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Macarthur JI, Carlstrom L, Hannan CJ, Wadeson A, Driscoll C, Neff B, Carlson ML, Rutherford SA, Link MJ, van Gompel JJ. Radiation-Associated Vestibular Schwannomas: Case Series and Literature Review. World Neurosurg 2024:S1878-8750(24)00876-3. [PMID: 38789032 DOI: 10.1016/j.wneu.2024.05.113] [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: 04/22/2024] [Revised: 05/17/2024] [Accepted: 05/18/2024] [Indexed: 05/26/2024]
Abstract
OBJECTIVES Radiation treatment, particularly at a young age, creates theoretical risk for long-term adverse radiation effects, including the development of malignancy. The literature is sparse on radiation-induced vestibular schwannomas (VSs). METHODS A retrospective review was performed for cases of suspected radiation-induced VS at 2 high-volume centers. Only cases where radiation included coverage of the posterior fossa were included with those diagnosed within 3 years of radiation treatment being excluded. Patient and tumor characteristics were collected. A systematic literature review was also performed for any previously published series on radiation-induced VS. RESULTS Eight cases of radiation-induced VS were identified with a median follow-up 125 months (range 7-131). The median age at incident radiation was 15 years (range 2-46). The median age at VS diagnosis was 57 years (range 26-83) with median interval from radiation to diagnosis of 51-years (range 15-66). The median tumor size was 6 mm (range 3-21). Two patients underwent surgical resection. Lesions were described as soft and highly vascular, with medium to high adherence to the facial nerve. Five articles with a total of 52 patients were identified, median age at VS diagnosis was 42-years (range 23-73) with a median interval from radiation to diagnosis of 19 years (range 15-23). CONCLUSIONS The development of VS following radiation exposure appears rare and our understanding of the condition remains incomplete. Further studies are required to determine the best management of these patients and determine whether there is a causative relationship between radiation exposure and the development of VS.
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Affiliation(s)
- Joshua I Macarthur
- Department of Neurosurgery, Manchester Centre for Clinical Neurosciences, Manchester, UK; Geoffrey Jefferson Brain Research Centre, University of Manchester, Manchester, UK.
| | - Lucas Carlstrom
- Department of Neurologic Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Cathal John Hannan
- Department of Neurosurgery, Manchester Centre for Clinical Neurosciences, Manchester, UK; Geoffrey Jefferson Brain Research Centre, University of Manchester, Manchester, UK
| | - Andrea Wadeson
- Department of Neurosurgery, Manchester Centre for Clinical Neurosciences, Manchester, UK
| | - Colin Driscoll
- Otolaryngology-Head and Neck Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Brian Neff
- Otolaryngology-Head and Neck Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Matthew L Carlson
- Otolaryngology-Head and Neck Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Scott A Rutherford
- Department of Neurosurgery, Manchester Centre for Clinical Neurosciences, Manchester, UK; Geoffrey Jefferson Brain Research Centre, University of Manchester, Manchester, UK
| | - Michael J Link
- Department of Neurologic Surgery, Mayo Clinic, Rochester, Minnesota, USA; Otolaryngology-Head and Neck Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Jamie J van Gompel
- Department of Neurologic Surgery, Mayo Clinic, Rochester, Minnesota, USA; Otolaryngology-Head and Neck Surgery, Mayo Clinic, Rochester, Minnesota, USA
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2
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Raj R, Kim HG, Xu M, Roach T, Liebner D, Konieczkowski D, Tinoco G. Clinical Characteristics, Patterns of Care, and Treatment Outcomes of Radiation-Associated Sarcomas. Cancers (Basel) 2024; 16:1918. [PMID: 38791996 PMCID: PMC11119080 DOI: 10.3390/cancers16101918] [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: 04/01/2024] [Revised: 05/16/2024] [Accepted: 05/16/2024] [Indexed: 05/26/2024] Open
Abstract
Radiation-associated sarcomas (RASs) are rare tumors with limited contemporary data to inform prognostication and management. We sought to identify the clinical presentation, patterns of care, and prognostic factors of RASs. RAS patients treated at a single institution from 2015 to 2021 were retrospectively reviewed for clinicopathologic variables, treatment strategies, and outcomes. Thirty-eight patients were identified with a median follow-up of 30.5 months. The median age at RAS diagnosis was 68.4 years (27.9-85.4), with a median latency from index radiotherapy (RT) of 9.1 years (3.7-46.3). RAS histologies included angiosarcoma (26%), undifferentiated pleomorphic sarcoma (21%), and osteosarcoma (18%). Most were high-grade (76%). Genomic profiling revealed low tumor mutational burden, frequent inactivating TP53 mutations (44%), CDKN2A deletions (26%), and MYC amplifications (22%), particularly in breast angiosarcomas. Of 38 patients, 33 presented with localized disease, 26 of whom were treated with curative intent. Overall, the median progression-free survival (PFS) was 9.5 months (1.4-34.7), and the overall survival (OS) was 11.1 months (0.6-31.6). Patients with localized vs. metastatic RASs had a longer PFS (HR, 3.0 [1.1-8.5]; p = 0.03) and OS (HR, 3.0 [1.04-8.68]; p = 0.03). Among localized RAS patients, high grade was associated with shorter OS (HR, 4.6 [1.04-20.30]; p = 0.03) and resection with longer OS (mean 58.8 vs. 6.1 months, HR, 0.1 [0.03-0.28]; p < 0.001). Among patients undergoing resection, negative margins were associated with improved OS (mean 71.0 vs. 15.5 months, HR, 5.1 [1.4-18.2]; p = 0.006). Patients with localized disease, particularly those undergoing R0 resection, demonstrated significantly better outcomes. Novel strategies are urgently needed to improve treatment outcomes in this challenging group of diseases.
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Affiliation(s)
- Rohit Raj
- Department of Radiation Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA; (R.R.); (D.K.)
| | - Han Gil Kim
- Department of Medical Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA; (H.G.K.); (M.X.); (D.L.)
| | - Menglin Xu
- Department of Medical Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA; (H.G.K.); (M.X.); (D.L.)
| | - Tyler Roach
- Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA;
| | - David Liebner
- Department of Medical Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA; (H.G.K.); (M.X.); (D.L.)
| | - David Konieczkowski
- Department of Radiation Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA; (R.R.); (D.K.)
| | - Gabriel Tinoco
- Department of Medical Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA; (H.G.K.); (M.X.); (D.L.)
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3
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Cox SN, Lo Giudice C, Lavecchia A, Poeta ML, Chiara M, Picardi E, Pesole G. Mitochondrial and Nuclear DNA Variants in Amyotrophic Lateral Sclerosis: Enrichment in the Mitochondrial Control Region and Sirtuin Pathway Genes in Spinal Cord Tissue. Biomolecules 2024; 14:411. [PMID: 38672428 PMCID: PMC11048214 DOI: 10.3390/biom14040411] [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: 02/01/2024] [Revised: 03/19/2024] [Accepted: 03/23/2024] [Indexed: 04/28/2024] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a progressive disease with prevalent mitochondrial dysfunctions affecting both upper and lower motor neurons in the motor cortex, brainstem, and spinal cord. Despite mitochondria having their own genome (mtDNA), in humans, most mitochondrial genes are encoded by the nuclear genome (nDNA). Our study aimed to simultaneously screen for nDNA and mtDNA genomes to assess for specific variant enrichment in ALS compared to control tissues. Here, we analysed whole exome (WES) and whole genome (WGS) sequencing data from spinal cord tissues, respectively, of 6 and 12 human donors. A total of 31,257 and 301,241 variants in nuclear-encoded mitochondrial genes were identified from WES and WGS, respectively, while mtDNA reads accounted for 73 and 332 variants. Despite technical differences, both datasets consistently revealed a specific enrichment of variants in the mitochondrial Control Region (CR) and in several of these genes directly associated with mitochondrial dynamics or with Sirtuin pathway genes within ALS tissues. Overall, our data support the hypothesis of a variant burden in specific genes, highlighting potential actionable targets for therapeutic interventions in ALS.
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Affiliation(s)
- Sharon Natasha Cox
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70126 Bari, Italy; (A.L.); (M.L.P.); (E.P.)
| | - Claudio Lo Giudice
- Institute of Biomedical Technologies, National Research Council, 70126 Bari, Italy;
| | - Anna Lavecchia
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70126 Bari, Italy; (A.L.); (M.L.P.); (E.P.)
| | - Maria Luana Poeta
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70126 Bari, Italy; (A.L.); (M.L.P.); (E.P.)
| | - Matteo Chiara
- Department of Biosciences, University of Milan, 20133 Milan, Italy;
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, National Research Council, 70126 Bari, Italy
| | - Ernesto Picardi
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70126 Bari, Italy; (A.L.); (M.L.P.); (E.P.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, National Research Council, 70126 Bari, Italy
| | - Graziano Pesole
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70126 Bari, Italy; (A.L.); (M.L.P.); (E.P.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, National Research Council, 70126 Bari, Italy
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4
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Numata Y, Akutsu N, Idogawa M, Wagatsuma K, Numata Y, Ishigami K, Nakamura T, Hirano T, Kawakami Y, Masaki Y, Murota A, Sasaki S, Nakase H. Genomic analysis of an aggressive hepatic leiomyosarcoma case following treatment for hepatocellular carcinoma. Hepatol Res 2024. [PMID: 38459823 DOI: 10.1111/hepr.14034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 02/05/2024] [Accepted: 02/17/2024] [Indexed: 03/10/2024]
Abstract
A 70-year-old man undergoing treatment for immunoglobulin G4-related disease developed a liver mass on computed tomography during routine imaging examination. The tumor was located in the hepatic S1/4 region, was 38 mm in size, and showed arterial enhancement on dynamic contrast-enhanced computed tomography. We performed a liver biopsy and diagnosed moderately differentiated hepatocellular carcinoma. The patient underwent proton beam therapy. The tumor remained unchanged but enlarged after 4 years. The patient was diagnosed with hepatocellular carcinoma recurrence and received hepatic arterial chemoembolization. However, 1 year later, the patient developed jaundice, and the liver tumor grew in size. Unfortunately, the patient passed away. Autopsy revealed that the tumor consisted of spindle-shaped cells exhibiting nuclear atypia and a fission pattern and tested positive for α-smooth muscle actin and vimentin. No hepatocellular carcinoma components were observed, and the patient was pathologically diagnosed with hepatic leiomyosarcoma. Next-generation sequencing revealed somatic mutations in CACNA2D4, CTNNB1, DOCK5, IPO8, MTMR1, PABPC5, SEMA6D, and ZFP36L1. Based on the genetic mutation, sarcomatoid hepatocarcinoma was the most likely pathogenesis in this case. This mutation is indicative of the transition from sarcomatoid hepatocarcinoma to hepatic leiomyosarcoma.
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Affiliation(s)
- Yuto Numata
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Noriyuki Akutsu
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Masashi Idogawa
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
- Department of Medical Genome Sciences, Cancer Research Institute, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Kohei Wagatsuma
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yasunao Numata
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Keisuike Ishigami
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Tomoya Nakamura
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Takehiro Hirano
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yujiro Kawakami
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yoshiharu Masaki
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Ayako Murota
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Shigeru Sasaki
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiroshi Nakase
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
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5
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George J, Maas L, Abedpour N, Cartolano M, Kaiser L, Fischer RN, Scheel AH, Weber JP, Hellmich M, Bosco G, Volz C, Mueller C, Dahmen I, John F, Alves CP, Werr L, Panse JP, Kirschner M, Engel-Riedel W, Jürgens J, Stoelben E, Brockmann M, Grau S, Sebastian M, Stratmann JA, Kern J, Hummel HD, Hegedüs B, Schuler M, Plönes T, Aigner C, Elter T, Toepelt K, Ko YD, Kurz S, Grohé C, Serke M, Höpker K, Hagmeyer L, Doerr F, Hekmath K, Strapatsas J, Kambartel KO, Chakupurakal G, Busch A, Bauernfeind FG, Griesinger F, Luers A, Dirks W, Wiewrodt R, Luecke A, Rodermann E, Diel A, Hagen V, Severin K, Ullrich RT, Reinhardt HC, Quaas A, Bogus M, Courts C, Nürnberg P, Becker K, Achter V, Büttner R, Wolf J, Peifer M, Thomas RK. Evolutionary trajectories of small cell lung cancer under therapy. Nature 2024; 627:880-889. [PMID: 38480884 PMCID: PMC10972747 DOI: 10.1038/s41586-024-07177-7] [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: 01/25/2023] [Accepted: 02/07/2024] [Indexed: 03/18/2024]
Abstract
The evolutionary processes that underlie the marked sensitivity of small cell lung cancer (SCLC) to chemotherapy and rapid relapse are unknown1-3. Here we determined tumour phylogenies at diagnosis and throughout chemotherapy and immunotherapy by multiregion sequencing of 160 tumours from 65 patients. Treatment-naive SCLC exhibited clonal homogeneity at distinct tumour sites, whereas first-line platinum-based chemotherapy led to a burst in genomic intratumour heterogeneity and spatial clonal diversity. We observed branched evolution and a shift to ancestral clones underlying tumour relapse. Effective radio- or immunotherapy induced a re-expansion of founder clones with acquired genomic damage from first-line chemotherapy. Whereas TP53 and RB1 alterations were exclusively part of the common ancestor, MYC family amplifications were frequently not constituents of the founder clone. At relapse, emerging subclonal mutations affected key genes associated with SCLC biology, and tumours harbouring clonal CREBBP/EP300 alterations underwent genome duplications. Gene-damaging TP53 alterations and co-alterations of TP53 missense mutations with TP73, CREBBP/EP300 or FMN2 were significantly associated with shorter disease relapse following chemotherapy. In summary, we uncover key processes of the genomic evolution of SCLC under therapy, identify the common ancestor as the source of clonal diversity at relapse and show central genomic patterns associated with sensitivity and resistance to chemotherapy.
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Affiliation(s)
- Julie George
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
- Department of Otorhinolaryngology, Head and Neck Surgery, Faculty of Medicine and University Hospital Cologne, University Hospital of Cologne, Cologne, Germany.
| | - Lukas Maas
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Nima Abedpour
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Department I of Internal Medicine, Centre for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University Hospital Cologne, Cologne, Germany
- Cancer Research Centre Cologne Essen, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Maria Cartolano
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Centre for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Laura Kaiser
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Rieke N Fischer
- Department I of Internal Medicine, Lung Cancer Group Cologne, University Hospital Cologne, Cologne, Germany
| | - Andreas H Scheel
- Institute of Pathology, Medical Faculty, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Jan-Philipp Weber
- Department I of Internal Medicine, Lung Cancer Group Cologne, University Hospital Cologne, Cologne, Germany
| | - Martin Hellmich
- Institute of Medical Statistics, and Computational Biology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Graziella Bosco
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Caroline Volz
- Department I of Internal Medicine, Centre for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University Hospital Cologne, Cologne, Germany
- Centre for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Christian Mueller
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Department of Otorhinolaryngology, Head and Neck Surgery, Faculty of Medicine and University Hospital Cologne, University Hospital of Cologne, Cologne, Germany
| | - Ilona Dahmen
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Felix John
- Department I of Internal Medicine, Lung Cancer Group Cologne, University Hospital Cologne, Cologne, Germany
| | - Cleidson Padua Alves
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Lisa Werr
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Jens Peter Panse
- Department of Haematology, Oncology, Haemostaseology and Stem Cell Transplantation, University Hospital RWTH Aachen, Aachen, Germany
- Centre for Integrated Oncology, Aachen Bonn Cologne Düsseldorf, Aachen, Germany
| | - Martin Kirschner
- Department of Haematology, Oncology, Haemostaseology and Stem Cell Transplantation, University Hospital RWTH Aachen, Aachen, Germany
- Centre for Integrated Oncology, Aachen Bonn Cologne Düsseldorf, Aachen, Germany
| | - Walburga Engel-Riedel
- Department of Pneumology, City of Cologne Municipal Hospitals, Lung Hospital Cologne Merheim, Cologne, Germany
| | - Jessica Jürgens
- Department of Pneumology, City of Cologne Municipal Hospitals, Lung Hospital Cologne Merheim, Cologne, Germany
| | - Erich Stoelben
- Thoraxclinic Cologne, Thoracic Surgery, St. Hildegardis-Krankenhaus, Cologne, Germany
| | - Michael Brockmann
- Department of Pathology, City of Cologne Municipal Hospitals, Witten/Herdecke University, Cologne, Germany
| | - Stefan Grau
- Department of General Neurosurgery, Centre of Neurosurgery, University Hospital Cologne, Cologne, Germany
- University Medicine Marburg - Campus Fulda, Department of Neurosurgery, Fulda, Germany
| | - Martin Sebastian
- Department of Medicine II, Haematology/Oncology, University Hospital Frankfurt, Goethe University, Frankfurt, Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt, Germany
- DKFZ, German Cancer Research Centre, German Cancer Consortium, Heidelberg, Germany
| | - Jan A Stratmann
- Department of Medicine II, Haematology/Oncology, University Hospital Frankfurt, Goethe University, Frankfurt, Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt, Germany
| | - Jens Kern
- Klinikum Würzburg Mitte - Missioklinik site, Pneumology and Respiratory Medicine, Würzburg, Germany
| | - Horst-Dieter Hummel
- Translational Oncology/Early Clinical Trial Unit, Comprehensive Cancer Centre Mainfranken, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Balazs Hegedüs
- Department of Thoracic Surgery, University Medicine Essen - Ruhrlandklinik, University Duisburg-Essen, Essen, Germany
| | - Martin Schuler
- DKFZ, German Cancer Research Centre, German Cancer Consortium, Heidelberg, Germany
- Department of Medical Oncology, West German Cancer Centre Essen, University Duisburg-Essen, Essen, Germany
| | - Till Plönes
- Department of Medical Oncology, West German Cancer Centre Essen, University Duisburg-Essen, Essen, Germany
- Division of Thoracic Surgery, Department of General, Thoracic and Vascular Surgery, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Clemens Aigner
- Department of Thoracic Surgery, University Medicine Essen - Ruhrlandklinik, University Duisburg-Essen, Essen, Germany
- Department of Thoracic Surgery, Medical University of Vienna, Vienna General Hospital, Vienna, Austria
| | - Thomas Elter
- Department I of Internal Medicine, Centre for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University Hospital Cologne, Cologne, Germany
| | - Karin Toepelt
- Department I of Internal Medicine, Centre for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University Hospital Cologne, Cologne, Germany
| | | | - Sylke Kurz
- Department of Respiratory Diseases, Evangelische Lungenklinik, Berlin, Germany
| | - Christian Grohé
- Department of Respiratory Diseases, Evangelische Lungenklinik, Berlin, Germany
| | - Monika Serke
- DGD Lungenklinik Hemer, Internal Medicine, Pneumology and Oncology, Hemer, Germany
| | - Katja Höpker
- Clinic III for Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Lars Hagmeyer
- Clinic of Pneumology and Allergology, Centre for Sleep Medicine and Respiratory Care, Bethanien Hospital Solingen, Solingen, Germany
| | - Fabian Doerr
- Department of Thoracic Surgery, University Medicine Essen - Ruhrlandklinik, University Duisburg-Essen, Essen, Germany
- Department of Cardiothoracic Surgery, University Hospital of Cologne, Cologne, Germany
| | - Khosro Hekmath
- Department of Cardiothoracic Surgery, University Hospital of Cologne, Cologne, Germany
| | - Judith Strapatsas
- Department of Haematology, Oncology and Clinical Immunology, University Hospital of Duesseldorf, Düsseldorf, Germany
| | | | | | - Annette Busch
- Medical Clinic III for Oncology, Haematology, Immune-Oncology and Rheumatology, Centre for Integrative Medicine, University Hospital Bonn, Bonn, Germany
| | - Franz-Georg Bauernfeind
- Medical Clinic III for Oncology, Haematology, Immune-Oncology and Rheumatology, Centre for Integrative Medicine, University Hospital Bonn, Bonn, Germany
| | - Frank Griesinger
- Pius-Hospital Oldenburg, Department of Haematology and Oncology, University Department Internal Medicine-Oncology, University Medicine Oldenburg, Oldenburg, Germany
| | - Anne Luers
- Pius-Hospital Oldenburg, Department of Haematology and Oncology, University Department Internal Medicine-Oncology, University Medicine Oldenburg, Oldenburg, Germany
| | - Wiebke Dirks
- Pius-Hospital Oldenburg, Department of Haematology and Oncology, University Department Internal Medicine-Oncology, University Medicine Oldenburg, Oldenburg, Germany
| | - Rainer Wiewrodt
- Pulmonary Division, Department of Medicine A, Münster University Hospital, Münster, Germany
| | - Andrea Luecke
- Pulmonary Division, Department of Medicine A, Münster University Hospital, Münster, Germany
| | - Ernst Rodermann
- Onkologie Rheinsieg, Praxisnetzwerk Hämatologie und Internistische Onkologie, Troisdorf, Germany
| | - Andreas Diel
- Onkologie Rheinsieg, Praxisnetzwerk Hämatologie und Internistische Onkologie, Troisdorf, Germany
| | - Volker Hagen
- Clinic II for Internal Medicine, St.-Johannes-Hospital Dortmund, Dortmund, Germany
| | - Kai Severin
- Haematologie und Onkologie Köln MV-Zentrum, Cologne, Germany
| | - Roland T Ullrich
- Department I of Internal Medicine, Centre for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University Hospital Cologne, Cologne, Germany
- Centre for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Hans Christian Reinhardt
- Department of Haematology and Stem Cell Transplantation, University Hospital Essen, Essen, Germany
- West German Cancer Centre, University Hospital Essen, Essen, Germany
| | - Alexander Quaas
- Institute of Pathology, Medical Faculty, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Magdalena Bogus
- Institute of Legal Medicine, University of Cologne, Cologne, Germany
| | - Cornelius Courts
- Institute of Legal Medicine, University of Cologne, Cologne, Germany
| | - Peter Nürnberg
- Cologne Centre for Genomics, West German Genome Centre, University of Cologne, Cologne, Germany
| | - Kerstin Becker
- Cologne Centre for Genomics, West German Genome Centre, University of Cologne, Cologne, Germany
| | - Viktor Achter
- Computing Centre, University of Cologne, Cologne, Germany
| | - Reinhard Büttner
- Institute of Pathology, Medical Faculty, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Jürgen Wolf
- Department I of Internal Medicine, Lung Cancer Group Cologne, University Hospital Cologne, Cologne, Germany
| | - Martin Peifer
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
- Centre for Molecular Medicine, University of Cologne, Cologne, Germany.
| | - Roman K Thomas
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
- Institute of Pathology, Medical Faculty, University Hospital Cologne, University of Cologne, Cologne, Germany.
- DKFZ, German Cancer Research Centre, German Cancer Consortium, Heidelberg, Germany.
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6
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Youk J, Kwon HW, Lim J, Kim E, Kim T, Kim R, Park S, Yi K, Nam CH, Jeon S, An Y, Choi J, Na H, Lee ES, Cho Y, Min DW, Kim H, Kang YR, Choi SH, Bae MJ, Lee CG, Kim JG, Kim YS, Yu T, Lee WC, Shin JY, Lee DS, Kim TY, Ku T, Kim SY, Lee JH, Koo BK, Lee H, Yi OV, Han EC, Chang JH, Kim KS, Son TG, Ju YS. Quantitative and qualitative mutational impact of ionizing radiation on normal cells. CELL GENOMICS 2024; 4:100499. [PMID: 38359788 PMCID: PMC10879144 DOI: 10.1016/j.xgen.2024.100499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 10/23/2023] [Accepted: 01/09/2024] [Indexed: 02/17/2024]
Abstract
The comprehensive genomic impact of ionizing radiation (IR), a carcinogen, on healthy somatic cells remains unclear. Using large-scale whole-genome sequencing (WGS) of clones expanded from irradiated murine and human single cells, we revealed that IR induces a characteristic spectrum of short insertions or deletions (indels) and structural variations (SVs), including balanced inversions, translocations, composite SVs (deletion-insertion, deletion-inversion, and deletion-translocation composites), and complex genomic rearrangements (CGRs), including chromoplexy, chromothripsis, and SV by breakage-fusion-bridge cycles. Our findings suggest that 1 Gy IR exposure causes an average of 2.33 mutational events per Gb genome, comprising 2.15 indels, 0.17 SVs, and 0.01 CGRs, despite a high level of inter-cellular stochasticity. The mutational burden was dependent on total irradiation dose, regardless of dose rate or cell type. The findings were further validated in IR-induced secondary cancers and single cells without clonalization. Overall, our study highlights a comprehensive and clear picture of IR effects on normal mammalian genomes.
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Affiliation(s)
- Jeonghwan Youk
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Hyun Woo Kwon
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea; Department of Nuclear Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Joonoh Lim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Genome Insight, Inc., San Diego, CA 92121, USA
| | - Eunji Kim
- Department of Radiation Oncology, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, 20, Boramae-ro 5 Gil, Dongjak-gu, Seoul 07061, Republic of Korea; Department of Radiation Oncology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Taewoo Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Ryul Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Genome Insight, Inc., San Diego, CA 92121, USA
| | - Seongyeol Park
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Genome Insight, Inc., San Diego, CA 92121, USA
| | - Kijong Yi
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Genome Insight, Inc., San Diego, CA 92121, USA
| | - Chang Hyun Nam
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Sara Jeon
- Department of Biological Sciences & IMBG, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Yohan An
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Jinwook Choi
- Wellcome - MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW Cambridge, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, CB2 3EL Cambridge, UK
| | - Hyelin Na
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Eon-Seok Lee
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Youngwon Cho
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea; Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Dong-Wook Min
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea; Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - HyoJin Kim
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Yeong-Rok Kang
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Si Ho Choi
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Min Ji Bae
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Chang Geun Lee
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Joon-Goon Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; KI for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Young Seo Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; KI for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Tosol Yu
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Radiation Oncology, Dongnam Institute of Radiological and Medical Science, Busan 46033, Republic of Korea
| | | | | | - Dong Soo Lee
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea; Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Tae-You Kim
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea; Cancer Research Institute, Seoul National University, Seoul, Republic of Korea; Department of Internal Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Taeyun Ku
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; KI for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Su Yeon Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Joo-Hyeon Lee
- Wellcome - MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW Cambridge, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, CB2 3EL Cambridge, UK
| | - Bon-Kyoung Koo
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Hyunsook Lee
- Department of Biological Sciences & IMBG, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - On Vox Yi
- Department of Breast Surgery, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Eon Chul Han
- Department of Surgery, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Ji Hyun Chang
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Radiation Oncology, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Kyung Su Kim
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Radiation Oncology, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Tae Gen Son
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea.
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Genome Insight, Inc., San Diego, CA 92121, USA.
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7
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Pierik AS, Poell JB, Brink A, Stigter-van Walsum M, de Roest RH, Poli T, Yaromin A, Lambin P, Leemans CR, Brakenhoff RH. Intratumor genetic heterogeneity and head and neck cancer relapse. Radiother Oncol 2024; 191:110087. [PMID: 38185257 DOI: 10.1016/j.radonc.2024.110087] [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: 08/02/2023] [Revised: 12/18/2023] [Accepted: 01/03/2024] [Indexed: 01/09/2024]
Abstract
BACKGROUND Head and neck squamous cell carcinomas are treated by surgery, radiotherapy (RT), chemoradiotherapy (CRT) or combinations thereof, but locoregional recurrences (LRs) occur in 30-40% of treated patients. We have previously shown that in approximately half of the LRs after CRT, cancer driver mutations are not shared with the index tumor. AIM To investigate two possible explanations for these genetically unrelated relapses, treatment-induced genetic changes and intratumor genetic heterogeneity. METHODS To investigate treatment-induced clonal DNA changes, we compared copy number alterations (CNAs) and mutations between primary and recurrent xenografted tumors after treatment with (C)RT. Intratumor genetic heterogeneity was studied by multi-region sequencing on DNA from 31 biopsies of 11 surgically treated tumors. RESULTS Induction of clonal DNA changes by (C)RT was not observed in the xenograft models. Multi-region sequencing demonstrated variations in CNA profiles between paired biopsies of individual tumors, with copy number heterogeneity scores varying from 0.027 to 0.333. In total, 32 cancer driver mutations could be identified and were shared in all biopsies of each tumor. Remarkably, multi-clonal mutations in these same cancer driver genes were observed in 6 of 11 tumors. Genetically distinct heterogeneous cell cultures could also be established from single tumors, with different biomarker profiles and drug sensitivities. CONCLUSION Intratumor genetic heterogeneity at the level of the cancer driver mutations might explain the discordant mutational profiles in LRs after CRT, while there are no indications in xenograft models that these changes are induced by CRT.
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Affiliation(s)
- A S Pierik
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Otolaryngology/Head and Neck Surgery, Head and Neck Cancer Biology and Immunology laboratory, De Boelelaan 1117, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology and Immunology, De Boelelaan 1117, Amsterdam, the Netherlands
| | - J B Poell
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Otolaryngology/Head and Neck Surgery, Head and Neck Cancer Biology and Immunology laboratory, De Boelelaan 1117, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology and Immunology, De Boelelaan 1117, Amsterdam, the Netherlands
| | - A Brink
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Otolaryngology/Head and Neck Surgery, Head and Neck Cancer Biology and Immunology laboratory, De Boelelaan 1117, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology and Immunology, De Boelelaan 1117, Amsterdam, the Netherlands
| | - M Stigter-van Walsum
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Otolaryngology/Head and Neck Surgery, Head and Neck Cancer Biology and Immunology laboratory, De Boelelaan 1117, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology and Immunology, De Boelelaan 1117, Amsterdam, the Netherlands
| | - R H de Roest
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Otolaryngology/Head and Neck Surgery, Head and Neck Cancer Biology and Immunology laboratory, De Boelelaan 1117, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology and Immunology, De Boelelaan 1117, Amsterdam, the Netherlands
| | - T Poli
- Maxillofacial Surgery Unit, Department of Medicine and Surgery - University of Parma, University Hospital of Parma, Via Gramsci 14, Parma, Italy
| | - A Yaromin
- Maastricht University, Department of Precision Medicine-UM & Radiology-MUMC, Universiteitssingel 40, Maastricht, the Netherlands
| | - P Lambin
- Maastricht University, Department of Precision Medicine-UM & Radiology-MUMC, Universiteitssingel 40, Maastricht, the Netherlands
| | - C R Leemans
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Otolaryngology/Head and Neck Surgery, Head and Neck Cancer Biology and Immunology laboratory, De Boelelaan 1117, Amsterdam, the Netherlands
| | - R H Brakenhoff
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Otolaryngology/Head and Neck Surgery, Head and Neck Cancer Biology and Immunology laboratory, De Boelelaan 1117, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology and Immunology, De Boelelaan 1117, Amsterdam, the Netherlands.
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8
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Bailey SM, Cross EM, Kinner-Bibeau L, Sebesta HC, Bedford JS, Tompkins CJ. Monitoring Genomic Structural Rearrangements Resulting from Gene Editing. J Pers Med 2024; 14:110. [PMID: 38276232 PMCID: PMC10817574 DOI: 10.3390/jpm14010110] [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: 11/30/2023] [Revised: 01/04/2024] [Accepted: 01/13/2024] [Indexed: 01/27/2024] Open
Abstract
The cytogenomics-based methodology of directional genomic hybridization (dGH) enables the detection and quantification of a more comprehensive spectrum of genomic structural variants than any other approach currently available, and importantly, does so on a single-cell basis. Thus, dGH is well-suited for testing and/or validating new advancements in CRISPR-Cas9 gene editing systems. In addition to aberrations detected by traditional cytogenetic approaches, the strand specificity of dGH facilitates detection of otherwise cryptic intra-chromosomal rearrangements, specifically small inversions. As such, dGH represents a powerful, high-resolution approach for the quantitative monitoring of potentially detrimental genomic structural rearrangements resulting from exposure to agents that induce DNA double-strand breaks (DSBs), including restriction endonucleases and ionizing radiations. For intentional genome editing strategies, it is critical that any undesired effects of DSBs induced either by the editing system itself or by mis-repair with other endogenous DSBs are recognized and minimized. In this paper, we discuss the application of dGH for assessing gene editing-associated structural variants and the potential heterogeneity of such rearrangements among cells within an edited population, highlighting its relevance to personalized medicine strategies.
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Affiliation(s)
- Susan M. Bailey
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA;
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
| | - Erin M. Cross
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
| | | | - Henry C. Sebesta
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
| | - Joel S. Bedford
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA;
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
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9
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Yamamori A, Murayama S, Takahashi I, Akaihata M, Kakuda Y, Sugino T, Aramaki T, Onoe T, Takahashi Y, Ishida Y. Young Adult Secondary Cancer After Proton Beam Therapy: A Case Study. Adv Radiat Oncol 2024; 9:101307. [PMID: 38260212 PMCID: PMC10801643 DOI: 10.1016/j.adro.2023.101307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/26/2023] [Indexed: 01/24/2024] Open
Affiliation(s)
- Ayako Yamamori
- Division of Pediatrics (and the AYA Generation), Shizuoka Cancer Center, Shizuoka, Japan
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | | | - Ikuko Takahashi
- Division of Pediatrics (and the AYA Generation), Shizuoka Cancer Center, Shizuoka, Japan
| | - Mitsuko Akaihata
- Division of Pediatrics (and the AYA Generation), Shizuoka Cancer Center, Shizuoka, Japan
| | | | | | - Takeshi Aramaki
- Interventional Radiology, Shizuoka Cancer Center, Shizuoka, Japan
| | | | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuji Ishida
- Division of Pediatrics (and the AYA Generation), Shizuoka Cancer Center, Shizuoka, Japan
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10
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Madkhali AM, Alaluan HF, Alnajeim MH, Al Saeed EF, Ajlan AM, Abdelwarith A, Abduh A, Albanyan S, Alqurashi A, Alkhalidi H. A New Sarcoma Shortly after Treatment for High-Grade Glioma with Adjuvant Chemoradiation: A Case Report. Case Rep Oncol 2024; 17:573-580. [PMID: 38665312 PMCID: PMC11045215 DOI: 10.1159/000538508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 01/31/2024] [Indexed: 04/28/2024] Open
Abstract
Introduction High-grade gliomas are central nervous system tumors conventionally treated with surgery followed by adjuvant chemoradiotherapy. Secondary cancer due to radiation therapy is a rare yet established phenomenon that typically occurs years after radiation therapy. Case Presentation In this case, we discuss an early presentation of a second cancer adjacent to the radiation field. This case report is of a 52-year-old male who developed a new scalp sarcoma at the site of primary surgery 8 months after radiation therapy. Genetic testing revealed a heterozygous missense variant in the NF1 gene, a variant of uncertain significance. The report highlights that this case does not conform to the expected criteria for postradiation sarcoma in terms of timing. Conclusion Secondary cancers may arise earlier than expected, even in phenotypically normal patients, as they may have unmanifested variants of relevant mutations. The question of pre-radiotherapy screening for radiosensitivity syndromes and diseases requires further study, as current data are limited and do not provide enough insight into the significance of different genetic variants.
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Affiliation(s)
- Abdossalam M. Madkhali
- Department of Medicine, Oncology, Hematology and Radiation Oncology Unit, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | | | | | - Eyad F. Al Saeed
- Department of Medicine, Oncology, Hematology and Radiation Oncology Unit, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Abdulrazag M. Ajlan
- Surgery Department, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | | | - Ali Abduh
- Department of Radiology, King Khalid University Hospital, King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Saleh Albanyan
- Department of Internal Medicine, College of Medicine and King Khalid University Hospital, King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Ashwag Alqurashi
- Division of Neurosurgery, Department of Surgery, King Saud University Medical City, Riyadh, Saudi Arabia
| | - Hisham Alkhalidi
- Department of Pathology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
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11
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Daniel AR, Su C, Williams NT, Li Z, Huang J, Lopez O, Luo L, Ma Y, Campos LDS, Selitsky SR, Modliszewski JL, Liu S, Hernansaiz-Ballesteros R, Mowery YM, Cardona DM, Lee CL, Kirsch DG. Temporary Knockdown of p53 During Focal Limb Irradiation Increases the Development of Sarcomas. CANCER RESEARCH COMMUNICATIONS 2023; 3:2455-2467. [PMID: 37982576 PMCID: PMC10697056 DOI: 10.1158/2767-9764.crc-23-0104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 09/21/2023] [Accepted: 11/14/2023] [Indexed: 11/21/2023]
Abstract
Approximately half of patients with cancer receive radiotherapy and, as cancer survivorship increases, the low rate of radiation-associated sarcomas is rising. Pharmacologic inhibition of p53 has been proposed as an approach to ameliorate acute injury of normal tissues from genotoxic therapies, but how this might impact the risk of therapy-induced cancer and normal tissue injuries remains unclear. We utilized mice that express a doxycycline (dox)-inducible p53 short hairpin RNA to reduce Trp53 expression temporarily during irradiation. Mice were placed on a dox diet 10 days prior to receiving 30 or 40 Gy hind limb irradiation in a single fraction and then returned to normal chow. Mice were examined weekly for sarcoma development and scored for radiation-induced normal tissue injuries. Radiation-induced sarcomas were subjected to RNA sequencing. Following single high-dose irradiation, 21% of animals with temporary p53 knockdown during irradiation developed a sarcoma in the radiation field compared with 2% of control animals. Following high-dose irradiation, p53 knockdown preserves muscle stem cells, and increases sarcoma development. Mice with severe acute radiation-induced injuries exhibit an increased risk of developing late persistent wounds, which were associated with sarcomagenesis. RNA sequencing revealed radiation-induced sarcomas upregulate genes related to translation, epithelial-mesenchymal transition (EMT), inflammation, and the cell cycle. Comparison of the transcriptomes of human and mouse sarcomas that arose in irradiated tissues revealed regulation of common gene programs, including elevated EMT pathway gene expression. These results suggest that blocking p53 during radiotherapy could minimize acute toxicity while exacerbating late effects including second cancers. SIGNIFICANCE Strategies to prevent or mitigate acute radiation toxicities include pharmacologic inhibition of p53 and other cell death pathways. Our data show that temporarily reducing p53 during irradiation increases late effects including sarcomagenesis.
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Affiliation(s)
- Andrea R. Daniel
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Chang Su
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Nerissa T. Williams
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Zhiguo Li
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina
| | - Jianguo Huang
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Omar Lopez
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Lixia Luo
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Yan Ma
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | | | - Sara R. Selitsky
- QuantBio LLC, Durham, North Carolina
- Tempus Labs, Inc., Chicago, Illinois
| | | | - Siyao Liu
- QuantBio LLC, Durham, North Carolina
- Tempus Labs, Inc., Chicago, Illinois
| | | | - Yvonne M. Mowery
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
- Department of Head and Neck Surgery & Communication Sciences, Duke University Medical Center, Durham, North Carolina
| | - Diana M. Cardona
- Department of Pathology, Duke University Medical Center, Durham, North Carolina
| | - Chang-Lung Lee
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
- Department of Pathology, Duke University Medical Center, Durham, North Carolina
| | - David G. Kirsch
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina
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12
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Rasche L, Weinhold N. When a solitary plasmacytoma is just the beginning…. Blood 2023; 142:1849-1850. [PMID: 38032673 DOI: 10.1182/blood.2023021859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023] Open
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13
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Yang Y, Feng T, Fan X, Wang C, Jiang Y, Zhou X, Bao W, Zhang D, Wang S, Yu J, Tao Y, Song G, Bao H, Yan J, Wu X, Shao Y, Qiu G, Su D, Chen Q. Genomic and Transcriptomic Remodeling by Neoadjuvant Chemoradiotherapy (nCRT) and the Indicative Role of Acquired INDEL Percentage for nCRT Efficacy in Esophageal Squamous Cell Carcinoma. Int J Radiat Oncol Biol Phys 2023; 117:979-993. [PMID: 37339686 DOI: 10.1016/j.ijrobp.2023.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 05/30/2023] [Accepted: 06/11/2023] [Indexed: 06/22/2023]
Abstract
PURPOSE The effect of genomic factors on the response of patients with esophageal squamous cell carcinoma (ESCC) to neoadjuvant chemoradiotherapy (nCRT), as well as how nCRT influences the genome and transcriptome of ESCC, remain largely unknown. METHODS AND MATERIALS In total, 137 samples from 57 patients with ESCC undergoing nCRT were collected and subjected to whole-exome sequencing and RNA sequencing analysis. Genetic and clinicopathologic factors were compared between the patients achieving pathologic complete response and patients not achieving pathologic complete response. Genomic and transcriptomic profiles before and after nCRT were analyzed. RESULTS Codeficiency of the DNA damage repair and HIPPO pathways synergistically sensitized ESCC to nCRT. nCRT induced small INDELs and focal chromosomal loss concurrently. Acquired INDEL% exhibited a decreasing trend with the increase of tumor regression grade (P = .06, Jonckheere's test). Multivariable Cox analysis indicated that higher acquired INDEL% was associated with better survival (adjusted hazard ratio [aHR], 0.93; 95% CI, 0.86-1.01; P = .067 for recurrence-free survival [RFS]; aHR, 0.86; 95% CI, 0.76-0.98; P = .028 for overall survival [OS], with 1% of acquired INDEL% as unit). The prognostic value of acquired INDEL% was confirmed by the Glioma Longitudinal AnalySiS data set (aHR, 0.95; 95% CI, 0.902-0.997; P = .037 for RFS; aHR, 0.96; 95% CI, 0.917-1.004; P = .076 for OS). Additionally, clonal expansion degree was negatively associated with patient survival (aHR, 5.87; 95% CI, 1.10-31.39; P = .038 for RFS; aHR, 9.09; 95% CI, 1.10-75.36; P = .041 for OS, with low clonal expression group as reference) and also negatively correlated with acquired INDEL% (Spearman ρ = -0.45; P = .02). The expression profile was changed after nCRT. The DNA replication gene set was downregulated, while the cell adhesion gene set was upregulated after nCRT. Acquired INDEL% was negatively correlated with the enrichment of the DNA replication gene set (Spearman ρ = -0.56; P = .003) but was positively correlated with the enrichment of the cell adhesion gene set (Spearman ρ = 0.40; P = .05) in posttreatment samples. CONCLUSIONS nCRT remodels the genome and transcriptome of ESCC. Acquired INDEL% is a potential biomarker to indicate the effectiveness of nCRT and radiation sensitivity.
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Affiliation(s)
- Yang Yang
- Department of Thoracic Radiotherapy, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China; Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, China
| | - TingTing Feng
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Xiaojun Fan
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc, Nanjing, China
| | - Changchun Wang
- Department of Thoracic Surgery, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Youhua Jiang
- Department of Thoracic Surgery, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Xia Zhou
- Department of Thoracic Radiotherapy, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China; Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, China
| | - Wu'an Bao
- Department of Thoracic Radiotherapy, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China; Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, China
| | - Danhong Zhang
- Department of Thoracic Radiotherapy, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China; Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, China
| | - Shi Wang
- Endoscopy Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Jiangping Yu
- Endoscopy Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Yali Tao
- Endoscopy Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Ge Song
- Department of Radiology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Hua Bao
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc, Nanjing, China
| | - Junrong Yan
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc, Nanjing, China
| | - Xue Wu
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc, Nanjing, China
| | - Yang Shao
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc, Nanjing, China
| | - Guoqin Qiu
- Department of Thoracic Radiotherapy, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China; Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, China.
| | - Dan Su
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China.
| | - Qixun Chen
- Department of Thoracic Surgery, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China.
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14
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Adler N, Bahcheli AT, Cheng KC, Al-Zahrani KN, Slobodyanyuk M, Pellegrina D, Schramek D, Reimand J. Mutational processes of tobacco smoking and APOBEC activity generate protein-truncating mutations in cancer genomes. SCIENCE ADVANCES 2023; 9:eadh3083. [PMID: 37922356 PMCID: PMC10624356 DOI: 10.1126/sciadv.adh3083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 10/04/2023] [Indexed: 11/05/2023]
Abstract
Mutational signatures represent a genomic footprint of endogenous and exogenous mutational processes through tumor evolution. However, their functional impact on the proteome remains incompletely understood. We analyzed the protein-coding impact of single-base substitution (SBS) signatures in 12,341 cancer genomes from 18 cancer types. Stop-gain mutations (SGMs) (i.e., nonsense mutations) were strongly enriched in SBS signatures of tobacco smoking, APOBEC cytidine deaminases, and reactive oxygen species. These mutational processes alter specific trinucleotide contexts and thereby substitute serines and glutamic acids with stop codons. SGMs frequently affect cancer hallmark pathways and tumor suppressors such as TP53, FAT1, and APC. Tobacco-driven SGMs in lung cancer correlate with smoking history and highlight a preventable determinant of these harmful mutations. APOBEC-driven SGMs are enriched in YTCA motifs and associate with APOBEC3A expression. Our study exposes SGM expansion as a genetic mechanism by which endogenous and carcinogenic mutational processes directly contribute to protein loss of function, oncogenesis, and tumor heterogeneity.
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Affiliation(s)
- Nina Adler
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Alexander T. Bahcheli
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Kevin C. L. Cheng
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | | | - Mykhaylo Slobodyanyuk
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Diogo Pellegrina
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Daniel Schramek
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada
| | - Jüri Reimand
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
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15
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Atajanova T, Rahman MM, Konieczkowski DJ, Morris ZS. Radiation-associated secondary malignancies: a novel opportunity for applying immunotherapies. Cancer Immunol Immunother 2023; 72:3445-3452. [PMID: 37658906 DOI: 10.1007/s00262-023-03532-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 08/16/2023] [Indexed: 09/05/2023]
Abstract
Radiation is commonly used as a treatment intended to cure or palliate cancer patients. Despite remarkable advances in the precision of radiotherapy delivery, even the most advanced forms inevitably expose some healthy tissues surrounding the target site to radiation. On rare occasions, this results in the development of radiation-associated secondary malignancies (RASM). RASM are typically high-grade and carry a poorer prognosis than their non-radiated counterparts. RASM are characterized by a high mutation burden, increased T cell infiltration, and a microenvironment that bears unique inflammatory signatures of prior radiation, including increased expression of various cytokines (e.g., TGF-β, TNF-α, IL4, and IL10). Interestingly, these cytokines have been shown to up-regulate the expression of PD-1 and/or PD-L1-an immune checkpoint receptor/ligand pair that is commonly targeted by immune checkpoint blocking immunotherapies. Here, we review the current understanding of the tumor-immune interactions in RASM, highlight the distinct clinical and molecular characteristics of RASM that may render them immunologically "hot," and propose a rationale for the formal testing of immune checkpoint blockade as a treatment approach for patients with RASM.
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Affiliation(s)
- Tavus Atajanova
- Biochemistry and Biophysics Program, Amherst College, Amherst, MA, 01002, USA
- Department of Sociology, Amherst College, Amherst, MA, 01002, USA
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI, 53726, USA
| | - Md Mahfuzur Rahman
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI, 53726, USA
| | - David J Konieczkowski
- Department of Radiation Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH, 43210, USA
| | - Zachary S Morris
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI, 53726, USA.
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16
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Mathew F, Manalad J, Yeo J, Galarneau L, Ybarra N, Wang YC, Tonin PN, Ragoussis I, Kildea J. Single-cell DNA sequencing-a potential dosimetric tool. RADIATION PROTECTION DOSIMETRY 2023; 199:2047-2052. [PMID: 37819315 DOI: 10.1093/rpd/ncad055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 02/02/2023] [Accepted: 02/13/2023] [Indexed: 10/13/2023]
Abstract
We hypothesised that single-cell whole-genome sequencing has the potential to detect mutational differences in the genomes of the cells that are irradiated with different doses of radiation and we set out to test our hypothesis using in silico and in vitro experiments. In this manuscript, we present our findings from a Monte Carlo single-cell irradiation simulation performed in TOPAS-nBio using a custom-built geometric nuclear deoxyribonucleic acid (DNA) model, which predicts a significant dose dependence of the number of cluster damages per cell as a function of radiation dose. We also present preliminary experimental results, obtained from single-cell whole-genome DNA sequencing analysis performed on cells irradiated with different doses of radiation, showing promising agreement with the simulation results.
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Affiliation(s)
- Felix Mathew
- Medical Physics Unit, McGill University, Montreal, Quebec, Canada
| | - James Manalad
- Medical Physics Unit, McGill University, Montreal, Quebec, Canada
| | - Jonathan Yeo
- Singapore Nuclear Research and Safety Initiative, National University of Singapore, Singapore
| | - Luc Galarneau
- Medical Physics Unit, McGill University, Montreal, Quebec, Canada
| | - Norma Ybarra
- Medical Physics Unit, McGill University, Montreal, Quebec, Canada
| | - Yu Chang Wang
- McGill Genome Centre, McGill University, Montreal, Quebec, Canada
| | - Patricia N Tonin
- Departments of Medicine and Human Genetics, McGill University, Montreal, Quebec, Canada
- Cancer Research Program, Research Institute-McGill University Health Centre, Montreal, Quebec, Canada
| | | | - John Kildea
- Medical Physics Unit, McGill University, Montreal, Quebec, Canada
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17
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Dermawan JK, Chi P, Tap WD, Rosenbaum E, D'Angelo S, Alektiar KM, Antonescu CR. Distinct genomic landscapes in radiation-associated angiosarcoma compared with other radiation-associated sarcoma histologies. J Pathol 2023; 260:465-477. [PMID: 37350195 PMCID: PMC10756077 DOI: 10.1002/path.6137] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/31/2023] [Accepted: 05/05/2023] [Indexed: 06/24/2023]
Abstract
MYC amplifications have been frequently detected in radiation (RT)-associated angiosarcomas (ASs) by low-resolution molecular methods. However, large-scale next-generation sequencing (NGS) studies to investigate the genomic landscape of RT-AS are scarce, particularly compared with other RT-associated sarcomas. We performed a detailed comparative genomic investigation of RT-AS versus other RT-associated histotypes, as well as sporadic sarcomas with similar histologies. Our institutional targeted DNA-NGS assay database was searched for RT-associated sarcomas. Clinical outcome data, pathologic diagnosis, and the types and frequencies of genomic alterations, including single nucleotide variants (SNVs) and copy number alterations (CNAs), were analyzed. The cohort consisted of 82 patients, 68 (83%) females and 14 (17%) males, aged 37-88 (mean 64) years. Forty-four RT-ASs (38 from breast) and 38 RT sarcomas of other histologies, including 12 malignant peripheral nerve sheath tumors (RT-MPNSTs), 14 undifferentiated pleomorphic sarcomas (RT-UPSs), and 12 osteosarcomas (RT-OSs), were included. Median time intervals from radiation to initial diagnosis in RT-AS (8.0 years) were significantly lower than those in RT-MPNST and RT-UPS (12.5 and 18.5 years), respectively. Each RT-sarcoma histotype harbored distinct mutations and CNAs. RT-associated AS had more frequent MYC, FLT4, CRKL, HRAS, and KMT2D alterations than sporadic AS (enriched in TP53, KDR, ATM, ATRX), whereas the mutational landscapes of MPNST, UPS, and OS were similar in both RT and non-RT settings. CDKN2A/B deletions and TP53 alterations were infrequent in RT-AS compared with other RT sarcomas. Among RT sarcomas, RT-AS harbored the lowest fraction of genome altered (FGA), while RT-MPNST showed the highest FGA. RT-AS had the lowest insertion:SNV and deletion:SNV ratios, while RT-UPS had the highest. The predominant mutational signatures were associated with errors in DNA repair and replication. In conclusion, RT-AS has a distinct genomic landscape compared with other RT sarcomas and sporadic AS. Potential molecular targets for precision medicine may be histotype-dependent. © 2023 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Josephine K Dermawan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ping Chi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - William D Tap
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Evan Rosenbaum
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Sandra D'Angelo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Kaled M Alektiar
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Cristina R Antonescu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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18
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Chow JCH, Cheuk W, Cho WCS, Wong CF, Au DWY, Tam AHP, Wong RCW, Chan JCH, Law SCC, Ngan RKC, Wong KH, Cheung KM. Comparison of Clinical Outcomes, Pathologic Characteristics, and Immune-Related Features of Postradiation vs Sporadic Oral Cavity Squamous Cell Carcinoma. JAMA Netw Open 2023; 6:e2323890. [PMID: 37459093 PMCID: PMC10352864 DOI: 10.1001/jamanetworkopen.2023.23890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 06/02/2023] [Indexed: 07/20/2023] Open
Abstract
Importance Postradiation oral cavity squamous cell carcinoma (OCSCC) is a common secondary malignant neoplasm affecting survivors of head and neck cancer who underwent radiotherapy. The clinical, pathologic, and immune-related features of postradiation OCSCC are poorly characterized, and treatment options are limited because of surgical difficulty and high morbidity associated with reirradiation. Objective To determine whether postradiation OCSCC has distinctive clinical, pathologic, and immune-related features compared with demographic-matched sporadic OCSCC. Design, Setting, and Participants This retrospective matched cohort study was conducted at a single tertiary oncology center in Hong Kong. Participants included consecutive patients with OCSCC diagnosed between 2000 and 2020. Patients with postradiation OCSCC were matched with patients with sporadic OCSCC using age, year of diagnosis, sex, and anatomic subsites. Data analysis was performed from July to December 2022. Exposure Head and neck irradiation involving the oral cavity before the diagnosis of OCSCC. Main Outcomes and Measures The primary outcomes were relapse pattern, survival, and causes of death. Pathologic features; immunohistochemical staining for programmed death-ligand 1, PD-1, MSH6, PMS2, FOXP3, and Ki67; and mRNA expression of 31 immune-related genes were also analyzed. Results A total of 173 patients, 60 with postradiation OCSCC (median [IQR] age, 63.8 [53.0-71.7] years; 43 men [71.7%]) and 113 with sporadic OCSCC (median [IQR] age, 64.4 [52.8-70.6] years; 83 men [73.5%]), were included. Patients with postradiation OCSCC had a higher proportion of N0 disease than those with sporadic OCSCC (50 patients [83.3%] vs 56 patients [49.6%]). With a median (IQR) follow-up of 10.2 (1.2-20.5) years, the 10-year relapse-free survival rates were lower in patients with postradiation OCSCC than sporadic OCSCC (29.6% [95% CI, 17.1%-43.2%] vs 52.4% [95% CI, 41.8%-62.0%]; P = .04), and the same was true for overall survival (30.5% [95% CI, 17.6%-44.4%] vs 52.3% [95% CI, 41.4%-62.1%]; P = .03). All relapses in patients with postradiation OCSCC were locoregional, whereas 35.2% of relapses (12 of 34 patients) in patients with sporadic OCSCC were distant. Despite similar 10-year disease-specific survival rates between the 2 groups (68.8% [95% CI, 55.8%-81.0%] vs 67.1% [95% CI, 57.5%-76.5%]; P = .91), patients with postradiation OCSCC had excess mortality due to pneumonia and cerebrovascular events. Postradiation OCSCC exhibited more adverse pathologic features (perineural invasion, worse pattern of invasion, and tumor budding), higher PD-1 expression, and higher gene expression of CD4 and TGF-β compared with sporadic OCSCC. Conclusions and Relevance This retrospective matched cohort study found distinctive pathologic characteristics and relapse patterns of postradiation OCSCC compared with sporadic OCSCC, which may be attributable to the lack of adjuvant radiotherapy, aggressive biologic phenotype, and different host immune response. Further exploration of the role of immune checkpoint therapy may be justified.
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Affiliation(s)
- James C. H. Chow
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong SAR, China
| | - Wah Cheuk
- Department of Pathology, Queen Elizabeth Hospital, Hong Kong SAR, China
| | - William C. S. Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong SAR, China
| | - Chi-Fai Wong
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong SAR, China
| | - Dennis W. Y. Au
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong SAR, China
| | - Anthony H. P. Tam
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong SAR, China
| | - Rachel C. W. Wong
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong SAR, China
| | - Jeffrey C. H. Chan
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong SAR, China
| | - Simon C. C. Law
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong SAR, China
| | - Roger K. C. Ngan
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Kam-Hung Wong
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong SAR, China
| | - Ka-Man Cheung
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong SAR, China
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19
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Delhomme TM, Munteanu M, Buonanno M, Grilj V, Biayna J, Supek F. Proton and alpha radiation-induced mutational profiles in human cells. Sci Rep 2023; 13:9791. [PMID: 37328655 PMCID: PMC10275862 DOI: 10.1038/s41598-023-36845-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 06/11/2023] [Indexed: 06/18/2023] Open
Abstract
Ionizing radiation is known to be DNA damaging and mutagenic, however less is known about which mutational footprints result from exposures of human cells to different types of radiation. We were interested in the mutagenic effects of particle radiation exposures on genomes of various human cell types, in order to gauge the genotoxic risks of galactic cosmic radiation, and of certain types of tumor radiotherapy. To this end, we exposed cultured cell lines from the human blood, breast and lung to fractionated proton and alpha particle (helium nuclei) beams at doses sufficient to considerably affect cell viability. Whole-genome sequencing revealed that mutation rates were not overall markedly increased upon proton and alpha exposures. However, there were modest changes in mutation spectra and distributions, such as the increases in clustered mutations and of certain types of indels and structural variants. The spectrum of mutagenic effects of particle beams may be cell-type and/or genetic background specific. Overall, the mutational effects of repeated exposures to proton and alpha radiation on human cells in culture appear subtle, however further work is warranted to understand effects of long-term exposures on various human tissues.
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Affiliation(s)
- Tiffany M Delhomme
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Maia Munteanu
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Manuela Buonanno
- Radiological Research Accelerator Facility (RARAF), Columbia University, New York, USA
| | - Veljko Grilj
- Radiological Research Accelerator Facility (RARAF), Columbia University, New York, USA
| | - Josep Biayna
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Fran Supek
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
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20
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Martínez-Jiménez F, Movasati A, Brunner SR, Nguyen L, Priestley P, Cuppen E, Van Hoeck A. Pan-cancer whole-genome comparison of primary and metastatic solid tumours. Nature 2023; 618:333-341. [PMID: 37165194 PMCID: PMC10247378 DOI: 10.1038/s41586-023-06054-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 04/05/2023] [Indexed: 05/12/2023]
Abstract
Metastatic cancer remains an almost inevitably lethal disease1-3. A better understanding of disease progression and response to therapies therefore remains of utmost importance. Here we characterize the genomic differences between early-stage untreated primary tumours and late-stage treated metastatic tumours using a harmonized pan-cancer analysis (or reanalysis) of two unpaired primary4 and metastatic5 cohorts of 7,108 whole-genome-sequenced tumours. Metastatic tumours in general have a lower intratumour heterogeneity and a conserved karyotype, displaying only a modest increase in mutations, although frequencies of structural variants are elevated overall. Furthermore, highly variable tumour-specific contributions of mutational footprints of endogenous (for example, SBS1 and APOBEC) and exogenous mutational processes (for example, platinum treatment) are present. The majority of cancer types had either moderate genomic differences (for example, lung adenocarcinoma) or highly consistent genomic portraits (for example, ovarian serous carcinoma) when comparing early-stage and late-stage disease. Breast, prostate, thyroid and kidney renal clear cell carcinomas and pancreatic neuroendocrine tumours are clear exceptions to the rule, displaying an extensive transformation of their genomic landscape in advanced stages. Exposure to treatment further scars the tumour genome and introduces an evolutionary bottleneck that selects for known therapy-resistant drivers in approximately half of treated patients. Our data showcase the potential of pan-cancer whole-genome analysis to identify distinctive features of late-stage tumours and provide a valuable resource to further investigate the biological basis of cancer and resistance to therapies.
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Affiliation(s)
- Francisco Martínez-Jiménez
- Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Hartwig Medical Foundation, Amsterdam, The Netherlands
| | - Ali Movasati
- Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sascha Remy Brunner
- Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Luan Nguyen
- Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
- Hartwig Medical Foundation Australia, Sydney, New South Wales, Australia
| | - Peter Priestley
- Hartwig Medical Foundation Australia, Sydney, New South Wales, Australia
| | - Edwin Cuppen
- Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands.
- Hartwig Medical Foundation, Amsterdam, The Netherlands.
| | - Arne Van Hoeck
- Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
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21
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Yanagihara H, Morioka T, Yamazaki S, Yamada Y, Tachibana H, Daino K, Tsuruoka C, Amasaki Y, Kaminishi M, Imaoka T, Kakinuma S. Interstitial deletion of the Apc locus in β-catenin-overexpressing cells is a signature of radiation-induced intestinal tumors in C3B6F1 ApcMin/+ mice†. JOURNAL OF RADIATION RESEARCH 2023; 64:622-631. [PMID: 37117033 DOI: 10.1093/jrr/rrad021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/13/2023] [Indexed: 05/27/2023]
Abstract
Recent studies have identified interstitial deletions in the cancer genome as a radiation-related mutational signature, although most of them do not fall on cancer driver genes. Pioneering studies in the field have indicated the presence of loss of heterozygosity (LOH) spanning Apc in a subset of sporadic and radiation-induced intestinal tumors of ApcMin/+ mice, albeit with a substantial subset in which LOH was not detected; whether copy number losses accompany such LOH has also been unclear. Herein, we analyzed intestinal tumors of C3B6F1 ApcMin/+ mice that were either left untreated or irradiated with 2 Gy of γ-rays. We observed intratumor mosaicism with respect to the nuclear/cytoplasmic accumulation of immunohistochemically detectable β-catenin, which is a hallmark of Apc+ allele loss. An immunoguided laser microdissection approach enabled the detection of LOH involving the Apc+ allele in β-catenin-overexpressing cells; in contrast, the LOH was not observed in the non-overexpressing cells. With this improvement, LOH involving Apc+ was detected in all 22 tumors analyzed, in contrast to what has been reported previously. The use of a formalin-free fixative facilitated the LOH and microarray-based DNA copy number analyses, enabling the classification of the aberrations as nondisjunction/mitotic recombination type or interstitial deletion type. Of note, the latter was observed only in radiation-induced tumors (nonirradiated, 0 of 8; irradiated, 11 of 14). Thus, an analysis considering intratumor heterogeneity identifies interstitial deletion involving the Apc+ allele as a causative radiation-related event in intestinal tumors of ApcMin/+ mice, providing an accurate approach for attributing individual tumors to radiation exposure.
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Affiliation(s)
- Hiromi Yanagihara
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Takamitsu Morioka
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Shunsuke Yamazaki
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Yutaka Yamada
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Hirotaka Tachibana
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
| | - Kazuhiro Daino
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
| | - Chizuru Tsuruoka
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Yoshiko Amasaki
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Mutsumi Kaminishi
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Tatsuhiko Imaoka
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Shizuko Kakinuma
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
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22
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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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23
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Patterson A, Elbasir A, Tian B, Auslander N. Computational Methods Summarizing Mutational Patterns in Cancer: Promise and Limitations for Clinical Applications. Cancers (Basel) 2023; 15:cancers15071958. [PMID: 37046619 PMCID: PMC10093138 DOI: 10.3390/cancers15071958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 02/24/2023] [Accepted: 03/09/2023] [Indexed: 03/29/2023] Open
Abstract
Since the rise of next-generation sequencing technologies, the catalogue of mutations in cancer has been continuously expanding. To address the complexity of the cancer-genomic landscape and extract meaningful insights, numerous computational approaches have been developed over the last two decades. In this review, we survey the current leading computational methods to derive intricate mutational patterns in the context of clinical relevance. We begin with mutation signatures, explaining first how mutation signatures were developed and then examining the utility of studies using mutation signatures to correlate environmental effects on the cancer genome. Next, we examine current clinical research that employs mutation signatures and discuss the potential use cases and challenges of mutation signatures in clinical decision-making. We then examine computational studies developing tools to investigate complex patterns of mutations beyond the context of mutational signatures. We survey methods to identify cancer-driver genes, from single-driver studies to pathway and network analyses. In addition, we review methods inferring complex combinations of mutations for clinical tasks and using mutations integrated with multi-omics data to better predict cancer phenotypes. We examine the use of these tools for either discovery or prediction, including prediction of tumor origin, treatment outcomes, prognosis, and cancer typing. We further discuss the main limitations preventing widespread clinical integration of computational tools for the diagnosis and treatment of cancer. We end by proposing solutions to address these challenges using recent advances in machine learning.
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Affiliation(s)
- Andrew Patterson
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- The Wistar Institute, Philadelphia, PA 19104, USA
| | | | - Bin Tian
- The Wistar Institute, Philadelphia, PA 19104, USA
| | - Noam Auslander
- The Wistar Institute, Philadelphia, PA 19104, USA
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Correspondence:
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24
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Sun Q, Chen Y, Li T, Ni B, Zhu X, Xu B, Li J. Risk and prognosis of secondary esophagus cancer after radiotherapy for breast cancer. Sci Rep 2023; 13:3968. [PMID: 36894590 PMCID: PMC9998633 DOI: 10.1038/s41598-023-30812-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 03/01/2023] [Indexed: 03/11/2023] Open
Abstract
Although radiation therapy (RT) improves locoregional recurrence and overall survival in breast cancer (BC), it is not yet clear whether RT affects the risk of patients with BC developing second esophageal cancer (SEC). We enrolled patients with BC as their first primary cancer from nine registries in the Surveillance, Epidemiology, and End Results (SEER) database between 1975 and 2018. Fine-Gray competing risk regressions were assessed to determine the cumulative incidence of SECs. The standardized incidence ratio (SIR) was used to compare the prevalence of SECs among BC survivors to that in the general population of the US. Kaplan-Meier survival analysis was applied to calculate the 10-year overall survival (OS) and cancer-specific survival (CSS) rates for SEC patients. Among the 523,502 BC patients considered herein, 255,135 were treated with surgery and RT, while 268,367 had surgery without radiotherapy. In a competing risk regression analysis, receiving RT was associated with a higher risk of developing an SEC in BC patients than that in the patients not receiving RT (P = .003). Compared to the general population of the US, the BC patients receiving RT showed a greater incidence of SEC (SIR, 1.52; 95% confidence interval [CI], 1.34-1.71, P < .05). The 10-year OS and CSS rates of SEC patients after RT were comparable to those of the SEC patients after no RT. Radiotherapy was related to an increased risk of developing SECs in patients with BC. Survival outcomes for patients who developed SEC after RT were similar to those after no RT.
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Affiliation(s)
- Qianhui Sun
- Oncology Department, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, No. 5, Beixian Pavilion, Xicheng District, Beijing, China
| | - Yunru Chen
- Centre for Evidence-Based Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Tingting Li
- Beijing University of Chinese Medicine, Beijing, China
| | - Baoyi Ni
- Oncology Department, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, No. 5, Beixian Pavilion, Xicheng District, Beijing, China
| | - Xiaoyu Zhu
- Oncology Department, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, No. 5, Beixian Pavilion, Xicheng District, Beijing, China
| | - Bowen Xu
- Oncology Department, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, No. 5, Beixian Pavilion, Xicheng District, Beijing, China.,Beijing University of Chinese Medicine, Beijing, China
| | - Jie Li
- Oncology Department, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, No. 5, Beixian Pavilion, Xicheng District, Beijing, China.
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25
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Liao YH, Hsu CL, Leu CY, Lai SF, Huang YL, Hsieh MS, Chen TC, Chen CN, Wang CP, Yang TL, Tsai MH, Lin MC, Lou PJ. Radiation-induced sarcoma of head and neck: Clinical characteristics and molecular signatures. Head Neck 2023; 45:638-646. [PMID: 36513597 DOI: 10.1002/hed.27279] [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: 09/20/2022] [Revised: 11/09/2022] [Accepted: 11/30/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Radiation-induced sarcoma of the head and neck (RISHN) is a rare yet devastating potential complication of radiotherapy treatment. We aimed to evaluate the clinicopathological characteristics and molecular signatures of RISHN in patients who underwent radiotherapy for head and neck cancer (HNC) to identify high-risk patients and enable earlier cancer detection. METHODS This study retrospectively evaluated 24 sarcoma patients who received radiotherapy for HNC between 1994 and 2019. Patients were divided into two groups based on RISHN latency period. Patient demographics, initial tumor staging, risk factors, and survival between groups were analyzed, and whole-exome sequencing (WES) of selected samples was performed. RESULTS The median age at diagnosis of RISHN was 54 years, and the male-to-female ratio was 2:1. The latency period ranged from 0.8 to 64.4 years (median 6.5 years), with a median survival of 21.5 months. Primary cancer in the oral cavity, treatment with alkylating agents, alcohol consumption, betel nut chewing, and smoking were identified as risk factors for short (<5 years) latency periods. The majority of RISHN cases occurred in the oral cavity (58.3%). WES analysis showed that tumor necrosis factor and cell cycle checkpoint pathways were differentially involved in both patient groups. CONCLUSIONS Although case numbers were small, our cohort represents the largest case series of RISHN from a single institution to date. Clinicians must be aware of factors affecting RISHN development and latency, and risk factor identification may lead to earlier detection and prevention in the future.
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Affiliation(s)
- Yu-Hao Liao
- Department of Otolaryngology, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan.,Department of Otolaryngology, National Taiwan University Hospital Hsin-Chu Biomedical Park Branch, Hsinchu, Taiwan
| | - Chia-Lang Hsu
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Chih-Yu Leu
- Department of Medical Education, National Taiwan University, Taipei, Taiwan
| | - Shih-Fan Lai
- Division of Radiation Oncology, Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
| | - Yen-Lin Huang
- Department of Pathology, National Taiwan University Cancer Center, Taipei, Taiwan
| | - Min-Shu Hsieh
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Tseng-Cheng Chen
- Department of Otolaryngology, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chun-Nan Chen
- Department of Otolaryngology, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Cheng-Ping Wang
- Department of Otolaryngology, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Tsung-Lin Yang
- Department of Otolaryngology, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Mong-Hsun Tsai
- Bioinformatics and Biostatistics Core, Center of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan
| | - Mei-Chun Lin
- Department of Otolaryngology, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Pei-Jen Lou
- Department of Otolaryngology, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
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26
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Eidemüller M, Becker J, Kaiser JC, Ulanowski A, Apostoaei AI, Hoffman FO. Concepts of association between cancer and ionising radiation: accounting for specific biological mechanisms. RADIATION AND ENVIRONMENTAL BIOPHYSICS 2023; 62:1-15. [PMID: 36633666 PMCID: PMC9950217 DOI: 10.1007/s00411-022-01012-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
The probability that an observed cancer was caused by radiation exposure is usually estimated using cancer rates and risk models from radioepidemiological cohorts and is called assigned share (AS). This definition implicitly assumes that an ongoing carcinogenic process is unaffected by the studied radiation exposure. However, there is strong evidence that radiation can also accelerate an existing clonal development towards cancer. In this work, we define different association measures that an observed cancer was newly induced, accelerated, or retarded. The measures were quantified exemplarily by Monte Carlo simulations that track the development of individual cells. Three biologically based two-stage clonal expansion (TSCE) models were applied. In the first model, radiation initiates cancer development, while in the other two, radiation has a promoting effect, i.e. radiation accelerates the clonal expansion of pre-cancerous cells. The parameters of the TSCE models were derived from breast cancer data from the atomic bomb survivors of Hiroshima and Nagasaki. For exposure at age 30, all three models resulted in similar estimates of AS at age 60. For the initiation model, estimates of association were nearly identical to AS. However, for the promotion models, the cancerous clonal development was frequently accelerated towards younger ages, resulting in associations substantially higher than AS. This work shows that the association between a given cancer and exposure in an affected person depends on the underlying biological mechanism and can be substantially larger than the AS derived from classic radioepidemiology.
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Affiliation(s)
- Markus Eidemüller
- Institute of Radiation Medicine, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.
| | - Janine Becker
- Institute of Radiation Medicine, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Jan Christian Kaiser
- Institute of Radiation Medicine, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Alexander Ulanowski
- Institute of Radiation Medicine, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
- International Atomic Energy Agency, IAEA Laboratories, Friedensstraße 1, 2444, Seibersdorf, Austria
| | - A Iulian Apostoaei
- Oak Ridge Center for Risk Analysis (ORRISK, Inc), 102 Donner Drive, Oak Ridge, TN, 37830, USA
| | - F Owen Hoffman
- Oak Ridge Center for Risk Analysis (ORRISK, Inc), 102 Donner Drive, Oak Ridge, TN, 37830, USA
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Copy number footprints of platinum-based anticancer therapies. PLoS Genet 2023; 19:e1010634. [PMID: 36780550 PMCID: PMC9956877 DOI: 10.1371/journal.pgen.1010634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/24/2023] [Accepted: 01/24/2023] [Indexed: 02/15/2023] Open
Abstract
Recently, distinct mutational footprints observed in metastatic tumors, secondary malignancies and normal human tissues have been demonstrated to be caused by the exposure to several chemotherapeutic drugs. These characteristic mutations originate from specific lesions caused by these chemicals to the DNA of exposed cells. However, it is unknown whether the exposure to these chemotherapies leads to a specific footprint of larger chromosomal aberrations. Here, we address this question exploiting whole genome sequencing data of metastatic tumors obtained from patients exposed to different chemotherapeutic drugs. As a result, we discovered a specific copy number footprint across tumors from patients previously exposed to platinum-based therapies. This footprint is characterized by a significant increase in the number of chromosomal fragments of copy number 1-4 and size smaller than 10 Mb in exposed tumors with respect to their unexposed counterparts (median 14-387% greater across tumor types). The number of chromosomal fragments characteristic of the platinum-associated CN footprint increases significantly with the activity of the well known platinum-related footprint of single nucleotide variants across exposed tumors.
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28
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Schimmel J, van Wezel MD, van Schendel R, Tijsterman M. Chromosomal breaks at the origin of small tandem DNA duplications. Bioessays 2023; 45:e2200168. [PMID: 36385254 DOI: 10.1002/bies.202200168] [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: 08/26/2022] [Revised: 11/01/2022] [Accepted: 11/03/2022] [Indexed: 11/18/2022]
Abstract
Small tandem DNA duplications in the range of 15 to 300 base-pairs play an important role in the aetiology of human disease and contribute to genome diversity. Here, we discuss different proposed mechanisms for their occurrence and argue that this type of structural variation mainly results from mutagenic repair of chromosomal breaks. This hypothesis is supported by both bioinformatical analysis of insertions occurring in the genome of different species and disease alleles, as well as by CRISPR/Cas9-based experimental data from different model systems. Recent work points to fill-in synthesis at double-stranded DNA breaks with complementary sequences, regulated by end-joining mechanisms, to account for small tandem duplications. We will review the prevalence of small tandem duplications in the population, and we will speculate on the potential sources of DNA damage that could give rise to this mutational signature. With the development of novel algorithms to analyse sequencing data, small tandem duplications are now more frequently detected in the human genome and identified as oncogenic gain-of-function mutations. Understanding their origin could lead to optimized treatment regimens to prevent therapy-induced activation of oncogenes and might expose novel vulnerabilities in cancer.
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Affiliation(s)
- Joost Schimmel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marloes D van Wezel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Robin van Schendel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
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29
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Whole-Genome Sequencing Reveals Mutational Signatures Related to Radiation-Induced Sarcomas and DNA-Damage-Repair Pathways. Mod Pathol 2023; 36:100004. [PMID: 36788076 DOI: 10.1016/j.modpat.2022.100004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 08/01/2022] [Accepted: 09/18/2022] [Indexed: 01/19/2023]
Abstract
Radiation-induced sarcoma (RIS) is a rare but serious late complication arising from radiotherapy. Despite unfavorable clinical outcomes, the genomic footprints of ionizing radiation in RIS development remain largely unknown. Hence, this study aimed to characterize RIS genomes and the genomic alterations in them. We analyzed whole-genome sequencing in 11 RIS genomes matched with normal genomes to identify somatic alterations potentially associated with RIS development. Furthermore, the abundance of mutations, mutation signatures, and structural variants in RIS were compared with those in radiation-naïve spontaneous sarcomas. The mutation abundance in RIS genomes, including one hypermutated genome, was variable. Cancer-related genes might show different types of genomic alterations. For instance, NF1, NF2, NOTCH1, NOTCH2, PIK3CA, RB1, and TP53 showed singleton somatic mutations; MYC, CDKN2A, RB1, and NF1 showed recurrent copy number alterations; and NF2, ARID1B, and RAD51B showed recurrent structural variations. The genomic footprints of nonhomologous end joining are prevalent at indels of RIS genomes compared with those in spontaneous sarcoma genomes, representing the genomic hallmark of RIS genomes. In addition, frequent chromothripsis was identified along with predisposing germline variants in the DNA-damage-repair pathways in RIS genomes. The characterization of RIS genomes on a whole-genome sequencing scale highlighted that the nonhomologous end joining pathway was associated with tumorigenesis, and it might pave the way for the development of advanced diagnostic and therapeutic strategies for RIS.
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30
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Thol K, Pawlik P, McGranahan N. Therapy sculpts the complex interplay between cancer and the immune system during tumour evolution. Genome Med 2022; 14:137. [PMID: 36476325 PMCID: PMC9730559 DOI: 10.1186/s13073-022-01138-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 11/09/2022] [Indexed: 12/12/2022] Open
Abstract
Cancer development is an evolutionary process. A key selection pressure is exerted by therapy, one of the few players in cancer evolution that can be controlled. As such, an understanding of how treatment acts to sculpt the tumour and its microenvironment and how this influences a tumour's subsequent evolutionary trajectory is critical. In this review, we examine cancer evolution and intra-tumour heterogeneity in the context of therapy. We focus on how radiotherapy, chemotherapy and immunotherapy shape both tumour development and the environment in which tumours evolve and how resistance can develop or be selected for during treatment.
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Affiliation(s)
- Kerstin Thol
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK
| | - Piotr Pawlik
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK.
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31
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Bartlett EK, Sharma A, Seier K, Antonescu CR, Agaram NP, Jadeja B, Rosenbaum E, Chi P, Brennan MF, Qin LX, Alektiar KM, Singer S. Histology-Specific Prognostication for Radiation-Associated Soft Tissue Sarcoma. JCO Precis Oncol 2022; 6:e2200087. [PMID: 36240470 PMCID: PMC9616643 DOI: 10.1200/po.22.00087] [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: 02/04/2022] [Revised: 04/29/2022] [Accepted: 07/21/2022] [Indexed: 11/07/2022] Open
Abstract
PURPOSE Radiation-associated sarcomas (RAS) are rare but aggressive malignancies. We sought to characterize the histology-specific presentation and behavior of soft tissue RAS to improve individualized prognostication. METHODS A single-institutional prospectively maintained database was queried for all patients with primary, nonmetastatic RAS treated with surgical resection from 1982 to 2019. Patients presenting with the five most common RAS histologies were propensity-matched to those with sporadic tumors of the same histology. Incidence of disease-specific death (DSD) was modeled using cumulative incidence analyses. RESULTS Among 259 patients with RAS, the five most common histologies were malignant peripheral nerve sheath tumor (MPNST; n = 19), myxofibrosarcoma (n = 20), leiomyosarcoma (n = 24), undifferentiated pleomorphic sarcoma (UPS; n = 55), and angiosarcoma (AS; n = 62). DSD varied significantly by histology (P = .002), with RAS MPNST and UPS having the highest DSD. In unadjusted analysis, RAS MPNST was associated with increased DSD compared with sporadic MPNST (75% v 38% 5-year DSD, P = .002), as was RAS UPS compared with sporadic UPS (49% v 28% 5-year DSD, P = .004). Unadjusted DSD was similar among patients with RAS AS, leiomyosarcoma, or myxofibrosarcoma and sporadic sarcoma of the same histology. After matching RAS to sporadic patients within each histology, DSD only differed between RAS and sporadic MPNST (83% v 46% 5-year DSD, P = .013). Patients with RAS AS presented in such a distinct manner to those with sporadic AS that a successful match was not possible. CONCLUSION The aggressive presentation of RAS is histology-specific, and DSD is driven by RAS MPNST and UPS histologies. Despite the aggressive presentation, standard prognostic factors can be used to estimate risk of DSD among most RAS. In MPNST, radiation association should be considered to independently associate with markedly higher risk of DSD.
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Affiliation(s)
- Edmund K. Bartlett
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Avinash Sharma
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kenneth Seier
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Bhumika Jadeja
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Evan Rosenbaum
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ping Chi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Murray F. Brennan
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Li-Xuan Qin
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kaled M. Alektiar
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Samuel Singer
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
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32
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Cisneros-Aguirre M, Ping X, Stark JM. To indel or not to indel: Factors influencing mutagenesis during chromosomal break end joining. DNA Repair (Amst) 2022; 118:103380. [PMID: 35926296 PMCID: PMC10105512 DOI: 10.1016/j.dnarep.2022.103380] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/22/2022] [Accepted: 07/24/2022] [Indexed: 12/16/2022]
Abstract
Chromosomal DNA double-strand breaks (DSBs) are the effective lesion of radiotherapy and other clastogenic cancer therapeutics, and are also the initiating event of many approaches to gene editing. Ligation of the DSBs by end joining (EJ) pathways can restore the broken chromosome, but the repair junctions can have insertion/deletion (indel) mutations. The indel patterns resulting from DSB EJ are likely defined by the initial structure of the DNA ends, how the ends are processed and synapsed prior to ligation, and the factors that mediate the ligation step. In this review, we describe key factors that influence these steps of DSB EJ in mammalian cells, which is significant both for understanding mutagenesis resulting from clastogenic cancer therapeutics, and for developing approaches to manipulating gene editing outcomes.
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Affiliation(s)
- Metztli Cisneros-Aguirre
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Xiaoli Ping
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA.
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Carvalho FL, Mossanen M, Van Allen EM, Mouw KW. Reply to Yuxuan Song, Yiqing Du, and Tao Xu’s Letter to the Editor re: Matthew Mossanen, Filipe L.F. Carvalho, Vinayak Muralidhar, et al. Genomic Features of Muscle-invasive Bladder Cancer Arising After Prostate Radiotherapy. Eur Urol 2022;81:466–73. Eur Urol 2022; 82:e141-e142. [DOI: 10.1016/j.eururo.2022.07.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 07/21/2022] [Indexed: 11/25/2022]
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34
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Wakeford R, Hauptmann M. The risk of cancer following high, and very high, doses of ionising radiation. JOURNAL OF RADIOLOGICAL PROTECTION : OFFICIAL JOURNAL OF THE SOCIETY FOR RADIOLOGICAL PROTECTION 2022; 42:020518. [PMID: 35671754 DOI: 10.1088/1361-6498/ac767b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
It is established that moderate-to-high doses of ionising radiation increase the risk of subsequent cancer in the exposed individual, but the question arises as to the risk of cancer from higher doses, such as those delivered during radiotherapy, accidents, or deliberate acts of malice. In general, the cumulative dose received during a course of radiation treatment is sufficiently high that it would kill a person if delivered as a single dose to the whole body, but therapeutic doses are carefully fractionated and high/very high doses are generally limited to a small tissue volume under controlled conditions. The very high cumulative doses delivered as fractions during radiation treatment are designed to inactivate diseased cells, but inevitably some healthy cells will also receive high/very high doses. How the doses (ranging from <1 Gy to tens of Gy) received by healthy tissues during radiotherapy affect the risk of second primary cancer is an increasingly important issue to address as more cancer patients survive the disease. Studies show that, except for a turndown for thyroid cancer, a linear dose-response for second primary solid cancers seems to exist over a cumulative gamma radiation dose range of tens of gray, but with a gradient of excess relative risk per Gy that varies with the type of second cancer, and which is notably shallower than that found in the Japanese atomic bomb survivors receiving a single moderate-to-high acute dose. The risk of second primary cancer consequent to high/very high doses of radiation is likely to be due to repopulation of heavily irradiated tissues by surviving stem cells, some of which will have been malignantly transformed by radiation exposure, although the exact mechanism is not known, and various models have been proposed. It is important to understand the mechanisms that lead to the raised risk of second primary cancers consequent to the receipt of high/very high doses, in particular so that the risks associated with novel radiation treatment regimens-for example, intensity modulated radiotherapy and volumetric modulated arc therapy that deliver high doses to the target volume while exposing relatively large volumes of healthy tissue to low/moderate doses, and treatments using protons or heavy ions rather than photons-may be properly assessed.
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Affiliation(s)
- Richard Wakeford
- Centre for Occupational and Environmental Health, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Michael Hauptmann
- Institute of Biostatistics and Registry Research, Brandenburg Medical School, Fehrbelliner Strasse 38, 16816 Neuruppin, Germany
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Guo JJ, Liu N, Ma Z, Gong ZJ, Liang YL, Cheng Q, Zhong XG, Yao ZJ. Dose-Response Effects of Low-Dose Ionizing Radiation on Blood Parameters in Industrial Irradiation Workers. Dose Response 2022; 20:15593258221105695. [PMID: 35693871 PMCID: PMC9174562 DOI: 10.1177/15593258221105695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 05/17/2022] [Indexed: 11/24/2022] Open
Abstract
While previous studies have focused on the health effects of occupational
exposure of radiations on medical radiation workers, few have analyzed the
dose-response relationship between low radiation doses and changes in blood
parameters. Even fewer studies have been conducted on industrial worker
populations. Using a prospective cohort study design, this study collected
health examination reports and personal dose monitoring data from 705 industrial
irradiation workers who underwent regular physical examinations at Dongguan
Sixth People’s Hospital. The dose-response effects of low-dose ionizing
radiation on blood parameters were assessed using a generalized linear model and
restricted cubic spline model. Red blood cell counts decreased then increased,
before decreasing again with increasing ionizing radiation. This was in contrast
to the curve of the total platelet count after irradiation. Additionally, a
radiation dose of 2.904 mSv was the turning point for the nonlinear curve of
hemoglobin count changes. In conclusion, long-term, low-dose ionizing radiation
affects blood cell levels in industrial irradiation workers. There is a
nonlinear dose-response relationship between red blood cell, platelet, and
hemoglobin counts and the cumulative radiation dose. These findings should alert
radiation workers to seek preventive medical treatment before the occurrence of
any serious hematopoietic disease.
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Affiliation(s)
- Jia-jia Guo
- Department of Epidemiology and Health Statistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Ning Liu
- Department of Epidemiology and Health Statistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Zheng Ma
- The Sixth People’s Hospital of Dongguan, Dongguan, China
| | - Zi-jun Gong
- Department of Epidemiology and Health Statistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Yue-lang Liang
- Department of Epidemiology and Health Statistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Qi Cheng
- Department of Epidemiology and Health Statistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | | | - Zhen-jiang Yao
- Department of Epidemiology and Health Statistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
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Cosenza MR, Rodriguez-Martin B, Korbel JO. Structural Variation in Cancer: Role, Prevalence, and Mechanisms. Annu Rev Genomics Hum Genet 2022; 23:123-152. [DOI: 10.1146/annurev-genom-120121-101149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Somatic rearrangements resulting in genomic structural variation drive malignant phenotypes by altering the expression or function of cancer genes. Pan-cancer studies have revealed that structural variants (SVs) are the predominant class of driver mutation in most cancer types, but because they are difficult to discover, they remain understudied when compared with point mutations. This review provides an overview of the current knowledge of somatic SVs, discussing their primary roles, prevalence in different contexts, and mutational mechanisms. SVs arise throughout the life history of cancer, and 55% of driver mutations uncovered by the Pan-Cancer Analysis of Whole Genomes project represent SVs. Leveraging the convergence of cell biology and genomics, we propose a mechanistic classification of somatic SVs, from simple to highly complex DNA rearrangement classes. The actions of DNA repair and DNA replication processes together with mitotic errors result in a rich spectrum of SV formation processes, with cascading effects mediating extensive structural diversity after an initiating DNA lesion has formed. Thanks to new sequencing technologies, including the sequencing of single-cell genomes, open questions about the molecular triggers and the biomolecules involved in SV formation as well as their mutational rates can now be addressed. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
| | | | - Jan O. Korbel
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
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Transcriptional Dynamics of DNA Damage Responsive Genes in Circulating Leukocytes during Radiotherapy. Cancers (Basel) 2022; 14:cancers14112649. [PMID: 35681629 PMCID: PMC9179543 DOI: 10.3390/cancers14112649] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/19/2022] [Accepted: 05/24/2022] [Indexed: 02/06/2023] Open
Abstract
Simple Summary In this study, the transcriptional response of a panel of radiation responsive genes was monitored over time in blood samples after radiation exposure in vivo. For this aim, cancer patients treated by radiotherapy were recruited after consent forms were obtained. Following the first fraction of radiotherapy, 2 mL blood samples were collected at different time points during the first 24h hours (before the second fraction was delivered) and at mid and end of treatment. Amongst the 9 genes studied, the gene FDXR stood out as the most sensitive and responsive to the low dose of radiation received from the localised radiation treatment by the circulating white blood cells. The activation of FDXR was found to depend on the volume of the body exposed with a peak of expression around 8–9 hours after irradiation was delivered. Finally results obtained ex vivo confirmed the results obtained in vivo. Abstract External beam radiation therapy leads to cellular activation of the DNA damage response (DDR). DNA double-strand breaks (DSBs) activate the ATM/CHEK2/p53 pathway, inducing the transcription of stress genes. The dynamic nature of this transcriptional response has not been directly observed in vivo in humans. In this study we monitored the messenger RNA transcript abundances of nine DNA damage-responsive genes (CDKN1A, GADD45, CCNG1, FDXR, DDB2, MDM2, PHPT1, SESN1, and PUMA), eight of them regulated by p53 in circulating blood leukocytes at different time points (2, 6–8, 16–18, and 24 h) in cancer patients (lung, neck, brain, and pelvis) undergoing radiotherapy. We discovered that, although the calculated mean physical dose to the blood was very low (0.038–0.169 Gy), an upregulation of Ferredoxin reductase (FDXR) gene transcription was detectable 2 h after exposure and was dose dependent from the lowest irradiated percentage of the body (3.5% whole brain) to the highest, (up to 19.4%, pelvic zone) reaching a peak at 6–8 h. The radiation response of the other genes was not strong enough after such low doses to provide meaningful information. Following multiple fractions, the expression level increased further and was still significantly up-regulated by the end of the treatment. Moreover, we compared FDXR transcriptional responses to ionizing radiation (IR) in vivo with healthy donors’ blood cells exposed ex vivo and found a good correlation in the kinetics of expression from the 8-hours time-point onward, suggesting that a molecular transcriptional regulation mechanism yet to be identified is involved. To conclude, we provided the first in vivo human report of IR-induced gene transcription temporal response of a panel of p53-dependant genes. FDXR was demonstrated to be the most responsive gene, able to reliably inform on the low doses following partial body irradiation of the patients, and providing an expression pattern corresponding to the % of body exposed. An extended study would provide individual biological dosimetry information and may reveal inter-individual variability to predict radiotherapy-associated adverse health outcomes.
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Abstract
Distilling biologically meaningful information from cancer genome sequencing data requires comprehensive identification of somatic alterations using rigorous computational methods. As the amount and complexity of sequencing data have increased, so has the number of tools for analysing them. Here, we describe the main steps involved in the bioinformatic analysis of cancer genomes, review key algorithmic developments and highlight popular tools and emerging technologies. These tools include those that identify point mutations, copy number alterations, structural variations and mutational signatures in cancer genomes. We also discuss issues in experimental design, the strengths and limitations of sequencing modalities and methodological challenges for the future.
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Klubo-Gwiezdzinska J. Childhood Exposure to Excess Ionizing Radiation Is Associated with Dose-Dependent Fusions as Molecular Drivers of Papillary Thyroid Cancer. Thyroid 2022; 34:161-164. [PMID: 36969797 PMCID: PMC10038615 DOI: 10.1089/ct.2022;34.161-164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Background Exposure to excess ionizing radiation has been identified as a risk factor for the development of thyroid cancer (1). However, there are no well-established biomarkers indicating exposure to radiation as the etiology of thyroid tumors that can be applied in clinical care or in legal claims. Morton et al. analyzed a large cohort of individuals who were exposed to a power plant accident in Chernobyl in 1986 in their childhood and who subsequently developed papillary thyroid cancer (PTC) (2). The goal of the study was to enhance our understanding of radiation-induced carcinogenesis based on assessment of the molecular drivers, transcriptomics, and epigenetic profile of PTC associated with excessive environmental radiation exposure. Methods The authors performed whole-genome sequencing, single-nucleotide polymorphism (SNP) microarray genotyping, mRNA and microRNA sequencing, methylation profiling, transcriptome analysis, and telomere-length quantification in 440 pathologically confirmed fresh-frozen PTC tissue samples for which matched normal tissue from either nontumor thyroid and/or blood was available. In the study group, 359 subjects were exposed to excess ionizing radiation in childhood or in utero; 81 individuals who were born more than 9 months after the Chernobyl accident served as a reference group. The data were analyzed adjusting for covariates that potentially affect PTC incidence, including sex, age at diagnosis, age at radiation exposure, and latency (defined as the time from exposure to PTC diagnosis). Results The median age at exposure to ionizing radiation was 7.3 years and the median latency before the diagnosis of PTC was 22.4 years. The exposure estimates (250 mGy on average and up to 8800 mGy) were based on direct measurements of the thyroid-absorbed dose within 8 weeks after the accident in 53 individuals, while for the remaining cohort, they were imputed from direct measurements in individuals living in a similar area.The molecular drivers were identified in the vast majority of the tumors (98.4%), mainly as a low mutation burden consisting of single candidates in the mitogen-activated protein kinase (MAPK) pathway. The most common driver was the BRAF V600E mutation, but fusions in RET proto-oncogene, receptor tyrosine kinase (RTK), such as NTRK1, NTRK3, ALK, as well as BRAF, PPRAG, and IGF2/IGF2BP3 accounted for the majority of the remaining drivers (41% of the tumors). Moreover, there was a significant association between fusion drivers and radiation dose, after adjustment for age at diagnosis and sex. Same significant association with radiation was observed for small deletions and balanced structural variants resulting from the nonhomologous end-joining repair of double-stranded DNA damage. In contrast, transcriptome, methylome, or telomere length were not significantly associated with the radiation dose, and all tumors were microsatellite-stable. No novel molecular signature unique for radiation-associated PTC has been identified. Conclusions The study reveals potential mechanisms behind radiation-associated PTC, consisting of DNA double-stranded breaks leading to nonhomologous end-joining repair mechanisms, that result in pathogenic gene fusions responsible for clonal growth. There is no unique signature of radiation-associated PTC that could serve as a biomarker of radiation-induced malignancy.
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Affiliation(s)
- Joanna Klubo-Gwiezdzinska
- Metabolic Disease Branch, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, U.S.A
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Mirjolet C, Diallo I, Bertaut A, Veres C, Sargos P, Helfre S, Sunyach MP, Truc G, Le Pechoux C, Paumier A, Ducassou A, Jolnerovski M, Thariat J, Lapeyre M, Cordoba A, Mahé MA, Maingon P. Treatment related factors associated with the risk of breast radio-induced-sarcoma. Radiother Oncol 2022; 171:14-21. [DOI: 10.1016/j.radonc.2022.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 03/14/2022] [Accepted: 04/03/2022] [Indexed: 10/18/2022]
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Tarabichi M, Demetter P, Craciun L, Maenhaut C, Detours V. Thyroid cancer under the scope of emerging technologies. Mol Cell Endocrinol 2022; 541:111491. [PMID: 34740746 DOI: 10.1016/j.mce.2021.111491] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 10/08/2021] [Accepted: 10/18/2021] [Indexed: 01/03/2023]
Abstract
The vast majority of thyroid cancers originate from follicular cells. We outline outstanding issues at each step along the path of cancer patient care, from prevention to post-treatment follow-up and highlight how emerging technologies will help address them in the coming years. Three directions will dominate the coming technological landscape. Genomics will reveal tumoral evolutionary history and shed light on how these cancers arise from the normal epithelium and the genomics alteration driving their progression. Transcriptomics will gain cellular and spatial resolution providing a full account of intra-tumor heterogeneity and opening a window on the microenvironment supporting thyroid tumor growth. Artificial intelligence will set morphological analysis on an objective quantitative ground laying the foundations of a systematic thyroid tumor classification system. It will also integrate into unified representations the molecular and morphological perspectives on thyroid cancer.
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Affiliation(s)
- Maxime Tarabichi
- Institute of Interdisciplinary Research (IRIBHM), Université Libre de Bruxelles, Brussels, Belgium.
| | - Pieter Demetter
- Department of Pathology, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Ligia Craciun
- Department of Pathology, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Carine Maenhaut
- Institute of Interdisciplinary Research (IRIBHM), Université Libre de Bruxelles, Brussels, Belgium.
| | - Vincent Detours
- Institute of Interdisciplinary Research (IRIBHM), Université Libre de Bruxelles, Brussels, Belgium.
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Genetic alterations associated with malignant transformation of sporadic vestibular schwannoma. Acta Neurochir (Wien) 2022; 164:343-352. [PMID: 34816314 PMCID: PMC8854236 DOI: 10.1007/s00701-021-05062-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 11/10/2021] [Indexed: 11/25/2022]
Abstract
Introduction Malignant peripheral nerve sheath tumor of the vestibulocochlear nerve (VN-MPNST) is exceedingly rare and carries a poor prognosis. Little is known about its underlying genetics and in particular the process of malignant transformation. There is an ongoing debate on whether the transformation is initiated by ionizing radiation. We present here the analysis and comparison of two post-radiation VN-MPNST and one undergoing spontaneous transformation. Methods Four tumors from three patients (radiation-naïve vestibular schwannoma before (VS) and after (VN-MPNST) malignant transformation in addition to two post-radiation VN-MPNST) were subjected to DNA whole-genome microarray and whole-exome sequencing and tumor-specific mutations were called. Mutational signatures were characterized using MuSiCa. Results The tumor genomes were characterized predominantly by copy-number aberrations with 36–81% of the genome affected. Even the VS genome was grossly aberrated. The spontaneous malignant transformation was characterized by a near-total whole-genome doubling, disappearance of NF2 mutation and new mutations in three cancer-related genes (GNAQ, FOXO4 and PDGFRB). All tumors had homozygous loss of the tumor suppressor CDKN2A. Neither mutational signature nor copy number profile was associated with ionizing radiation. Conclusion The VN-MPNST genome in our cases is characterized by large copy-number aberrations and homozygous deletion of CDKN2A. Our study demonstrates a VS with genetic alterations similar to its malignant counterpart, suggesting the existence of premalignant VS. No consistent mutational signature was associated with ionizing radiation.
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Brady SW, Gout AM, Zhang J. Therapeutic and prognostic insights from the analysis of cancer mutational signatures. Trends Genet 2022; 38:194-208. [PMID: 34483003 PMCID: PMC8752466 DOI: 10.1016/j.tig.2021.08.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 02/08/2023]
Abstract
The somatic mutations in each cancer genome are caused by multiple mutational processes, each of which leaves a characteristic imprint (or 'signature'), potentially caused by specific etiologies or exposures. Deconvolution of these signatures offers a glimpse into the evolutionary history of individual tumors. Recent work has shown that mutational signatures may also yield therapeutic and prognostic insights, including the identification of cell-intrinsic signatures as biomarkers of drug response and prognosis. For example, mutational signatures indicating homologous recombination deficiency are associated with poly(ADP)-ribose polymerase (PARP) inhibitor sensitivity, whereas APOBEC-associated signatures are associated with ataxia telangiectasia and Rad3-related kinase (ATR) inhibitor sensitivity. Furthermore, therapy-induced mutational signatures implicated in cancer progression have also been uncovered, including the identification of thiopurine-induced TP53 mutations in leukemia. In this review, we explore the various ways mutational signatures can reveal new therapeutic and prognostic insights, thus extending their traditional role in identifying disease etiology.
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Affiliation(s)
- Samuel W Brady
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Alexander M Gout
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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Muscle-invasive Bladder Cancer Arising After Prostate Radiotherapy: A Rare Entity with Unique Genomic Features. Eur Urol 2022; 81:474-475. [PMID: 35109971 DOI: 10.1016/j.eururo.2022.01.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 01/13/2022] [Indexed: 11/24/2022]
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Schipper LJ, Monkhorst K, Samsom KG, Bosch LJ, Snaebjornsson P, van Boven H, Roepman P, van der Kolk LE, van Houdt WJ, van der Graaf WT, Meijer GA, Voest EE. Clinical Impact of Prospective Whole Genome Sequencing in Sarcoma Patients. Cancers (Basel) 2022; 14:436. [PMID: 35053600 PMCID: PMC8773512 DOI: 10.3390/cancers14020436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/12/2022] [Accepted: 01/14/2022] [Indexed: 12/21/2022] Open
Abstract
With more than 70 different histological sarcoma subtypes, accurate classification can be challenging. Although characteristic genetic events can largely facilitate pathological assessment, large-scale molecular profiling generally is not part of regular diagnostic workflows for sarcoma patients. We hypothesized that whole genome sequencing (WGS) optimizes clinical care of sarcoma patients by detection of diagnostic and actionable genomic characteristics, and of underlying hereditary conditions. WGS of tumor and germline DNA was incorporated in the diagnostic work-up of 83 patients with a (presumed) sarcomas in a tertiary referral center. Clinical follow-up data were collected prospectively to assess impact of WGS on clinical decision making. In 12/83 patients (14%), the genomic profile led to revision of cancer diagnosis, with change of treatment plan in eight. All twelve patients had undergone multiple tissue retrieval procedures and immunohistopathological assessments by regional and expert pathologists prior to WGS analysis. Actionable biomarkers with therapeutic potential were identified for 30/83 patients. Pathogenic germline variants were present in seven patients. In conclusion, unbiased genomic characterization with WGS identifies genomic biomarkers with direct clinical implications for sarcoma patients. Given the diagnostic complexity and high unmet need for new treatment opportunities in sarcoma patients, WGS can be an important extension of the diagnostic arsenal of pathologists.
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Affiliation(s)
- Luuk J. Schipper
- Department of Molecular Oncology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
- Oncode Institute, 3521 AL Utrecht, The Netherlands
| | - Kim Monkhorst
- Department of Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; (K.M.); (K.G.S.); (L.J.W.B.); (P.S.); (H.v.B.); (G.A.M.)
| | - Kris G. Samsom
- Department of Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; (K.M.); (K.G.S.); (L.J.W.B.); (P.S.); (H.v.B.); (G.A.M.)
| | - Linda J.W. Bosch
- Department of Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; (K.M.); (K.G.S.); (L.J.W.B.); (P.S.); (H.v.B.); (G.A.M.)
| | - Petur Snaebjornsson
- Department of Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; (K.M.); (K.G.S.); (L.J.W.B.); (P.S.); (H.v.B.); (G.A.M.)
| | - Hester van Boven
- Department of Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; (K.M.); (K.G.S.); (L.J.W.B.); (P.S.); (H.v.B.); (G.A.M.)
| | - Paul Roepman
- Hartwig Medical Foundation, 1098 XH Amsterdam, The Netherlands;
| | - Lizet E. van der Kolk
- Family Cancer Clinic, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
| | - Winan J. van Houdt
- Department of Surgical Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
| | | | - Gerrit A. Meijer
- Department of Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; (K.M.); (K.G.S.); (L.J.W.B.); (P.S.); (H.v.B.); (G.A.M.)
| | - Emile E. Voest
- Department of Molecular Oncology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
- Oncode Institute, 3521 AL Utrecht, The Netherlands
- Department of Medical Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
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Mismatch Repair Deficiency and Somatic Mutations in Human Sinonasal Tumors. Cancers (Basel) 2021; 13:cancers13236081. [PMID: 34885191 PMCID: PMC8657279 DOI: 10.3390/cancers13236081] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 01/12/2023] Open
Abstract
Simple Summary Sinonasal carcinomas are rare tumors with an overall poor prognosis. Due to limitations in local therapeutic approaches, systemic neo-adjuvant or adjuvant therapies are becoming increasingly important in order to improve patient outcome. This study aimed to examine potentially therapeutic targetable molecular alterations in different sinonasal tumors, including deficiency in mismatch repair proteins and microsatellite instability as well as driver mutations. According to our results, immunohistochemical (IHC) analysis of mismatch repair (MMR) proteins and sequencing-based panel analysis should be integrated into the diagnostics of clinically aggressive inverted sinonasal papilloma (ISP) and sinonasal squamous cell carcinoma (SNSCC) in order to enable the therapeutic possibility of a targeted therapy. Abstract Due to limitations in local therapy approaches for sinonasal tumors, improvement in systemic therapies plays a pivotal role for prolongation of the patient’s survival. The aim of this study was to examine potential biomarkers, including deficiency in mismatch repair proteins (dMMR)/microsatellite instability (MSI-H) in sinonasal cancers and their precancerous lesions. A comprehensive analysis of 10 sinonasal cancer cell lines by whole exome sequencing, screening 174 sinonasal tumors by immunohistochemistry (IHC) for mismatch repair deficiency and next generation sequencing (NGS) of 136 tumor samples revealed a dMMR/MSI-H sinonasal squamous cell carcinoma (SNSCC) cell line based on a somatic missense mutation in MLH1 and an overall frequency of dMMR/MSI-H SNSCC of 3.2% (4/125). Targetable EGFR mutations were found in 89.3% (25/28) of inverted sinonasal papilloma (ISP) and in 60% (6/10) of ISP-associated carcinomas. While PIK3CA and EGFR mutations were not mutually exclusive, KRAS mutated tumors were an EGFR-wildtype. The effect of potential driver mutations in FGFR2, FGFR3, BRAF, HRAS, MAP2K1, PTEN, NOTCH1 and CARD11 need further investigation. Our results suggest that biomarker testing, including MMR-IHC and NGS panel analysis, should be integrated into the diagnostics of clinically aggressive ISPs and SNSCC to assess prognosis and facilitate therapeutic decisions.
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Poland SG, Guth AA, Feinberg JA, Ebina W, Chiu E, Levine J, Gonzalez LM, Muggia F. Basal cell carcinoma after breast radiation: An uncommon disease with varying clinical presentations. CURRENT PROBLEMS IN CANCER: CASE REPORTS 2021. [DOI: 10.1016/j.cpccr.2021.100111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
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Genomic Features of Muscle-invasive Bladder Cancer Arising After Prostate Radiotherapy. Eur Urol 2021; 81:466-473. [PMID: 34953602 PMCID: PMC9018481 DOI: 10.1016/j.eururo.2021.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 11/12/2021] [Accepted: 12/04/2021] [Indexed: 11/24/2022]
Abstract
BACKGROUND Muscle-invasive bladder cancer (MIBC) is a rare but serious event following definitive radiation for prostate cancer. Radiation-associated MIBC (RA-MIBC) can be difficult to manage given the challenges of delivering definitive therapy to a previously irradiated pelvis. The genomic landscape of RA-MIBC and whether it is distinct from non-RA-MIBC are unknown. OBJECTIVE To define mutational features of RA-MIBC and compare the genomic landscape of RA-MIBC with that of non-RA-MIBC. DESIGN, SETTING, AND PARTICIPANTS We identified patients from our institution who received radiotherapy for prostate cancer and subsequently developed MIBC. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS We performed whole exome sequencing of bladder tumors from RA-MIBC patients. Tumor genetic alterations including mutations, copy number alterations, and mutational signatures were identified and were compared with genetic features of non-RA-MIBC. We used the Kaplan-Meier method to estimate recurrence-free (RFS) and overall (OS) survival. RESULTS AND LIMITATIONS We identified 19 RA-MIBC patients with available tumor tissue (n = 22 tumors) and clinical data. The median age was 76 yr, and the median time from prostate cancer radiation to RA-MIBC was 12 yr. The median RFS was 14.5 mo and the median OS was 22.0 mo. Compared with a cohort of non-RA-MIBC analyzed in parallel, there was no difference in tumor mutational burden, but RA-MIBCs had a significantly increased number of short insertions and deletions (indels) consistent with previous radiation exposure. We identified mutation signatures characteristic of APOBEC-mediated mutagenesis, aging, and homologous recombination deficiency. The frequency of mutations in many known bladder cancer genes, including TP53, KDM6A, and RB1, as well as copy number alterations such as CDKN2A loss was similar in RA-MIBC and non-RA-MIBC. CONCLUSIONS We identified unique mutational properties that likely contribute to the distinct biological and clinical features of RA-MIBC. PATIENT SUMMARY Bladder cancer is a rare but serious diagnosis following radiation for prostate cancer. We characterized genetic features of bladder tumors arising after prostate radiotherapy, and identify similarities with and differences from bladder tumors from patients without previous radiation.
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Smith JB, Cass LM, Simpson MC, Osazuwa-Peters N, Ward GM, Massa ST. Radiation-Associated Sarcoma of the Head and Neck: Incidence, Latency, and Survival. Laryngoscope 2021; 132:1034-1041. [PMID: 34779517 DOI: 10.1002/lary.29942] [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: 08/23/2021] [Revised: 10/29/2021] [Accepted: 11/03/2021] [Indexed: 11/10/2022]
Abstract
OBJECTIVES/HYPOTHESIS Radiation-associated sarcomas of the head and neck (RASHN) are known but rare sequelae after radiation for squamous cell carcinoma. The purpose of this study was to characterize RASHN, estimate the risk of RASHN in head and neck squamous cell patients after therapeutic radiation, and compare their survival to that of patients with de novo sarcomas of the head and neck (dnSHN). STUDY DESIGN Retrospective database analysis. METHODS RASHN and dnSHN cases were collected from the Surveillance, Epidemiology, and End Results Database to identify risk factors and calculate incidence and latency. Survival was compared between RASHN and dnSHN. RESULTS The risk of RASHN was 20.0 per 100,000 person-years. The average latency period was 124.2 months (range 38-329). The cumulative incidence of RASHN at 20 years was 0.13%. Oral cavity and oropharynx primaries demonstrate increased risk. Five-year overall survival of RASHN was 22.4% compared to 64.5% for dnSHN. CONCLUSIONS RASHN are confirmed to be rare. RASHN have poor overall survival and worse survival compared to dnSHN. The impact of intensity-modulated radiation therapy protocols on this risk is unknown. Modifiable risk factors of smoking and alcohol consumption continue to dwarf radiation therapy as risk factors of second primary head and neck cancers. LEVEL OF EVIDENCE 3 Laryngoscope, 2021.
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Affiliation(s)
- Joshua B Smith
- Department of Otolaryngology-Head and Neck Surgery, Saint Louis University School of Medicine, St. Louis, Missouri, U.S.A
| | - Lauren M Cass
- Department of Otolaryngology-Head and Neck Surgery, Saint Louis University School of Medicine, St. Louis, Missouri, U.S.A
| | - Matthew C Simpson
- Department of Otolaryngology-Head and Neck Surgery, Saint Louis University School of Medicine, St. Louis, Missouri, U.S.A
| | - Nosayaba Osazuwa-Peters
- Department of Head and Neck Surgery and Communication Sciences, Duke University School of Medicine, Durham, North Carolina, U.S.A
| | - Gregory M Ward
- Department of Otolaryngology-Head and Neck Surgery, Saint Louis University School of Medicine, St. Louis, Missouri, U.S.A
| | - Sean T Massa
- Department of Otolaryngology-Head and Neck Surgery, Saint Louis University School of Medicine, St. Louis, Missouri, U.S.A
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Thompson C, Hakim MO, Infante-Mendez J, Kesmodel S, Goel N. Radiation-Associated Sarcoma of the Breast in a Patient With a Germline Tumor Protein p53 Mutation. Cureus 2021; 13:e18563. [PMID: 34765345 PMCID: PMC8575327 DOI: 10.7759/cureus.18563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2021] [Indexed: 11/18/2022] Open
Abstract
Radiation-induced sarcoma of the breast is a rare complication that is primarily treated with surgical resection but in patients with advanced disease, a multimodality treatment approach is often required. This case report discusses a 37-year-old female with a history of a pT3N3M0, estrogen receptor (ER)+, progesterone receptor (PR)+, human epidermal growth factor receptor 2 (HER2)+, right breast cancer, and a germline tumor protein (TP) p53 mutation who underwent right modified radical mastectomy, adjuvant systemic therapy, and radiation therapy, and subsequently developed a radiation-induced sarcoma. The patient is a 37-year-old female who has a history of pT3N3M0, ER/PR+, HER2+, and right breast cancer diagnosed in 2014. At the time of diagnosis, she had locally advanced disease and underwent right modified radical mastectomy followed by adjuvant chemotherapy, radiation, delayed right breast implant-based reconstruction, and left breast augmentation with mastopexy. Upon completion of adjuvant chemotherapy, she was started on hormonal therapy. In February 2020, she underwent genetic testing given her early onset of breast cancer and was found to have a germline TP53 mutation. Routine MRI for breast implant evaluation showed two irregular enhancing masses with an additional satellite lesion in the right breast. Right breast ultrasound (US)-guided biopsy revealed two separate foci of high-grade pleomorphic fibroblastic/myofibroblastic sarcoma. Further staging workup with a whole-body MRI was negative for evidence of metastatic disease. Her case was discussed in multidisciplinary sarcoma tumor board and consensus was for surgical resection. She underwent radical resection of the right chest wall masses and subcutaneous tissue, removal of right breast implant and capsulectomy, and left breast mastectomy with left breast implant removal and capsulectomy. The final pathology revealed two separate foci of high-grade pleomorphic fibroblastic/myofibroblastic sarcoma, 1.2 cm and 1.1 cm in their greatest dimensions with negative margins. Her case was re-discussed in multidisciplinary sarcoma tumor board and due to T1 size of the tumors and the negative resection margins, close surveillance with annual whole-body MRI and quarterly chest MRI imaging was recommended. In patients with a germline TP53 mutation and breast cancer, the utilization of adjuvant radiotherapy should be considered cautiously given the increased risk of radiation-associated sarcoma.
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Affiliation(s)
- Cheyenne Thompson
- Surgical Oncology, University of Miami Sylvester Comprehensive Cancer Center, Miami, USA.,Surgical Oncology, University of Miami Hospital, Miami, USA
| | | | | | - Susan Kesmodel
- Surgical Oncology, University of Miami Sylvester Comprehensive Cancer Center, Miami, USA.,Surgical Oncology, University of Miami Hospital, Miami, USA
| | - Neha Goel
- Surgical Oncology, University of Miami Sylvester Comprehensive Cancer Center, Miami, USA.,Surgical Oncology, University of Miami Hospital, Miami, USA
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