1
|
Schlieben LD, Carta MG, Moskalev EA, Stöhr R, Metzler M, Besendörfer M, Meidenbauer N, Semrau S, Janka R, Grützmann R, Wiemann S, Hartmann A, Agaimy A, Haller F, Ferrazzi F. Machine Learning-Supported Diagnosis of Small Blue Round Cell Sarcomas Using Targeted RNA Sequencing. J Mol Diagn 2024; 26:387-398. [PMID: 38395409 DOI: 10.1016/j.jmoldx.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/25/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Small blue round cell sarcomas (SBRCSs) are a heterogeneous group of tumors with overlapping morphologic features but markedly varying prognosis. They are characterized by distinct chromosomal alterations, particularly rearrangements leading to gene fusions, whose detection currently represents the most reliable diagnostic marker. Ewing sarcomas are the most common SBRCSs, defined by gene fusions involving EWSR1 and transcription factors of the ETS family, and the most frequent non-EWSR1-rearranged SBRCSs harbor a CIC rearrangement. Unfortunately, currently the identification of CIC::DUX4 translocation events, the most common CIC rearrangement, is challenging. Here, we present a machine-learning approach to support SBRCS diagnosis that relies on gene expression profiles measured via targeted sequencing. The analyses on a curated cohort of 69 soft-tissue tumors showed markedly distinct expression patterns for SBRCS subgroups. A random forest classifier trained on Ewing sarcoma and CIC-rearranged cases predicted probabilities of being CIC-rearranged >0.9 for CIC-rearranged-like sarcomas and <0.6 for other SBRCSs. Testing on a retrospective cohort of 1335 routine diagnostic cases identified 15 candidate CIC-rearranged tumors with a probability >0.75, all of which were supported by expert histopathologic reassessment. Furthermore, the multigene random forest classifier appeared advantageous over using high ETV4 expression alone, previously proposed as a surrogate to identify CIC rearrangement. Taken together, the expression-based classifier can offer valuable support for SBRCS pathologic diagnosis.
Collapse
Affiliation(s)
- Lea D Schlieben
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany
| | - Maria Giulia Carta
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany
| | - Evgeny A Moskalev
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany
| | - Robert Stöhr
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany
| | - Markus Metzler
- Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany; Department of Pediatrics, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Manuel Besendörfer
- Department of Pediatric Surgery, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Norbert Meidenbauer
- Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany; Department of Internal Medicine 5-Hematology and Oncology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Sabine Semrau
- Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany; Department of Radiation Oncology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Rolf Janka
- Department of Radiology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Robert Grützmann
- Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany; Department of Pediatric Surgery, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Department of Surgery, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Stefan Wiemann
- Division of Molecular Genome Analysis, German Cancer Research Center, Heidelberg, Germany
| | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany
| | - Abbas Agaimy
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany
| | - Florian Haller
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany
| | - Fulvia Ferrazzi
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany; Department of Nephropathology, Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
| |
Collapse
|
2
|
Hirose T, Ikegami M, Kojima S, Yoshida A, Endo M, Shimada E, Kanahori M, Oyama R, Matsumoto Y, Nakashima Y, Kawai A, Mano H, Kohsaka S. Extensive analysis of 59 sarcoma-related fusion genes identified pazopanib as a potential inhibitor to COL1A1-PDGFB fusion gene. Cancer Sci 2023; 114:4089-4100. [PMID: 37592448 PMCID: PMC10551592 DOI: 10.1111/cas.15915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 07/02/2023] [Accepted: 07/05/2023] [Indexed: 08/19/2023] Open
Abstract
Sarcomas are malignant mesenchymal tumors that are extremely rare and divergent. Fusion genes are involved in approximately 30% of sarcomas as driver oncogenes; however, their detailed functions are not fully understood. In this study, we determined the functional significance of 59 sarcoma-related fusion genes. The transforming potential and drug sensitivities of these fusion genes were evaluated using a focus formation assay (FFA) and the mixed-all-nominated-in-one (MANO) method, respectively. The transcriptome was also examined using RNA sequencing of 3T3 cells transduced with each fusion gene. Approximately half (28/59, 47%) of the fusion genes exhibited transformation in the FFA assay, which was classified into five types based on the resulting phenotype. The sensitivity to 12 drugs including multityrosine kinase inhibitors was assessed using the MANO method and pazopanib was found to be more effective against cells expressing the COL1A1-PDGFB fusion gene compared with the others. The downstream MAPK/AKT pathway was suppressed at the protein level following pazopanib treatment. The fusion genes were classified into four subgroups by cluster analysis of the gene expression data and gene set enrichment analysis. In summary, the oncogenicity and drug sensitivity of 59 fusion genes were simultaneously evaluated using a high-throughput strategy. Pazopanib was selected as a candidate drug for sarcomas harboring the COL1A1-PDGFB fusion gene. This assessment could be useful as a screening platform and provides a database to evaluate customized therapy for fusion gene-associated sarcomas.
Collapse
Affiliation(s)
- Takeshi Hirose
- Division of Cellular SignalingNational Cancer Center Research InstituteTokyoJapan
- Department of Orthopaedic Surgery, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Masachika Ikegami
- Division of Cellular SignalingNational Cancer Center Research InstituteTokyoJapan
| | - Shinya Kojima
- Division of Cellular SignalingNational Cancer Center Research InstituteTokyoJapan
| | - Akihiko Yoshida
- Department of Diagnostic PathologyNational Cancer Center HospitalTokyoJapan
| | - Makoto Endo
- Department of Orthopaedic Surgery, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Eijiro Shimada
- Department of Orthopaedic Surgery, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Masaya Kanahori
- Department of Orthopaedic Surgery, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Ryunosuke Oyama
- Department of Orthopaedic Surgery, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Yoshihiro Matsumoto
- Department of Orthopaedic Surgery, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Yasuharu Nakashima
- Department of Orthopaedic Surgery, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Akira Kawai
- Department of Musculoskeletal OncologyNational Cancer Center HospitalTokyoJapan
| | - Hiroyuki Mano
- Division of Cellular SignalingNational Cancer Center Research InstituteTokyoJapan
| | - Shinji Kohsaka
- Division of Cellular SignalingNational Cancer Center Research InstituteTokyoJapan
| |
Collapse
|
3
|
刘 磊, 邱 海, 惠 明, 江 枫, 王 代, 林 玉, 杨 新, 姚 俊. [A case report of adult primary soft tissue sarcoma of the head and neck]. LIN CHUANG ER BI YAN HOU TOU JING WAI KE ZA ZHI = JOURNAL OF CLINICAL OTORHINOLARYNGOLOGY, HEAD, AND NECK SURGERY 2023; 37:146-149. [PMID: 36756833 PMCID: PMC10208871 DOI: 10.13201/j.issn.2096-7993.2023.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Indexed: 02/10/2023]
Abstract
Head and neck primary soft tissue sarcoma is a rare adult connective tissue malignant tumor derived from mesenchymal tissue, which can occur in the paranasal sinuses, throat or neck space.The clinical manifestations are local spread masses in the head and neck or difficulty breathing, swallowing, etc al. MRI and enhanced CT examination are the most commonly used to diagnose such diseases. Pathological diagnosis requires immunohistochemistry combined with FISH to detect MDM2 and CDK4. In this report,two cases of primary soft tissue sarcoma were reported,one is parotid high-differentiated liposarcoma and the other is laryngeal dedifferentiated leiomyosarcoma, introducing the characteristics diagnosis and treatment, and reviewing the relevant literature.
Collapse
Affiliation(s)
- 磊峰 刘
- 广东医科大学附属医院耳鼻咽喉头颈外科(广东湛江,524000)Department of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, China
| | - 海涛 邱
- 广东医科大学附属医院耳鼻咽喉头颈外科(广东湛江,524000)Department of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, China
| | - 明朗 惠
- 广东医科大学附属医院耳鼻咽喉头颈外科(广东湛江,524000)Department of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, China
| | - 枫 江
- 广东医科大学附属医院耳鼻咽喉头颈外科(广东湛江,524000)Department of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, China
| | - 代红 王
- 广东医科大学研究生院Graduate School of Guangdong Medical University
| | - 玉英 林
- 广东医科大学研究生院Graduate School of Guangdong Medical University
| | - 新建 杨
- 广东医科大学研究生院Graduate School of Guangdong Medical University
| | - 俊 姚
- 广东医科大学附属医院耳鼻咽喉头颈外科(广东湛江,524000)Department of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, China
| |
Collapse
|
4
|
PANAGOPOULOS IOANNIS, HEIM SVERRE. Neoplasia-associated Chromosome Translocations Resulting in Gene Truncation. Cancer Genomics Proteomics 2022; 19:647-672. [PMID: 36316036 PMCID: PMC9620447 DOI: 10.21873/cgp.20349] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 11/27/2022] Open
Abstract
Chromosomal translocations in cancer as well as benign neoplasias typically lead to the formation of fusion genes. Such genes may encode chimeric proteins when two protein-coding regions fuse in-frame, or they may result in deregulation of genes via promoter swapping or translocation of the gene into the vicinity of a highly active regulatory element. A less studied consequence of chromosomal translocations is the fusion of two breakpoint genes resulting in an out-of-frame chimera. The breaks then occur in one or both protein-coding regions forming a stop codon in the chimeric transcript shortly after the fusion point. Though the latter genetic events and mechanisms at first awoke little research interest, careful investigations have established them as neither rare nor inconsequential. In the present work, we review and discuss the truncation of genes in neoplastic cells resulting from chromosomal rearrangements, especially from seemingly balanced translocations.
Collapse
Affiliation(s)
- IOANNIS PANAGOPOULOS
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - SVERRE HEIM
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| |
Collapse
|
5
|
Roy S, Laroche-Clary A, Verbeke S, Derieppe MA, Italiano A. MDM2 Antagonists Induce a Paradoxical Activation of Erk1/2 through a P53-Dependent Mechanism in Dedifferentiated Liposarcomas: Implications for Combinatorial Strategies. Cancers (Basel) 2020; 12:cancers12082253. [PMID: 32806555 PMCID: PMC7465494 DOI: 10.3390/cancers12082253] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/03/2020] [Accepted: 08/09/2020] [Indexed: 12/13/2022] Open
Abstract
The MDM2 gene is amplified in dedifferentiated liposarcoma (DDLPS). Treatment with MDM2 antagonists is a promising strategy to treat DDLPS; however, drug resistance is a major limitation when these drugs are used as a single agent. This study examined the impact of MDM2 antagonists on the mitogen-activated protein kinase (MAPK) pathway in DDLPS and investigated the potential synergistic activity of a MAPK kinase (MEK) inhibitor in combination with MDM2 antagonists. We identified a synergistic effect and identified the mechanism behind it. Combination effects of MDM2 antagonists and a MEK inhibitor were analyzed in a patient-derived xenograft mouse model and in DDLPS and leiomyosarcoma cell lines using different cell proliferation assays and immunoblot analysis. MDM2 antagonist (RG7388)-resistant IB115 [P4] cells and p53-silenced DDLPS cells were also established to understand the importance of functional p53. We found that MDM2 antagonists induced an upregulation of phosphorylated extracellular signal-regulated kinase (p-ERK) in DDLPS cells. The upregulation of p-ERK occurred due to mitochondrial translocation of p53, which resulted in increased production of reactive oxygen species, causing the activation of receptor tyrosine kinases (RTKs). Activated RTKs led to the activation of the downstream MEK/ERK signaling pathway. Treatment with a MEK inhibitor resulted in decreased expression of p-ERK, causing significant anti-tumor synergy when combined with MDM2 antagonists. Our results provide a framework for designing clinical studies of combination therapies in DDLPS patients.
Collapse
Affiliation(s)
- Shomereeta Roy
- Sarcoma Unit, Institut Bergonié, 33000 Bordeaux, France; (S.R.); (A.L.-C.); (S.V.)
- University of Bordeaux, 33400 Talence, France
| | - Audrey Laroche-Clary
- Sarcoma Unit, Institut Bergonié, 33000 Bordeaux, France; (S.R.); (A.L.-C.); (S.V.)
- Sarcoma Unit, INSERM U1218, Institut Bergonié, 33000 Bordeaux, France
| | - Stephanie Verbeke
- Sarcoma Unit, Institut Bergonié, 33000 Bordeaux, France; (S.R.); (A.L.-C.); (S.V.)
- Sarcoma Unit, INSERM U1218, Institut Bergonié, 33000 Bordeaux, France
| | | | - Antoine Italiano
- Sarcoma Unit, Institut Bergonié, 33000 Bordeaux, France; (S.R.); (A.L.-C.); (S.V.)
- University of Bordeaux, 33400 Talence, France
- Sarcoma Unit, INSERM U1218, Institut Bergonié, 33000 Bordeaux, France
- Department of Medical Oncology, Institut Bergonié, 33000 Bordeaux, France
- Correspondence:
| |
Collapse
|
6
|
Unachukwu U, Chada K, D’Armiento J. High Mobility Group AT-Hook 2 (HMGA2) Oncogenicity in Mesenchymal and Epithelial Neoplasia. Int J Mol Sci 2020; 21:ijms21093151. [PMID: 32365712 PMCID: PMC7246488 DOI: 10.3390/ijms21093151] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 12/31/2022] Open
Abstract
High mobility group AT-hook 2 (HMGA2) has been associated with increased cell proliferation and cell cycle dysregulation, leading to the ontogeny of varied tumor types and their metastatic potentials, a frequently used index of disease prognosis. In this review, we deepen our understanding of HMGA2 pathogenicity by exploring the mechanisms by which HMGA2 misexpression and ectopic expression induces mesenchymal and epithelial tumorigenesis respectively and distinguish the pathogenesis of benign from malignant mesenchymal tumors. Importantly, we highlight the regulatory role of let-7 microRNA family of tumor suppressors in determining HMGA2 misexpression events leading to tumor pathogenesis and focused on possible mechanisms by which HMGA2 could propagate lymphangioleiomyomatosis (LAM), benign mesenchymal tumors of the lungs. Lastly, we discuss potential therapeutic strategies for epithelial and mesenchymal tumorigenesis based on targeting the HMGA2 signaling pathway.
Collapse
Affiliation(s)
- Uchenna Unachukwu
- Department of Anesthesiology, Columbia University Medical Center, 630 West 168th Street, P&S 12-402, New York, NY 10032, USA;
| | - Kiran Chada
- Department of Biochemistry & Molecular Biology; Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, NJ 08854, USA;
| | - Jeanine D’Armiento
- Department of Anesthesiology, Columbia University Medical Center, 630 West 168th Street, P&S 12-402, New York, NY 10032, USA;
- Correspondence: ; Tel.: +212-305-3745
| |
Collapse
|
7
|
The Hidden Genomic and Transcriptomic Plasticity of Giant Marker Chromosomes in Cancer. Genetics 2017; 208:951-961. [PMID: 29279323 DOI: 10.1534/genetics.117.300552] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 12/11/2017] [Indexed: 01/16/2023] Open
Abstract
Genome amplification in the form of rings or giant rod-shaped marker chromosomes (RGMs) is a common genetic alteration in soft tissue tumors. The mitotic stability of these structures is often rescued by perfectly functioning analphoid neocentromeres, which therefore significantly contribute to cancer progression. Here, we disentangled the genomic architecture of many neocentromeres stabilizing marker chromosomes in well-differentiated liposarcoma and lung sarcomatoid carcinoma samples. In cells carrying heavily rearranged RGMs, these structures were assembled as patchworks of multiple short amplified sequences, disclosing an extremely high level of complexity and definitely ruling out the existence of regions prone to neocentromere seeding. Moreover, by studying two well-differentiated liposarcoma samples derived from the onset and the recurrence of the same tumor, we documented an expansion of the neocentromeric domain that occurred during tumor progression, which reflects a strong selective pressure acting toward the improvement of the neocentromeric functionality in cancer. In lung sarcomatoid carcinoma cells we documented, extensive "centromere sliding" phenomena giving rise to multiple, closely mapping neocentromeric epialleles on separate coexisting markers occur, likely due to the instability of neocentromeres arising in cancer cells. Finally, by investigating the transcriptional activity of neocentromeres, we came across a burst of chimeric transcripts, both by extremely complex genomic rearrangements, and cis/trans-splicing events. Post-transcriptional editing events have been reported to expand and variegate the genetic repertoire of higher eukaryotes, so they might have a determining role in cancer. The increased incidence of fusion transcripts, might act as a driving force for the genomic amplification process, together with the increased transcription of oncogenes.
Collapse
|
8
|
Son HY, Hwangbo Y, Yoo SK, Im SW, Yang SD, Kwak SJ, Park MS, Kwak SH, Cho SW, Ryu JS, Kim J, Jung YS, Kim TH, Kim SJ, Lee KE, Park DJ, Cho NH, Sung J, Seo JS, Lee EK, Park YJ, Kim JI. Genome-wide association and expression quantitative trait loci studies identify multiple susceptibility loci for thyroid cancer. Nat Commun 2017; 8:15966. [PMID: 28703219 PMCID: PMC5511346 DOI: 10.1038/ncomms15966] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 05/16/2017] [Indexed: 01/12/2023] Open
Abstract
Thyroid cancer is the most common cancer in Korea. Several susceptibility loci of differentiated thyroid cancer (DTC) were identified by previous genome-wide association studies (GWASs) in Europeans only. Here we conducted a GWAS and a replication study in Koreans using a total of 1,085 DTC cases and 8,884 controls, and validated these results using expression quantitative trait loci (eQTL) analysis and clinical phenotypes. The most robust associations were observed in the NRG1 gene (rs6996585, P=1.08 × 10-10) and this SNP was also associated with NRG1 expression in thyroid tissues. In addition, we confirmed three previously reported loci (FOXE1, NKX2-1 and DIRC3) and identified seven novel susceptibility loci (VAV3, PCNXL2, INSR, MRSB3, FHIT, SEPT11 and SLC24A6) associated with DTC. Furthermore, we identified specific variants of DTC that have different effects according to cancer type or ethnicity. Our findings provide deeper insight into the genetic contribution to thyroid cancer in different populations.
Collapse
Affiliation(s)
- Ho-Young Son
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
| | - Yul Hwangbo
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Center for Thyroid Cancer, National Cancer Center, Goyang 10408, Republic of Korea
| | - Seong-Keun Yoo
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Republic of Korea
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul 03080, Republic of Korea
| | - Sun-Wha Im
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
| | - San Duk Yang
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Republic of Korea
| | - Soo-Jung Kwak
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Republic of Korea
| | - Min Seon Park
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
- Graduate Program in Genetic Counseling, Northwestern University, Chicago, Illinois 60637, USA
| | - Soo Heon Kwak
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Sun Wook Cho
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Jun Sun Ryu
- Center for Thyroid Cancer, National Cancer Center, Goyang 10408, Republic of Korea
| | - Jeongseon Kim
- Molecular Epidemiology Branch, Division of Cancer Epidemiology and Prevention, Research Institute, National Cancer Center, Goyang 10408, Republic of Korea
| | - Yuh-Seog Jung
- Center for Thyroid Cancer, National Cancer Center, Goyang 10408, Republic of Korea
| | - Tae Hyun Kim
- Center for Thyroid Cancer, National Cancer Center, Goyang 10408, Republic of Korea
| | - Su-jin Kim
- Department of Surgery, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Kyu Eun Lee
- Department of Surgery, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Do Joon Park
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Nam Han Cho
- Department of Preventive Medicine Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Joohon Sung
- Department of Epidemiology and Institute of Environment and Health, School of Public Health, Seoul National University, Seoul 08826, Republic of Korea
| | - Jeong-Sun Seo
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Republic of Korea
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul 03080, Republic of Korea
| | - Eun Kyung Lee
- Center for Thyroid Cancer, National Cancer Center, Goyang 10408, Republic of Korea
| | - Young Joo Park
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul 03080, Republic of Korea
| | - Jong-Il Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| |
Collapse
|
9
|
Tisato V, Voltan R, Gonelli A, Secchiero P, Zauli G. MDM2/X inhibitors under clinical evaluation: perspectives for the management of hematological malignancies and pediatric cancer. J Hematol Oncol 2017; 10:133. [PMID: 28673313 PMCID: PMC5496368 DOI: 10.1186/s13045-017-0500-5] [Citation(s) in RCA: 189] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 06/20/2017] [Indexed: 02/07/2023] Open
Abstract
The two murine double minute (MDM) family members MDM2 and MDMX are at the center of an intense clinical assessment as molecular target for the management of cancer. Indeed, the two proteins act as regulators of P53, a well-known key controller of the cell cycle regulation and cell proliferation that, when altered, plays a direct role on cancer development and progression. Several evidence demonstrated that functional aberrations of P53 in tumors are in most cases the consequence of alterations on the MDM2 and MDMX regulatory proteins, in particular in patients with hematological malignancies where TP53 shows a relatively low frequency of mutation while MDM2 and MDMX are frequently found amplified/overexpressed. The pharmacological targeting of these two P53-regulators in order to restore or increase P53 expression and activity represents therefore a strategy for cancer therapy. From the discovery of the Nutlins in 2004, several compounds have been developed and reported with the ability of targeting the P53-MDM2/X axis by inhibiting MDM2 and/or MDMX. From natural compounds up to small molecules and stapled peptides, these MDM2/X pharmacological inhibitors have been extensively studied, revealing different biological features and different rate of efficacy when tested in in vitro and in vivo experimental tumor models. The data/evidence coming from the preclinical experimentation have allowed the identification of the most promising molecules and the setting of clinical studies for their evaluation as monotherapy or in therapeutic combination with conventional chemotherapy or with innovative therapeutic protocols in different tumor settings. Preliminary results have been recently published reporting data about safety, tolerability, potential side effects, and efficacy of such therapeutic approaches. In this light, the aim of this review is to give an updated overview about the state of the art of the clinical evaluation of MDM2/X inhibitor compounds with a special attention to hematological malignancies and to the potential for the management of pediatric cancers.
Collapse
Affiliation(s)
- Veronica Tisato
- Department of Morphology, Surgery and Experimental Medicine and LTTA Centre, University of Ferrara, Via Fossato di Mortara 66, 44121, Ferrara, Italy.
| | - Rebecca Voltan
- Department of Morphology, Surgery and Experimental Medicine and LTTA Centre, University of Ferrara, Via Fossato di Mortara 66, 44121, Ferrara, Italy
| | - Arianna Gonelli
- Department of Morphology, Surgery and Experimental Medicine and LTTA Centre, University of Ferrara, Via Fossato di Mortara 66, 44121, Ferrara, Italy
| | - Paola Secchiero
- Department of Morphology, Surgery and Experimental Medicine and LTTA Centre, University of Ferrara, Via Fossato di Mortara 66, 44121, Ferrara, Italy
| | - Giorgio Zauli
- Department of Morphology, Surgery and Experimental Medicine and LTTA Centre, University of Ferrara, Via Fossato di Mortara 66, 44121, Ferrara, Italy
| |
Collapse
|
10
|
Panagopoulos I, Gorunova L, Lobmaier I, Bjerkehagen B, Heim S. Identification of SETD2-NF1 fusion gene in a pediatric spindle cell tumor with the chromosomal translocation t(3;17)(p21;q12). Oncol Rep 2017; 37:3181-3188. [PMID: 28498454 PMCID: PMC5442398 DOI: 10.3892/or.2017.5628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Accepted: 03/29/2017] [Indexed: 01/20/2023] Open
Abstract
Spindle cell tumors are clinically heterogeneous but morphologically similar neoplasms. The term refers to the tumor cells' long and slender microscopic appearance. Distinct subgroups of spindle cell tumors are characterized by chromosomal translocations and also fusion genes. Other spindle cell tumors exist that have not yet been found to have characteristic, let alone pathognomonic, genetic or pathogenetic features. Continuous examination of spindle cell tumors is likely to reveal other subgroups that may, in the future, be seen to correspond to meaningful clinical differences and may even be therapeutically decisive. We analyzed genetically a pediatric spindle cell tumor. Karyotyping showed the tumor cells to carry a t(3;17)(p21;q12) chromosomal translocation whereas RNA sequencing identified a SETD2-NF1 fusion gene caused by the translocation. RT-PCR together with Sanger sequencing verified the presence of the above-mentioned fusion transcript. Interphase FISH analysis confirmed the existence of the chimeric gene and showed that there was no reciprocal fusion. The fusion transcript codes for a protein in which the last 114 amino acids of SETD2, i.e., the entire Set2 Rpb1 interacting (SRI) domain of SETD2, are replaced by 30 amino acids encoded by the NF1 sequence. The result would be similar to that seen with truncating SETD2 mutations in leukemias. Absence of the SRI domain would result in inability to recruit SETD2 to its target gene locus through binding to the phosphor-C-terminal repeat domain of elongating RNA polymerase II and may affect H3K36 methylation. Alternatively, loss of one of two functional SETD2 alleles might be the crucial tumorigenic factor.
Collapse
Affiliation(s)
- Ioannis Panagopoulos
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Ludmila Gorunova
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Ingvild Lobmaier
- Department of Pathology, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Bodil Bjerkehagen
- Department of Pathology, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Sverre Heim
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| |
Collapse
|
11
|
Jiang Q, Tong HX, Zhang Y, Hou YY, Li JL, Wang JY, Zhou YH, Lu WQ. Successful establishment of patient-derived tumor xenografts from gastrointestinal stromal tumor-a single center experience. Am J Cancer Res 2016; 6:533-543. [PMID: 27186422 PMCID: PMC4858539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Accepted: 01/12/2016] [Indexed: 06/05/2023] Open
Abstract
Patient-derived tumor xenografts (PDTX) generally represent a kind of more reliable model of human disease, by which a potential drugs' preclinical efficacy could be evaluated. To date, no stable gastrointestinal stromal tumor (GIST) PDTX models have been reported. In this study, we aimed to establish stable GIST PDTX models and to evaluate whether these models accurately reflected the histological feature of the corresponding patient tumors and create a reliable GIST PDTX models for our future experiment. By engrafting fresh patient GIST tissues into immune-compromised mice (BALB/c athymic mice), 4 PDTX models were established. Histological features were assessed by a qualified pathologist based on H&E staining, CD117 and DOG-1. We also conduct whole exome sequencing(WES) for the 4 established GIST PDTX models to test if the model still harbored the same mutation detected in corresponding patient tumors and get a more intensive vision for the genetic profile of the models we have established, which will help a lot for our future experiment. To explore the tumorigenesis mechanism for GIST, we also have a statistical analysis for the genes detected as nonsynchronous-mutated simultaneously in 4 samples. All 4 GIST PDTX models retained the histological features of the corresponding human tumors, with original morphology type and positive stains for CD117 and DOG-1. Between the GIST PDTX models and their parental tumors, a same mutation site was detected, which confirmed the genetic consistency. The stability of molecular profiles observed within the GIST PDTX models provides confidence in the utility and translational significance of these models for in vivo testing of personalized therapies. To date, we conducted the first study to successfully establish a GIST PDTX model whose genetic profiles were revealed by whole exome sequencing. Our experience could be of great use.
Collapse
Affiliation(s)
- Quan Jiang
- Department of General Surgery, Zhongshan Hospital, Fudan UniversityShanghai 200032, China
| | - Han-Xing Tong
- Department of General Surgery, Zhongshan Hospital, Fudan UniversityShanghai 200032, China
| | - Yong Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan UniversityShanghai 200032, China
| | - Ying-Yong Hou
- Department of Pathology, Zhongshan Hospital, Fudan UniversityShanghai 200032, China
| | - Jing-Lei Li
- Department of General Surgery, Zhongshan Hospital, Fudan UniversityShanghai 200032, China
| | - Jiong-Yuan Wang
- Department of General Surgery, Zhongshan Hospital, Fudan UniversityShanghai 200032, China
| | - Yu-Hong Zhou
- Department of Oncology, Zhongshan Hospital, Fudan UniversityShanghai 200032, China
| | - Wei-Qi Lu
- Department of General Surgery, Zhongshan Hospital, Fudan UniversityShanghai 200032, China
| |
Collapse
|
12
|
Depletion of three combined THOC5 mRNA export protein target genes synergistically induces human hepatocellular carcinoma cell death. Oncogene 2015; 35:3872-9. [PMID: 26549021 DOI: 10.1038/onc.2015.433] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 10/01/2015] [Accepted: 10/11/2015] [Indexed: 12/15/2022]
Abstract
Hepatocellular carcinoma (HCC) is a frequent form of cancer with a poor prognosis and with limited possibilities of medical intervention. It has been shown that over 100 putative driver genes are associated with multiple recurrently altered pathways in HCC, suggesting that multiple pathways will need to be inhibited for any therapeutic method. mRNA processing is regulated by a complex RNA-protein network that is essential for the maintenance of homeostasis. THOC5, a member of mRNA export complex, has a role in less than 1% of mRNA processing, and is required for cell growth and differentiation, but not for cell survival in normal fibroblasts, hepatocytes and macrophages. In this report, we show that 50% depletion of THOC5 in human HCC cell lines Huh7 and HepG2 induced apoptosis. Transcriptome analysis using THOC5-depleted cells revealed that 396 genes, such as transmembrane BAX inhibitor motif containing 4 (TMBIM4), transmembrane emp24-like trafficking protein 10 (Tmed10) and D-tyrosyl-tRNA deacylase 2 (Dtd2) genes were downregulated in both cell lines. The depletion of one of these THOC5 target genes in Huh7 or HepG2 did not significantly induce cell death, suggesting that these may be fine tuners for HCC cell survival. However, the depletion of a combination of these genes synergistically increased the number of TUNEL (terminal deoxynucleotidyl transferase dUTP nick end labeling)-positive HCC. It must be noted that the depletion of these genes did not induce cell death in the hepatocyte cell line, THLE-2 cells. THOC5 expression was enhanced in 78% of cytological differentiation grading G2 and G3 tumor in primary HCC. Furthermore, the expression of a putative glycoprotein, Tmed10, is correlated to THOC5 expression level in primary HCCs, suggesting that this protein may be a novel biomarker for HCC. These data imply that the suppression of the multiple THOC5 target genes may represent a novel strategy for HCC therapy.
Collapse
|