1
|
Lim WC, Marques Da Costa ME, Godefroy K, Jacquet E, Gragert L, Rondof W, Marchais A, Nhiri N, Dalfovo D, Viard M, Labaied N, Khan AM, Dessen P, Romanel A, Pasqualini C, Schleiermacher G, Carrington M, Zitvogel L, Scoazec JY, Geoerger B, Salmon J. Divergent HLA variations and heterogeneous expression but recurrent HLA loss-of- heterozygosity and common HLA-B and TAP transcriptional silencing across advanced pediatric solid cancers. Front Immunol 2024; 14:1265469. [PMID: 38318504 PMCID: PMC10839790 DOI: 10.3389/fimmu.2023.1265469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 11/06/2023] [Indexed: 02/07/2024] Open
Abstract
The human leukocyte antigen (HLA) system is a major factor controlling cancer immunosurveillance and response to immunotherapy, yet its status in pediatric cancers remains fragmentary. We determined high-confidence HLA genotypes in 576 children, adolescents and young adults with recurrent/refractory solid tumors from the MOSCATO-01 and MAPPYACTS trials, using normal and tumor whole exome and RNA sequencing data and benchmarked algorithms. There was no evidence for narrowed HLA allelic diversity but discordant homozygosity and allele frequencies across tumor types and subtypes, such as in embryonal and alveolar rhabdomyosarcoma, neuroblastoma MYCN and 11q subtypes, and high-grade glioma, and several alleles may represent protective or susceptibility factors to specific pediatric solid cancers. There was a paucity of somatic mutations in HLA and antigen processing and presentation (APP) genes in most tumors, except in cases with mismatch repair deficiency or genetic instability. The prevalence of loss-of-heterozygosity (LOH) ranged from 5.9 to 7.7% in HLA class I and 8.0 to 16.7% in HLA class II genes, but was widely increased in osteosarcoma and glioblastoma (~15-25%), and for DRB1-DQA1-DQB1 in Ewing sarcoma (~23-28%) and low-grade glioma (~33-50%). HLA class I and HLA-DR antigen expression was assessed in 194 tumors and 44 patient-derived xenografts (PDXs) by immunochemistry, and class I and APP transcript levels quantified in PDXs by RT-qPCR. We confirmed that HLA class I antigen expression is heterogeneous in advanced pediatric solid tumors, with class I loss commonly associated with the transcriptional downregulation of HLA-B and transporter associated with antigen processing (TAP) genes, whereas class II antigen expression is scarce on tumor cells and occurs on immune infiltrating cells. Patients with tumors expressing sufficient HLA class I and TAP levels such as some glioma, osteosarcoma, Ewing sarcoma and non-rhabdomyosarcoma soft-tissue sarcoma cases may more likely benefit from T cell-based approaches, whereas strategies to upregulate HLA expression, to expand the immunopeptidome, and to target TAP-independent epitopes or possibly LOH might provide novel therapeutic opportunities in others. The consequences of HLA class II expression by immune cells remain to be established. Immunogenetic profiling should be implemented in routine to inform immunotherapy trials for precision medicine of pediatric cancers.
Collapse
Affiliation(s)
- Wan Ching Lim
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Bioinformatics Platform, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- School of Data Sciences, Perdana University, Kuala Lumpur, Malaysia
| | | | - Karine Godefroy
- Department of Pathology and Laboratory Medicine, Translational Research Laboratory and Biobank, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Eric Jacquet
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Loren Gragert
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Windy Rondof
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Bioinformatics Platform, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Antonin Marchais
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Bioinformatics Platform, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Naima Nhiri
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Davide Dalfovo
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Mathias Viard
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, United States
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
| | - Nizar Labaied
- Department of Pathology and Laboratory Medicine, Translational Research Laboratory and Biobank, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Asif M. Khan
- School of Data Sciences, Perdana University, Kuala Lumpur, Malaysia
| | - Philippe Dessen
- Bioinformatics Platform, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Alessandro Romanel
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Claudia Pasqualini
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Gudrun Schleiermacher
- INSERM U830, Recherche Translationnelle en Oncologie Pédiatrique (RTOP), and SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), PSL Research University, Institut Curie, Paris, France
| | - Mary Carrington
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, United States
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Cambridge, MA, United States
| | - Laurence Zitvogel
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Jean-Yves Scoazec
- Department of Pathology and Laboratory Medicine, Translational Research Laboratory and Biobank, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Birgit Geoerger
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Jerome Salmon
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| |
Collapse
|
2
|
Zhuang G, Zhang X, Du W, Xu L, Ma J, Luo H, Tang H, Wang W, Wang P, Li M, Yang X, Wu D, Fang S. A benchmarking framework for the accurate and cost-effective detection of clinically-relevant structural variants for cancer target identification and diagnosis. J Transl Med 2024; 22:65. [PMID: 38229122 PMCID: PMC10792779 DOI: 10.1186/s12967-024-04865-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: 09/28/2023] [Accepted: 01/06/2024] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Accurate clinical structural variant (SV) calling is essential for cancer target identification and diagnosis but has been historically challenging due to the lack of ground truth for clinical specimens. Meanwhile, reduced clinical-testing cost is the key to the widespread clinical utility. METHODS We analyzed massive data from tumor samples of 476 patients and developed a computational framework for accurate and cost-effective detection of clinically-relevant SVs. In addition, standard materials and classical experiments including immunohistochemistry and/or fluorescence in situ hybridization were used to validate the developed computational framework. RESULTS We systematically evaluated the common algorithms for SV detection and established an expert-reviewed SV call set of 1,303 tumor-specific SVs with high-evidence levels. Moreover, we developed a random-forest-based decision model to improve the true positive of SVs. To independently validate the tailored 'two-step' strategy, we utilized standard materials and classical experiments. The accuracy of the model was over 90% (92-99.78%) for all types of data. CONCLUSION Our study provides a valuable resource and an actionable guide to improve cancer-specific SV detection accuracy and clinical applicability.
Collapse
Affiliation(s)
- Guiwu Zhuang
- Department of Gastrointestinal Surgery, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, China
| | - Xiaotao Zhang
- Department of Radiotherapy, Qingdao Central Hospital, University of Health and Rehabilitation Sciences, Qingdao, China
| | - Wenjing Du
- Department of Radiotherapy, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Libin Xu
- Department of Orthopedic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiyong Ma
- Department of Respiration, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Haitao Luo
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, YuceBio Technology Co., Ltd., Shenzhen, China
| | - Hongzhen Tang
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, YuceBio Technology Co., Ltd., Shenzhen, China
| | - Wei Wang
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, YuceBio Technology Co., Ltd., Shenzhen, China
| | - Peng Wang
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, YuceBio Technology Co., Ltd., Shenzhen, China
| | - Miao Li
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, YuceBio Technology Co., Ltd., Shenzhen, China
| | - Xu Yang
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, YuceBio Technology Co., Ltd., Shenzhen, China
| | - Dongfang Wu
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, YuceBio Technology Co., Ltd., Shenzhen, China
| | - Shencun Fang
- Department of Respiratory Medicine, Nanjing Chest Hospital, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China.
| |
Collapse
|
3
|
Edsjö A, Holmquist L, Geoerger B, Nowak F, Gomon G, Alix-Panabières C, Ploeger C, Lassen U, Le Tourneau C, Lehtiö J, Ott PA, von Deimling A, Fröhling S, Voest E, Klauschen F, Dienstmann R, Alshibany A, Siu LL, Stenzinger A. Precision cancer medicine: Concepts, current practice, and future developments. J Intern Med 2023; 294:455-481. [PMID: 37641393 DOI: 10.1111/joim.13709] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Precision cancer medicine is a multidisciplinary team effort that requires involvement and commitment of many stakeholders including the society at large. Building on the success of significant advances in precision therapy for oncological patients over the last two decades, future developments will be significantly shaped by improvements in scalable molecular diagnostics in which increasingly complex multilayered datasets require transformation into clinically useful information guiding patient management at fast turnaround times. Adaptive profiling strategies involving tissue- and liquid-based testing that account for the immense plasticity of cancer during the patient's journey and also include early detection approaches are already finding their way into clinical routine and will become paramount. A second major driver is the development of smart clinical trials and trial concepts which, complemented by real-world evidence, rapidly broaden the spectrum of therapeutic options. Tight coordination with regulatory agencies and health technology assessment bodies is crucial in this context. Multicentric networks operating nationally and internationally are key in implementing precision oncology in clinical practice and support developing and improving the ecosystem and framework needed to turn invocation into benefits for patients. The review provides an overview of the diagnostic tools, innovative clinical studies, and collaborative efforts needed to realize precision cancer medicine.
Collapse
Affiliation(s)
- Anders Edsjö
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
- Division of Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
- Genomic Medicine Sweden (GMS), Kristianstad, Sweden
| | - Louise Holmquist
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
- Genomic Medicine Sweden (GMS), Kristianstad, Sweden
| | - Birgit Geoerger
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | | | - Georgy Gomon
- Department of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
- Department of Medical Oncology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Catherine Alix-Panabières
- Laboratory of Rare Human Circulating Cells, University Medical Center of Montpellier, Montpellier, France
- CREEC, MIVEGEC, University of Montpellier, Montpellier, France
| | - Carolin Ploeger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Centers for Personalized Medicine (ZPM), Heidelberg, Germany
| | - Ulrik Lassen
- Department of Oncology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Christophe Le Tourneau
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
- INSERM U900 Research Unit, Saint-Cloud, France
- Faculty of Medicine, Paris-Saclay University, Paris, France
| | - Janne Lehtiö
- Department of Oncology Pathology, Karolinska Institutet, Science for Life Laboratory, Stockholm, Sweden
| | - Patrick A Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
| | - Andreas von Deimling
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan Fröhling
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Emile Voest
- Department of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Frederick Klauschen
- Institute of Pathology, Charite - Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- BIFOLD - Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
- Institute of Pathology, Ludwig-Maximilians-University, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Munich Partner Site, Heidelberg, Germany
| | | | | | - Lillian L Siu
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Centers for Personalized Medicine (ZPM), Heidelberg, Germany
| |
Collapse
|
4
|
Mukherjee S, Mukherjee SB, Frenkel-Morgenstern M. Functional and regulatory impact of chimeric RNAs in human normal and cancer cells. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1777. [PMID: 36633099 DOI: 10.1002/wrna.1777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 12/21/2022] [Accepted: 12/27/2022] [Indexed: 01/13/2023]
Abstract
Fusions of two genes can lead to the generation of chimeric RNAs, which may have a distinct functional role from their original molecules. Chimeric RNAs could encode novel functional proteins or serve as novel long noncoding RNAs (lncRNAs). The appearance of chimeric RNAs in a cell could help to generate new functionality and phenotypic diversity that might facilitate this cell to survive against new environmental stress. Several recent studies have demonstrated the functional roles of various chimeric RNAs in cancer progression and are considered as biomarkers for cancer diagnosis and sometimes even drug targets. Further, the growing evidence demonstrated the potential functional association of chimeric RNAs with cancer heterogeneity and drug resistance cancer evolution. Recent studies highlighted that chimeric RNAs also have functional potentiality in normal physiological processes. Several functionally potential chimeric RNAs were discovered in human cancer and normal cells in the last two decades. This could indicate that chimeric RNAs are the hidden layer of the human transcriptome that should be explored from the functional insights to better understand the functional evolution of the genome and disease development that could facilitate clinical practice improvements. This review summarizes the current knowledge of chimeric RNAs and highlights their functional, regulatory, and evolutionary impact on different cancers and normal physiological processes. Further, we will discuss the potential functional roles of a recently discovered novel class of chimeric RNAs named sense-antisense/cross-strand chimeric RNAs generated by the fusion of the bi-directional transcripts of the same gene. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
Collapse
Affiliation(s)
- Sumit Mukherjee
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
- Department of Computer Science, Ben-Gurion University, Beer-Sheva, Israel
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Sunanda Biswas Mukherjee
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Milana Frenkel-Morgenstern
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| |
Collapse
|
5
|
van Belzen IAEM, Cai C, van Tuil M, Badloe S, Strengman E, Janse A, Verwiel ETP, van der Leest DFM, Kester L, Molenaar JJ, Meijerink J, Drost J, Peng WC, Kerstens HHD, Tops BBJ, Holstege FCP, Kemmeren P, Hehir-Kwa JY. Systematic discovery of gene fusions in pediatric cancer by integrating RNA-seq and WGS. BMC Cancer 2023; 23:618. [PMID: 37400763 DOI: 10.1186/s12885-023-11054-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 03/08/2023] [Indexed: 07/05/2023] Open
Abstract
BACKGROUND Gene fusions are important cancer drivers in pediatric cancer and their accurate detection is essential for diagnosis and treatment. Clinical decision-making requires high confidence and precision of detection. Recent developments show RNA sequencing (RNA-seq) is promising for genome-wide detection of fusion products but hindered by many false positives that require extensive manual curation and impede discovery of pathogenic fusions. METHODS We developed Fusion-sq to overcome existing disadvantages of detecting gene fusions. Fusion-sq integrates and "fuses" evidence from RNA-seq and whole genome sequencing (WGS) using intron-exon gene structure to identify tumor-specific protein coding gene fusions. Fusion-sq was then applied to the data generated from a pediatric pan-cancer cohort of 128 patients by WGS and RNA sequencing. RESULTS In a pediatric pan-cancer cohort of 128 patients, we identified 155 high confidence tumor-specific gene fusions and their underlying structural variants (SVs). This includes all clinically relevant fusions known to be present in this cohort (30 patients). Fusion-sq distinguishes healthy-occurring from tumor-specific fusions and resolves fusions in amplified regions and copy number unstable genomes. A high gene fusion burden is associated with copy number instability. We identified 27 potentially pathogenic fusions involving oncogenes or tumor-suppressor genes characterized by underlying SVs, in some cases leading to expression changes indicative of activating or disruptive effects. CONCLUSIONS Our results indicate how clinically relevant and potentially pathogenic gene fusions can be identified and their functional effects investigated by combining WGS and RNA-seq. Integrating RNA fusion predictions with underlying SVs advances fusion detection beyond extensive manual filtering. Taken together, we developed a method for identifying candidate gene fusions that is suitable for precision oncology applications. Our method provides multi-omics evidence for assessing the pathogenicity of tumor-specific gene fusions for future clinical decision making.
Collapse
Affiliation(s)
| | - Casey Cai
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Marc van Tuil
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Shashi Badloe
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Eric Strengman
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Alex Janse
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | | | - Lennart Kester
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Jan J Molenaar
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Jules Meijerink
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Weng Chuan Peng
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - Bastiaan B J Tops
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - Patrick Kemmeren
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
- Center for Molecular Medicine, UMC Utrecht and Utrecht University, Utrecht, The Netherlands.
| | - Jayne Y Hehir-Kwa
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
| |
Collapse
|
6
|
da Costa MEM, Droit R, Khneisser P, Gomez-Brouchet A, Adam-de-Beaumais T, Nolla M, Signolles N, Torrejon J, Lombard B, Loew D, Ayrault O, Scoazec JY, Geoerger B, Vassal G, Marchais A, Gaspar N. Longitudinal characterization of primary osteosarcoma and derived subcutaneous and orthotopic relapsed patient-derived xenograft models. Front Oncol 2023; 13:1166063. [PMID: 37377921 PMCID: PMC10291137 DOI: 10.3389/fonc.2023.1166063] [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: 02/14/2023] [Accepted: 04/25/2023] [Indexed: 06/29/2023] Open
Abstract
Osteosarcoma is a rare bone cancer in adolescents and young adults with a dismal prognosis because of metastatic disease and chemoresistance. Despite multiple clinical trials, no improvement in outcome has occurred in decades. There is an urgent need to better understand resistant and metastatic disease and to generate in vivo models from relapsed tumors. We developed eight new patient-derived xenograft (PDX) subcutaneous and orthotopic/paratibial models derived from patients with recurrent osteosarcoma and compared the genetic and transcriptomic landscapes of the disease progression at diagnosis and relapse with the matching PDX. Whole exome sequencing showed that driver and copy-number alterations are conserved from diagnosis to relapse, with the emergence of somatic alterations of genes mostly involved in DNA repair, cell cycle checkpoints, and chromosome organization. All PDX patients conserve most of the genetic alterations identified at relapse. At the transcriptomic level, tumor cells maintain their ossification, chondrocytic, and trans-differentiation programs during progression and implantation in PDX models, as identified at the radiological and histological levels. A more complex phenotype, like the interaction with immune cells and osteoclasts or cancer testis antigen expression, seemed conserved and was hardly identifiable by histology. Despite NSG mouse immunodeficiency, four of the PDX models partially reconstructed the vascular and immune-microenvironment observed in patients, among which the macrophagic TREM2/TYROBP axis expression, recently linked to immunosuppression. Our multimodal analysis of osteosarcoma progression and PDX models is a valuable resource to understand resistance and metastatic spread mechanisms, as well as for the exploration of novel therapeutic strategies for advanced osteosarcoma.
Collapse
Affiliation(s)
- Maria Eugenia Marques da Costa
- INSERM U1015, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Robin Droit
- INSERM U1015, Université Paris-Saclay, Villejuif, France
| | - Pierre Khneisser
- Department of Medical Biology and Pathology, Gustave Roussy Cancer Campus, Villejuif, France
| | - Anne Gomez-Brouchet
- Department of Pathology, IUCT-Oncopole, CHU Toulouse and University Toulouse, Pharmacology and Structural Biology Institute, CNRS UMR5089, Toulouse, France
| | - Tiphaine Adam-de-Beaumais
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Marie Nolla
- Department of Pediatric Hemato-oncology, CHU Toulouse, Toulouse, France
| | - Nicolas Signolles
- Department of Medical Biology and Pathology, Gustave Roussy Cancer Campus, Villejuif, France
| | - Jacob Torrejon
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France
- Université Paris Sud, Université Paris-Saclay, CNRS UMR, INSERM, Orsay, France
| | - Bérangère Lombard
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Paris, France
| | - Damarys Loew
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Paris, France
| | - Olivier Ayrault
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France
- Université Paris Sud, Université Paris-Saclay, CNRS UMR, INSERM, Orsay, France
| | - Jean-Yves Scoazec
- Department of Medical Biology and Pathology, Gustave Roussy Cancer Campus, Villejuif, France
| | - Birgit Geoerger
- INSERM U1015, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Gilles Vassal
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Antonin Marchais
- INSERM U1015, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Nathalie Gaspar
- INSERM U1015, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| |
Collapse
|
7
|
Veluvolu SM, Grohar PJ. Importance of pharmacologic considerations in the development of targeted anticancer agents for children. Curr Opin Pediatr 2023; 35:91-96. [PMID: 36562272 DOI: 10.1097/mop.0000000000001208] [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] [Indexed: 12/24/2022]
Abstract
PURPOSE OF REVIEW The purpose of this review is to describe key pharmacologic considerations to inform strategies in drug development for pediatric cancer. RECENT FINDINGS Main themes that will be discussed include considering patient specific factors, epigenetic/genetic tumor context, and drug schedule when optimizing protocols to treat pediatric cancers. SUMMARY Considering these factors will allow us to more effectively translate novel targeted therapies to benefit pediatric patients.
Collapse
Affiliation(s)
- Sridhar M Veluvolu
- Division of Oncology, Center of Childhood Cancer Research, Children's Hospital of Philadelphia
| | - Patrick J Grohar
- Division of Oncology, Center of Childhood Cancer Research, Children's Hospital of Philadelphia
- University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| |
Collapse
|
8
|
Hiemcke-Jiwa LS, Meister MT, Martin E, Dierselhuis MP, Haveman LM, Meijers RWJ, Tops BBJ, Wesseling P, van Diest PJ, van Gorp JM, Hehir-Kwa JY, van Belzen IAEM, Bonenkamp JJ, van Noesel MM, Flucke U, Kester LA. NTRK rearrangements in a subset of NF1-related malignant peripheral nerve sheath tumors as novel actionable target. Acta Neuropathol 2023; 145:149-152. [PMID: 36331594 PMCID: PMC9807516 DOI: 10.1007/s00401-022-02515-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/21/2022] [Accepted: 10/22/2022] [Indexed: 11/06/2022]
Affiliation(s)
- L S Hiemcke-Jiwa
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands. .,Department of Pathology, Utrecht University Hospital, Utrecht, The Netherlands.
| | - M T Meister
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands.,Oncode Institute, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - E Martin
- Department of Reconstructive Surgery, Utrecht University Hospital, Utrecht, The Netherlands
| | - M P Dierselhuis
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - L M Haveman
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - R W J Meijers
- Department of Pathology, Utrecht University Hospital, Utrecht, The Netherlands
| | - B B J Tops
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - P Wesseling
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands.,Department of Pathology, Amsterdam University Medical Centers/Location VUmc, Amsterdam, The Netherlands
| | - P J van Diest
- Department of Pathology, Utrecht University Hospital, Utrecht, The Netherlands
| | - J M van Gorp
- Department of Pathology, St. Antonius Hospital, Nieuwegein, The Netherlands
| | - J Y Hehir-Kwa
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - I A E M van Belzen
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - J J Bonenkamp
- Department of Surgery, Radboud University Medical Center, Nijmegen, The Netherlands
| | - M M van Noesel
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands.,Division Imaging and Cancer, Utrecht University Hospital, Utrecht, the Netherlands
| | - U Flucke
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands.,Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - L A Kester
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| |
Collapse
|
9
|
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
|
10
|
Fusion Genes in Prostate Cancer: A Comparison in Men of African and European Descent. BIOLOGY 2022; 11:biology11050625. [PMID: 35625354 PMCID: PMC9137560 DOI: 10.3390/biology11050625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/03/2022] [Accepted: 04/06/2022] [Indexed: 11/21/2022]
Abstract
Simple Summary Men of African origin have a 2–3 times greater chance of developing prostate cancer than those of European origin, and of patients that are diagnosed with the disease, men of African descent are 2 times more likely to die compared to white men. Men of African origin are still greatly underrepresented in genetic studies and clinical trials. This, unfortunately, means that new discoveries in cancer treatment are missing key information on the group with a greater chance of mortality. A fusion gene is a hybrid gene formed from two previously independent genes. Fusion genes have been found to be common in all main types of human cancer. The objective of this study was to increase our knowledge of fusion genes in prostate cancer using computational approaches and to compare fusion genes between men of African and European origin. This identified novel gene fusions unique to men of African origin and suggested that this group has a greater number of fusion genes. Abstract Prostate cancer is one of the most prevalent cancers worldwide, particularly affecting men living a western lifestyle and of African descent, suggesting risk factors that are genetic, environmental, and socioeconomic in nature. In the USA, African American (AA) men are disproportionately affected, on average suffering from a higher grade of the disease and at a younger age compared to men of European descent (EA). Fusion genes are chimeric products formed by the merging of two separate genes occurring as a result of chromosomal structural changes, for example, inversion or trans/cis-splicing of neighboring genes. They are known drivers of cancer and have been identified in 20% of cancers. Improvements in genomics technologies such as RNA-sequencing coupled with better algorithms for prediction of fusion genes has added to our knowledge of specific gene fusions in cancers. At present AA are underrepresented in genomic studies of prostate cancer. The primary goal of this study was to examine molecular differences in predicted fusion genes in a cohort of AA and EA men in the context of prostate cancer using computational approaches. RNA was purified from prostate tissue specimens obtained at surgery from subjects enrolled in the study. Fusion gene predictions were performed using four different fusion gene detection programs. This identified novel putative gene fusions unique to AA and suggested that the fusion gene burden was higher in AA compared to EA men.
Collapse
|
11
|
RNA-Seq for the detection of gene fusions in solid tumors: development and validation of the JAX FusionSeq™ 2.0 assay. J Mol Med (Berl) 2022; 100:323-335. [PMID: 35013752 DOI: 10.1007/s00109-021-02149-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/30/2021] [Accepted: 10/05/2021] [Indexed: 10/19/2022]
Abstract
Whole transcriptome sequencing (RNA-Seq) has gained prominence for the detection of fusions in solid tumors. Here, we describe the development and validation of an in-house RNA-Seq-based test system (FusionSeq™ 2.0) for the detection of clinically actionable gene fusions, in formalin-fixed paraffin-embedded (FFPE) specimens, using seventy tumor samples with varying fusion status. Conditions were optimized for RNA input of 50 ng, shown to be adequate to call known fusions at as low as 20% neoplastic content. Evaluation of assay performance between FFPE and fresh-frozen (FF) tissues exhibited little to no difference in fusion calling capability. Performance analysis of the assay validation data determined 100% accuracy, sensitivity, specificity, and reproducibility. This clinically developed and validated RNA-Seq-based approach for fusion detection in FPPE samples was shown to be on par if not superior to off-the-shelf commercially offered assays. With gene fusions implicated in a variety of cancer types, offering high-quality, low-cost molecular testing services for FFPE specimens will serve to best benefit the patient and the advancement of precision medicine in molecular oncology. KEY MESSAGES: A custom RNA-Seq-based test system (FusionSeq™ 2.0) for the detection of clinically actionable gene fusions, Evaluation of assay performance between FFPE and fresh-frozen (FF) tissues exhibited little to no difference in fusion calling capability. The assay can be performed with low RNA input and neoplastic content. Performance characteristics of the assay validation data determined 100% accuracy, sensitivity, specificity, and reproducibility.
Collapse
|
12
|
Angione SDA, Akalu AY, Gartrell J, Fletcher EP, Burckart GJ, Reaman GH, Leong R, Stewart CF. Fusion Oncoproteins in Childhood Cancers: Potential Role in Targeted Therapy. J Pediatr Pharmacol Ther 2021; 26:541-555. [PMID: 34421403 DOI: 10.5863/1551-6776-26.6.541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/03/2021] [Indexed: 11/11/2022]
Abstract
Cancer remains the leading cause of death from disease in children. Historically, in contrast to their adult counterparts, the causes of pediatric malignancies have remained largely unknown, with most pediatric cancers displaying low mutational burdens. Research related to molecular genetics in pediatric cancers is advancing our understanding of potential drivers of tumorigenesis and opening new opportunities for targeted therapies. One such area is fusion oncoproteins, which are a product of chromosomal rearrangements resulting in the fusion of different genes. They have been identified as oncogenic drivers in several sarcomas and leukemias. Continued advancement in the understanding of the biology of fusion oncoproteins will contribute to the discovery and development of new therapies for childhood cancers. Here we review the current scientific knowledge on fusion oncoproteins, focusing on pediatric sarcomas and hematologic cancers, and highlight the challenges and current efforts in developing drugs to target fusion oncoproteins.
Collapse
|
13
|
Hegvik TA, Waløen K, Pandey SK, Faraone SV, Haavik J, Zayats T. Druggable genome in attention deficit/hyperactivity disorder and its co-morbid conditions. New avenues for treatment. Mol Psychiatry 2021; 26:4004-4015. [PMID: 31628418 PMCID: PMC7165040 DOI: 10.1038/s41380-019-0540-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 05/26/2019] [Accepted: 06/10/2019] [Indexed: 01/22/2023]
Abstract
Attention-Deficit/Hyperactivity Disorder (ADHD) is a common neurodevelopmental disorder with only symptomatic care available. Genome-wide association (GWA) studies can provide a starting point in the search for novel drug targets and possibilities of drug repurposing. Here, we explored the druggable genome in ADHD by utilising GWA studies on ADHD and its co-morbid conditions. First, we explored whether the genes targeted by current ADHD drugs show association with the disorder and/or its co-morbidities. Second, we aimed to identify genes and pathways involved in the biological processes underlying ADHD that can be targeted by pharmacological agents. These ADHD-associated druggable genes and pathways were also examined in co-morbidities of ADHD, as commonalities in their aetiology and management may lead to novel pharmacological insights. Strikingly, none of the genes encoding targets of first-line pharmacotherapeutics for ADHD were significantly associated with the disorder, suggesting that FDA-approved ADHD drugs may act through different mechanisms than those underlying ADHD. In the examined druggable genome, three loci on chromosomes 1, 4 and 12 revealed significant association with ADHD and contained nine druggable genes, five of which encode established drug targets for malignancies, autoimmune and neurodevelopmental disorders. To conclude, we present a framework to assess the druggable genome in a disorder, exemplified by ADHD. We highlight signal transduction and cell adhesion as potential novel avenues for ADHD treatment. Our findings add to knowledge on known ADHD drugs and present the exploration of druggable genome associated with ADHD, which may offer interventions at the aetiological level of the disorder.
Collapse
Affiliation(s)
- Tor-Arne Hegvik
- K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Kai Waløen
- K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Sunil K Pandey
- K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Stephen V Faraone
- K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, Department of Biomedicine, University of Bergen, Bergen, Norway
- Departments of Psychiatry and of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Jan Haavik
- K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, Department of Biomedicine, University of Bergen, Bergen, Norway
- Division of Psychiatry, Haukeland University Hospital, Bergen, Norway
| | - Tetyana Zayats
- K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, Department of Biomedicine, University of Bergen, Bergen, Norway.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
| |
Collapse
|
14
|
Wang MY, Huang M, Wang CY, Tang XY, Wang JG, Yang YD, Xiong X, Gao CW. Transcriptome Analysis Reveals MFGE8-HAPLN3 Fusion as a Novel Biomarker in Triple-Negative Breast Cancer. Front Oncol 2021; 11:682021. [PMID: 34211850 PMCID: PMC8239224 DOI: 10.3389/fonc.2021.682021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/24/2021] [Indexed: 12/27/2022] Open
Abstract
Background Triple-negative breast cancer (TNBC) is a highly aggressive cancer with poor prognosis. The lack of effective targeted therapies for TNBC remains a profound clinical challenge. Fusion transcripts play critical roles in carcinogenesis and serve as valuable diagnostic and therapeutic targets in cancer. The present study aimed to identify novel fusion transcripts in TNBC. Methods We analyzed the RNA sequencing data of 360 TNBC samples to identify and filter fusion candidates through SOAPfuse and ChimeraScan analysis. The characteristics, including recurrence, fusion type, chromosomal localization, TNBC subgroup distribution, and clinicopathological correlations, were analyzed in all candidates. Furthermore, we selected the promising fusion transcript and predicted its fusion type and protein coding capacity. Results Using the RNA sequencing data, we identified 189 fusion transcripts in TNBC, among which 22 were recurrent fusions. Compared to para-tumor tissues, TNBC tumor tissues accumulated more fusion events, especially in high-grade tumors. Interestingly, these events were enriched at specific chromosomal loci, and the distribution pattern varied in different TNBC subtypes. The vast majority of fusion partners were discovered on chromosomes 1p, 11q, 19p, and 19q. Besides, fusion events mainly clustered on chromosome 11 in the immunomodulatory subtype and chromosome 19 in the luminal androgen receptor subtype of TNBC. Considering the tumor specificity and frameshift mutation, we selected MFGE8-HAPLN3 as a novel biomarker and further validated it in TNBC samples using PCR and Sanger sequencing. Further, we successfully identified three types of MFGE8-HAPLN3 (E6-E2, E5-E3, and E6-E3) and predicted the ORF of E6-E2, which could encode a protein of 712 amino acids, suggesting its critical role in TNBC. Conclusions Improved bioinformatic stratification and comprehensive analysis identified the fusion transcript MFGE8-HAPLN3 as a novel biomarker with promising clinical application in the future.
Collapse
Affiliation(s)
- Meng-Yuan Wang
- Department of Breast Surgery, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Man Huang
- Department of Breast Surgery, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Chao-Yi Wang
- Department of Breast Surgery, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Xiao-Ying Tang
- Department of Breast Surgery, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Jian-Gen Wang
- Department of Breast Surgery, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Yong-De Yang
- Department of Breast Surgery, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Xin Xiong
- Department of Breast Surgery, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Chao-Wei Gao
- Department of Breast Surgery, Chongqing University Three Gorges Hospital, Chongqing, China
| |
Collapse
|
15
|
Blattner-Johnson M, Jones DTW, Pfaff E. Precision medicine in pediatric solid cancers. Semin Cancer Biol 2021; 84:214-227. [PMID: 34116162 DOI: 10.1016/j.semcancer.2021.06.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 12/18/2022]
Abstract
Despite huge advances in the diagnosis and treatment of pediatric cancers over the past several decades, it remains one of the leading causes of death during childhood in developed countries. The development of new targeted treatments for these diseases has been hampered by two major factors. First, the extremely heterogeneous nature of the types of tumors encountered in this age group, and their fundamental differences from common adult carcinomas, has made it hard to truly get a handle on the complexities of the underlying biology driving tumor growth. Second, a reluctance of the pharmaceutical industry to develop products or trials for this population due to the relatively small size of the 'market', and a too-easy mechanism of obtaining waivers for pediatric development of adult oncology drugs based on disease type rather than mechanism of action, led to significant difficulties in getting access to new drugs. Thankfully, the field has now started to change, both scientifically and from a regulatory perspective, in order to address some of these challenges. In this review, we will examine some of the recent insights into molecular features which make pediatric tumors so unique and how these might represent therapeutic targets; highlight ongoing international initiatives for providing comprehensive, personalized genomic profiling of childhood tumors in a clinically-relevant timeframe, and look briefly at where the field of pediatric precision oncology may be heading in future.
Collapse
Affiliation(s)
- Mirjam Blattner-Johnson
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany; Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany; Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Elke Pfaff
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany; Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| |
Collapse
|
16
|
van Belzen IAEM, Schönhuth A, Kemmeren P, Hehir-Kwa JY. Structural variant detection in cancer genomes: computational challenges and perspectives for precision oncology. NPJ Precis Oncol 2021; 5:15. [PMID: 33654267 PMCID: PMC7925608 DOI: 10.1038/s41698-021-00155-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 01/12/2021] [Indexed: 01/31/2023] Open
Abstract
Cancer is generally characterized by acquired genomic aberrations in a broad spectrum of types and sizes, ranging from single nucleotide variants to structural variants (SVs). At least 30% of cancers have a known pathogenic SV used in diagnosis or treatment stratification. However, research into the role of SVs in cancer has been limited due to difficulties in detection. Biological and computational challenges confound SV detection in cancer samples, including intratumor heterogeneity, polyploidy, and distinguishing tumor-specific SVs from germline and somatic variants present in healthy cells. Classification of tumor-specific SVs is challenging due to inconsistencies in detected breakpoints, derived variant types and biological complexity of some rearrangements. Full-spectrum SV detection with high recall and precision requires integration of multiple algorithms and sequencing technologies to rescue variants that are difficult to resolve through individual methods. Here, we explore current strategies for integrating SV callsets and to enable the use of tumor-specific SVs in precision oncology.
Collapse
Affiliation(s)
| | - Alexander Schönhuth
- Genome Data Science, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Patrick Kemmeren
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Jayne Y Hehir-Kwa
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
| |
Collapse
|
17
|
Van AAN, Kunkel MT, Baffi TR, Lordén G, Antal CE, Banerjee S, Newton AC. Protein kinase C fusion proteins are paradoxically loss of function in cancer. J Biol Chem 2021; 296:100445. [PMID: 33617877 PMCID: PMC8008189 DOI: 10.1016/j.jbc.2021.100445] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 02/11/2021] [Accepted: 02/18/2021] [Indexed: 12/02/2022] Open
Abstract
Within the AGC kinase superfamily, gene fusions resulting from chromosomal rearrangements have been most frequently described for protein kinase C (PKC), with gene fragments encoding either the C-terminal catalytic domain or the N-terminal regulatory moiety fused to other genes. Kinase fusions that eliminate regulatory domains are typically gain of function and often oncogenic. However, several quality control pathways prevent accumulation of aberrant PKC, suggesting that PKC fusions may paradoxically be loss of function. To explore this topic, we used biochemical, cellular, and genome editing approaches to investigate the function of fusions that retain the portion of the gene encoding either the catalytic domain or regulatory domain of PKC. Overexpression studies revealed that PKC catalytic domain fusions were constitutively active but vulnerable to degradation. Genome editing of endogenous genes to generate a cancer-associated PKC fusion resulted in cells with detectable levels of fusion transcript but no detectable protein. Hence, PKC catalytic domain fusions are paradoxically loss of function as a result of their instability, preventing appreciable accumulation of protein in cells. Overexpression of a PKC regulatory domain fusion suppressed both basal and agonist-induced endogenous PKC activity, acting in a dominant-negative manner by competing for diacylglycerol. For both catalytic and regulatory domain fusions, the PKC component of the fusion proteins mediated the effects of the full-length fusions on the parameters examined, suggesting that the partner protein is dispensable in these contexts. Taken together, our findings reveal that PKC gene fusions are distinct from oncogenic fusions and present a mechanism by which loss of PKC function occurs in cancer.
Collapse
Affiliation(s)
- An-Angela N Van
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA; Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, California, USA
| | - Maya T Kunkel
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA
| | - Timothy R Baffi
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA; Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, California, USA
| | - Gema Lordén
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA
| | - Corina E Antal
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA; Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, California, USA
| | - Sourav Banerjee
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA
| | - Alexandra C Newton
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA.
| |
Collapse
|
18
|
Zhao G, Chen L, Xiao M, Yang S. Rare coexistence of three novel CDCA7-ALK, FSIP2-ALK, ALK-ERLEC1 fusions in a lung adenocarcinoma patient who responded to Crizotinib. Lung Cancer 2020; 152:189-192. [PMID: 33419583 DOI: 10.1016/j.lungcan.2020.12.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 12/13/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Guojiang Zhao
- Department of Oncology and Hematology, Panzhihua Central Hospital, Panzhihua, 617000, China
| | - Lin Chen
- The State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, 210002, China
| | - Mingzhe Xiao
- The State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, 210002, China
| | - Shengli Yang
- Department of Oncology and Hematology, Panzhihua Central Hospital, Panzhihua, 617000, China.
| |
Collapse
|
19
|
Oldrini B, Vaquero-Siguero N, Mu Q, Kroon P, Zhang Y, Galán-Ganga M, Bao Z, Wang Z, Liu H, Sa JK, Zhao J, Kim H, Rodriguez-Perales S, Nam DH, Verhaak RGW, Rabadan R, Jiang T, Wang J, Squatrito M. MGMT genomic rearrangements contribute to chemotherapy resistance in gliomas. Nat Commun 2020; 11:3883. [PMID: 32753598 PMCID: PMC7403430 DOI: 10.1038/s41467-020-17717-0] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 07/16/2020] [Indexed: 12/21/2022] Open
Abstract
Temozolomide (TMZ) is an oral alkylating agent used for the treatment of glioblastoma and is now becoming a chemotherapeutic option in patients diagnosed with high-risk low-grade gliomas. The O-6-methylguanine-DNA methyltransferase (MGMT) is responsible for the direct repair of the main TMZ-induced toxic DNA adduct, the O6-Methylguanine lesion. MGMT promoter hypermethylation is currently the only known biomarker for TMZ response in glioblastoma patients. Here we show that a subset of recurrent gliomas carries MGMT genomic rearrangements that lead to MGMT overexpression, independently from changes in its promoter methylation. By leveraging the CRISPR/Cas9 technology we generated some of these MGMT rearrangements in glioma cells and demonstrated that the MGMT genomic rearrangements contribute to TMZ resistance both in vitro and in vivo. Lastly, we showed that such fusions can be detected in tumor-derived exosomes and could potentially represent an early detection marker of tumor recurrence in a subset of patients treated with TMZ.
Collapse
Affiliation(s)
- Barbara Oldrini
- Seve Ballesteros Foundation Brain Tumor Group, Molecular Oncology Programme, Spanish National Cancer Research Center, CNIO, 28029, Madrid, Spain
| | - Nuria Vaquero-Siguero
- Seve Ballesteros Foundation Brain Tumor Group, Molecular Oncology Programme, Spanish National Cancer Research Center, CNIO, 28029, Madrid, Spain
| | - Quanhua Mu
- Division of Life Science, Department of Chemical and Biological Engineering, Center of Systems Biology and Human Health and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Paula Kroon
- Seve Ballesteros Foundation Brain Tumor Group, Molecular Oncology Programme, Spanish National Cancer Research Center, CNIO, 28029, Madrid, Spain
| | - Ying Zhang
- Beijing Neurosurgical Institute, Capital Medical University, 100050, Beijing, China
| | - Marcos Galán-Ganga
- Seve Ballesteros Foundation Brain Tumor Group, Molecular Oncology Programme, Spanish National Cancer Research Center, CNIO, 28029, Madrid, Spain
| | - Zhaoshi Bao
- Division of Life Science, Department of Chemical and Biological Engineering, Center of Systems Biology and Human Health and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China.,Beijing Neurosurgical Institute, Capital Medical University, 100050, Beijing, China
| | - Zheng Wang
- Beijing Neurosurgical Institute, Capital Medical University, 100050, Beijing, China
| | - Hanjie Liu
- Beijing Neurosurgical Institute, Capital Medical University, 100050, Beijing, China
| | - Jason K Sa
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06531, Korea.,Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Korea
| | - Junfei Zhao
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
| | - Hoon Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Sandra Rodriguez-Perales
- Molecular Cytogenetics Group, Human Cancer Genetics Program, Spanish National Cancer Research Center, CNIO, 28029, Madrid, Spain
| | - Do-Hyun Nam
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06531, Korea
| | - Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Raul Rabadan
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
| | - Tao Jiang
- Beijing Neurosurgical Institute, Capital Medical University, 100050, Beijing, China.
| | - Jiguang Wang
- Division of Life Science, Department of Chemical and Biological Engineering, Center of Systems Biology and Human Health and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China.
| | - Massimo Squatrito
- Seve Ballesteros Foundation Brain Tumor Group, Molecular Oncology Programme, Spanish National Cancer Research Center, CNIO, 28029, Madrid, Spain.
| |
Collapse
|
20
|
Powers MP. The ever-changing world of gene fusions in cancer: a secondary gene fusion and progression. Oncogene 2019; 38:7197-7199. [DOI: 10.1038/s41388-019-1057-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 09/30/2019] [Accepted: 10/02/2019] [Indexed: 11/09/2022]
|
21
|
Dupain C, Gracia C, Harttrampf AC, Rivière J, Geoerger B, Massaad-Massade L. Newly identified LMO3-BORCS5 fusion oncogene in Ewing sarcoma at relapse is a driver of tumor progression. Oncogene 2019; 38:7200-7215. [PMID: 31488873 DOI: 10.1038/s41388-019-0914-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/29/2019] [Accepted: 05/29/2019] [Indexed: 12/25/2022]
Abstract
Recently, we detected a new fusion transcript LMO3-BORCS5 in a patient with Ewing sarcoma within a cohort of relapsed pediatric cancers. LMO3-BORCS5 was as highly expressed as the characteristic fusion oncogene EWS/FLI1. However, the expression level of LMO3-BORCS5 at diagnosis was very low. Sanger sequencing depicted two LMO3-BORCS5 variants leading to loss of the functional domain LIM2 in LMO3 gene, and disruption of BORCS5. In vitro studies showed that LMO3-BORCS5 (i) increases proliferation, (ii) decreases expression of apoptosis-related genes and treatment sensitivity, and (iii) downregulates genes involved in differentiation and upregulates proliferative and extracellular matrix-related pathways. Remarkably, in vivo LMO3-BORCS5 demonstrated its high oncogenic potential by inducing tumors in mouse fibroblastic NIH-3T3 cell line. Moreover, BORCS5 probably acts, in vivo, as a tumor-suppressor gene. In conclusion, functional studies of fusion oncogenes at relapse are of great importance to define mechanisms involved in tumor progression and resistance to conventional treatments.
Collapse
Affiliation(s)
- Célia Dupain
- Laboratoire de Vectorologie et Thérapeutiques Anticancéreuses, Université Paris-Sud 11, CNRS UMR 8203, Gustave Roussy Cancer Center, 94805, Villejuif, France
| | - Céline Gracia
- Laboratoire de Vectorologie et Thérapeutiques Anticancéreuses, Université Paris-Sud 11, CNRS UMR 8203, Gustave Roussy Cancer Center, 94805, Villejuif, France
| | - Anne C Harttrampf
- Laboratoire de Vectorologie et Thérapeutiques Anticancéreuses, Université Paris-Sud 11, CNRS UMR 8203, Gustave Roussy Cancer Center, 94805, Villejuif, France
| | - Julie Rivière
- INSERM U1170, Gustave Roussy Cancer Center, Villejuif, France
| | - Birgit Geoerger
- Laboratoire de Vectorologie et Thérapeutiques Anticancéreuses, Université Paris-Sud 11, CNRS UMR 8203, Gustave Roussy Cancer Center, 94805, Villejuif, France.,Gustave Roussy, Department of Pediatric and Adolescent Oncology, Villejuif, France
| | - Liliane Massaad-Massade
- Laboratoire de Vectorologie et Thérapeutiques Anticancéreuses, Université Paris-Sud 11, CNRS UMR 8203, Gustave Roussy Cancer Center, 94805, Villejuif, France. .,U1195 INSERM, 20 rue du Général Leclerc, 94276, le Kremlin-Bicêtre, France.
| |
Collapse
|
22
|
Wang SS, Bandopadhayay P, Jenkins MR. Towards Immunotherapy for Pediatric Brain Tumors. Trends Immunol 2019; 40:748-761. [PMID: 31229353 DOI: 10.1016/j.it.2019.05.009] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 05/12/2019] [Accepted: 05/28/2019] [Indexed: 12/25/2022]
Abstract
Pediatric brain tumors are the leading cause of childhood cancer-related death. Immunotherapy is a powerful new approach for treating some refractory cancers; applying this 'fourth pillar' of cancer treatment to pediatric brain tumors is an exciting but challenging prospect. This review offers new perspectives on moving towards successful immunotherapy for pediatric brain tumors, focusing on pediatric high-grade glioma (HGG), a subgroup with universally poor outcomes. We cover chimeric antigen receptor T cell (CAR-T) therapy, vaccine therapy, and checkpoint inhibition in this context, and focus on the need for intimately understanding the growing brain and its immune system. We highlight the challenges associated with the application of immunotherapy in pediatric neuro-oncology, as well as the tissue-specific challenges to be overcome, to achieve improved outcomes.
Collapse
Affiliation(s)
- Stacie Shiqi Wang
- Immunology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
| | - Pratiti Bandopadhayay
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Misty Rayna Jenkins
- Immunology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia; La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3083, Australia.
| |
Collapse
|