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Polychronopoulos PA, Bedoya-Reina OC, Johnsen JI. The Neuroblastoma Microenvironment, Heterogeneity and Immunotherapeutic Approaches. Cancers (Basel) 2024; 16:1863. [PMID: 38791942 PMCID: PMC11119056 DOI: 10.3390/cancers16101863] [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: 04/08/2024] [Revised: 05/02/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Neuroblastoma is a peripheral nervous system tumor that almost exclusively occurs in young children. Although intensified treatment modalities have led to increased patient survival, the prognosis for patients with high-risk disease is still around 50%, signifying neuroblastoma as a leading cause of cancer-related deaths in children. Neuroblastoma is an embryonal tumor and is shaped by its origin from cells within the neural crest. Hence, neuroblastoma usually presents with a low mutational burden and is, in the majority of cases, driven by epigenetically deregulated transcription networks. The recent development of Omic techniques has given us detailed knowledge of neuroblastoma evolution, heterogeneity, and plasticity, as well as intra- and intercellular molecular communication networks within the neuroblastoma microenvironment. Here, we discuss the potential of these recent discoveries with emphasis on new treatment modalities, including immunotherapies which hold promise for better future treatment regimens.
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Affiliation(s)
- Panagiotis Alkinoos Polychronopoulos
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, 11883 Stockholm, Sweden; (P.A.P.); (O.C.B.-R.)
| | - Oscar C. Bedoya-Reina
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, 11883 Stockholm, Sweden; (P.A.P.); (O.C.B.-R.)
- School of Medical Sciences, Örebro University, 70182 Örebro, Sweden
| | - John Inge Johnsen
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, 11883 Stockholm, Sweden; (P.A.P.); (O.C.B.-R.)
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2
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Perotti D, Williams RD, Wegert J, Brzezinski J, Maschietto M, Ciceri S, Gisselsson D, Gadd S, Walz AL, Furtwaengler R, Drost J, Al-Saadi R, Evageliou N, Gooskens SL, Hong AL, Murphy AJ, Ortiz MV, O'Sullivan MJ, Mullen EA, van den Heuvel-Eibrink MM, Fernandez CV, Graf N, Grundy PE, Geller JI, Dome JS, Perlman EJ, Gessler M, Huff V, Pritchard-Jones K. Hallmark discoveries in the biology of Wilms tumour. Nat Rev Urol 2024; 21:158-180. [PMID: 37848532 DOI: 10.1038/s41585-023-00824-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2023] [Indexed: 10/19/2023]
Abstract
The modern study of Wilms tumour was prompted nearly 50 years ago, when Alfred Knudson proposed the 'two-hit' model of tumour development. Since then, the efforts of researchers worldwide have substantially expanded our knowledge of Wilms tumour biology, including major advances in genetics - from cloning the first Wilms tumour gene to high-throughput studies that have revealed the genetic landscape of this tumour. These discoveries improve understanding of the embryonal origin of Wilms tumour, familial occurrences and associated syndromic conditions. Many efforts have been made to find and clinically apply prognostic biomarkers to Wilms tumour, for which outcomes are generally favourable, but treatment of some affected individuals remains challenging. Challenges are also posed by the intratumoural heterogeneity of biomarkers. Furthermore, preclinical models of Wilms tumour, from cell lines to organoid cultures, have evolved. Despite these many achievements, much still remains to be discovered: further molecular understanding of relapse in Wilms tumour and of the multiple origins of bilateral Wilms tumour are two examples of areas under active investigation. International collaboration, especially when large tumour series are required to obtain robust data, will help to answer some of the remaining unresolved questions.
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Affiliation(s)
- Daniela Perotti
- Predictive Medicine: Molecular Bases of Genetic Risk, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.
| | - Richard D Williams
- Developmental Biology and Cancer Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
- Section of Genetics and Genomics, Faculty of Medicine, Imperial College London, London, UK
| | - Jenny Wegert
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, Wuerzburg University, Wuerzburg, Germany
| | - Jack Brzezinski
- Division of Haematology/Oncology, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Mariana Maschietto
- Research Center, Boldrini Children's Hospital, Campinas, São Paulo, Brazil
| | - Sara Ciceri
- Predictive Medicine: Molecular Bases of Genetic Risk, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - David Gisselsson
- Cancer Cell Evolution Unit, Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Clinical Genetics, Pathology and Molecular Diagnostics, Office of Medical Services, Skåne, Sweden
| | - Samantha Gadd
- Department of Pathology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Amy L Walz
- Division of Hematology,Oncology, Neuro-Oncology, and Stem Cell Transplant, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Rhoikos Furtwaengler
- Division of Pediatric Oncology and Hematology, Department of Pediatrics, Inselspital Bern University, Bern, Switzerland
| | - Jarno Drost
- Princess Máxima Center for Paediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Reem Al-Saadi
- Developmental Biology and Cancer Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
- Department of Histopathology, Great Ormond Street Hospital for Children, London, UK
| | - Nicholas Evageliou
- Divisions of Hematology and Oncology, Children's Hospital of Philadelphia, CHOP Specialty Care Center, Vorhees, NJ, USA
| | - Saskia L Gooskens
- Princess Máxima Center for Paediatric Oncology, Utrecht, Netherlands
| | - Andrew L Hong
- Aflac Cancer and Blood Disorders Center, Emory University and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Andrew J Murphy
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael V Ortiz
- Department of Paediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maureen J O'Sullivan
- Histology Laboratory, Children's Health Ireland at Crumlin, Dublin, Ireland
- Trinity Translational Medicine Institute, Trinity College, Dublin, Ireland
| | - Elizabeth A Mullen
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | | | - Conrad V Fernandez
- Division of Paediatric Hematology Oncology, IWK Health Centre and Dalhousie University, Halifax, Nova Scotia, Canada
| | - Norbert Graf
- Department of Paediatric Oncology and Hematology, Saarland University Hospital, Homburg, Germany
| | - Paul E Grundy
- Department of Paediatrics Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - James I Geller
- Division of Oncology, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Jeffrey S Dome
- Division of Oncology, Center for Cancer and Blood Disorders, Children's National Hospital and the Department of Paediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Elizabeth J Perlman
- Department of Pathology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Manfred Gessler
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, Wuerzburg University, Wuerzburg, Germany
- Comprehensive Cancer Center Mainfranken, Wuerzburg, Germany
| | - Vicki Huff
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kathy Pritchard-Jones
- Developmental Biology and Cancer Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
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3
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Saba KH, Difilippo V, Kovac M, Cornmark L, Magnusson L, Nilsson J, van den Bos H, Spierings DC, Bidgoli M, Jonson T, Sumathi VP, Brosjö O, Staaf J, Foijer F, Styring E, Nathrath M, Baumhoer D, Nord KH. Disruption of the TP53 locus in osteosarcoma leads to TP53 promoter gene fusions and restoration of parts of the TP53 signalling pathway. J Pathol 2024; 262:147-160. [PMID: 38010733 DOI: 10.1002/path.6219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/24/2023] [Accepted: 09/19/2023] [Indexed: 11/29/2023]
Abstract
TP53 is the most frequently mutated gene in human cancer. This gene shows not only loss-of-function mutations but also recurrent missense mutations with gain-of-function activity. We have studied the primary bone malignancy osteosarcoma, which harbours one of the most rearranged genomes of all cancers. This is odd since it primarily affects children and adolescents who have not lived the long life thought necessary to accumulate massive numbers of mutations. In osteosarcoma, TP53 is often disrupted by structural variants. Here, we show through combined whole-genome and transcriptome analyses of 148 osteosarcomas that TP53 structural variants commonly result in loss of coding parts of the gene while simultaneously preserving and relocating the promoter region. The transferred TP53 promoter region is fused to genes previously implicated in cancer development. Paradoxically, these erroneously upregulated genes are significantly associated with the TP53 signalling pathway itself. This suggests that while the classical tumour suppressor activities of TP53 are lost, certain parts of the TP53 signalling pathway that are necessary for cancer cell survival and proliferation are retained. In line with this, our data suggest that transposition of the TP53 promoter is an early event that allows for a new normal state of genome-wide rearrangements in osteosarcoma. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Karim H Saba
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Valeria Difilippo
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Michal Kovac
- Bone Tumour Reference Centre at the Institute of Pathology, University Hospital and University of Basel, Basel, Switzerland
- Faculty of Informatics and Information Technologies, Slovak University of Technology, Bratislava, Slovakia
| | - Louise Cornmark
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Linda Magnusson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Jenny Nilsson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Hilda van den Bos
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Diana Cj Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Mahtab Bidgoli
- Department of Clinical Genetics and Pathology, Laboratory Medicine, Medical Services, Skåne University Hospital, Lund, Sweden
| | - Tord Jonson
- Department of Clinical Genetics and Pathology, Laboratory Medicine, Medical Services, Skåne University Hospital, Lund, Sweden
| | - Vaiyapuri P Sumathi
- Department of Musculoskeletal Pathology, Royal Orthopaedic Hospital, Birmingham, UK
| | - Otte Brosjö
- Department of Orthopedics, Karolinska University Hospital, Stockholm, Sweden
| | - Johan Staaf
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Emelie Styring
- Department of Orthopedics, Lund University, Skåne University Hospital, Lund, Sweden
| | - Michaela Nathrath
- Children's Cancer Research Centre and Department of Pediatrics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Department of Pediatric Oncology, Klinikum Kassel, Kassel, Germany
| | - Daniel Baumhoer
- Bone Tumour Reference Centre at the Institute of Pathology, University Hospital and University of Basel, Basel, Switzerland
| | - Karolin H Nord
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
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4
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Uno K, Rastegar B, Jansson C, Durand G, Valind A, Chattopadhyay S, Bertolotti A, Ciceri S, Spreafico F, Collini P, Perotti D, Mengelbier LH, Gisselsson D. A Gradual Transition Toward Anaplasia in Wilms Tumor Through Tolerance to Genetic Damage. Mod Pathol 2024; 37:100382. [PMID: 37951357 DOI: 10.1016/j.modpat.2023.100382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 10/23/2023] [Accepted: 11/06/2023] [Indexed: 11/14/2023]
Abstract
Patients with Wilms tumor (WT) in general have excellent survival, but the prognosis of patients belonging to the subgroup of WT with diffuse anaplasia (DA) is poor due to frequent resistance to chemotherapy. We hypothesized that DA WT cells might undergo changes, such as acquiring a persistent tolerance to DNA damage and copy number aberrations (CNAs), which could eventually lead to their resistance to chemotherapy treatment. Tissue sections from chemotherapy-treated DA WTs (n = 12) were compared with chemotherapy-treated nonanaplastic WTs (n = 15) in a tissue microarray system, enabling analysis of 769 tumor regions. All regions were scored for anaplastic features and immunohistochemistry was used to quantify p53 expression, proliferation index (Ki67), and DNA double-strand breaks (γH2AX). CNAs were assessed by array-based genotyping and TP53 mutations using targeted sequencing. Proliferation index and the frequency of DNA double-strand breaks (γH2AX dot expression) increased with higher anaplasia scores. Almost all (95.6%) areas with full-scale anaplasia had TP53 mutations or loss of heterozygosity, along with an increased amount of CNAs. Interestingly, areas with wild-type TP53 with loss of heterozygosity and only one feature of anaplasia (anaplasia score 1) also had significantly higher proliferation indices, more DNA double-strand breaks, and more CNAs than regions without any anaplastic features (score 0); such areas may be preanaplastic cell populations under selective pressure for TP53 mutations. In conclusion, we suggest that chemoresistance of DA WTs may be partly explained by a high proliferative capability of anaplastic cells, which also have a high burden of double-stranded DNA breaks and CNAs, and that there is a gradual emergence of anaplasia in WT.
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Affiliation(s)
- Kaname Uno
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden; Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, Japan.
| | - Bahar Rastegar
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Caroline Jansson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Geoffroy Durand
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Anders Valind
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden; Now with Childhood Cancer Center, Skåne University Hospital, Lund, Sweden
| | - Subhayan Chattopadhyay
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Alessia Bertolotti
- Diagnostic and Molecular Research Lab, Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Sara Ciceri
- Molecular Bases of Genetic Risk and Genetic Testing Unit, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy; Now with Predictive Medicine: Molecular Bases of Genetic Risk, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Filippo Spreafico
- Pediatric Oncology Unit, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Paola Collini
- Soft Tissue Tumor Pathology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Daniela Perotti
- Molecular Bases of Genetic Risk and Genetic Testing Unit, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy; Now with Predictive Medicine: Molecular Bases of Genetic Risk, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - David Gisselsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden; Division of Oncology-Pathology, Department of Clinical Science, Lund University, Lund, Sweden; Division of Clinical Genetics and Pathology, Department of Laboratory Medicine, Lund University Hospital, Skåne Healthcare Region, Lund, Sweden
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5
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Rastegar B, Andersson N, Petersson A, Karlsson J, Chattopadhyay S, Valind A, Jansson C, Durand G, Romerius P, Jirström K, Holmquist Mengelbier L, Gisselsson D. Resolving the Pathogenesis of Anaplastic Wilms Tumors through Spatial Mapping of Cancer Cell Evolution. Clin Cancer Res 2023; 29:2668-2677. [PMID: 37140929 PMCID: PMC10345961 DOI: 10.1158/1078-0432.ccr-23-0311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/31/2023] [Accepted: 05/02/2023] [Indexed: 05/05/2023]
Abstract
PURPOSE While patients with intermediate-risk (IR) Wilms tumors now have an overall survival (OS) rate of almost 90%, those affected by high-stage tumors with diffuse anaplasia have an OS of only around 50%. We here identify key events in the pathogenesis of diffuse anaplasia by mapping cancer cell evolution over anatomic space in Wilms tumors. EXPERIMENTAL DESIGN We spatially mapped subclonal landscapes in a retrospective cohort of 20 Wilms tumors using high-resolution copy-number profiling and TP53 mutation analysis followed by clonal deconvolution and phylogenetic reconstruction. Tumor whole-mount sections (WMS) were utilized to characterize the distribution of subclones across anatomically distinct tumor compartments. RESULTS Compared with non-diffuse anaplasia Wilms tumors, tumors with diffuse anaplasia showed a significantly higher number of genetically distinct tumor cell subpopulations and more complex phylogenetic trees, including high levels of phylogenetic species richness, divergence, and irregularity. All regions with classical anaplasia showed TP53 alterations. TP53 mutations were frequently followed by saltatory evolution and parallel loss of the remaining wild-type (WT) allele in different regions. Morphologic features of anaplasia increased with copy-number aberration (CNA) burden and regressive features. Compartments demarcated by fibrous septae or necrosis/regression were frequently (73%) associated with the emergence of new clonal CNAs, although clonal sweeps were rare within these compartments. CONCLUSIONS Wilms tumors with diffuse anaplasia display significantly more complex phylogenies compared with non-diffuse anaplasia Wilms tumors, including features of saltatory and parallel evolution. The subclonal landscape of individual tumors was constrained by anatomic compartments, which should be considered when sampling tissue for precision diagnostics.
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Affiliation(s)
- Bahar Rastegar
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Pediatrics, Skåne University Hospital, Lund, Sweden
| | - Natalie Andersson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Alexandra Petersson
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Jenny Karlsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Subhayan Chattopadhyay
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Anders Valind
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Pediatrics, Skåne University Hospital, Lund, Sweden
| | - Caroline Jansson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Geoffroy Durand
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Patrik Romerius
- Department of Pediatrics, Skåne University Hospital, Lund, Sweden
| | - Karin Jirström
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | | | - David Gisselsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
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6
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Gundem G, Levine MF, Roberts SS, Cheung IY, Medina-Martínez JS, Feng Y, Arango-Ossa JE, Chadoutaud L, Rita M, Asimomitis G, Zhou J, You D, Bouvier N, Spitzer B, Solit DB, Dela Cruz F, LaQuaglia MP, Kushner BH, Modak S, Shukla N, Iacobuzio-Donahue CA, Kung AL, Cheung NKV, Papaemmanuil E. Clonal evolution during metastatic spread in high-risk neuroblastoma. Nat Genet 2023:10.1038/s41588-023-01395-x. [PMID: 37169874 DOI: 10.1038/s41588-023-01395-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 04/12/2023] [Indexed: 05/13/2023]
Abstract
Patients with high-risk neuroblastoma generally present with widely metastatic disease and often relapse despite intensive therapy. As most studies to date focused on diagnosis-relapse pairs, our understanding of the genetic and clonal dynamics of metastatic spread and disease progression remain limited. Here, using genomic profiling of 470 sequential and spatially separated samples from 283 patients, we characterize subtype-specific genetic evolutionary trajectories from diagnosis through progression and end-stage metastatic disease. Clonal tracing timed disease initiation to embryogenesis. Continuous acquisition of structural variants at disease-defining loci (MYCN, TERT, MDM2-CDK4) followed by convergent evolution of mutations targeting shared pathways emerged as the predominant feature of progression. At diagnosis metastatic clones were already established at distant sites where they could stay dormant, only to cause relapses years later and spread via metastasis-to-metastasis and polyclonal seeding after therapy.
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Affiliation(s)
- Gunes Gundem
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Max F Levine
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Stephen S Roberts
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Irene Y Cheung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Juan S Medina-Martínez
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yi Feng
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Juan E Arango-Ossa
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Loic Chadoutaud
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mathieu Rita
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Georgios Asimomitis
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joe Zhou
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daoqi You
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nancy Bouvier
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Barbara Spitzer
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David B Solit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, New York, NY, USA
| | - Filemon Dela Cruz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael P LaQuaglia
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brian H Kushner
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shakeel Modak
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Neerav Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christine A Iacobuzio-Donahue
- The David M. Rubenstein Center for Pancreatic Cancer Research, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew L Kung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nai-Kong V Cheung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elli Papaemmanuil
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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7
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Körber V, Stainczyk SA, Kurilov R, Henrich KO, Hero B, Brors B, Westermann F, Höfer T. Neuroblastoma arises in early fetal development and its evolutionary duration predicts outcome. Nat Genet 2023; 55:619-630. [PMID: 36973454 PMCID: PMC10101850 DOI: 10.1038/s41588-023-01332-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 02/06/2023] [Indexed: 03/29/2023]
Abstract
AbstractNeuroblastoma, the most frequent solid tumor in infants, shows very diverse outcomes from spontaneous regression to fatal disease. When these different tumors originate and how they evolve are not known. Here we quantify the somatic evolution of neuroblastoma by deep whole-genome sequencing, molecular clock analysis and population-genetic modeling in a comprehensive cohort covering all subtypes. We find that tumors across the entire clinical spectrum begin to develop via aberrant mitoses as early as the first trimester of pregnancy. Neuroblastomas with favorable prognosis expand clonally after short evolution, whereas aggressive neuroblastomas show prolonged evolution during which they acquire telomere maintenance mechanisms. The initial aneuploidization events condition subsequent evolution, with aggressive neuroblastoma exhibiting early genomic instability. We find in the discovery cohort (n = 100), and validate in an independent cohort (n = 86), that the duration of evolution is an accurate predictor of outcome. Thus, insight into neuroblastoma evolution may prospectively guide treatment decisions.
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8
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Aaltonen K, Radke K, Adamska A, Seger A, Mañas A, Bexell D. Patient-derived models: Advanced tools for precision medicine in neuroblastoma. Front Oncol 2023; 12:1085270. [PMID: 36776363 PMCID: PMC9910084 DOI: 10.3389/fonc.2022.1085270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/21/2022] [Indexed: 01/27/2023] Open
Abstract
Neuroblastoma is a childhood cancer derived from the sympathetic nervous system. High-risk neuroblastoma patients have a poor overall survival and account for ~15% of childhood cancer deaths. There is thus a need for clinically relevant and authentic models of neuroblastoma that closely resemble the human disease to further interrogate underlying mechanisms and to develop novel therapeutic strategies. Here we review recent developments in patient-derived neuroblastoma xenograft models and in vitro cultures. These models can be used to decipher mechanisms of metastasis and treatment resistance, for drug screening, and preclinical drug testing. Patient-derived neuroblastoma models may also provide useful information about clonal evolution, phenotypic plasticity, and cell states in relation to neuroblastoma progression. We summarize current opportunities for, but also barriers to, future model development and application. Integration of patient-derived models with patient data holds promise for the development of precision medicine treatment strategies for children with high-risk neuroblastoma.
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9
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Walz AL, Maschietto M, Crompton B, Evageliou N, Dix D, Tytgat G, Gessler M, Gisselsson D, Daw NC, Wegert J. Tumor biology, biomarkers, and liquid biopsy in pediatric renal tumors. Pediatr Blood Cancer 2023; 70 Suppl 2:e30130. [PMID: 36592003 DOI: 10.1002/pbc.30130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 11/10/2022] [Accepted: 11/12/2022] [Indexed: 01/03/2023]
Abstract
The expansion of knowledge regarding driver mutations for Wilms tumor (WT) and malignant rhabdoid tumor of the kidney (MRT) and various translocations for other pediatric renal tumors opens up new possibilities for diagnosis and treatment. In addition, there are growing data surrounding prognostic factors that can be used to stratify WT treatment to improve outcomes. Here, we review the molecular landscape of WT and other pediatric renal tumors as well as WT prognostic factors. We also review incorporation of circulating tumor DNA/liquid biopsies to leverage this molecular landscape, with potential use in the future for distinguishing renal tumors at the time of diagnosis and elucidating intratumor heterogeneity, which is not well evaluated with standard biopsies. Incorporation of liquid biopsies will require longitudinal collection of multiple biospecimens. Further preclinical research, identification and validation of biomarkers, molecular studies, and data sharing among investigators are crucial to inform therapeutic strategies that improve patient outcomes.
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Affiliation(s)
- Amy L Walz
- Division of Hematology, Oncology, Neuro-Oncology, and Stem Cell Transplant, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Mariana Maschietto
- Research Center, Boldrini Children's Hospital, Campinas, São Paulo, Brazil
| | - Brian Crompton
- Department of Pediatric Oncology, Dana-Farber/Harvard Cancer Center, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Nicholas Evageliou
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - David Dix
- British Columbia Children's Hospital, Vancouver, British Columbia, Canada
| | - Godelieve Tytgat
- Princess Máxima Center for Pediatric Oncology, CS Utrecht, The Netherlands
| | - Manfred Gessler
- Comprehensive Cancer Center Mainfranken, Wuerzburg, Germany.,Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, University of Wuerzburg, Wuerzburg, Germany
| | - David Gisselsson
- Cancer Cell Evolution Unit, Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Najat C Daw
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jenny Wegert
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, University of Wuerzburg, Wuerzburg, Germany
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10
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Valind A, Verhoeven BM, Enoksson J, Karlsson J, Christensson G, Mañas A, Aaltonen K, Jansson C, Bexell D, Baryawno N, Gisselsson D, Hagerling C. Macrophage infiltration promotes regrowth in MYCN-amplified neuroblastoma after chemotherapy. Oncoimmunology 2023; 12:2184130. [PMID: 36875552 PMCID: PMC9980604 DOI: 10.1080/2162402x.2023.2184130] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023] Open
Abstract
Despite aggressive treatment, the 5-year event-free survival rate for children with high-risk neuroblastoma is <50%. While most high-risk neuroblastoma patients initially respond to treatment, often with complete clinical remission, many eventually relapse with therapy-resistant tumors. Novel therapeutic alternatives that prevent the recurrence of therapy-resistant tumors are urgently needed. To understand the adaptation of neuroblastoma under therapy, we analyzed the transcriptomic landscape in 46 clinical tumor samples collected before (PRE) or after (POST) treatment from 22 neuroblastoma patients. RNA sequencing revealed that many of the top-upregulated biological processes in POST MYCN amplified (MNA+) tumors compared to PRE MNA+ tumors were immune-related, and there was a significant increase in numerous genes associated with macrophages. The infiltration of macrophages was corroborated by immunohistochemistry and spatial digital protein profiling. Moreover, POST MNA+ tumor cells were more immunogenic compared to PRE MNA+ tumor cells. To find support for the macrophage-induced outgrowth of certain subpopulations of immunogenic tumor cells following treatment, we examined the genetic landscape in multiple clinical PRE and POST tumor samples from nine neuroblastoma patients revealing a significant correlation between an increased amount of copy number aberrations (CNA) and macrophage infiltration in POST MNA+ tumor samples. Using an in vivo neuroblastoma patient-derived xenograft (PDX) chemotherapy model, we further show that inhibition of macrophage recruitment with anti-CSF1R treatment prevents the regrowth of MNA+ tumors following chemotherapy. Taken together, our work supports a therapeutic strategy for fighting the relapse of MNA+ neuroblastoma by targeting the immune microenvironment.
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Affiliation(s)
- Anders Valind
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Sweden Karolinska Institute, Lund, Sweden.,Department of Pediatrics, Skåne University Hospital, Lund, Sweden
| | - Bronte Manouk Verhoeven
- Childhood Cancer Research Unit, Department of Women's and Children's Healthy, Karolinska Institute, Stockholm, Sweden
| | - Jens Enoksson
- Department of Pathology, Laboratory Medicine, Skåne University Hospital, Lund, Sweden
| | - Jenny Karlsson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Sweden Karolinska Institute, Lund, Sweden
| | - Gustav Christensson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Sweden Karolinska Institute, Lund, Sweden
| | - Adriana Mañas
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Kristina Aaltonen
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Caroline Jansson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Sweden Karolinska Institute, Lund, Sweden
| | - Daniel Bexell
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Ninib Baryawno
- Childhood Cancer Research Unit, Department of Women's and Children's Healthy, Karolinska Institute, Stockholm, Sweden
| | - David Gisselsson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Sweden Karolinska Institute, Lund, Sweden.,Department of Pathology, Laboratory Medicine, Skåne University Hospital, Lund, Sweden
| | - Catharina Hagerling
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Sweden Karolinska Institute, Lund, Sweden.,Department of Pathology, Laboratory Medicine, Skåne University Hospital, Lund, Sweden
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11
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Targeted Epigenetic Interventions in Cancer with an Emphasis on Pediatric Malignancies. Biomolecules 2022; 13:biom13010061. [PMID: 36671446 PMCID: PMC9855367 DOI: 10.3390/biom13010061] [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: 11/26/2022] [Revised: 12/16/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
Over the past two decades, novel hallmarks of cancer have been described, including the altered epigenetic landscape of malignant diseases. In addition to the methylation and hyd-roxymethylation of DNA, numerous novel forms of histone modifications and nucleosome remodeling have been discovered, giving rise to a wide variety of targeted therapeutic interventions. DNA hypomethylating drugs, histone deacetylase inhibitors and agents targeting histone methylation machinery are of distinguished clinical significance. The major focus of this review is placed on targeted epigenetic interventions in the most common pediatric malignancies, including acute leukemias, brain and kidney tumors, neuroblastoma and soft tissue sarcomas. Upcoming novel challenges include specificity and potential undesirable side effects. Different epigenetic patterns of pediatric and adult cancers should be noted. Biological significance of epigenetic alterations highly depends on the tissue microenvironment and widespread interactions. An individualized treatment approach requires detailed genetic, epigenetic and metabolomic evaluation of cancer. Advances in molecular technologies and clinical translation may contribute to the development of novel pediatric anticancer treatment strategies, aiming for improved survival and better patient quality of life.
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12
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Seferbekova Z, Lomakin A, Yates LR, Gerstung M. Spatial biology of cancer evolution. Nat Rev Genet 2022; 24:295-313. [PMID: 36494509 DOI: 10.1038/s41576-022-00553-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2022] [Indexed: 12/13/2022]
Abstract
The natural history of cancers can be understood through the lens of evolution given that the driving forces of cancer development are mutation and selection of fitter clones. Cancer growth and progression are spatial processes that involve the breakdown of normal tissue organization, invasion and metastasis. For these reasons, spatial patterns are an integral part of histological tumour grading and staging as they measure the progression from normal to malignant disease. Furthermore, tumour cells are part of an ecosystem of tumour cells and their surrounding tumour microenvironment. A range of new spatial genomic, transcriptomic and proteomic technologies offers new avenues for the study of cancer evolution with great molecular and spatial detail. These methods enable precise characterizations of the tumour microenvironment, cellular interactions therein and micro-anatomical structures. In conjunction with spatial genomics, it emerges that tumours and microenvironments co-evolve, which helps explain observable patterns of heterogeneity and offers new routes for therapeutic interventions.
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13
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Ciceri S, Carenzo A, Iannó MF, Bertolotti A, Morosi C, Luksch R, Spreafico F, Collini P, Radice P, Massimino M, De Cecco L, Perotti D. Gene expression-based dissection of inter-histotypes, intra-histotype and intra-tumor heterogeneity in pediatric tumors. Sci Rep 2022; 12:17837. [PMID: 36284197 PMCID: PMC9596396 DOI: 10.1038/s41598-022-20536-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/14/2022] [Indexed: 02/07/2023] Open
Abstract
Intra-tumor heterogeneity (ITH) fosters tumor evolution, resistance to therapy, and relapse. Recently, many evidence have been accumulated on the occurrence of genetic ITH in pediatric cancers. With this study we aimed to address the downstream effects that genetic and epigenetic ITH, and tumor-microenvironment interactions may produce within a tumor mass. To this aim, we investigated by high-throughput gene expression multiple samples of 5 hepatoblastomas, 5 neuroblastomas, 5 rhabdomyosarcomas, and 5 Wilms tumors. Principal component analysis, single sample hallmark gene sets analysis, and weighted gene co-expression network analysis were performed on gene expression data. We observed that the different tumors clustered by histotype, and then by case, and in addition, a variable degree of ITH was visible in all the investigated cases. The ITH highlighted in this study can represent a challenge in tumor treatment since we demonstrated that different druggable hallmarks and targets may be heterogeneously present within the same tumor mass, and this can potentially lead to therapeutic failure. Despite this heterogeneity, we could highlight some commonalities among the different histotypes investigated, supporting the feasibility to move in the clinic from a histotype-driven to a target-driven, sometimes agnostic, approach at least in some cases.
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Affiliation(s)
- Sara Ciceri
- grid.417893.00000 0001 0807 2568Molecular Bases of Genetic Risk and Genetic Testing Unit, Department of Research, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Venezian 1, 20133 Milano, Italy
| | - Andrea Carenzo
- grid.417893.00000 0001 0807 2568Molecular Mechanisms Unit, Department of Research, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Venezian 1, 20133 Milano, Italy
| | - Maria Federica Iannó
- grid.417893.00000 0001 0807 2568Integrated Biology Platform, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Alessia Bertolotti
- grid.417893.00000 0001 0807 2568Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Carlo Morosi
- grid.417893.00000 0001 0807 2568Department of Radiology, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Roberto Luksch
- grid.417893.00000 0001 0807 2568Pediatric Oncology Unit, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Filippo Spreafico
- grid.417893.00000 0001 0807 2568Pediatric Oncology Unit, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Paola Collini
- grid.417893.00000 0001 0807 2568Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Paolo Radice
- grid.417893.00000 0001 0807 2568Molecular Bases of Genetic Risk and Genetic Testing Unit, Department of Research, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Venezian 1, 20133 Milano, Italy
| | - Maura Massimino
- grid.417893.00000 0001 0807 2568Pediatric Oncology Unit, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Loris De Cecco
- grid.417893.00000 0001 0807 2568Molecular Mechanisms Unit, Department of Research, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Venezian 1, 20133 Milano, Italy
| | - Daniela Perotti
- grid.417893.00000 0001 0807 2568Molecular Bases of Genetic Risk and Genetic Testing Unit, Department of Research, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Venezian 1, 20133 Milano, Italy
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14
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Gomez RL, Ibragimova S, Ramachandran R, Philpott A, Ali FR. Tumoral heterogeneity in neuroblastoma. Biochim Biophys Acta Rev Cancer 2022; 1877:188805. [PMID: 36162542 DOI: 10.1016/j.bbcan.2022.188805] [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: 04/06/2022] [Revised: 08/28/2022] [Accepted: 09/17/2022] [Indexed: 10/31/2022]
Abstract
Neuroblastoma is a solid, neuroendocrine tumor with divergent clinical behavior ranging from asymptomatic to fatal. The diverse clinical presentations of neuroblastoma are directly linked to the high intra- and inter-tumoral heterogeneity it presents. This heterogeneity is strongly associated with therapeutic resistance and continuous relapses, often leading to fatal outcomes. The development of successful risk assessment and tailored treatment strategies lies in evaluating the extent of heterogeneity via the accurate genetic and epigenetic profiling of distinct cell subpopulations present in the tumor. Recent studies have focused on understanding the molecular mechanisms that drive tumoral heterogeneity in pursuing better therapeutic and diagnostic approaches. This review describes the cellular, genetic, and epigenetic aspects of neuroblastoma heterogeneity. In addition, we summarize the recent findings on three crucial factors that can lead to heterogeneity in solid tumors: the inherent diversity of the progenitor cells, the presence of cancer stem cells, and the influence of the tumor microenvironment.
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Affiliation(s)
- Roshna Lawrence Gomez
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Healthcare City, Dubai, United Arab Emirates
| | - Shakhzada Ibragimova
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Healthcare City, Dubai, United Arab Emirates
| | - Revathy Ramachandran
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Healthcare City, Dubai, United Arab Emirates
| | - Anna Philpott
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom; Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Center, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Fahad R Ali
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Healthcare City, Dubai, United Arab Emirates.
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15
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Oliver TRW, Chappell L, Sanghvi R, Deighton L, Ansari-Pour N, Dentro SC, Young MD, Coorens THH, Jung H, Butler T, Neville MDC, Leongamornlert D, Sanders MA, Hooks Y, Cagan A, Mitchell TJ, Cortes-Ciriano I, Warren AY, Wedge DC, Heer R, Coleman N, Murray MJ, Campbell PJ, Rahbari R, Behjati S. Clonal diversification and histogenesis of malignant germ cell tumours. Nat Commun 2022; 13:4272. [PMID: 35953478 PMCID: PMC9372159 DOI: 10.1038/s41467-022-31375-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 06/13/2022] [Indexed: 12/21/2022] Open
Abstract
Germ cell tumours (GCTs) are a collection of benign and malignant neoplasms derived from primordial germ cells. They are uniquely able to recapitulate embryonic and extraembryonic tissues, which carries prognostic and therapeutic significance. The developmental pathways underpinning GCT initiation and histogenesis are incompletely understood. Here, we study the relationship of histogenesis and clonal diversification in GCTs by analysing the genomes and transcriptomes of 547 microdissected histological units. We find no correlation between genomic and histological heterogeneity. However, we identify unifying features including the retention of fetal developmental transcripts across tissues, expression changes on chromosome 12p, and a conserved somatic evolutionary sequence of whole genome duplication followed by clonal diversification. While this pattern is preserved across all GCTs, the developmental timing of the duplication varies between prepubertal and postpubertal cases. In addition, tumours of younger children exhibit distinct substitution signatures which may lend themselves as potential biomarkers for risk stratification. Our findings portray the extensive diversification of GCT tissues and genetic subclones as randomly distributed, while identifying overarching transcriptional and genomic features.
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Affiliation(s)
- Thomas R W Oliver
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | | | | | - Naser Ansari-Pour
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Stefan C Dentro
- Wellcome Sanger Institute, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | | | | | | | | | | | | | - Mathijs A Sanders
- Wellcome Sanger Institute, Hinxton, UK
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | | | - Thomas J Mitchell
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Isidro Cortes-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Anne Y Warren
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - David C Wedge
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Manchester Cancer Research Centre, Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Rakesh Heer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Newcastle Urology, Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Nicholas Coleman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Matthew J Murray
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | | | | | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK.
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16
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Hambraeus M, Karlsson J, Kasselaki I, Hagerling C, Hagander L, Gisselsson D. Differential Activation of Immune Effector Processes in Mature Compared to Immature Sacrococcygeal Teratomas. Fetal Pediatr Pathol 2022; 41:413-425. [PMID: 33063585 DOI: 10.1080/15513815.2020.1831661] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Objective: This study aims to characterize the molecular signatures of sacrococcygeal teratomas (SCTs). Methods: Three SCTs were analyzed with whole genome genotyping. RNA sequencing of 10 SCTs dominated by mature, immature and neuroglial elements was analyzed. Expression in SCT-samples with different elements were compared to each other and to a reference group of malignant pediatric tumors. Macrophages, T- and B-lymphocytes were detected by immunohistochemistry. Results: No chromosomal imbalances were detected. SCTs showed overexpression of genes involved in neurosignaling, DNA-binding molecules and pathways of early germ cells. Genes associated with immune effector processes were overexpressed in mature compared to immature SCTs, and immune cell infiltration was found predominantly around mature epithelial elements. Conclusion: The broad repertoire of histological elements in SCTs reflects differences in transcriptional regulation rather than differences in gene copy numbers. A paucity of immune response in immature SCTs may be a factor contributing to their uninhibited growth.
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Affiliation(s)
- Mette Hambraeus
- Department of Pediatric Surgery, Lund University Hospital, Lund, Sweden.,Department of Clinical Sciences, Section of Pediatrics, Lund University, Lund, Sweden
| | - Jenny Karlsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Ioanna Kasselaki
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University Hospital, Lund, Sweden
| | - Catharina Hagerling
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Lars Hagander
- Department of Pediatric Surgery, Lund University Hospital, Lund, Sweden.,Department of Clinical Sciences, Section of Pediatrics, Lund University, Lund, Sweden
| | - David Gisselsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Department of Clinical Sciences, Division of Oncology and Pathology, Lund University Hospital, Lund, Sweden
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17
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Abstract
Purpose of Review The evolving information of the initiation, tumor cell heterogeneity, and plasticity of childhood neuroblastoma has opened up new perspectives for developing therapies based on detailed knowledge of the disease. Recent Findings The cellular origin of neuroblastoma has begun to unravel and there have been several reports on tumor cell heterogeneity based on transcriptional core regulatory circuitries that have given us important information on the biology of neuroblastoma as a developmental disease. This together with new insight of the tumor microenvironment which acts as a support for neuroblastoma growth has given us the prospect for designing better treatment approaches for patients with high-risk neuroblastoma. Here, we discuss these new discoveries and highlight some emerging therapeutic options. Summary Neuroblastoma is a disease with multiple facets. Detailed biological and molecular knowledge on neuroblastoma initiation, heterogeneity, and the communications between cells in the tumor microenvironment holds promise for better therapies.
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18
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Laganà A. Computational Approaches for the Investigation of Intra-tumor Heterogeneity and Clonal Evolution from Bulk Sequencing Data in Precision Oncology Applications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1361:101-118. [DOI: 10.1007/978-3-030-91836-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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19
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Noble R, Burri D, Le Sueur C, Lemant J, Viossat Y, Kather JN, Beerenwinkel N. Spatial structure governs the mode of tumour evolution. Nat Ecol Evol 2022; 6:207-217. [PMID: 34949822 PMCID: PMC8825284 DOI: 10.1038/s41559-021-01615-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/10/2021] [Indexed: 12/12/2022]
Abstract
Characterizing the mode-the way, manner or pattern-of evolution in tumours is important for clinical forecasting and optimizing cancer treatment. Sequencing studies have inferred various modes, including branching, punctuated and neutral evolution, but it is unclear why a particular pattern predominates in any given tumour. Here we propose that tumour architecture is key to explaining the variety of observed genetic patterns. We examine this hypothesis using spatially explicit population genetics models and demonstrate that, within biologically relevant parameter ranges, different spatial structures can generate four tumour evolutionary modes: rapid clonal expansion, progressive diversification, branching evolution and effectively almost neutral evolution. Quantitative indices for describing and classifying these evolutionary modes are presented. Using these indices, we show that our model predictions are consistent with empirical observations for cancer types with corresponding spatial structures. The manner of cell dispersal and the range of cell-cell interactions are found to be essential factors in accurately characterizing, forecasting and controlling tumour evolution.
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Affiliation(s)
- Robert Noble
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland. .,SIB Swiss Institute of Bioinformatics, Basel, Switzerland. .,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland. .,Department of Mathematics, City, University of London, London, UK.
| | - Dominik Burri
- grid.5801.c0000 0001 2156 2780Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland ,grid.6612.30000 0004 1937 0642Biozentrum, University of Basel, Basel, Switzerland
| | - Cécile Le Sueur
- grid.5801.c0000 0001 2156 2780Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Jeanne Lemant
- grid.5801.c0000 0001 2156 2780Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Yannick Viossat
- grid.11024.360000000120977052Ceremade, Université Paris Dauphine-PSL, Paris, France
| | - Jakob Nikolas Kather
- grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Applied Tumor Immunity, German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.412301.50000 0000 8653 1507Internal Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland. .,SIB Swiss Institute of Bioinformatics, Basel, Switzerland.
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20
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Schmelz K, Toedling J, Huska M, Cwikla MC, Kruetzfeldt LM, Proba J, Ambros PF, Ambros IM, Boral S, Lodrini M, Chen CY, Burkert M, Guergen D, Szymansky A, Astrahantseff K, Kuenkele A, Haase K, Fischer M, Deubzer HE, Hertwig F, Hundsdoerfer P, Henssen AG, Schwarz RF, Schulte JH, Eggert A. Spatial and temporal intratumour heterogeneity has potential consequences for single biopsy-based neuroblastoma treatment decisions. Nat Commun 2021; 12:6804. [PMID: 34815394 PMCID: PMC8611017 DOI: 10.1038/s41467-021-26870-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 10/18/2021] [Indexed: 01/12/2023] Open
Abstract
Intratumour heterogeneity is a major cause of treatment failure in cancer. We present in-depth analyses combining transcriptomic and genomic profiling with ultra-deep targeted sequencing of multiregional biopsies in 10 patients with neuroblastoma, a devastating childhood tumour. We observe high spatial and temporal heterogeneity in somatic mutations and somatic copy-number alterations which are reflected on the transcriptomic level. Mutations in some druggable target genes including ALK and FGFR1 are heterogeneous at diagnosis and/or relapse, raising the issue whether current target prioritization and molecular risk stratification procedures in single biopsies are sufficiently reliable for therapy decisions. The genetic heterogeneity in gene mutations and chromosome aberrations observed in deep analyses from patient courses suggest clonal evolution before treatment and under treatment pressure, and support early emergence of metastatic clones and ongoing chromosomal instability during disease evolution. We report continuous clonal evolution on mutational and copy number levels in neuroblastoma, and detail its implications for therapy selection, risk stratification and therapy resistance.
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Affiliation(s)
- Karin Schmelz
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- The German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany
- The German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Joern Toedling
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- The German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany
- The German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matt Huska
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Maja C Cwikla
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | | | - Jutta Proba
- Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Peter F Ambros
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, 1090, Vienna, Austria
| | - Inge M Ambros
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, 1090, Vienna, Austria
| | - Sengül Boral
- Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Marco Lodrini
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- The German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany
- The German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Celine Y Chen
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- Experimental and Clinical Research Center (ECRC) of the Charité and Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Martin Burkert
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Dennis Guergen
- Experimental Pharmacology and Oncology Berlin-Buch GmbH (EPO), Berlin, Germany
| | | | | | - Annette Kuenkele
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- The German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany
- The German Cancer Research Center (DKFZ), Heidelberg, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Kerstin Haase
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- The German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany
- The German Cancer Research Center (DKFZ), Heidelberg, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, Medical Faculty, University Children's Hospital of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Hedwig E Deubzer
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- The German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany
- The German Cancer Research Center (DKFZ), Heidelberg, Germany
- Experimental and Clinical Research Center (ECRC) of the Charité and Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Falk Hertwig
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- The German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany
- The German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patrick Hundsdoerfer
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- Helios Klinikum Berlin-Buch, Berlin, Germany
| | - Anton G Henssen
- Charité-Universitätsmedizin Berlin, Berlin, Germany.
- The German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany.
- The German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
- Experimental and Clinical Research Center (ECRC) of the Charité and Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
- Berlin Institute of Health (BIH), Berlin, Germany.
| | - Roland F Schwarz
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
- BIFOLD-Berlin Institute for the Foundations of Learning and Data, Berlin, Germany.
| | - Johannes H Schulte
- Charité-Universitätsmedizin Berlin, Berlin, Germany.
- The German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany.
- The German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Berlin Institute of Health (BIH), Berlin, Germany.
| | - Angelika Eggert
- Charité-Universitätsmedizin Berlin, Berlin, Germany.
- The German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany.
- The German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Berlin Institute of Health (BIH), Berlin, Germany.
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21
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Chattopadhyay S, Karlsson J, Valind A, Andersson N, Gisselsson D. Tracing the evolution of aneuploid cancers by multiregional sequencing with CRUST. Brief Bioinform 2021; 22:bbab292. [PMID: 34343239 PMCID: PMC8981300 DOI: 10.1093/bib/bbab292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/16/2021] [Accepted: 07/09/2021] [Indexed: 12/20/2022] Open
Abstract
Clonal deconvolution of mutational landscapes is crucial to understand the evolutionary dynamics of cancer. Two limiting factors for clonal deconvolution that have remained unresolved are variation in purity and chromosomal copy number across different samples of the same tumor. We developed a semi-supervised algorithm that tracks variant calls through multi-sample spatiotemporal tumor data. While normalizing allele frequencies based on purity, it also adjusts for copy number changes at clonal deconvolution. Absent à priori copy number data, it renders in silico copy number estimations from bulk sequences. Using published and simulated tumor sequences, we reliably segregated clonal/subclonal variants even at a low sequencing depth (~50×). Given at least one pure tumor sample (>70% purity), we could normalize and deconvolve paired samples down to a purity of 40%. This renders a reliable clonal reconstruction well adapted to multi-regionally sampled solid tumors, which are often aneuploid and contaminated by non-cancer cells.
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Affiliation(s)
- Subhayan Chattopadhyay
- Division of Clinical Genetics, Department of Laboratory
Medicine, Lund University, Lund, Sweden
| | - Jenny Karlsson
- Division of Clinical Genetics, Department of Laboratory
Medicine, Lund University, Lund, Sweden
| | - Anders Valind
- Division of Clinical Genetics, Department of Laboratory
Medicine, Lund University, Lund, Sweden
- Department of Pediatrics, Skåne University
Hospital, Lund, Sweden
| | - Natalie Andersson
- Division of Clinical Genetics, Department of Laboratory
Medicine, Lund University, Lund, Sweden
| | - David Gisselsson
- Division of Clinical Genetics, Department of Laboratory
Medicine, Lund University, Lund, Sweden
- Division of Oncology and Pathology, Department of Clinical
Sciences, Lund University, Lund, Sweden
- Clinical Genetics and Pathology, Laboratory Medicine,
Lund University Hospital, Lund, Sweden
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22
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Andersson N, Chattopadhyay S, Valind A, Karlsson J, Gisselsson D. DEVOLUTION-A method for phylogenetic reconstruction of aneuploid cancers based on multiregional genotyping data. Commun Biol 2021; 4:1103. [PMID: 34545199 PMCID: PMC8452746 DOI: 10.1038/s42003-021-02637-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 09/03/2021] [Indexed: 02/05/2023] Open
Abstract
Phylogenetic reconstruction of cancer cell populations remains challenging. There is a particular lack of tools that deconvolve clones based on copy number aberration analyses of multiple tumor biopsies separated in time and space from the same patient. This has hampered investigations of tumors rich in aneuploidy but few point mutations, as in many childhood cancers and high-risk adult cancer. Here, we present DEVOLUTION, an algorithm for subclonal deconvolution followed by phylogenetic reconstruction from bulk genotyping data. It integrates copy number and sequencing information across multiple tumor regions throughout the inference process, provided that the mutated clone fraction for each mutation is known. We validate DEVOLUTION on data from 56 pediatric tumors comprising 253 tumor biopsies and show a robust performance on simulations of bulk genotyping data. We also benchmark DEVOLUTION to similar bioinformatic tools using an external dataset. DEVOLUTION holds the potential to facilitate insights into the development, progression, and response to treatment, particularly in tumors with high burden of chromosomal copy number alterations.
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Affiliation(s)
- Natalie Andersson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.
| | - Subhayan Chattopadhyay
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Anders Valind
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Pediatrics, Skåne University Hospital, Lund, Sweden
| | - Jenny Karlsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - David Gisselsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Division of Oncology-Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
- Clinical Genetics and Pathology, Laboratory Medicine, Lund University Hospital, Skåne Healthcare Region, Lund, Sweden
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23
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Langenberg KPS, Looze EJ, Molenaar JJ. The Landscape of Pediatric Precision Oncology: Program Design, Actionable Alterations, and Clinical Trial Development. Cancers (Basel) 2021; 13:4324. [PMID: 34503139 PMCID: PMC8431194 DOI: 10.3390/cancers13174324] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 12/20/2022] Open
Abstract
Over the last years, various precision medicine programs have been developed for pediatric patients with high-risk, relapsed, or refractory malignancies, selecting patients for targeted treatment through comprehensive molecular profiling. In this review, we describe characteristics of these initiatives, demonstrating the feasibility and potential of molecular-driven precision medicine. Actionable events are identified in a significant subset of patients, although comparing results is complicated due to the lack of a standardized definition of actionable alterations and the different molecular profiling strategies used. The first biomarker-driven trials for childhood cancer have been initiated, but until now the effect of precision medicine on clinical outcome has only been reported for a small number of patients, demonstrating clinical benefit in some. Future perspectives include the incorporation of novel approaches such as liquid biopsies and immune monitoring as well as innovative collaborative trial design including combination strategies, and the development of agents specifically targeting aberrations in childhood malignancies.
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Affiliation(s)
- Karin P. S. Langenberg
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands; (E.J.L.); (J.J.M.)
| | - Eleonora J. Looze
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands; (E.J.L.); (J.J.M.)
| | - Jan J. Molenaar
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands; (E.J.L.); (J.J.M.)
- Department of Pharmaceutical Sciences, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands
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24
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Dziak JJ, Coffman DL, Lanza ST, Li R, Jermiin LS. Sensitivity and specificity of information criteria. Brief Bioinform 2021; 21:553-565. [PMID: 30895308 DOI: 10.1093/bib/bbz016] [Citation(s) in RCA: 188] [Impact Index Per Article: 62.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/04/2019] [Accepted: 01/21/2019] [Indexed: 11/14/2022] Open
Abstract
Information criteria (ICs) based on penalized likelihood, such as Akaike's information criterion (AIC), the Bayesian information criterion (BIC) and sample-size-adjusted versions of them, are widely used for model selection in health and biological research. However, different criteria sometimes support different models, leading to discussions about which is the most trustworthy. Some researchers and fields of study habitually use one or the other, often without a clearly stated justification. They may not realize that the criteria may disagree. Others try to compare models using multiple criteria but encounter ambiguity when different criteria lead to substantively different answers, leading to questions about which criterion is best. In this paper we present an alternative perspective on these criteria that can help in interpreting their practical implications. Specifically, in some cases the comparison of two models using ICs can be viewed as equivalent to a likelihood ratio test, with the different criteria representing different alpha levels and BIC being a more conservative test than AIC. This perspective may lead to insights about how to interpret the ICs in more complex situations. For example, AIC or BIC could be preferable, depending on the relative importance one assigns to sensitivity versus specificity. Understanding the differences and similarities among the ICs can make it easier to compare their results and to use them to make informed decisions.
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Affiliation(s)
| | - Donna L Coffman
- Department of Epidemiology and Biostatistics at Temple University
| | - Stephanie T Lanza
- Department of Biobehavioral Health and a principal investigator at the Methodology Center
| | - Runze Li
- Department of Statistics and a principal investigator in the Methodology Center at Penn State
| | - Lars S Jermiin
- Research School of Biology at the Australian National University and a visiting researcher at the Earth Institute and School of Biology and Environmental Science, University College Dublin
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25
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Discovery of Spatial Peptide Signatures for Neuroblastoma Risk Assessment by MALDI Mass Spectrometry Imaging. Cancers (Basel) 2021; 13:cancers13133184. [PMID: 34202325 PMCID: PMC8269054 DOI: 10.3390/cancers13133184] [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: 04/23/2021] [Revised: 06/16/2021] [Accepted: 06/22/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary The childhood tumor, neuroblastoma, has a broad clinical presentation. Risk assessment at diagnosis is particularly difficult in molecularly heterogeneous high-risk cases. Here we investigate the potential of imaging mass spectrometry to directly detect intratumor heterogeneity on the protein level in tissue sections. We show that this approach can produce discriminatory peptide signatures separating high- from low- and intermediate-risk tumors, identify 8 proteins aassociated with these signatures and validate two marker proteins using tissue immunostaining that have promise for further basic and translational research in neuroblastoma. We provide proof-of-concept that mass spectrometry-based technology could assist early risk assessment in neuroblastoma and provide insights into peptide signature-based detection of intratumor heterogeneity. Abstract Risk classification plays a crucial role in clinical management and therapy decisions in children with neuroblastoma. Risk assessment is currently based on patient criteria and molecular factors in single tumor biopsies at diagnosis. Growing evidence of extensive neuroblastoma intratumor heterogeneity drives the need for novel diagnostics to assess molecular profiles more comprehensively in spatial resolution to better predict risk for tumor progression and therapy resistance. We present a pilot study investigating the feasibility and potential of matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) to identify spatial peptide heterogeneity in neuroblastoma tissues of divergent current risk classification: high versus low/intermediate risk. Univariate (receiver operating characteristic analysis) and multivariate (segmentation, principal component analysis) statistical strategies identified spatially discriminative risk-associated MALDI-based peptide signatures. The AHNAK nucleoprotein and collapsin response mediator protein 1 (CRMP1) were identified as proteins associated with these peptide signatures, and their differential expression in the neuroblastomas of divergent risk was immunohistochemically validated. This proof-of-concept study demonstrates that MALDI-MSI combined with univariate and multivariate analysis strategies can identify spatially discriminative risk-associated peptide signatures in neuroblastoma tissues. These results suggest a promising new analytical strategy improving risk classification and providing new biological insights into neuroblastoma intratumor heterogeneity.
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26
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Park JH, de Lomana ALG, Marzese DM, Juarez T, Feroze A, Hothi P, Cobbs C, Patel AP, Kesari S, Huang S, Baliga NS. A Systems Approach to Brain Tumor Treatment. Cancers (Basel) 2021; 13:3152. [PMID: 34202449 PMCID: PMC8269017 DOI: 10.3390/cancers13133152] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/11/2021] [Accepted: 06/17/2021] [Indexed: 12/12/2022] Open
Abstract
Brain tumors are among the most lethal tumors. Glioblastoma, the most frequent primary brain tumor in adults, has a median survival time of approximately 15 months after diagnosis or a five-year survival rate of 10%; the recurrence rate is nearly 90%. Unfortunately, this prognosis has not improved for several decades. The lack of progress in the treatment of brain tumors has been attributed to their high rate of primary therapy resistance. Challenges such as pronounced inter-patient variability, intratumoral heterogeneity, and drug delivery across the blood-brain barrier hinder progress. A comprehensive, multiscale understanding of the disease, from the molecular to the whole tumor level, is needed to address the intratumor heterogeneity resulting from the coexistence of a diversity of neoplastic and non-neoplastic cell types in the tumor tissue. By contrast, inter-patient variability must be addressed by subtyping brain tumors to stratify patients and identify the best-matched drug(s) and therapies for a particular patient or cohort of patients. Accomplishing these diverse tasks will require a new framework, one involving a systems perspective in assessing the immense complexity of brain tumors. This would in turn entail a shift in how clinical medicine interfaces with the rapidly advancing high-throughput (HTP) technologies that have enabled the omics-scale profiling of molecular features of brain tumors from the single-cell to the tissue level. However, several gaps must be closed before such a framework can fulfill the promise of precision and personalized medicine for brain tumors. Ultimately, the goal is to integrate seamlessly multiscale systems analyses of patient tumors and clinical medicine. Accomplishing this goal would facilitate the rational design of therapeutic strategies matched to the characteristics of patients and their tumors. Here, we discuss some of the technologies, methodologies, and computational tools that will facilitate the realization of this vision to practice.
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Affiliation(s)
- James H. Park
- Institute for Systems Biology, Seattle, WA 98109, USA; (J.H.P.); (S.H.)
| | | | - Diego M. Marzese
- Balearic Islands Health Research Institute (IdISBa), 07010 Palma, Spain;
| | - Tiffany Juarez
- St. John’s Cancer Institute, Santa Monica, CA 90401, USA; (T.J.); (S.K.)
| | - Abdullah Feroze
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA; (A.F.); (A.P.P.)
| | - Parvinder Hothi
- Swedish Neuroscience Institute, Seattle, WA 98122, USA; (P.H.); (C.C.)
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Seattle, WA 98122, USA
| | - Charles Cobbs
- Swedish Neuroscience Institute, Seattle, WA 98122, USA; (P.H.); (C.C.)
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Seattle, WA 98122, USA
| | - Anoop P. Patel
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA; (A.F.); (A.P.P.)
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Brotman-Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA
| | - Santosh Kesari
- St. John’s Cancer Institute, Santa Monica, CA 90401, USA; (T.J.); (S.K.)
| | - Sui Huang
- Institute for Systems Biology, Seattle, WA 98109, USA; (J.H.P.); (S.H.)
| | - Nitin S. Baliga
- Institute for Systems Biology, Seattle, WA 98109, USA; (J.H.P.); (S.H.)
- Departments of Microbiology, Biology, and Molecular Engineering Sciences, University of Washington, Seattle, WA 98105, USA
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27
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Hansson K, Radke K, Aaltonen K, Saarela J, Mañas A, Sjölund J, Smith EM, Pietras K, Påhlman S, Wennerberg K, Gisselsson D, Bexell D. Therapeutic targeting of KSP in preclinical models of high-risk neuroblastoma. Sci Transl Med 2021; 12:12/562/eaba4434. [PMID: 32967973 DOI: 10.1126/scitranslmed.aba4434] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 05/11/2020] [Accepted: 07/30/2020] [Indexed: 01/05/2023]
Abstract
Neuroblastoma is a childhood malignancy with often dismal prognosis; relapse is common despite intense treatment. Here, we used human tumor organoids representing multiple MYCN-amplified high-risk neuroblastomas to perform a high-throughput drug screen with approved or emerging oncology drugs. Tumor-selective effects were calculated using drug sensitivity scores. Several drugs with previously unreported anti-neuroblastoma effects were identified by stringent selection criteria. ARRY-520, an inhibitor of kinesin spindle protein (KSP), was among those causing reduced viability. High expression of the KSP-encoding gene KIF11 was associated with poor outcome in neuroblastoma. Genome-scale loss-of-function screens in hundreds of human cancer cell lines across 22 tumor types revealed that KIF11 is particularly important for neuroblastoma cell viability. KSP inhibition in neuroblastoma patient-derived xenograft (PDX) cells resulted in the formation of abnormal monoastral spindles, mitotic arrest, up-regulation of mitosis-associated genes, and apoptosis. In vivo, KSP inhibition caused regression of MYCN-amplified neuroblastoma PDX tumors. Furthermore, treatment of mice harboring orthotopic neuroblastoma PDX tumors resulted in increased survival. Our results suggested that KSP inhibition could be a promising treatment strategy in children with high-risk neuroblastoma.
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Affiliation(s)
- Karin Hansson
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 223 81 Lund, Sweden
| | - Katarzyna Radke
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 223 81 Lund, Sweden
| | - Kristina Aaltonen
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 223 81 Lund, Sweden
| | - Jani Saarela
- Institute for Molecular Medicine Finland, University of Helsinki, 00290 Helsinki, Finland
| | - Adriana Mañas
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 223 81 Lund, Sweden
| | - Jonas Sjölund
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 223 81 Lund, Sweden
| | - Emma M Smith
- Division of Molecular Medicine and Gene Therapy, Lund Strategic Center for Stem Cell Biology, Lund University, 221 84 Lund, Sweden
| | - Kristian Pietras
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 223 81 Lund, Sweden
| | - Sven Påhlman
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 223 81 Lund, Sweden
| | - Krister Wennerberg
- Institute for Molecular Medicine Finland, University of Helsinki, 00290 Helsinki, Finland.,BRIC - Biotech Research and Innovation Centre, University of Copenhagen, 2200 Copenhagen, Denmark
| | - David Gisselsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, 221 85 Lund, Sweden.,Department of Pathology, Laboratory Medicine, Medical Services, University Hospital, 221 84 Lund, Sweden
| | - Daniel Bexell
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 223 81 Lund, Sweden.
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28
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Radke K, Hansson K, Sjölund J, Wolska M, Karlsson J, Esfandyari J, Pietras K, Aaltonen K, Gisselsson D, Bexell D. Anti-tumor effects of rigosertib in high-risk neuroblastoma. Transl Oncol 2021; 14:101149. [PMID: 34118691 PMCID: PMC8207190 DOI: 10.1016/j.tranon.2021.101149] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/27/2021] [Accepted: 06/02/2021] [Indexed: 11/16/2022] Open
Abstract
High-risk neuroblastoma has a poor prognosis despite intense treatment, demonstrating the need for new therapeutic strategies. Here we evaluated the effects of rigosertib (ON-01910.Na) in preclinical models of high-risk neuroblastoma. Among several hundred cancer cell lines representing 24 tumor types, neuroblastoma was the most sensitive to rigosertib. Treatment of MYCN-amplified neuroblastoma organoids resulted in organoid disintegration, decreased cell viability, and increased apoptotic cell death. Neuroblastoma response to rigosertib involved G2M cell cycle arrest and decreased phosphorylation of AKT (Ser473) and ERK1/2 (Thr202/Tyr204). Rigosertib delayed tumor growth and prolonged survival of mice carrying neuroblastoma MYCN-amplified PDX tumors (median survival: 31 days, treated; 22 days, vehicle) accompanied with increased apoptosis in treated tumors. We further identified vincristine and rigosertib as a potential promising drug combination treatment. Our results show that rigosertib might be a useful therapeutic agent for MYCN-amplified neuroblastomas, especially in combination with existing agents.
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Affiliation(s)
- Katarzyna Radke
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Karin Hansson
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Jonas Sjölund
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Magdalena Wolska
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Jenny Karlsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Javanshir Esfandyari
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Kristian Pietras
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Kristina Aaltonen
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - David Gisselsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden; Department of Pathology, Laboratory Medicine, Medical Services, University Hospital, Lund, Sweden
| | - Daniel Bexell
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden.
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29
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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.
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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
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30
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Valind A, Gisselsson D. Immune checkpoint inhibitors in Wilms' tumor and Neuroblastoma: What now? Cancer Rep (Hoboken) 2021; 4:e1397. [PMID: 33932141 PMCID: PMC8714551 DOI: 10.1002/cnr2.1397] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/13/2021] [Accepted: 03/25/2021] [Indexed: 12/12/2022] Open
Abstract
Background Therapeutic activation of tumor‐infiltrating lymphocytes using monoclonal antibodies targeting PD1 or PD‐L1 (immune checkpoint inhibitors—ICIs) has revolutionized treatment of specific solid tumors in adult cancer patients, and much hope has been placed on a similar effect in relapsed or refractory solid pediatric tumors. Recent clinical trials have disappointingly shown an almost nonexistent response rate, while case reports have demonstrated that some pediatric patients do achieve durable responses when treated with this type of drug. Aim To elucidate this paradox, we mapped the landscape of expressed neoantigens as well as the levels of immune cell infiltration in the two most common extracranial solid pediatric tumors: Wilms tumor and neuroblastoma using state‐of‐the‐art in silico analysis of a large cohort of patients with these tumors. Methods By integration of whole exome sequencing and RNA‐sequencing, we mapped the landscape of neoantigens in the TARGET cohorts for these diagnoses and correlated these findings with known genetic prognostic markers. Results Our analysis shows that these tumors typically have much lower levels of expressed neoantigens than commonly seen in adult cancers, but we also identify subgroups with significantly higher levels of neoantigens. For neuroblastomas, the cases with higher levels of neoantigens were confined to the group without MYCN‐amplification and for Wilms tumor restricted to the TP53‐mutated cases. Furthermore, we demonstrate that neuroblastomas have an unexpectedly high level of CD8+ tumor‐infiltrating lymphocytes, even when compared to adult tumor types where ICI is an approved treatment. Conclusion These results could be important to consider when designing future clinical trials of ICI treatment in pediatric patients with relapsed or refractory solid tumors.
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Affiliation(s)
- Anders Valind
- Division of Clinical Genetics, Lund University, Lund, Sweden.,Department of Pediatrics, Skåne University Hospital, Lund, Sweden
| | - David Gisselsson
- Division of Clinical Genetics, Lund University, Lund, Sweden.,Department of Pathology, Laboratory Medicine Skåne, Lund, Sweden
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31
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Tucker ER, George S, Angelini P, Bruna A, Chesler L. The Promise of Patient-Derived Preclinical Models to Accelerate the Implementation of Personalised Medicine for Children with Neuroblastoma. J Pers Med 2021; 11:248. [PMID: 33808071 PMCID: PMC8065808 DOI: 10.3390/jpm11040248] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 01/02/2023] Open
Abstract
Patient-derived preclinical models are now a core component of cancer research and have the ability to drastically improve the predictive power of preclinical therapeutic studies. However, their development and maintenance can be challenging, time consuming, and expensive. For neuroblastoma, a developmental malignancy of the neural crest, it is possible to establish patient-derived models as xenografts in mice and zebrafish, and as spheroids and organoids in vitro. These varied approaches have contributed to comprehensive packages of preclinical evidence in support of new therapeutics for neuroblastoma. We discuss here the ethical and technical considerations for the creation of patient-derived models of neuroblastoma and how their use can be optimized for the study of tumour evolution and preclinical therapies. We also discuss how neuroblastoma patient-derived models might become avatars for personalised medicine for children with this devastating disease.
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Affiliation(s)
- Elizabeth R. Tucker
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, Cotswold Road, London SM2 5NG, UK; (E.R.T.); (S.G.)
| | - Sally George
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, Cotswold Road, London SM2 5NG, UK; (E.R.T.); (S.G.)
| | - Paola Angelini
- Children and Young People’s Unit, The Royal Marsden, Downs Road, Sutton, Surrey SM2 5PT, UK;
| | - Alejandra Bruna
- Preclinical Paediatric Cancer Evolution, Centre for Cancer Drug Discovery, The Institute of Cancer Research, Cotswold Road, London SM2 5NG, UK;
| | - Louis Chesler
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, Cotswold Road, London SM2 5NG, UK; (E.R.T.); (S.G.)
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32
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Kaminska K, Akrap N, Staaf J, Alves CL, Ehinger A, Ebbesson A, Hedenfalk I, Beumers L, Veerla S, Harbst K, Ehmsen S, Borgquist S, Borg Å, Pérez-Fidalgo A, Ditzel HJ, Bosch A, Honeth G. Distinct mechanisms of resistance to fulvestrant treatment dictate level of ER independence and selective response to CDK inhibitors in metastatic breast cancer. Breast Cancer Res 2021; 23:26. [PMID: 33602273 PMCID: PMC7893923 DOI: 10.1186/s13058-021-01402-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/31/2021] [Indexed: 11/23/2022] Open
Abstract
Background Resistance to endocrine treatment in metastatic breast cancer is a major clinical challenge. Clinical tools to predict both drug resistance and possible treatment combination approaches to overcome it are lacking. This unmet need is mainly due to the heterogeneity underlying both the mechanisms involved in resistance development and breast cancer itself. Methods To study the complexity of the mechanisms involved in the resistance to the selective estrogen receptor degrader (SERD) fulvestrant, we performed comprehensive biomarker analyses using several in vitro models that recapitulate the heterogeneity of developed resistance. We further corroborated our findings in tissue samples from patients treated with fulvestrant. Results We found that different in vitro models of fulvestrant resistance show variable stability in their phenotypes, which corresponded with distinct genomic alterations. Notably, the studied models presented adaptation at different cell cycle nodes to facilitate progression through the cell cycle and responded differently to CDK inhibitors. Cyclin E2 overexpression was identified as a biomarker of a persistent fulvestrant-resistant phenotype. Comparison of pre- and post-treatment paired tumor biopsies from patients treated with fulvestrant revealed an upregulation of cyclin E2 upon development of resistance. Moreover, overexpression of this cyclin was found to be a prognostic factor determining resistance to fulvestrant and shorter progression-free survival. Conclusions These data highlight the complexity of estrogen receptor positive breast cancer and suggest that the development of diverse resistance mechanisms dictate levels of ER independence and potentially cross-resistance to CDK inhibitors. Supplementary Information The online version contains supplementary material available at 10.1186/s13058-021-01402-1.
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Affiliation(s)
- Kamila Kaminska
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Nina Akrap
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Johan Staaf
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Carla L Alves
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Anna Ehinger
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.,Division of Clinical Genetics and Pathology, Department of Laboratory Medicine, Skåne University Hospital, Lund, Sweden
| | - Anna Ebbesson
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Ingrid Hedenfalk
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Lukas Beumers
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Srinivas Veerla
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Katja Harbst
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Sidse Ehmsen
- Department of Oncology, Odense University Hospital, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Signe Borgquist
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.,Aarhus University Hospital, Aarhus, Denmark
| | - Åke Borg
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | | | - Henrik J Ditzel
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark.,Department of Oncology, Odense University Hospital, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Ana Bosch
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden. .,Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden.
| | - Gabriella Honeth
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.
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33
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Liao G, Liang X, Ping Y, Zhang Y, Liao J, Wang Y, Hou X, Jiang Z, Dong X, Xu C, Xiao Y. Revealing the subtyping of non-small cell lung cancer based on genomic evolutionary patterns by multi-region sequencing. Cancer Med 2020; 9:9485-9498. [PMID: 33078899 PMCID: PMC7774747 DOI: 10.1002/cam4.3541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 09/12/2020] [Accepted: 09/28/2020] [Indexed: 12/16/2022] Open
Abstract
Accurately classifying patients with non-small cell lung cancer (NSCLC) from the perspective of tumor evolution has not been systematically studied to date. Here, we reconstructed phylogenetic relationships of somatic mutations in 100 early NSCLC patients (327 lesions) through reanalyzing the TRACERx data. Based on the genomic evolutionary patterns presented on the phylogenetic trees, we grouped NSCLC patients into three evolutionary subtypes. The phylogenetic trees among three subtypes exhibited distinct branching structures, with one subtype representing branched evolution and another reflecting the early accumulation of genomic variation. However, in the evolutionary pattern of the third subtype, some mutations experienced selective sweeps and were gradually replaced by multiple newly formed subclonal populations. The subtype patients with poor prognosis had higher intra-tumor heterogeneity and subclonal diversity. We combined genomic heterogeneity with clinical phenotypes analysis and found that subclonal expansion results in the progression and deterioration of the tumor. The molecular mechanisms of subtype-specific Early Driver Feature (EDF) genes differed across the evolutionary subtypes, reflecting the characteristics of the subtype itself. In summary, our study provided new insights on the stratification of NSCLC patients based on genomic evolution that can be valuable for us to understand the development of pulmonary tumor profoundly.
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Affiliation(s)
- Gaoming Liao
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinHeilongjiangChina
| | - Xin Liang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinHeilongjiangChina
| | - Yanyan Ping
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinHeilongjiangChina
| | - Yong Zhang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinHeilongjiangChina
| | - Jianlong Liao
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinHeilongjiangChina
| | - Yihan Wang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinHeilongjiangChina
| | - Xiaobo Hou
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinHeilongjiangChina
| | - Zedong Jiang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinHeilongjiangChina
| | - Xiaoqiu Dong
- The Fourth Hospital of Harbin Medical UniversityHarbinChina
| | - Chaohan Xu
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinHeilongjiangChina
| | - Yun Xiao
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinHeilongjiangChina
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34
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Zhang Y, Xie A, Quan F, Hou X, Liao J, Zhu S, Pang L, Liang X, Zhu X, Cheng P, Li X, Xiao Y. Identifying bifurcated paths with differential function impact in glioblastomas evolution. Int J Cancer 2020; 147:3139-3151. [PMID: 32875565 DOI: 10.1002/ijc.33276] [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: 12/17/2019] [Revised: 08/19/2020] [Accepted: 08/19/2020] [Indexed: 11/10/2022]
Abstract
The evolutionary dynamics of human cancers has been investigated popularly and several bifurcated paths in cancer evolutionary trajectories are revealed to be with differential outcomes and phenotypes. However, whether such bifurcated paths exist in glioblastoma (GBM) remains unclear. In 385 GBM samples, through determining the clonal status of cancer driver events and inferring their temporal order, we constructed a temporal map of evolutionary trajectories at the patient population level. By investigating the differential impact on clinical outcome, we identified four key bifurcated paths, namely, "chromosome 10 copy number loss (ie, 10 loss) → chromosome 19 copy number gain (ie, 19 gain): 10 loss → 13q loss"; "10 loss → 19 gain: 10 loss → 15q loss"; "10 loss → 19 gain: 10 loss → 6q loss" and "10 loss → 19 gain: 10 loss → 16q loss". They formed a core multibranches path, with 10 loss being regarded as the common earliest event followed by 19 gain and four other departure events (13q loss, 15q loss, 6q loss and 16q loss), which may account for their difference in genome instability and patient survival time. Compared to "10 loss → 19 gain", the patients with "10 loss → 13q loss" had higher telomerase activity. Notably, there were obvious discrepancies in immune activity and immune cell infiltration level between patients with "10 loss → 13q/16q loss" and "10 loss → 19 gain", highlighting the bifurcated paths' effect on tumor immune microenvironment. In summary, our study identifies four key bifurcated paths in GBM for the first time, suggesting the feasibility of patient stratification and prognosis prediction based on key bifurcated paths.
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Affiliation(s)
- Yong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Aimin Xie
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Fei Quan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Xiaobo Hou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Jianlong Liao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Shiwei Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Lin Pang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Xin Liang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Xiaojing Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Peng Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China.,Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, Harbin, Heilongjiang, China
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China.,Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, Harbin, Heilongjiang, China
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35
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Clinical, Genomic, and Pharmacological Study of MYCN-Amplified RB1 Wild-Type Metastatic Retinoblastoma. Cancers (Basel) 2020; 12:cancers12092714. [PMID: 32971811 PMCID: PMC7565107 DOI: 10.3390/cancers12092714] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/11/2020] [Accepted: 08/23/2020] [Indexed: 12/15/2022] Open
Abstract
An uncommon subgroup of unilateral retinoblastomas with highly aggressive histological features, lacking aberrations in RB1 gene with high-level amplification of MYCN (MCYNamplRB1+/+) has only been described as intra-ocular cases treated with initial enucleation. Here, we present a comprehensive clinical, genomic, and pharmacological analysis of two cases of MCYNamplRB1+/+ with orbital and cervical lymph node involvement, but no central nervous system spread, rapidly progressing to fatal disease due to chemoresistance. Both patients showed in common MYCN high amplification and chromosome 16q and 17p loss. A somatic mutation in TP53, in homozygosis by LOH, and high chromosomal instability leading to aneuploidy was identified in the primary ocular tumor and sites of dissemination of one patient. High-throughput pharmacological screening was performed in a primary cell line derived from the lymph node dissemination of one case. This cell line showed resistance to broad spectrum chemotherapy consistent with the patient's poor response but sensitivity to the synergistic effects of panobinostat-bortezomib and carboplatin-panobinostat associations. From these cells we established a cell line derived xenograft model that closely recapitulated the tumor dissemination pattern of the patient and served to evaluate whether triple chemotherapy significantly prolonged survival of the animals. We report novel genomic alterations in two cases of metastatic MCYNamplRB1+/+ that may be associated with chemotherapy resistance and in vitro/in vivo models that serve as basis for tailoring therapy in these cases.
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36
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Yasui H, Valind A, Karlsson J, Pietras C, Jansson C, Wille J, Romerius P, Backman T, Gisselsson D. A dynamic mutational landscape associated with an inter-regionally diverse immune response in malignant rhabdoid tumour. J Pathol 2020; 252:22-28. [PMID: 32542645 DOI: 10.1002/path.5490] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/11/2020] [Accepted: 06/03/2020] [Indexed: 12/19/2022]
Abstract
Malignant rhabdoid tumour (MRT) is a childhood neoplasm of high malignancy characterised by biallelic mutation and/or loss of the epigenetic master regulator SMARCB1, accompanied by no or few other oncogenic drivers. In spite of their generally low mutational burden, an intratumoural T-cell response has been reported in a subset of MRTs, indicating that immune checkpoint inhibition may be considered a viable therapy option for some patients. We assess here the evolution over time and space of predicted neoantigens and indicators of immune checkpoint status in two MRT patients who progressed under treatment. Both patients showed an accumulation of novel clonal and subclonal mutations, including predicted neoantigens, in metastases compared to their inferred ancestral clones in the primary tumours. The first patient had peritoneal metastases from an MRT of the liver. Clonal deconvolution revealed polyclonal seeding from the primary tumour to a single metastatic site, followed by a local subclonal burst of mutations. The second patient had a renal MRT with multiple pulmonary metastases, each of which could be traced back to a single genetically unique founder cell, with formation of novel subclones in two metastases. Both patients showed a regionally heterogeneous landscape of predicted neoantigens and of tumour-infiltrating lymphocytes expressing CD8 and PD1. In both patients, some tumour regions fulfilled established criteria for PD-L1 positivity (> 1% of tumour cells), while others did not. This suggests that even in a tumour type like MRT, with a single driver mutation, there can be heterogeneity in neoantigen repertoire, immune response, and biomarkers for checkpoint blockade among sampled locations. This must be taken into account when assessing progressed MRT patients for checkpoint inhibition therapy. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Hiroaki Yasui
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Department of Obstetrics and Gynaecology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Anders Valind
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Department of Paediatrics, Skåne University Hospital, Lund, Sweden
| | - Jenny Karlsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Christina Pietras
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Caroline Jansson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Joakim Wille
- Paediatric Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Patrik Romerius
- Paediatric Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Torbjörn Backman
- Paediatric Surgery, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - David Gisselsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
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37
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Terry RL, Meyran D, Ziegler DS, Haber M, Ekert PG, Trapani JA, Neeson PJ. Immune profiling of pediatric solid tumors. J Clin Invest 2020; 130:3391-3402. [PMID: 32538896 PMCID: PMC7324195 DOI: 10.1172/jci137181] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Pediatric cancers, particularly high-risk solid tumors, urgently need effective and specific therapies. Their outlook has not appreciably improved in decades. Immunotherapies such as immune checkpoint inhibitors offer much promise, but most are only approved for use in adults. Though several hundred clinical trials have tested immune-based approaches in childhood cancers, few have been guided by biomarkers or clinical-grade assays developed to predict patient response and, ultimately, to help select those most likely to benefit. There is extensive evidence in adults to show that immune profiling has substantial predictive value, but few studies focus on childhood tumors, because of the relatively small disease population and restricted use of immune-based therapies. For instance, only one published study has retrospectively examined the immune profiles of pediatric brain tumors after immunotherapy. Furthermore, application and integration of advanced multiplex techniques has been extremely limited. Here, we review the current status of immune profiling of pediatric solid tumors, with emphasis on tumor types that represent enormous unmet clinical need, primarily in the context of immune checkpoint inhibitor therapy. Translating optimized and informative immune profiling into standard practice and access to personalized combination therapy will be critical if childhood cancers are to be treated effectively and affordably.
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Affiliation(s)
- Rachael L. Terry
- Children’s Cancer Institute, Randwick, New South Wales, Australia
| | - Deborah Meyran
- Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia
- Université de Paris, Inserm, U976 HIPI Unit, Institut de Recherche Saint-Louis, Paris, France
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - David S. Ziegler
- Children’s Cancer Institute, Randwick, New South Wales, Australia
- Kids Cancer Center, Sydney Children’s Hospital, Randwick, New South Wales, Australia
| | - Michelle Haber
- Children’s Cancer Institute, Randwick, New South Wales, Australia
| | - Paul G. Ekert
- Children’s Cancer Institute, Randwick, New South Wales, Australia
- Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia
| | - Joseph A. Trapani
- Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Paul J. Neeson
- Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
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38
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Hau SO, Petersson A, Nodin B, Karnevi E, Boman K, Williamsson C, Eberhard J, Leandersson K, Gisselsson D, Heby M, Jirström K. Chemotherapy, host response and molecular dynamics in periampullary cancer: the CHAMP study. BMC Cancer 2020; 20:308. [PMID: 32293352 PMCID: PMC7161011 DOI: 10.1186/s12885-020-06807-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 03/30/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Pancreatic cancer is a devastating disease with a dismal prognosis. Despite profound medical advances in systemic therapies for other types of aggressive tumours during recent years, a diagnosis of pancreatic cancer is still often synonymous with a fatal outcome. The term periampullary cancer includes pancreatic cancer and applies to the group of tumours found in proximity to the ampulla of Vater. Molecular events and immune response in the host during chemotherapy remain largely unexplored in this group of tumours. Therefore, the "Chemotherapy, Host Response and Molecular Dynamics in Periampullary Cancer (CHAMP)" study aims to monitor these processes to gain new insight into this perplexing disease. METHODS The CHAMP study is a prospective, single-arm observational study. All patients diagnosed with pancreatic or other periampullary adenocarcinoma undergoing adjuvant or palliative chemotherapy treatment in the Department of Oncology, Skåne University Hospital, are invited to participate. Clinical and pathological data will be compiled at study entry. A single tissue microarray (TMA) block is constructed for each patient with a resected tumour and blood samples are drawn before, during and after chemotherapy in order to sample peripheral blood mononuclear cells (PBMC), cytokines and circulating tumour DNA (ctDNA). Next generation sequencing will be performed on tumour tissue and ctDNA to detect changes in the clonal landscape over space and time. DISCUSSION Despite the recent emergence of some promising biomarkers for periampullary cancer, there has been a lack of success in clinical implementation. Cancer cells continuously adapt and become resistant to treatment during chemotherapy. To be able to keep pace with and hopefully overtake this rapid evolution we must, with the help of new diagnostic tools, be ready to adapt and alter treatment accordingly. It seems to us that the only way forward is to gain a better understanding of the dynamics of the disease during treatment. With insights gained from the CHAMP study we hope to find answers to key questions in this largely unexplored territory. TRIAL REGISTRATION This study has been registered 30th October 2018 at clinicaltrials.gov as NCT03724994.
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Affiliation(s)
- Sofie Olsson Hau
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences, Lund University, SE-221 85, Lund, Sweden.
| | - Alexandra Petersson
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences, Lund University, SE-221 85, Lund, Sweden
| | - Björn Nodin
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences, Lund University, SE-221 85, Lund, Sweden
| | - Emelie Karnevi
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences, Lund University, SE-221 85, Lund, Sweden
| | - Karolina Boman
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences, Lund University, SE-221 85, Lund, Sweden
| | - Caroline Williamsson
- Division of Surgery, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Jakob Eberhard
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences, Lund University, SE-221 85, Lund, Sweden
| | - Karin Leandersson
- Cancer Immunology, Department of Translational Medicine, Lund University, Malmö, Sweden
| | - David Gisselsson
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences, Lund University, SE-221 85, Lund, Sweden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Margareta Heby
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences, Lund University, SE-221 85, Lund, Sweden
| | - Karin Jirström
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences, Lund University, SE-221 85, Lund, Sweden
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39
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Calandrini C, Schutgens F, Oka R, Margaritis T, Candelli T, Mathijsen L, Ammerlaan C, van Ineveld RL, Derakhshan S, de Haan S, Dolman E, Lijnzaad P, Custers L, Begthel H, Kerstens HHD, Visser LL, Rookmaaker M, Verhaar M, Tytgat GAM, Kemmeren P, de Krijger RR, Al-Saadi R, Pritchard-Jones K, Kool M, Rios AC, van den Heuvel-Eibrink MM, Molenaar JJ, van Boxtel R, Holstege FCP, Clevers H, Drost J. An organoid biobank for childhood kidney cancers that captures disease and tissue heterogeneity. Nat Commun 2020; 11:1310. [PMID: 32161258 PMCID: PMC7066173 DOI: 10.1038/s41467-020-15155-6] [Citation(s) in RCA: 159] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 02/21/2020] [Indexed: 01/02/2023] Open
Abstract
Kidney tumours are among the most common solid tumours in children, comprising distinct subtypes differing in many aspects, including cell-of-origin, genetics, and pathology. Pre-clinical cell models capturing the disease heterogeneity are currently lacking. Here, we describe the first paediatric cancer organoid biobank. It contains tumour and matching normal kidney organoids from over 50 children with different subtypes of kidney cancer, including Wilms tumours, malignant rhabdoid tumours, renal cell carcinomas, and congenital mesoblastic nephromas. Paediatric kidney tumour organoids retain key properties of native tumours, useful for revealing patient-specific drug sensitivities. Using single cell RNA-sequencing and high resolution 3D imaging, we further demonstrate that organoid cultures derived from Wilms tumours consist of multiple different cell types, including epithelial, stromal and blastemal-like cells. Our organoid biobank captures the heterogeneity of paediatric kidney tumours, providing a representative collection of well-characterised models for basic cancer research, drug-screening and personalised medicine. Pre-clinical cell culture models capturing the heterogeneity of childhood kidney tumours are limited. Here, the authors establish and characterise an organoid biobank of tumour and matched normal organoid cultures from over 50 children with different subtypes of kidney cancer.
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Affiliation(s)
- Camilla Calandrini
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Frans Schutgens
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.,University Medical Center, Department of Nephrology and Hypertension, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Rurika Oka
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Thanasis Margaritis
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Tito Candelli
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Luka Mathijsen
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Carola Ammerlaan
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.,University Medical Center, Department of Nephrology and Hypertension, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Ravian L van Ineveld
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Sepide Derakhshan
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Sanne de Haan
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Emmy Dolman
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Philip Lijnzaad
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Lars Custers
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Harry Begthel
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Hindrik H D Kerstens
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Lindy L Visser
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Maarten Rookmaaker
- University Medical Center, Department of Nephrology and Hypertension, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Marianne Verhaar
- University Medical Center, Department of Nephrology and Hypertension, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Godelieve A M Tytgat
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Patrick Kemmeren
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Ronald R de Krijger
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands.,University Medical Center, Department of Pathology, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Reem Al-Saadi
- University College London, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London, WC1N 1EH, UK
| | - Kathy Pritchard-Jones
- University College London, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London, WC1N 1EH, UK
| | - Marcel Kool
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands.,Hopp Children's Cancer Center (KiTZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Research Consortium (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Anne C Rios
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | | | - Jan J Molenaar
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Ruben van Boxtel
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Frank C P Holstege
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Hans Clevers
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands.,Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Jarno Drost
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands.
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40
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Andersson N, Bakker B, Karlsson J, Valind A, Holmquist Mengelbier L, Spierings DCJ, Foijer F, Gisselsson D. Extensive Clonal Branching Shapes the Evolutionary History of High-Risk Pediatric Cancers. Cancer Res 2020; 80:1512-1523. [PMID: 32041836 DOI: 10.1158/0008-5472.can-19-3468] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/18/2019] [Accepted: 02/04/2020] [Indexed: 11/16/2022]
Abstract
Darwinian evolution of tumor cells remains underexplored in childhood cancer. We here reconstruct the evolutionary histories of 56 pediatric primary tumors, including 24 neuroblastomas, 24 Wilms tumors, and 8 rhabdomyosarcomas. Whole-genome copy-number and whole-exome mutational profiling of multiple regions per tumor were performed, followed by clonal deconvolution to reconstruct a phylogenetic tree for each tumor. Overall, 88% of the tumors exhibited genetic variation among primary tumor regions. This variability typically emerged through collateral phylogenetic branching, leading to spatial variability in the distribution of more than 50% (96/173) of detected diagnostically informative genetic aberrations. Single-cell sequencing of 547 individual cancer cells from eight solid pediatric tumors confirmed branching evolution to be a fundamental underlying principle of genetic variation in all cases. Strikingly, cell-to-cell genetic diversity was almost twice as high in aggressive compared with clinically favorable tumors (median Simpson index of diversity 0.45 vs. 0.88; P = 0.029). Similarly, a comparison of multiregional sampling data from a total of 274 tumor regions showed that new phylogenetic branches emerge at a higher frequency per sample and carry a higher mutational load in high-risk than in low-risk tumors. Timelines based on spatial genetic variation showed that the mutations most influencing relapse risk occur at initiation of clonal expansion in neuroblastoma and rhabdomyosarcoma, whereas in Wilms tumor, they are late events. Thus, from an evolutionary standpoint, some high-risk childhood cancers are born bad, whereas others grow worse over time. SIGNIFICANCE: Different pediatric cancers with a high risk of relapse share a common generic pattern of extensively branching evolution of somatic mutations. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/7/1512/F1.large.jpg.
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Affiliation(s)
- Natalie Andersson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Bjorn Bakker
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jenny Karlsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Anders Valind
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Department of Pediatrics, Skåne University Hospital, Lund, Sweden
| | | | - Diana C J Spierings
- 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
| | - David Gisselsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden. .,Division of Oncology-Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Clinical Genetics and Pathology, Laboratory Medicine, Lund University Hospital, Skåne Healthcare Region, Lund, Sweden
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41
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Murphy AJ, Chen X, Pinto EM, Williams JS, Clay MR, Pounds SB, Cao X, Shi L, Lin T, Neale G, Morton CL, Woolard MA, Mulder HL, Gil HJ, Rehg JE, Billups CA, Harlow ML, Dome JS, Houghton PJ, Easton J, Zhang J, George RE, Zambetti GP, Davidoff AM. Forty-five patient-derived xenografts capture the clinical and biological heterogeneity of Wilms tumor. Nat Commun 2019; 10:5806. [PMID: 31862972 PMCID: PMC6925259 DOI: 10.1038/s41467-019-13646-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 11/19/2019] [Indexed: 12/22/2022] Open
Abstract
The lack of model systems has limited the preclinical discovery and testing of therapies for Wilms tumor (WT) patients who have poor outcomes. Herein, we establish 45 heterotopic WT patient-derived xenografts (WTPDX) in CB17 scid-/- mice that capture the biological heterogeneity of Wilms tumor (WT). Among these 45 total WTPDX, 6 from patients with diffuse anaplastic tumors, 9 from patients who experienced disease relapse, and 13 from patients with bilateral disease are included. Early passage WTPDX show evidence of clonal selection, clonal evolution and enrichment of blastemal gene expression. Favorable histology WTPDX are sensitive, whereas unfavorable histology WTPDX are resistant to conventional chemotherapy with vincristine, actinomycin-D, and doxorubicin given singly or in combination. This WTPDX library is a unique scientific resource that retains the spectrum of biological heterogeneity present in WT and provides an essential tool to test targeted therapies for WT patient groups with poor outcomes. The progress in pre-clinical drug discovery for Wilms tumor (WT) is limited by a lack of disease models. Here, the authors develop 45 heterotopic WT patient-derived xenografts including several anaplastic models that recapitulate the biological heterogeneity of WT, and propose this as a resource for evaluating future therapeutics for WT.
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Affiliation(s)
- Andrew J Murphy
- Department of Surgery, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA. .,Division of Pediatric Surgery, Department of Surgery, University of Tennessee Health Science Center, 910 Madison Ave. 2nd floor, Memphis, TN, 38163, USA.
| | - Xiang Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Emilia M Pinto
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Justin S Williams
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Michael R Clay
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Stanley B Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Xueyuan Cao
- Department of Biostatistics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.,College of Nursing, University of Tennessee Health Science Center, 920 Madison Ave, Memphis, TN, 38163, USA
| | - Lei Shi
- Department of Biostatistics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Tong Lin
- Department of Biostatistics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Geoffrey Neale
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Christopher L Morton
- Department of Surgery, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Mary A Woolard
- Department of Surgery, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Heather L Mulder
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Hyea Jin Gil
- Department of Surgery, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Jerold E Rehg
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Catherine A Billups
- Department of Biostatistics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Matthew L Harlow
- Department of Pediatric Hematology and Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, 450 Brookline Avenue, Room D640E, Boston, MA, 02215, USA
| | - Jeffrey S Dome
- Division of Oncology, Children's National Medical Center, 111 Michigan Avenue NW, Washington, DC, 20010, USA
| | - Peter J Houghton
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, 8403 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Rani E George
- Department of Pediatric Hematology and Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, 450 Brookline Avenue, Room D640E, Boston, MA, 02215, USA
| | - Gerard P Zambetti
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Andrew M Davidoff
- Department of Surgery, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.,Division of Pediatric Surgery, Department of Surgery, University of Tennessee Health Science Center, 910 Madison Ave. 2nd floor, Memphis, TN, 38163, USA
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42
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Mohlin S, Hansson K, Radke K, Martinez S, Blanco-Apiricio C, Garcia-Ruiz C, Welinder C, Esfandyari J, O'Neill M, Pastor J, von Stedingk K, Bexell D. Anti-tumor effects of PIM/PI3K/mTOR triple kinase inhibitor IBL-302 in neuroblastoma. EMBO Mol Med 2019; 11:e10058. [PMID: 31310053 PMCID: PMC6685085 DOI: 10.15252/emmm.201810058] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 06/04/2019] [Accepted: 06/24/2019] [Indexed: 11/12/2022] Open
Abstract
The PI3K pathway is a major driver of cancer progression. However, clinical resistance to PI3K inhibition is common. IBL‐302 is a novel highly specific triple PIM, PI3K, and mTOR inhibitor. Screening IBL‐302 in over 700 cell lines representing 47 tumor types identified neuroblastoma as a strong candidate for PIM/PI3K/mTOR inhibition. IBL‐302 was more effective than single PI3K inhibition in vitro, and IBL‐302 treatment of neuroblastoma patient‐derived xenograft (PDX) cells induced apoptosis, differentiated tumor cells, and decreased N‐Myc protein levels. IBL‐302 further enhanced the effect of the common cytotoxic chemotherapies cisplatin, doxorubicin, and etoposide. Global genome, proteome, and phospho‐proteome analyses identified crucial biological processes, including cell motility and apoptosis, targeted by IBL‐302 treatment. While IBL‐302 treatment alone reduced tumor growth in vivo, combination therapy with low‐dose cisplatin inhibited neuroblastoma PDX growth. Complementing conventional chemotherapy treatment with PIM/PI3K/mTOR inhibition has the potential to improve clinical outcomes and reduce severe late effects in children with high‐risk neuroblastoma.
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Affiliation(s)
- Sofie Mohlin
- Division of Pediatrics, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Karin Hansson
- Department of Laboratory Medicine, Translational Cancer Research, Lund University Cancer Center, Lund University, Lund, Sweden
| | - Katarzyna Radke
- Department of Laboratory Medicine, Translational Cancer Research, Lund University Cancer Center, Lund University, Lund, Sweden
| | - Sonia Martinez
- Experimental Therapeutics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Carmen Blanco-Apiricio
- Experimental Therapeutics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Cristian Garcia-Ruiz
- Department of Laboratory Medicine, Translational Cancer Research, Lund University Cancer Center, Lund University, Lund, Sweden
| | - Charlotte Welinder
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Javanshir Esfandyari
- Department of Laboratory Medicine, Translational Cancer Research, Lund University Cancer Center, Lund University, Lund, Sweden
| | | | - Joaquin Pastor
- Experimental Therapeutics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Kristoffer von Stedingk
- Division of Pediatrics, Department of Clinical Sciences, Lund University, Lund, Sweden.,Department of Oncogenomics, University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Daniel Bexell
- Department of Laboratory Medicine, Translational Cancer Research, Lund University Cancer Center, Lund University, Lund, Sweden
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43
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Abstract
Wilms tumour is the most common renal malignancy of childhood. The disease is curable in the majority of cases, albeit at considerable cost in terms of late treatment-related effects in some children. However, one in ten children with Wilms tumour will die of their disease despite modern treatment approaches. The genetic changes that underpin Wilms tumour have been defined by studies of familial cases and by unbiased DNA sequencing of tumour genomes. Together, these approaches have defined the landscape of cancer genes that are operative in Wilms tumour, many of which are intricately linked to the control of fetal nephrogenesis. Advances in our understanding of the germline and somatic genetic changes that underlie Wilms tumour may translate into better patient outcomes. Improvements in risk stratification have already been seen through the introduction of molecular biomarkers into clinical practice. A host of additional biomarkers are due to undergo clinical validation. Identifying actionable mutations has led to potential new targets, with some novel compounds undergoing testing in early phase trials. Avenues that warrant further exploration include targeting Wilms tumour cancer genes with a non-redundant role in nephrogenesis and targeting the fetal renal transcriptome.
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Affiliation(s)
- Taryn Dora Treger
- Wellcome Sanger Institute, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Tanzina Chowdhury
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Kathy Pritchard-Jones
- UCL Great Ormond Street Institute of Child Health, London, UK.
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.
| | - Sam Behjati
- Wellcome Sanger Institute, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
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44
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Fittall MW, Van Loo P. Translating insights into tumor evolution to clinical practice: promises and challenges. Genome Med 2019; 11:20. [PMID: 30925887 PMCID: PMC6440005 DOI: 10.1186/s13073-019-0632-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Accelerating technological advances have allowed the widespread genomic profiling of tumors. As yet, however, the vast catalogues of mutations that have been identified have made only a modest impact on clinical medicine. Massively parallel sequencing has informed our understanding of the genetic evolution and heterogeneity of cancers, allowing us to place these mutational catalogues into a meaningful context. Here, we review the methods used to measure tumor evolution and heterogeneity, and the potential and challenges for translating the insights gained to achieve clinical impact for cancer therapy, monitoring, early detection, risk stratification, and prevention. We discuss how tumor evolution can guide cancer therapy by targeting clonal and subclonal mutations both individually and in combination. Circulating tumor DNA and circulating tumor cells can be leveraged for monitoring the efficacy of therapy and for tracking the emergence of resistant subclones. The evolutionary history of tumors can be deduced for late-stage cancers, either directly by sampling precursor lesions or by leveraging computational approaches to infer the timing of driver events. This approach can identify recurrent early driver mutations that represent promising avenues for future early detection strategies. Emerging evidence suggests that mutational processes and complex clonal dynamics are active even in normal development and aging. This will make discriminating developing malignant neoplasms from normal aging cell lineages a challenge. Furthermore, insight into signatures of mutational processes that are active early in tumor evolution may allow the development of cancer-prevention approaches. Research and clinical studies that incorporate an appreciation of the complex evolutionary patterns in tumors will not only produce more meaningful genomic data, but also better exploit the vulnerabilities of cancer, resulting in improved treatment outcomes.
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Affiliation(s)
- Matthew W Fittall
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,University College London Cancer Institute, 72 Huntley Street, London, WC1E 6DD, UK.,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Peter Van Loo
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK. .,University of Leuven, Herestraat 49, B-3000, Leuven, Belgium.
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45
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Sweet-Cordero EA, Biegel JA. The genomic landscape of pediatric cancers: Implications for diagnosis and treatment. Science 2019; 363:1170-1175. [PMID: 30872516 PMCID: PMC7757338 DOI: 10.1126/science.aaw3535] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The past decade has witnessed a major increase in our understanding of the genetic underpinnings of childhood cancer. Genomic sequencing studies have highlighted key differences between pediatric and adult cancers. Whereas many adult cancers are characterized by a high number of somatic mutations, pediatric cancers typically have few somatic mutations but a higher prevalence of germline alterations in cancer predisposition genes. Also noteworthy is the remarkable heterogeneity in the types of genetic alterations that likely drive the growth of pediatric cancers, including copy number alterations, gene fusions, enhancer hijacking events, and chromoplexy. Because most studies have genetically profiled pediatric cancers only at diagnosis, the mechanisms underlying tumor progression, therapy resistance, and metastasis remain poorly understood. We discuss evidence that points to a need for more integrative approaches aimed at identifying driver events in pediatric cancers at both diagnosis and relapse. We also provide an overview of key aspects of germline predisposition for cancer in this age group.
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Affiliation(s)
- E Alejandro Sweet-Cordero
- Department of Pediatrics, Division of Hematology and Oncology, University of California, San Francisco, CA 94158, USA.
| | - Jaclyn A Biegel
- Department of Pathology and Laboratory Medicine, Children's Hospital of Los Angeles, and Keck School of Medicine, University of Southern California, Los Angeles, CA 90027, USA.
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46
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von Stedingk K, Gisselsson D, Bexell D. Multidimensional intratumour heterogeneity in neuroblastoma. Oncotarget 2019; 10:3-5. [PMID: 30713595 PMCID: PMC6343759 DOI: 10.18632/oncotarget.26524] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 12/20/2018] [Indexed: 12/16/2022] Open
Affiliation(s)
- Kristoffer von Stedingk
- Daniel Bexell: Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University, Lund, Sweden.,Kristoffer von Stedingk: Division of Pediatric Oncology, Department of Clinical Sciences, Lund University, University Hospital, Lund, Sweden; Department of Oncogenomics, Amsterdam UMC, location AMC, University of Amsterdam, The Netherlands
| | - David Gisselsson
- Daniel Bexell: Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University, Lund, Sweden.,Kristoffer von Stedingk: Division of Pediatric Oncology, Department of Clinical Sciences, Lund University, University Hospital, Lund, Sweden; Department of Oncogenomics, Amsterdam UMC, location AMC, University of Amsterdam, The Netherlands
| | - Daniel Bexell
- Daniel Bexell: Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University, Lund, Sweden.,Kristoffer von Stedingk: Division of Pediatric Oncology, Department of Clinical Sciences, Lund University, University Hospital, Lund, Sweden; Department of Oncogenomics, Amsterdam UMC, location AMC, University of Amsterdam, The Netherlands
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47
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Gisselsson D, Lichtenzstejn D, Kachko P, Karlsson J, Manor E, Mai S. Clonal evolution through genetic bottlenecks and telomere attrition: Potential threats to in vitro data reproducibility. Genes Chromosomes Cancer 2018; 58:452-461. [PMID: 30255964 DOI: 10.1002/gcc.22685] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/20/2018] [Accepted: 09/20/2018] [Indexed: 12/20/2022] Open
Abstract
Tissue cultures of immortalized human cells, also known as established cell lines, are broadly accessible and cost-efficient tools for biomedical research. We here review potential genetic sources of systematic error in cell line experiments due to clonal evolution in vitro. In particular, the authors highlight alterations in telomere function over prolonged culture and population bottlenecks, respectively, as two commonly overlooked phenomena that can result in significant alterations in cell line genotypes over just one or a few passages in vitro. These alterations may include changes in mutation status of oncogenes and large scale chromosomal imbalances. We introduce a simple list of factors to be avoided in order to reduce the risk of data misinterpretation due to clonal evolution, including unacknowledged in vitro selection pressures, prolonged culture per se, harsh population size reductions, experiments at early phases after establishment, and the employment of cell lines not sufficiently analyzed by high resolution genetic techniques.
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Affiliation(s)
- David Gisselsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Division of Oncology-Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Daniel Lichtenzstejn
- Cell Biology, Research Institute of Oncology and Hematology, The Genomic Centre for Cancer Research and Diagnosis, CancerCare Manitoba, University of Manitoba, Winnipeg, Canada
| | - Polina Kachko
- Shraga Segal Department of Microbiology, Immunology and Genetics, Ben Gurion University of the Negev, Beer-Sheva, Israel
| | - Jenny Karlsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Esther Manor
- Shraga Segal Department of Microbiology, Immunology and Genetics, Ben Gurion University of the Negev, Beer-Sheva, Israel
| | - Sabine Mai
- Cell Biology, Research Institute of Oncology and Hematology, The Genomic Centre for Cancer Research and Diagnosis, CancerCare Manitoba, University of Manitoba, Winnipeg, Canada
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48
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Valind A, Wessman S, Pal N, Karlsson J, Jonson T, Sandstedt B, Gisselsson D. Convergent evolution of 11p allelic loss in multifocal Wilms tumors arising in WT1 mutation carriers. Pediatr Blood Cancer 2018; 65:e27301. [PMID: 29968962 DOI: 10.1002/pbc.27301] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 05/31/2018] [Accepted: 06/01/2018] [Indexed: 11/08/2022]
Abstract
Wilms tumors in patients with constitutional WT1 mutations are examples of Knudson's tumor suppressor paradigm, with somatic inactivation of the second allele occurring through 11p loss of heterozygosity. The time point of this second hit has remained unknown. We analyzed seven Wilms tumors from two patients with constitutional WT1 mutations by whole exome sequencing and genomic array. All tumors exhibited wild type WT1 loss through uniparental isodisomy. Each tumor had a unique genomic breakpoint in 11p, typically accompanied by a private activating mutation of CTNNB1. Hence, convergent evolution rather than field carcinogenesis underlies multifocal tumors in WT1 mutation carriers.
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Affiliation(s)
- Anders Valind
- Divison of Clinical Genetics, Department of Laboratory Medicine, BMC C13, Lund University, Lund, Sweden
| | - Sandra Wessman
- Department of Pathology, Karolinska University Hospital, Solna, Sweden
| | - Niklas Pal
- Department of Women's and Children's Health, Karolinska Institute, Stockholm, Sweden
| | - Jenny Karlsson
- Divison of Clinical Genetics, Department of Laboratory Medicine, BMC C13, Lund University, Lund, Sweden
| | - Tord Jonson
- Divison of Clinical Genetics, Department of Laboratory Medicine, BMC C13, Lund University, Lund, Sweden
| | - Bengt Sandstedt
- Department of Women's and Children's Health, Karolinska Institute, Stockholm, Sweden
| | - David Gisselsson
- Divison of Clinical Genetics, Department of Laboratory Medicine, BMC C13, Lund University, Lund, Sweden.,Division of Oncology and Pathology, Department of Clinical Sciences, Skåne University Hospital, Lund, Sweden
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49
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Valind A, Öra I, Mertens F, Gisselsson D. Neuroblastoma with flat genomic profile: a question of representativity? BMJ Case Rep 2018; 2018:bcr-2018-225568. [PMID: 30196258 DOI: 10.1136/bcr-2018-225568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Neuroblastoma is one of the most common paediatric malignancies. Detection of somatic genetic alterations in this tumour is instrumental for its risk stratification and treatment. On the other hand, an absence of detected chromosomal imbalances in neuroblastoma biopsies is difficult to interpret because it is unclear whether this situation truly reflects the tumour genome or if it is due to suboptimal sampling. We here present a neuroblastoma in the left adrenal of a newborn. The tumour was subjected to single-nucleotide polymorphism array analysis of five tumour regions with >80% tumour cells in histological mirror sections. This revealed no aberrations compared with a normal reference sample from the patient. Whole exome sequencing identified two single-nucleotide variants present in most tumour regions, corroborating that the tumour resulted from monoclonal expansion. Our data provide proof-of-principle that rare cases of neuroblastoma can have a normal whole genome copy number and allelic profile.
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Affiliation(s)
- Anders Valind
- Division of Clinical Genetics, Lunds Universitet, Lund, Sweden
| | - Ingrid Öra
- Division of Clinical Genetics, Lunds Universitet, Lund, Sweden
| | - Fredrik Mertens
- Division of Clinical Genetics, Lunds Universitet, Lund, Sweden
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Braekeveldt N, von Stedingk K, Fransson S, Martinez-Monleon A, Lindgren D, Axelson H, Levander F, Willforss J, Hansson K, Øra I, Backman T, Börjesson A, Beckman S, Esfandyari J, Berbegall AP, Noguera R, Karlsson J, Koster J, Martinsson T, Gisselsson D, Påhlman S, Bexell D. Patient-Derived Xenograft Models Reveal Intratumor Heterogeneity and Temporal Stability in Neuroblastoma. Cancer Res 2018; 78:5958-5969. [PMID: 30154149 DOI: 10.1158/0008-5472.can-18-0527] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 07/06/2018] [Accepted: 08/23/2018] [Indexed: 11/16/2022]
Abstract
Patient-derived xenografts (PDX) and the Avatar, a single PDX mirroring an individual patient, are emerging tools in preclinical cancer research. However, the consequences of intratumor heterogeneity for PDX modeling of biomarkers, target identification, and treatment decisions remain underexplored. In this study, we undertook serial passaging and comprehensive molecular analysis of neuroblastoma orthotopic PDXs, which revealed strong intrinsic genetic, transcriptional, and phenotypic stability for more than 2 years. The PDXs showed preserved neuroblastoma-associated gene signatures that correlated with poor clinical outcome in a large cohort of patients with neuroblastoma. Furthermore, we captured spatial intratumor heterogeneity using ten PDXs from a single high-risk patient tumor. We observed diverse growth rates, transcriptional, proteomic, and phosphoproteomic profiles. PDX-derived transcriptional profiles were associated with diverse clinical characteristics in patients with high-risk neuroblastoma. These data suggest that high-risk neuroblastoma contains elements of both temporal stability and spatial intratumor heterogeneity, the latter of which complicates clinical translation of personalized PDX-Avatar studies into preclinical cancer research.Significance: These findings underpin the complexity of PDX modeling as a means to advance translational applications against neuroblastoma. Cancer Res; 78(20); 5958-69. ©2018 AACR.
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Affiliation(s)
- Noémie Braekeveldt
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University, Lund, Sweden
| | - Kristoffer von Stedingk
- Department of Clinical Sciences, Division of Pediatric Oncology, Lund University, University Hospital, Lund, Sweden. .,Department of Oncogenomics, Amsterdam UMC, University of Amsterdam, the Netherlands
| | - Susanne Fransson
- Department of Pathology and Genetics, University of Gothenburg, Gothenburg, Sweden
| | | | - David Lindgren
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University, Lund, Sweden
| | - Håkan Axelson
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University, Lund, Sweden
| | | | - Jakob Willforss
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Karin Hansson
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Ingrid Øra
- Department of Clinical Sciences, Division of Pediatric Oncology, Lund University, University Hospital, Lund, Sweden
| | - Torbjörn Backman
- Division of Pediatric Surgery, Department of Clinical Sciences, Lund University, University Hospital, Lund, Sweden
| | - Anna Börjesson
- Division of Pediatric Surgery, Department of Clinical Sciences, Lund University, University Hospital, Lund, Sweden
| | - Siv Beckman
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University, Lund, Sweden
| | - Javanshir Esfandyari
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University, Lund, Sweden
| | - Ana P Berbegall
- Department of Pathology, Medical School, University of Valencia/INCLIVA/CIBERONC, Madrid, Spain
| | - Rosa Noguera
- Department of Pathology, Medical School, University of Valencia/INCLIVA/CIBERONC, Madrid, Spain
| | - Jenny Karlsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Jan Koster
- Department of Oncogenomics, Amsterdam UMC, University of Amsterdam, the Netherlands
| | - Tommy Martinsson
- Department of Pathology and Genetics, University of Gothenburg, Gothenburg, Sweden
| | - David Gisselsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Department of Pathology, Laboratory Medicine, Medical Services, University Hospital, Lund, Sweden
| | - Sven Påhlman
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University, Lund, Sweden
| | - Daniel Bexell
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University, Lund, Sweden. .,Department of Pathology, Laboratory Medicine, Medical Services, University Hospital, Lund, Sweden
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