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Sydow S, Piccinelli P, Mitra S, Tsagkozis P, Hesla A, B R De Mattos C, Köster J, Magnusson L, Nilsson J, Ameur A, Wardenaar R, Foijer F, Spierings D, Mertens F. MDM2 amplification in rod-shaped chromosomes provides clues to early stages of circularized gene amplification in liposarcoma. Commun Biol 2024; 7:606. [PMID: 38769442 PMCID: PMC11106292 DOI: 10.1038/s42003-024-06307-1] [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: 09/27/2023] [Accepted: 05/08/2024] [Indexed: 05/22/2024] Open
Abstract
Well-differentiated liposarcoma (WDLS) displays amplification of genes on chromosome 12 (Chr12) in supernumerary ring or giant marker chromosomes. These structures have been suggested to develop through chromothripsis, followed by circularization and breakage-fusion-bridge (BFB) cycles. To test this hypothesis, we compared WDLSs with Chr12 amplification in rod-shaped chromosomes with WDLSs with rings. Both types of amplicons share the same spectrum of structural variants (SVs), show higher SV frequencies in Chr12 than in co-amplified segments, have SVs that fuse the telomeric ends of co-amplified chromosomes, and lack interspersed deletions. Combined with the finding of cells with transient rod-shaped structures in tumors with ring chromosomes, this suggests a stepwise process starting with the gain of Chr12 material that, after remodeling which does not fit with classical chromothripsis, forms a dicentric structure with other chromosomes. Depending on if and when telomeres from other chromosomes are captured, circularized or linear gain of 12q sequences will predominate.
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Affiliation(s)
- Saskia Sydow
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, 221 84, Lund, Sweden.
| | - Paul Piccinelli
- Department of Clinical Genetics and Pathology, Office for Medical Services, Region Skåne, 221 85, Lund, Sweden
| | - Shamik Mitra
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, 221 84, Lund, Sweden
| | - Panagiotis Tsagkozis
- Department of Orthopedics, Karolinska University Hospital, Solna, 17176, Stockholm, Sweden
| | - Asle Hesla
- Department of Orthopedics, Karolinska University Hospital, Solna, 17176, Stockholm, Sweden
| | | | - Jan Köster
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, 221 84, Lund, Sweden
- Department of Clinical Genetics and Pathology, Office for Medical Services, Region Skåne, 221 85, Lund, Sweden
| | - Linda Magnusson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, 221 84, Lund, Sweden
| | - Jenny Nilsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, 221 84, Lund, Sweden
| | - Adam Ameur
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - René Wardenaar
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Floris Foijer
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Diana Spierings
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Fredrik Mertens
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, 221 84, Lund, Sweden
- Department of Clinical Genetics and Pathology, Office for Medical Services, Region Skåne, 221 85, Lund, Sweden
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2
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Ranji P, Jonasson E, Andersson L, Filges S, Luna Santamaría M, Vannas C, Dolatabadi S, Gustafsson A, Myklebost O, Håkansson J, Fagman H, Landberg G, Åman P, Ståhlberg A. Deciphering the role of FUS::DDIT3 expression and tumor microenvironment in myxoid liposarcoma development. J Transl Med 2024; 22:389. [PMID: 38671504 PMCID: PMC11046918 DOI: 10.1186/s12967-024-05211-w] [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: 01/10/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Myxoid liposarcoma (MLS) displays a distinctive tumor microenvironment and is characterized by the FUS::DDIT3 fusion oncogene, however, the precise functional contributions of these two elements remain enigmatic in tumor development. METHODS To study the cell-free microenvironment in MLS, we developed an experimental model system based on decellularized patient-derived xenograft tumors. We characterized the cell-free scaffold using mass spectrometry. Subsequently, scaffolds were repopulated using sarcoma cells with or without FUS::DDIT3 expression that were analyzed with histology and RNA sequencing. RESULTS Characterization of cell-free MLS scaffolds revealed intact structure and a large variation of protein types remaining after decellularization. We demonstrated an optimal culture time of 3 weeks and showed that FUS::DDIT3 expression decreased cell proliferation and scaffold invasiveness. The cell-free MLS microenvironment and FUS::DDIT3 expression both induced biological processes related to cell-to-cell and cell-to-extracellular matrix interactions, as well as chromatin remodeling, immune response, and metabolism. Data indicated that FUS::DDIT3 expression more than the microenvironment determined the pre-adipocytic phenotype that is typical for MLS. CONCLUSIONS Our experimental approach opens new means to study the tumor microenvironment in detail and our findings suggest that FUS::DDIT3-expressing tumor cells can create their own extracellular niche.
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Affiliation(s)
- Parmida Ranji
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Emma Jonasson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Lisa Andersson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Stefan Filges
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Manuel Luna Santamaría
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Christoffer Vannas
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Department of Oncology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Soheila Dolatabadi
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Anna Gustafsson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Ola Myklebost
- Department of Tumor Biology, Oslo University Hospital, Oslo, Norway
- Institute for Clinical Science, University of Bergen, Bergen, Norway
| | - Joakim Håkansson
- RISE Unit of Biological Function, Division Materials and Production, RISE Research Institutes of Sweden, Borås, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry and Molecular Biology, Faculty of Science at University of Gothenburg, Gothenburg, Sweden
| | - Henrik Fagman
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Pathology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Göran Landberg
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Pathology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Pierre Åman
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.
- Department of Clinical Genetics and Genomics, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden.
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3
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Park C, Kim R, Choi J, Kim M, Kim TM, Han I, Kim JI, Kim HS. Case Series of Soft Tissue Sarcoma Patients with Brain Metastasis with Implications from Genomic and Transcriptomic Analysis. Cancer Res Treat 2024; 56:665-674. [PMID: 37752792 PMCID: PMC11016652 DOI: 10.4143/crt.2023.864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/26/2023] [Indexed: 09/28/2023] Open
Abstract
PURPOSE Brain metastasis rarely occurs in soft tissue sarcoma (STS). Here, we present five cases of STS with brain metastases with genetic profiles. MATERIALS AND METHODS We included five patients from Seoul National University Hospital who were diagnosed with STS with metastasis to the brain. Tissue from the brain metastasis along with that from the primary site or other metastases were used for DNA and RNA sequencing to identify genetic profiles. Gene expression profiles were compared with sarcoma samples from The Cancer Genome Atlas. RESULTS The overall survival after diagnosis of brain metastasis ranged from 2.2 to 34.3 months. Comparison of mutational profiles between brain metastases and matched primary or other metastatic samples showed similar profiles. In two patients, copy number variation profiles between brain metastasis and other tumors showed several differences including MYCL, JUN, MYC, and DDR2 amplification. Gene ontology analysis showed that the group of genes significantly highly expressed in the brain metastasis samples was enriched in the G-protein coupled receptor activity, structural constituent of chromatin, protein heterodimerization activity, and binding of DNA, RNA, and protein. Gene set enrichment analysis showed enrichment in the pathway of neuroactive ligand-receptor interaction and systemic lupus erythematosus. CONCLUSION The five patients had variable ranges of clinical courses and outcomes. Genomic and transcriptomic analysis of STS with brain metastasis implicates possible involvement of complex expression modification and epigenetic changes rather than the addition of single driver gene alteration.
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Affiliation(s)
- Changhee Park
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Rokhyun Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea
| | - Jaeyong Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea
| | - Miso Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Tae Min Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Ilkyu Han
- Department of Orthopaedic Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jong-Il Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Han-Soo Kim
- Department of Orthopaedic Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
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Mandahl N, Mertens F, Mitelman F. Gene amplification in neoplasia: A cytogenetic survey of 80 131 cases. Genes Chromosomes Cancer 2024; 63:e23214. [PMID: 38050922 DOI: 10.1002/gcc.23214] [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: 10/02/2023] [Revised: 10/26/2023] [Accepted: 11/10/2023] [Indexed: 12/07/2023] Open
Abstract
Gene amplification is a crucial process in cancer development, leading to the overexpression of oncogenes. It manifests cytogenetically as extrachromosomal double minutes (dmin), homogeneously staining regions (hsr), or ring chromosomes (r). This study investigates the prevalence and distribution of these amplification markers in a survey of 80 131 neoplasms spanning hematologic disorders, and benign and malignant solid tumors. The study reveals distinct variations in the frequency of dmin, hsr, and r among different tumor types. Rings were the most common (3.4%) sign of amplification, followed by dmin (1.3%), and hsr (0.8%). Rings were particularly frequent in malignant mesenchymal tumors, especially liposarcomas (47.5%) and osteosarcomas (23.4%), dmin were prevalent in neuroblastoma (30.9%) and pancreatic carcinoma (21.9%), and hsr frequencies were highest in head and neck carcinoma (14.0%) and neuroblastoma (9.0%). Combining all three amplification markers (dmin/hsr/r), malignant solid tumors consistently exhibited higher frequencies than hematologic disorders and benign solid tumors. The structural characteristics of these amplification markers and their potential role in tumorigenesis and tumor progression highlight the complex interplay between cancer-initiating gene-level alterations, for example, fusion genes, and subsequent amplification dynamics. Further research integrating cytogenetic and molecular approaches is warranted to better understand the underlying mechanisms of these amplifications, in particular, the enigmatic question of why certain malignancies display certain types of amplification. Comparing the present results with molecular genetic data proved challenging because of the diversity in definitions of amplification across studies. This study underscores the need for standardized definitions in future work.
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Affiliation(s)
- Nils Mandahl
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Fredrik Mertens
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Division of Laboratory Medicine, Department of Clinical Genetics and Pathology, University Hospital, Lund, Sweden
| | - Felix Mitelman
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
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Kojima N, Kubo T, Mori T, Satomi K, Matsushita Y, Iwata S, Yatabe Y, Ichimura K, Kawai A, Ichikawa H, Yoshida A. Myxoid liposarcoma with nuclear pleomorphism: a clinicopathological and molecular study. Virchows Arch 2024; 484:71-81. [PMID: 37704823 DOI: 10.1007/s00428-023-03631-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/14/2023] [Accepted: 08/19/2023] [Indexed: 09/15/2023]
Abstract
Myxoid liposarcoma (MLS) is a common type of liposarcoma. It is characterized by variably lipogenic uniform cells in myxoid stroma with arborizing capillaries and DDIT3 fusion. Nuclear uniformity is the rule, which is maintained even in high-grade round cell examples. In this study, we conducted an in-depth investigation of four MLS tumors that demonstrated nuclear pleomorphism in three patients. These cases accounted for 2.1% of 142 patients with MLS. All patients were male aged 26, 33, and 49 years. Nuclear pleomorphism was observed in both primary and metastatic tumors in one patient, a primary tumor in one patient, and a metastatic tumor in another patient. Pleomorphism was severe in three tumors and moderate in one. Histology resembled that of dedifferentiated liposarcoma with myxoid features, pleomorphic liposarcoma with myxoid features, or myxoid pleomorphic liposarcoma in two tumors, pleomorphic sarcoma with focal cartilaginous and rhabdomyoblastic differentiation in one tumor, and epithelioid pleomorphic liposarcoma in one tumor. All tumors harbored FUS::DDIT3 fusions and immunohistochemically expressed DDIT3. All tumors had TP53 mutations, whereas previous specimens with uniform cytology from the same patients lacked TP53 mutations. One tumor showed RB1 deletion and complete loss of Rb expression, which was unclassifiable using DNA methylation-based methods. The rare occurrence of nuclear pleomorphism is underrecognized in MLS and increases the complexity to the diagnosis of liposarcoma. DDIT3 evaluation can be liberally considered in liposarcoma assessment even in the presence of nuclear pleomorphism.
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Affiliation(s)
- Naoki Kojima
- Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Takashi Kubo
- Department of Clinical Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Taisuke Mori
- Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Kaishi Satomi
- Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
- Department of Pathology, Kyorin University Faculty of Medicine, Tokyo, Japan
| | - Yuko Matsushita
- Department of Brain Disease Translational Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Shintaro Iwata
- Department of Musculoskeletal Oncology, National Cancer Center Hospital, Tokyo, Japan
- Rare Cancer Center, National Cancer Center, Tokyo, Japan
| | - Yasushi Yatabe
- Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Koichi Ichimura
- Department of Brain Disease Translational Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Akira Kawai
- Department of Musculoskeletal Oncology, National Cancer Center Hospital, Tokyo, Japan
- Rare Cancer Center, National Cancer Center, Tokyo, Japan
| | - Hitoshi Ichikawa
- Department of Clinical Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Akihiko Yoshida
- Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
- Rare Cancer Center, National Cancer Center, Tokyo, Japan.
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Dermawan JK, Rubin BP. The spectrum and significance of secondary (co-occurring) genetic alterations in sarcomas: the hallmarks of sarcomagenesis. J Pathol 2023; 260:637-648. [PMID: 37345731 DOI: 10.1002/path.6140] [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: 04/11/2023] [Revised: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 06/23/2023]
Abstract
Bone and soft tissue tumors are generally classified into complex karyotype sarcomas versus those with recurrent genetic alterations, often in the form of gene fusions. In this review, we provide an overview of important co-occurring genomic alterations, organized by biological mechanisms and covering a spectrum of genomic alteration types: mutations (single-nucleotide variations or indels) in oncogenes or tumor suppressor genes, copy number alterations, transcriptomic signatures, genomic complexity indices (e.g. CINSARC), and complex genomic structural variants. We discuss the biological and prognostic roles of these so-called secondary or co-occurring alterations, arguing that recognition and detection of these alterations may be significant for our understanding and management of mesenchymal tumors. On a related note, we also discuss major recurrent alterations in so-called complex karyotype sarcomas. These secondary alterations are essential to sarcomagenesis via a variety of mechanisms, such as inactivation of tumor suppressors, activation of proliferative signal transduction, telomere maintenance, and aberrant regulation of epigenomic/chromatin remodeling players. The use of comprehensive genomic profiling, including targeted next-generation sequencing panels or whole-exome sequencing, may be incorporated into clinical workflows to offer more comprehensive, potentially clinically actionable information. © 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)
- Josephine K Dermawan
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Brian P Rubin
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
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7
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Watson S, Gruel N, Le Loarer F. New developments in the pathology and molecular biology of retroperitoneal sarcomas. EUROPEAN JOURNAL OF SURGICAL ONCOLOGY 2023; 49:1053-1060. [PMID: 35151525 DOI: 10.1016/j.ejso.2022.02.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/22/2022] [Accepted: 02/02/2022] [Indexed: 02/07/2023]
Abstract
Retroperitoneal sarcomas (RPS) refer to a heterogeneous group of malignancies of mesenchymal origin developing from retroperitoneal tissues and vessels. The most frequent RPS are well differentiated/dedifferentiated liposarcomas and leiomyosarcomas, but other rare histological subtypes can be observed. Over the last decade, significant advances have been made in the pathological and molecular characterization of sarcomas. These advances have led to major changes in their diagnostic management as well as in the development of new therapeutic strategies based on tumor biology and microenvironment. This review describes the current knowledge and recent findings in the pathology and molecular biology of the most frequent RPS subtypes.
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Affiliation(s)
- Sarah Watson
- INSERM U830, Équipe Labellisée Ligue Nationale Contre le Cancer, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, Institut Curie Research Center, Paris, France; Department of Medical Oncology, Institut Curie Hospital, Paris, France.
| | - Nadege Gruel
- INSERM U830, Équipe Labellisée Ligue Nationale Contre le Cancer, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, Institut Curie Research Center, Paris, France; Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - François Le Loarer
- Department of Pathology, Institut Bergonie, Bordeaux, France; INSERM U1218, Unité ACTION, Institut Bergonie, Bordeaux, France; University of Bordeaux, Talence, France
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8
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Vanni S, De Vita A, Gurrieri L, Fausti V, Miserocchi G, Spadazzi C, Liverani C, Cocchi C, Calabrese C, Bongiovanni A, Riva N, Mercatali L, Pieri F, Casadei R, Lucarelli E, Ibrahim T. Myxofibrosarcoma landscape: diagnostic pitfalls, clinical management and future perspectives. Ther Adv Med Oncol 2022; 14:17588359221093973. [PMID: 35782752 PMCID: PMC9244941 DOI: 10.1177/17588359221093973] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 01/12/2022] [Indexed: 12/26/2022] Open
Abstract
Myxofibrosarcoma (MFS) is a common entity of adult soft tissue sarcomas (STS) characterized by a predilection of the extremities and a high local recurrence rate. Originally classified as a myxoid variant of malignant fibrous histiocytoma, this musculoskeletal tumor has been recognized since 2002 as a distinct histotype showing a spectrum of malignant fibroblastic lesions with myxoid stroma, pleomorphism and curvilinear vessels. Currently, the molecular pathogenesis of MFS is still poorly understood and its genomic profile exhibits a complex karyotype with a number of aberrations including amplifications, deletions and loss of function. The diagnosis is challenging due to the unavailability of specific immunohistochemical markers and is based on the analysis of cytomorphologic features. The mainstay of treatment for localized disease is represented by surgical resection, with (neo)-adjuvant radio- and chemotherapy. In the metastatic setting, chemotherapy represents the backbone of treatments, however its role is still controversial and the outcome is very poor. Recent advent of genomic profiling, targeted therapies and larger enrollment of patients in translational and clinical studies, have improved the understanding of biological behavior and clinical outcome of such a disease. This review will provide an overview of current diagnostic pitfalls and clinical management of MFS. Finally, a look at future directions will be discussed.
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Affiliation(s)
- Silvia Vanni
- Osteoncology Unit, Bioscience Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) 'Dino Amadori', Meldola, Italy
| | - Alessandro De Vita
- Osteoncology Unit, Bioscience Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) 'Dino Amadori', Via P. Maroncelli 40, Meldola 47014, Forlì-Cesena, Italy
| | - Lorena Gurrieri
- Osteoncology Unit, Bioscience Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) 'Dino Amadori', Meldola, Italy
| | - Valentina Fausti
- Osteoncology Unit, Bioscience Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) 'Dino Amadori', Meldola, Italy
| | - Giacomo Miserocchi
- Osteoncology Unit, Bioscience Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) 'Dino Amadori', Meldola, Italy
| | - Chiara Spadazzi
- Osteoncology Unit, Bioscience Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) 'Dino Amadori', Meldola, Italy
| | - Chiara Liverani
- Osteoncology Unit, Bioscience Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) 'Dino Amadori', Meldola, Italy
| | - Claudia Cocchi
- Osteoncology Unit, Bioscience Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) 'Dino Amadori', Meldola, Italy
| | - Chiara Calabrese
- Osteoncology Unit, Bioscience Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) 'Dino Amadori', Meldola, Italy
| | - Alberto Bongiovanni
- Osteoncology Unit, Bioscience Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) 'Dino Amadori', Meldola, Italy
| | - Nada Riva
- Osteoncology Unit, Bioscience Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) 'Dino Amadori', Meldola, Italy
| | - Laura Mercatali
- Osteoncology Unit, Bioscience Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) 'Dino Amadori', Meldola, Italy
| | - Federica Pieri
- Pathology Unit, 'Morgagni-Pierantoni' Hospital, Forlì, Italy
| | - Roberto Casadei
- Orthopedic Unit, 'Morgagni-Pierantoni' Hospital, Forlì, Italy
| | - Enrico Lucarelli
- Osteoncology, Bone and Soft Tissue Sarcomas and Innovative Therapies Unit, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Toni Ibrahim
- Osteoncology, Bone and Soft Tissue Sarcomas and Innovative Therapies Unit, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
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9
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Eisenhardt AE, Schmid A, Esser J, Brugger Z, Lausch U, Kiefer J, Braig M, Runkel A, Wehrle J, Claus R, Bronsert P, Leithner A, Liegl-Atzwanger B, Zeller J, Papini R, von Laffert M, Pfitzner BM, Koulaxouzidis G, Giunta RE, Eisenhardt SU, Braig D. Targeted next-generation sequencing of circulating free DNA enables non-invasive tumor detection in myxoid liposarcomas. Mol Cancer 2022; 21:50. [PMID: 35164780 PMCID: PMC8842903 DOI: 10.1186/s12943-022-01523-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/26/2022] [Indexed: 12/17/2022] Open
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10
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The diagnostic utility of DNA copy number analysis of core needle biopsies from soft tissue and bone tumors. J Transl Med 2022; 102:838-845. [PMID: 35318454 PMCID: PMC9309094 DOI: 10.1038/s41374-022-00770-2] [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: 11/30/2021] [Revised: 01/26/2022] [Accepted: 02/08/2022] [Indexed: 12/03/2022] Open
Abstract
Morphologic and immunohistochemical analysis of preoperative core needle biopsies (CNB) is important in the management of patients with soft tissue and bone tumors (STBTs). Most SBTB subtypes have more or less extensive DNA copy number aberrations (CNA), potentially providing useful diagnostic information. To evaluate the technical feasibility of single nucleotide polymorphism (SNP) array analysis and the diagnostic usefulness of the copy number profiles, we studied CNBs from 171 patients with suspected STBTs. SNP array analysis could be performed on 168 (98%) of the samples. The CNA profile was compatible with the CNB diagnosis in 87% of the cases. Discrepant cases were dominated by false-negative results due to nonrepresentative material or contamination with normal cells. 70 genomic profiles were indicative of specific histopathologic tumor entities and in agreement with the corresponding CNB diagnoses in 83%. In 96 of the cases with aberrant CNA profiles, the SNP profiles were of sufficient quality for segmentation, allowing clustering analysis on the basis of the Jaccard similarity index. The analysis of these segment files showed three major CNA clusters, based on the complexity levels and the predominance of gains versus losses. For 43 of these CNB samples, we had SNP array data also from their corresponding surgical samples. In 33 of these pairs, the two corresponding samples clustered next to each other, with Jaccard scores ranging from 0.61 to 0.99 (median 0.96). Also, for those tumor pairs that did not cluster together, the Jaccard scores were relatively high (median 0.9). 10 cases showed discrepant results, mainly due to varying degrees of normal cell contamination or technical issues. Thus, the copy number profile seen in a CNB is typically highly representative of the major cell population in the tumor.
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Ghannoum S, Leoncio Netto W, Fantini D, Ragan-Kelley B, Parizadeh A, Jonasson E, Ståhlberg A, Farhan H, Köhn-Luque A. DIscBIO: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics. Int J Mol Sci 2021; 22:ijms22031399. [PMID: 33573289 PMCID: PMC7866810 DOI: 10.3390/ijms22031399] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/08/2021] [Accepted: 01/28/2021] [Indexed: 02/08/2023] Open
Abstract
The growing attention toward the benefits of single-cell RNA sequencing (scRNA-seq) is leading to a myriad of computational packages for the analysis of different aspects of scRNA-seq data. For researchers without advanced programing skills, it is very challenging to combine several packages in order to perform the desired analysis in a simple and reproducible way. Here we present DIscBIO, an open-source, multi-algorithmic pipeline for easy, efficient and reproducible analysis of cellular sub-populations at the transcriptomic level. The pipeline integrates multiple scRNA-seq packages and allows biomarker discovery with decision trees and gene enrichment analysis in a network context using single-cell sequencing read counts through clustering and differential analysis. DIscBIO is freely available as an R package. It can be run either in command-line mode or through a user-friendly computational pipeline using Jupyter notebooks. We showcase all pipeline features using two scRNA-seq datasets. The first dataset consists of circulating tumor cells from patients with breast cancer. The second one is a cell cycle regulation dataset in myxoid liposarcoma. All analyses are available as notebooks that integrate in a sequential narrative R code with explanatory text and output data and images. R users can use the notebooks to understand the different steps of the pipeline and will guide them to explore their scRNA-seq data. We also provide a cloud version using Binder that allows the execution of the pipeline without the need of downloading R, Jupyter or any of the packages used by the pipeline. The cloud version can serve as a tutorial for training purposes, especially for those that are not R users or have limited programing skills. However, in order to do meaningful scRNA-seq analyses, all users will need to understand the implemented methods and their possible options and limitations.
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Affiliation(s)
- Salim Ghannoum
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0372 Oslo, Norway; (A.P.); (H.F.)
- Correspondence: (S.G.); (A.K.-L.); Tel.: +46-76-5770129 (S.G.)
| | - Waldir Leoncio Netto
- Oslo Centre for Biostatistics and Epidemiology, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway;
| | - Damiano Fantini
- Department of Urology, Northwestern University, Chicago, IL 60611, USA;
| | | | - Amirabbas Parizadeh
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0372 Oslo, Norway; (A.P.); (H.F.)
| | - Emma Jonasson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, SE-41390 Gothenburg, Sweden; (E.J.); (A.S.)
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, SE-41390 Gothenburg, Sweden; (E.J.); (A.S.)
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-41390 Gothenburg, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, SE-41390 Gothenburg, Sweden
| | - Hesso Farhan
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0372 Oslo, Norway; (A.P.); (H.F.)
| | - Alvaro Köhn-Luque
- Oslo Centre for Biostatistics and Epidemiology, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway;
- Correspondence: (S.G.); (A.K.-L.); Tel.: +46-76-5770129 (S.G.)
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12
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Genome wide methylation profiling of selected matched soft tissue sarcomas identifies methylation changes in metastatic and recurrent disease. Sci Rep 2021; 11:667. [PMID: 33436720 PMCID: PMC7804318 DOI: 10.1038/s41598-020-79648-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/10/2020] [Indexed: 02/07/2023] Open
Abstract
In this study we used the Illumina Infinium Methylation array to investigate in a cohort of matched archival human tissue samples (n = 32) from 14 individuals with soft tissue sarcomas if genome-wide methylation changes occur during metastatic and recurrent (Met/Rec) disease. A range of sarcoma types were selected for this study: leiomyosarcoma (LMS), myxofibrosarcoma (MFS), rhabdomyosarcoma (RMS) and synovial sarcoma (SS). We identified differential methylation in all Met/Rec matched samples, demonstrating that epigenomic differences develop during the clonal evolution of sarcomas. Differentially methylated regions and genes were detected, not been previously implicated in sarcoma progression, including at PTPRN2 and DAXX in LMS, WT1-AS and TNXB in SS, VENTX and NTRK3 in pleomorphic RMS and MEST and the C14MC / miR-379/miR-656 in MFS. Our overall findings indicate the presence of objective epigenetic differences across primary and Met/Rec human tissue samples not previously reported.
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Köster J, Arbajian E, Viklund B, Isaksson A, Hofvander J, Haglund F, Bauer H, Magnusson L, Mandahl N, Mertens F. Genomic and transcriptomic features of dermatofibrosarcoma protuberans: Unusual chromosomal origin of the COL1A1-PDGFB fusion gene and synergistic effects of amplified regions in tumor development. Cancer Genet 2019; 241:34-41. [PMID: 31870844 DOI: 10.1016/j.cancergen.2019.12.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 11/06/2019] [Accepted: 12/06/2019] [Indexed: 12/11/2022]
Abstract
The dermatofibrosarcoma protuberans family of tumors (DPFT) comprises cutaneous soft tissue neoplasms associated with aberrant PDGFBR signaling, typically through a COL1A1-PDGFB fusion. The aim of the present study was to obtain a better understanding of the chromosomal origin of this fusion and to assess the spectrum of secondary mutations at the chromosome and nucleotide levels. We thus investigated 42 tumor samples from 35 patients using chromosome banding, fluorescence in situ hybridization, single nucleotide polymorphism arrays, and/or massively parallel sequencing (gene panel, whole exome and transcriptome sequencing) methods. We confirmed the age-associated differences in the origin of the COL1A1-PDGFB fusion and could show that it in most cases must arise after DNA synthesis, i.e., in the S or G2 phase of the cell cycle. Whereas there was a non-random pattern of secondary chromosomal rearrangements, single nucleotide variants seem to have little impact on tumor progression. No clear genomic differences between low-grade and high-grade DPFT were found, but the number of chromosomes and chromosomal imbalances as well as the frequency of 9p deletions all tended to be greater among the latter. Gene expression profiling of tumors with COL1A1-PDGFB fusions associated with unbalanced translocations or ring chromosomes identified several transcriptionally up-regulated genes in the amplified regions of chromosomes 17 and 22, including TBX2, PRKCA, MSI2, SOX9, SOX10, and PRAME.
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Affiliation(s)
- Jan Köster
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden; Department of Clinical Genetics and Pathology, Division of Laboratory Medicine, Lund, Sweden.
| | - Elsa Arbajian
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Björn Viklund
- Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Sweden
| | - Anders Isaksson
- Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Sweden
| | - Jakob Hofvander
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Felix Haglund
- Department of Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden
| | - Henrik Bauer
- Department of Orthopedics, Karolinska University Hospital, Stockholm, Sweden
| | - Linda Magnusson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Nils Mandahl
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Fredrik Mertens
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden; Department of Clinical Genetics and Pathology, Division of Laboratory Medicine, Lund, Sweden
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14
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Yu JSE, Colborne S, Hughes CS, Morin GB, Nielsen TO. The FUS-DDIT3 Interactome in Myxoid Liposarcoma. Neoplasia 2019; 21:740-751. [PMID: 31220736 PMCID: PMC6584455 DOI: 10.1016/j.neo.2019.05.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/10/2019] [Accepted: 05/13/2019] [Indexed: 12/13/2022] Open
Abstract
Myxoid liposarcoma is a malignant lipogenic tumor that develops in deep soft tissues. While local control rates are good, current chemotherapy options remain ineffective against metastatic disease. Myxoid liposarcoma is characterized by the FUS-DDIT3 fusion oncoprotein that is proposed to function as an aberrant transcription factor, but its exact mechanism of action has remained unclear. To identify the key functional interacting partners of FUS-DDIT3, this study utilized immunoprecipitation-mass spectrometry (IP-MS) to identify the FUS-DDIT3 interactome in whole cell lysates of myxoid liposarcoma cells, and results showed an enrichment of RNA processing proteins. Further quantitative MS analyses of FUS-DDIT3 complexes isolated from nuclear lysates showed that members of several chromatin regulatory complexes were present in the FUS-DDIT3 interactome, including NuRD, SWI/SNF, PRC1, PRC2, and MLL1 COMPASS-like complexes. Co-immunoprecipitation validated the associations of FUS-DDIT3 with BRG1/SMARCA4, BAF155/SMARCC1, BAF57/SMARCE1, and KDM1A. Data from this study provides candidates for functional validation as potential therapeutic targets, particularly for emerging epigenetic drugs.
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Affiliation(s)
- Jamie S E Yu
- Department of Pathology, University of British Columbia, Vancouver, BC V5Z 1M9, Canada.
| | - Shane Colborne
- British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
| | | | - Gregg B Morin
- British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada.
| | - Torsten O Nielsen
- Department of Pathology, University of British Columbia, Vancouver, BC V5Z 1M9, Canada.
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