We demonstrated how the FasL+ lung microenvironment can be leveraged for therapeutic intent through the upregulation of Fas expression. To this end, we demonstrated that the histone deacetylase inhibitor entinostat upregulated Fas expression on OS cells, reduced their ability to form lung metastases, and induced regression of established micrometastases. Fas expression in OS cells is regulated epigenetically by the microRNA miR-20a. We showed that expressions of Fas and miR-20a are inversely correlated, and that delivery of anti-miR-20a in vivo to mice with established osteosarcoma lung metastases resulted in upregulation of Fas and tumor regression. Therefore, targeting the Fas signaling pathway may present therapeutic opportunities, which target the lung microenvironment for elimination of OS lung metastases. We have also shown that in addition to being critically involved in the metastatic potential, the Fas signaling pathway may also contribute to the efficacy of chemotherapy. We demonstrated that the chemotherapeutic agent gemcitabine (GCB) increased Fas expression in both human and mouse OS cells in vitro. In vivo, aerosol GCB therapy induced upregulation of Fas expression and the regression of established osteosarcoma lung metastases. The therapeutic efficacy of GCB was contingent upon a FasL+ lung microenvironment as aerosol GCB had no effect in FasL-deficient mice. Manipulation of Fas expression and the Fas pathway should be considered, as this concept may provide additional novel therapeutic approaches for treating patients with OS lung metastases.
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34
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Wang L, Wang P, Su X, Zhao B. Circ_0001658 promotes the proliferation and metastasis of osteosarcoma cells via regulating miR‐382‐5p/YB‐1 axis. Cell Biochem Funct 2019; 38:77-86. [PMID: 31758574 DOI: 10.1002/cbf.3452] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/06/2019] [Accepted: 10/13/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Lisong Wang
- Department of OrthopaedicsShangluo Central Hospital Shangluo Shanxi Province China
| | - Pengbin Wang
- Department of OrthopaedicsShangluo Central Hospital Shangluo Shanxi Province China
| | - Xiujun Su
- Department of OrthopaedicsShangluo Central Hospital Shangluo Shanxi Province China
| | - Bo Zhao
- Department of OrthopaedicsShangluo Central Hospital Shangluo Shanxi Province China
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35
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Hattinger CM, Patrizio MP, Magagnoli F, Luppi S, Serra M. An update on emerging drugs in osteosarcoma: towards tailored therapies? Expert Opin Emerg Drugs 2019; 24:153-171. [PMID: 31401903 DOI: 10.1080/14728214.2019.1654455] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Introduction: Current treatment of conventional and non-conventional high-grade osteosarcoma (HGOS) is based on the surgical removal of primary tumor and, when possible, of metastases and local reccurrence, together with systemic pre- and post-operative chemotherapy with drugs that have been used since decades. Areas covered: This review is intended to summarize the new agents and therapeutic strategies that are under clinical evaluation in HGOS, with the aim to increase the cure probability of this highly malignant bone tumor, which has not significantly improved during the last 30-40 years. The list of drugs, compounds and treatment modalities presented and discussed here has been generated by considering only those that are included in presently ongoing and recruiting clinical trials, or which have been completed in the last 2 years with reported results, on the basis of the information obtained from different and continuously updated databases. Expert opinion: Despite HGOS is a rare tumor, several clinical trials are presently evaluating different treatment strategies, which may hopefully positively impact on the outcome of patients who experience unfavorable prognosis when treated with conventional therapies.
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Affiliation(s)
- Claudia Maria Hattinger
- Laboratory of Experimental Oncology, Pharmacogenomics and Pharmacogenetics Research Unit, IRCCS Istituto Ortopedico Rizzoli , Bologna , Italy
| | - Maria Pia Patrizio
- Laboratory of Experimental Oncology, Pharmacogenomics and Pharmacogenetics Research Unit, IRCCS Istituto Ortopedico Rizzoli , Bologna , Italy
| | - Federica Magagnoli
- Laboratory of Experimental Oncology, Pharmacogenomics and Pharmacogenetics Research Unit, IRCCS Istituto Ortopedico Rizzoli , Bologna , Italy
| | - Silvia Luppi
- Laboratory of Experimental Oncology, Pharmacogenomics and Pharmacogenetics Research Unit, IRCCS Istituto Ortopedico Rizzoli , Bologna , Italy
| | - Massimo Serra
- Laboratory of Experimental Oncology, Pharmacogenomics and Pharmacogenetics Research Unit, IRCCS Istituto Ortopedico Rizzoli , Bologna , Italy
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