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Ma W, Tang W, Kwok JS, Tong AH, Lo CW, Chu AT, Chung BH. A review on trends in development and translation of omics signatures in cancer. Comput Struct Biotechnol J 2024; 23:954-971. [PMID: 38385061 PMCID: PMC10879706 DOI: 10.1016/j.csbj.2024.01.024] [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: 10/27/2023] [Revised: 01/31/2024] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
The field of cancer genomics and transcriptomics has evolved from targeted profiling to swift sequencing of individual tumor genome and transcriptome. The steady growth in genome, epigenome, and transcriptome datasets on a genome-wide scale has significantly increased our capability in capturing signatures that represent both the intrinsic and extrinsic biological features of tumors. These biological differences can help in precise molecular subtyping of cancer, predicting tumor progression, metastatic potential, and resistance to therapeutic agents. In this review, we summarized the current development of genomic, methylomic, transcriptomic, proteomic and metabolic signatures in the field of cancer research and highlighted their potentials in clinical applications to improve diagnosis, prognosis, and treatment decision in cancer patients.
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Affiliation(s)
- Wei Ma
- Hong Kong Genome Institute, Hong Kong, China
| | - Wenshu Tang
- Hong Kong Genome Institute, Hong Kong, China
| | | | | | | | | | - Brian H.Y. Chung
- Hong Kong Genome Institute, Hong Kong, China
- Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Hong Kong Genome Project
- Hong Kong Genome Institute, Hong Kong, China
- Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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2
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Yang M, Gunnarsson R, Duployez N, Zaliova M, Zuna J, Johansson B, Paulsson K. Postnatal origin of the chromosomal gains in older patients with high hyperdiploid acute lymphoblastic leukemia. Haematologica 2024; 109:1951-1955. [PMID: 38356456 PMCID: PMC11141671 DOI: 10.3324/haematol.2023.284128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 02/08/2024] [Indexed: 02/16/2024] Open
Abstract
Not available.
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Affiliation(s)
- Minjun Yang
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund
| | - Rebeqa Gunnarsson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund
| | - Nicolas Duployez
- Laboratory of Hematology, Centre Hospitalier Universitaire (CHU) Lille, University of Lille, INSERM Unite 1277 Canther, Lille
| | - Marketa Zaliova
- Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University/University Hospital Motol, Prague, Czech Republic; Childhood Leukaemia Investigation Prague (CLIP), Prague, Czech Republic
| | - Jan Zuna
- Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University/University Hospital Motol, Prague, Czech Republic; Childhood Leukaemia Investigation Prague (CLIP), Prague, Czech Republic
| | - Bertil Johansson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden; Department of Clinical Genetics and Pathology, Office for Medical Services, Region Skane, Lund
| | - Kajsa Paulsson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund.
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3
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Anelo OM, Ma J, Neary JL, Koo SC, Inaba H, Pinto SN, Nguyen NT, Hoang TN, Bui LN, Klco JM, Gheorghe G, Blackburn PR. Pediatric Erythroid Sarcoma Diagnostically Confirmed by Identification of a Recurrent NFIA::CBFA2T3 Fusion. Genes Chromosomes Cancer 2024; 63:e23251. [PMID: 38884198 DOI: 10.1002/gcc.23251] [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: 03/21/2024] [Revised: 05/15/2024] [Accepted: 05/22/2024] [Indexed: 06/18/2024] Open
Abstract
Erythroid sarcoma (ES) is exceedingly rare in the pediatric population with only a handful of reports of de novo cases, mostly occurring in the central nervous system (CNS) or orbit. It is clinically and pathologically challenging and can masquerade as a nonhematopoietic small round blue cell tumor. Clinical presentation of ES without bone marrow involvement makes diagnosis particularly difficult. We describe a 22-month-old female with ES who presented with a 2-cm mass involving the left parotid region and CNS. The presence of crush/fixation artifact from the initial biopsy made definitive classification of this highly proliferative and malignant neoplasm challenging despite an extensive immunohistochemical workup. Molecular studies including RNA-sequencing revealed a NFIA::CBFA2T3 fusion. This fusion has been identified in several cases of de novo acute erythroid leukemia (AEL) and gene expression analysis comparing this case to other AELs revealed a similar transcriptional profile. Given the diagnostically challenging nature of this tumor, clinical RNA-sequencing was essential for establishing a diagnosis.
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Affiliation(s)
- Obianuju Mercy Anelo
- Department of Pathology, University of Tennessee Health Science Center (UTHSC), Memphis, Tennessee, USA
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jennifer L Neary
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Selene C Koo
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Hiroto Inaba
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Soniya N Pinto
- Department of Diagnostic Imaging, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Nga Thi Nguyen
- Pediatric Oncology Center, Vietnam National Children's Hospital, Hanoi, Vietnam
| | - Thach Ngoc Hoang
- Pathology Department, Vietnam National Children's Hospital, Hanoi, Vietnam
| | - Lan Ngoc Bui
- Pediatric Oncology Center, Vietnam National Children's Hospital, Hanoi, Vietnam
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Gabriela Gheorghe
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Patrick R Blackburn
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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Ma J, Liu YC, Voss RK, Ma J, Palagani A, Caldwell E, Rosikiewicz W, Cardenas M, Foy S, Umeda M, Wilkinson MR, Inaba H, Klco JM, Rubnitz JE, Wang L. Genomic and global gene expression profiling in pediatric and young adult acute leukemia with PICALM::MLLT10 Fusion. Leukemia 2024; 38:981-990. [PMID: 38429501 DOI: 10.1038/s41375-024-02194-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 03/03/2024]
Abstract
PICALM MLLT10 fusion is a rare but recurrent genetic driver in acute leukemias. To better understand the genomic landscape of PICALM::MLLT10 (PM) positive acute leukemia, we performed genomic profiling and gene expression profiling in twenty PM-positive patients, including AML (n = 10), T-ALL/LLy (n = 8), Mixed-phenotype acute leukemia (MPAL), T/B (n = 1) and acute undifferentiated leukemia (AUL) (n = 1). Besides confirming the known activation of HOXA, differential gene expression analysis compared to hematopoietic stem cells demonstrated the enrichment of genes associated with cell proliferation-related pathways and relatively high expression of XPO1 in PM-AML and PM-T-ALL/LLy. Our study also suggested PHF6 disruption as a key cooperating event in PICALM::MLLT10-positive leukemias. In addition, we demonstrated differences in gene expression profiles as well as remarkably different spectra of co-occurring mutations between PM-AML and PM-T-ALL/LLy. Alterations affecting TP53 and NF1, hallmarks of PM-AML, are strongly associated with disease progression and relapse, whereas EZH2 alterations are highly enriched in PM-T-ALL/LLy. This comprehensive genomic and transcriptomic profiling provides insights into the pathogenesis and development of PICALM::MLLT10 positive acute leukemia.
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Affiliation(s)
- Jingqun Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yen-Chun Liu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Rebecca K Voss
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ajay Palagani
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Elizabeth Caldwell
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wojciech Rosikiewicz
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Maria Cardenas
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Scott Foy
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Masayuki Umeda
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mark R Wilkinson
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hiroto Inaba
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jeffrey E Rubnitz
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lu Wang
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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5
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Ragnarsson C, Yang M, Moura-Castro LH, Aydın E, Gunnarsson R, Olsson-Arvidsson L, Lilljebjörn H, Fioretos T, Duployez N, Zaliova M, Zuna J, Castor A, Johansson B, Paulsson K. Constitutional and acquired genetic variants in ARID5B in pediatric B-cell precursor acute lymphoblastic leukemia. Genes Chromosomes Cancer 2024; 63:e23242. [PMID: 38738968 DOI: 10.1002/gcc.23242] [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: 02/27/2024] [Revised: 04/06/2024] [Accepted: 04/22/2024] [Indexed: 05/14/2024] Open
Abstract
Constitutional polymorphisms in ARID5B are associated with an increased risk of developing high hyperdiploid (HeH; 51-67 chromosomes) pediatric B-cell precursor acute lymphoblastic leukemia (BCP ALL). Here, we investigated constitutional and somatic ARID5B variants in 1335 BCP ALL cases from five different cohorts, with a particular focus on HeH cases. In 353 HeH ALL that were heterozygous for risk alleles and trisomic for chromosome 10, where ARID5B is located, a significantly higher proportion of risk allele duplication was seen for the SNPs rs7090445 (p = 0.009), rs7089424 (p = 0.005), rs7073837 (p = 0.03), and rs10740055 (p = 0.04). Somatic ARID5B deletions were seen in 16/1335 cases (1.2%), being more common in HeH than in other genetic subtypes (2.2% vs. 0.4%; p = 0.002). The expression of ARID5B in HeH cases with genomic deletions was reduced, consistent with a functional role in leukemogenesis. Whole-genome sequencing and RNA-sequencing in HeH revealed additional somatic events involving ARID5B, resulting in a total frequency of 3.6% of HeH cases displaying a somatic ARID5B aberration. Overall, our results show that both constitutional and somatic events in ARID5B are involved in the leukemogenesis of pediatric BCP ALL, particularly in the HeH subtype.
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Affiliation(s)
- Charlotte Ragnarsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Paediatrics, Skåne University Hospital, Lund University, Lund, Sweden
| | - Minjun Yang
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | | | - Efe Aydın
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Rebeqa Gunnarsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Linda Olsson-Arvidsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology, and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Henrik Lilljebjörn
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Thoas Fioretos
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology, and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Nicolas Duployez
- Laboratory of Haematology, Centre Hospitalier Universitaire (CHU) Lille, University of Lille, INSERM Unité 1277 Canther, Lille, France
| | - Marketa Zaliova
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University/University Hospital Motol, Prague, Czech Republic
- Childhood Leukaemia Investigation Prague (CLIP), Prague, Czech Republic
| | - Jan Zuna
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University/University Hospital Motol, Prague, Czech Republic
- Childhood Leukaemia Investigation Prague (CLIP), Prague, Czech Republic
| | - Anders Castor
- Department of Paediatrics, Skåne University Hospital, Lund University, Lund, Sweden
| | - Bertil Johansson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology, and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Kajsa Paulsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
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Walker M, Mayr EM, Koppermann ML, Terron A, Wagner Y, Kling C, Pfarr N. [Molecular pathological analysis through the ages]. PATHOLOGIE (HEIDELBERG, GERMANY) 2024; 45:173-179. [PMID: 38619582 PMCID: PMC11045621 DOI: 10.1007/s00292-024-01326-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/18/2024] [Indexed: 04/16/2024]
Abstract
BACKGROUND Molecular pathological examinations of tumor samples encompass a wide range of diagnostic analyses. Especially in recent years, numerous new biomarkers have come to the forefront-the analysis of which is crucial for therapy decisions. OBJECTIVES Within the field of molecular pathology, the demands of next generation sequencing (NGS)-based requirements have experienced massive growth in recent years. To meet this demand, methods are constantly being adapted and further developed. The following sections aim to illuminate how this trend arises and which analyses are gaining importance. METHODS The article provides an overview of the essential nucleic acid-based analysis techniques in the field of massive parallel sequencing. Terms such as DNA- and RNA-based techniques, as well as the associated analysis methods, are described, particularly with regard to their use in routine molecular pathological diagnostics. RESULTS The breadth of genomic sequencing has been steadily growing in recent years, particularly due to the increasing relevance of personalized medicine, along with the rising approvals of targeted therapeutics. This necessitates, among other things, the analysis of new biomarkers. The diagnostics as part of interdisciplinary molecular tumor boards (MTB) are now based on large gene panels (> 1 megabase). Furthermore, through the "Modellvorhaben Genomsequenzierung" § 64e, whole exome or whole genome sequencing has been made available for oncological patients. Given these developments, it is evident that future analyses will require the integration of additional omics fields, such as whole transcriptome analysis, epigenomics, and proteomics. CONCLUSION The challenges of personalized medicine along with the necessity of simultaneously assessing numerous new biomarkers require the implementation and execution of new techniques in molecular pathology whose complexity is steadily increasing.
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Affiliation(s)
- Maria Walker
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland
| | - Eva-Maria Mayr
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland
| | - Mai-Lan Koppermann
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland
| | - Ana Terron
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland
| | - Yoko Wagner
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland
| | - Charlotte Kling
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland
- Deutsches Konsortium für Translationale Krebsforschung (DKTK), Heidelberg, Deutschland
| | - Nicole Pfarr
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland.
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Hammad R, Nobre L, Ryall S, Arnoldo A, Siddaway R, Bennett J, Tabori U, Hawkins C. The Clinical Utility of a Tiered Approach to Pediatric Glioma Molecular Characterization for Resource-Limited Settings. JCO Glob Oncol 2024; 10:e2300269. [PMID: 38754050 DOI: 10.1200/go.23.00269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 02/09/2024] [Accepted: 02/23/2024] [Indexed: 05/18/2024] Open
Abstract
PURPOSE Molecular characterization is key to optimally diagnose and manage cancer. The complexity and cost of routine genomic analysis have unfortunately limited its use and denied many patients access to precision medicine. A possible solution is to rationalize use-creating a tiered approach to testing which uses inexpensive techniques for most patients and limits expensive testing to patients with the highest needs. Here, we tested the utility of this approach to molecularly characterize pediatric glioma in a cost- and time-sensitive manner. METHODS We used a tiered testing pipeline of immunohistochemistry (IHC), customized fusion panels or fluorescence in situ hybridization (FISH), and targeted RNA sequencing in pediatric gliomas. Two distinct diagnostic algorithms were used for low- and high-grade gliomas (LGGs and HGGs). The percentage of driver alterations identified, associated testing costs, and turnaround time (TAT) are reported. RESULTS The tiered approach successfully characterized 96% (95 of 99) of gliomas. For 82 LGGs, IHC, targeted fusion panel or FISH, and targeted RNA sequencing solved 35% (29 of 82), 29% (24 of 82), and 30% (25 of 82) of cases, respectively. A total of 64% (53 of 82) of samples were characterized without targeted RNA sequencing. Of 17 HGG samples, 13 were characterized by IHC and four were characterized by targeted RNA sequencing. The average cost per sample was more affordable when using the tiered approach as compared with up-front targeted RNA sequencing in LGG ($405 US dollars [USD] v $745 USD) and HGGs ($282 USD v $745 USD). The average TAT per sample was also shorter using the tiered approach (10 days for LGG, 5 days for HGG v 14 days for targeted RNA sequencing). CONCLUSION Our tiered approach molecularly characterized 96% of samples in a cost- and time-sensitive manner. Such an approach may be feasible in neuro-oncology centers worldwide, particularly in resource-limited settings.
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Affiliation(s)
- Rawan Hammad
- Haematology Department, Faculty of Medicine, King Abdulaziz University Hospital, King Abdulaziz University, Jeddah, Saudi Arabia
- Division of Pediatric Haematology Oncology, The Hospital for Sick Children, Toronto, Canada
| | - Liana Nobre
- Division of Pediatric Haematology Oncology, The Hospital for Sick Children, Toronto, Canada
- Division of Hematology, Oncology and Palliative Care, Department of Pediatrics, University of Alberta & Stollery Children's Hospital, Edmonton, Canada
| | - Scott Ryall
- Division of Pathology, Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada
- The Hospital for Sick Children, Arthur and Sonia Labatt Brain Tumour Research Centre, Toronto, Canada
| | - Anthony Arnoldo
- Division of Pathology, Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Robert Siddaway
- Division of Pathology, Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada
- The Hospital for Sick Children, Arthur and Sonia Labatt Brain Tumour Research Centre, Toronto, Canada
| | - Julie Bennett
- Division of Pediatric Haematology Oncology, The Hospital for Sick Children, Toronto, Canada
- The Hospital for Sick Children, Arthur and Sonia Labatt Brain Tumour Research Centre, Toronto, Canada
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Canada
| | - Uri Tabori
- Division of Pediatric Haematology Oncology, The Hospital for Sick Children, Toronto, Canada
- The Hospital for Sick Children, Arthur and Sonia Labatt Brain Tumour Research Centre, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Cynthia Hawkins
- Division of Pathology, Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada
- The Hospital for Sick Children, Arthur and Sonia Labatt Brain Tumour Research Centre, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
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Jacobs JE, Davis L, McWeeney S. Single nucleotide variants in nuclear pore complex disassembly pathway associated with poor survival in osteosarcoma. Front Genet 2024; 15:1303404. [PMID: 38562379 PMCID: PMC10982431 DOI: 10.3389/fgene.2024.1303404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 03/01/2024] [Indexed: 04/04/2024] Open
Abstract
Introduction The bone tumor, osteosarcoma, remains challenging to treat in children and young adults, especially when patients present with metastatic disease. Developing new therapies based on genomic data from sequencing projects has proven difficult given the lack of recurrent genetic lesions across tumors. MYC overexpression has been associated with poor outcomes in osteosarcoma. However, other genomic markers of disease severity are lacking. Materials and Methods We utilized whole genome sequencing of 106 tumors and matched normal controls in order to define genomic characteristics that correlate with overall survival. Single nucleotide variants were overlaid onto annotated molecular pathways in order to define aberrant pathway signatures specific to aggressive osteosarcoma. Additionally, we calculated differential gene expression in a subsample of 71 tumors. Differentially expressed genes were then queried for known MYC-responsive genes. Results Molecular pathways specific to nuclear pore complex disassembly (NPCD) show significant correlation with poor overall survival in osteosarcoma when mutations were present. Genes involved in immune response and immune regulation are enriched in the differential expression analysis of samples with and without NPCD pathway aberrations. Furthermore, neither MYC nor MYC-responsive genes show differential expression between NPCD-aberrant and non-aberrant groups. The NPCD pathway mutations are dominated by regulatory region variants rather than protein-altering mutations, suggesting that dysregulation of genetic regulatory networks may be the underlying mechanism for their relation to osteosarcoma phenotype. Discussion Overall survival is significantly worse in patients whose tumors show aberrations in the NPCD pathway. Moreover, this difference in survival is not driven by MYC-overexpression, suggesting a novel mechanism for some aggressive osteosarcomas. These findings add light to the evolving understanding of the drivers of osteosarcoma and may aid in the search for new treatments based on patient-specific genetic data.
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Affiliation(s)
- James E. Jacobs
- Oregon Health & Science University, Portland, OR, United States
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Arslan S, Schmidt J, Bass C, Mehrotra D, Geraldes A, Singhal S, Hense J, Li X, Raharja-Liu P, Maiques O, Kather JN, Pandya P. A systematic pan-cancer study on deep learning-based prediction of multi-omic biomarkers from routine pathology images. COMMUNICATIONS MEDICINE 2024; 4:48. [PMID: 38491101 PMCID: PMC10942985 DOI: 10.1038/s43856-024-00471-5] [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: 11/25/2022] [Accepted: 02/29/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND The objective of this comprehensive pan-cancer study is to evaluate the potential of deep learning (DL) for molecular profiling of multi-omic biomarkers directly from hematoxylin and eosin (H&E)-stained whole slide images. METHODS A total of 12,093 DL models predicting 4031 multi-omic biomarkers across 32 cancer types were trained and validated. The study included a broad range of genetic, transcriptomic, and proteomic biomarkers, as well as established prognostic markers, molecular subtypes, and clinical outcomes. RESULTS Here we show that 50% of the models achieve an area under the curve (AUC) of 0.644 or higher. The observed AUC for 25% of the models is at least 0.719 and exceeds 0.834 for the top 5%. Molecular profiling with image-based histomorphological features is generally considered feasible for most of the investigated biomarkers and across different cancer types. The performance appears to be independent of tumor purity, sample size, and class ratio (prevalence), suggesting a degree of inherent predictability in histomorphology. CONCLUSIONS The results demonstrate that DL holds promise to predict a wide range of biomarkers across the omics spectrum using only H&E-stained histological slides of solid tumors. This paves the way for accelerating diagnosis and developing more precise treatments for cancer patients.
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Affiliation(s)
| | | | | | - Debapriya Mehrotra
- Panakeia Technologies, London, UK
- Department of Pathology, Barking, Havering and Redbridge University NHS Trust, Romford, UK
| | | | - Shikha Singhal
- Panakeia Technologies, London, UK
- Department of Pathology, The Royal Wolverhampton NHS Trust, Wolverhampton, UK
| | | | - Xiusi Li
- Panakeia Technologies, London, UK
| | | | - Oscar Maiques
- Cytoskeleton and Cancer Metastasis Group, Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
- Cancer Biomarkers & Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, John Vane Science Building, London, UK
| | - Jakob Nikolas Kather
- Medical Oncology, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
- Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
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Furtado LV, Cardenas M, Santiago T, Ruiz RE, Shi Z, Pappo A, Kacar M. Novel MED15::ATF1 fusion in a pediatric melanoma with spitzoid features and aggressive presentation. Genes Chromosomes Cancer 2024; 63:e23230. [PMID: 38459940 DOI: 10.1002/gcc.23230] [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: 10/04/2023] [Revised: 02/13/2024] [Accepted: 02/17/2024] [Indexed: 03/11/2024] Open
Abstract
Childhood melanoma is a rare and biologically heterogeneous pediatric malignancy. The differential diagnosis of pediatric melanoma is usually broad, including a wide variety of spindle cell or epithelioid neoplasms. Different molecular alterations affecting the MAPK and PI3K/AKT/mTOR pathways, tumor suppressor genes, and telomerase reactivation have been implicated in melanoma tumorigenesis and progression. Here, we report a novel MED15::ATF1 fusion in a pediatric melanoma with spitzoid features and an aggressive clinical course.
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Affiliation(s)
- Larissa V Furtado
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Maria Cardenas
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Teresa Santiago
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Robert E Ruiz
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Zonggao Shi
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Alberto Pappo
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Marija Kacar
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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Kolekar P, Balagopal V, Dong L, Liu Y, Foy S, Tran Q, Mulder H, Huskey AL, Plyler E, Liang Z, Ma J, Nakitandwe J, Gu J, Namwanje M, Maciaszek J, Payne-Turner D, Mallampati S, Wang L, Easton J, Klco JM, Ma X. SJPedPanel: A pan-cancer gene panel for childhood malignancies. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.11.27.23299068. [PMID: 38076942 PMCID: PMC10705664 DOI: 10.1101/2023.11.27.23299068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Background Large scale genomics projects have identified driver alterations for most childhood cancers that provide reliable biomarkers for clinical diagnosis and disease monitoring using targeted sequencing. However, there is lack of a comprehensive panel that matches the list of known driver genes. Here we fill this gap by developing SJPedPanel for childhood cancers. Results SJPedPanel covers 5,275 coding exons of 357 driver genes, 297 introns frequently involved in rearrangements that generate fusion oncoproteins, commonly amplified/deleted regions (e.g., MYCN for neuroblastoma, CDKN2A and PAX5 for B-/T-ALL, and SMARCB1 for AT/RT), and 7,590 polymorphism sites for interrogating tumors with aneuploidy, such as hyperdiploid and hypodiploid B-ALL or 17q gain neuroblastoma. We used driver alterations reported from an established real-time clinical genomics cohort (n=253) to validate this gene panel. Among the 485 pathogenic variants reported, our panel covered 417 variants (86%). For 90 rearrangements responsible for oncogenic fusions, our panel covered 74 events (82%). We re-sequenced 113 previously characterized clinical specimens at an average depth of 2,500X using SJPedPanel and recovered 354 (91%) of the 389 reported pathogenic variants. We then investigated the power of this panel in detecting mutations from specimens with low tumor purity (as low as 0.1%) using cell line-based dilution experiments and discovered that this gene panel enabled us to detect ∼80% variants with allele fraction of 0.2%, while the detection rate decreases to ∼50% when the allele fraction is 0.1%. We finally demonstrate its utility in disease monitoring on clinical specimens collected from AML patients in morphologic remission. Conclusions SJPedPanel enables the detection of clinically relevant genetic alterations including rearrangements responsible for subtype-defining fusions for childhood cancers by targeted sequencing of ∼0.15% of human genome. It will enhance the analysis of specimens with low tumor burdens for cancer monitoring and early detection.
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12
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Umeda M, Ma J, Westover T, Ni Y, Song G, Maciaszek JL, Rusch M, Rahbarinia D, Foy S, Huang BJ, Walsh MP, Kumar P, Liu Y, Yang W, Fan Y, Wu G, Baker SD, Ma X, Wang L, Alonzo TA, Rubnitz JE, Pounds S, Klco JM. A new genomic framework to categorize pediatric acute myeloid leukemia. Nat Genet 2024; 56:281-293. [PMID: 38212634 PMCID: PMC10864188 DOI: 10.1038/s41588-023-01640-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 12/05/2023] [Indexed: 01/13/2024]
Abstract
Recent studies on pediatric acute myeloid leukemia (pAML) have revealed pediatric-specific driver alterations, many of which are underrepresented in the current classification schemas. To comprehensively define the genomic landscape of pAML, we systematically categorized 887 pAML into 23 mutually distinct molecular categories, including new major entities such as UBTF or BCL11B, covering 91.4% of the cohort. These molecular categories were associated with unique expression profiles and mutational patterns. For instance, molecular categories characterized by specific HOXA or HOXB expression signatures showed distinct mutation patterns of RAS pathway genes, FLT3 or WT1, suggesting shared biological mechanisms. We show that molecular categories were strongly associated with clinical outcomes using two independent cohorts, leading to the establishment of a new prognostic framework for pAML based on these updated molecular categories and minimal residual disease. Together, this comprehensive diagnostic and prognostic framework forms the basis for future classification of pAML and treatment strategies.
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Affiliation(s)
- Masayuki Umeda
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Tamara Westover
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yonghui Ni
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Guangchun Song
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jamie L Maciaszek
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Delaram Rahbarinia
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Scott Foy
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Benjamin J Huang
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Michael P Walsh
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Priyadarshini Kumar
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yanling Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wenjian Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yiping Fan
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Gang Wu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sharyn D Baker
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lu Wang
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Todd A Alonzo
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jeffrey E Rubnitz
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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13
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Fujii M, Sekine S, Sato T. Decoding the basis of histological variation in human cancer. Nat Rev Cancer 2024; 24:141-158. [PMID: 38135758 DOI: 10.1038/s41568-023-00648-5] [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] [Accepted: 11/21/2023] [Indexed: 12/24/2023]
Abstract
Molecular abnormalities that shape human neoplasms dissociate their phenotypic landscape from that of the healthy counterpart. Through the lens of a microscope, tumour pathology optically captures such aberrations projected onto a tissue slide and has categorized human epithelial neoplasms into distinct histological subtypes based on the diverse morphogenetic and molecular programmes that they manifest. Tumour histology often reflects tumour aggressiveness, patient prognosis and therapeutic vulnerability, and thus has been used as a de facto diagnostic tool and for making clinical decisions. However, it remains elusive how the diverse histological subtypes arise and translate into pleiotropic biological phenotypes. Molecular analysis of clinical tumour tissues and their culture, including patient-derived organoids, and add-back genetic reconstruction of tumorigenic pathways using gene engineering in culture models and rodents further elucidated molecular mechanisms that underlie morphological variations. Such mechanisms include genetic mutations and epigenetic alterations in cellular identity codes that erode hard-wired morphological programmes and histologically digress tumours from the native tissues. Interestingly, tumours acquire the ability to grow independently of the niche-driven stem cell ecosystem along with these morphological alterations, providing a biological rationale for histological diversification during tumorigenesis. This Review comprehensively summarizes our current understanding of such plasticity in the histological and lineage commitment fostered cooperatively by molecular alterations and the tumour environment, and describes basic and clinical implications for future cancer therapy.
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Affiliation(s)
- Masayuki Fujii
- Department of Integrated Medicine and Biochemistry, Keio University School of Medicine, Tokyo, Japan.
| | - Shigeki Sekine
- Division of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan
| | - Toshiro Sato
- Department of Integrated Medicine and Biochemistry, Keio University School of Medicine, Tokyo, Japan.
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14
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Huang D, Zhu X, Ye S, Zhang J, Liao J, Zhang N, Zeng X, Wang J, Yang B, Zhang Y, Lao L, Chen J, Xin M, Nie Y, Saw PE, Su S, Song E. Tumour circular RNAs elicit anti-tumour immunity by encoding cryptic peptides. Nature 2024; 625:593-602. [PMID: 38093017 DOI: 10.1038/s41586-023-06834-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/03/2023] [Indexed: 12/23/2023]
Abstract
Emerging data have shown that previously defined noncoding genomes might encode peptides that bind human leukocyte antigen (HLA) as cryptic antigens to stimulate adaptive immunity1,2. However, the significance and mechanisms of action of cryptic antigens in anti-tumour immunity remain unclear. Here mass spectrometry of the HLA class I (HLA-I) peptidome coupled with ribosome sequencing of human breast cancer samples identified HLA-I-binding cryptic antigenic peptides that were noncanonically translated by a tumour-specific circular RNA (circRNA): circFAM53B. The cryptic peptides efficiently primed naive CD4+ and CD8+ T cells in an antigen-specific manner and induced anti-tumour immunity. Clinically, the expression of circFAM53B and its encoded peptides was associated with substantial infiltration of antigen-specific CD8+ T cells and better survival in patients with breast cancer and patients with melanoma. Mechanistically, circFAM53B-encoded peptides had strong binding affinity to both HLA-I and HLA-II molecules. In vivo, administration of vaccines consisting of tumour-specific circRNA or its encoded peptides in mice bearing breast cancer tumours or melanoma induced enhanced infiltration of tumour-antigen-specific cytotoxic T cells, which led to effective tumour control. Overall, our findings reveal that noncanonical translation of circRNAs can drive efficient anti-tumour immunity, which suggests that vaccination exploiting tumour-specific circRNAs may serve as an immunotherapeutic strategy against malignant tumours.
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Affiliation(s)
- Di Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Xiaofeng Zhu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Shuying Ye
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jiahui Zhang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jianyou Liao
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Ning Zhang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Xin Zeng
- Program of Molecular Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Jiawen Wang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Bing Yang
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yin Zhang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Liyan Lao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jianing Chen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Min Xin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yan Nie
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Phei Er Saw
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Shicheng Su
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.
- Department of Infectious Diseases, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.
- Biotherapy Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
| | - Erwei Song
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
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15
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Paramasivam G, Sanmugam A, Palem VV, Sevanan M, Sairam AB, Nachiappan N, Youn B, Lee JS, Nallal M, Park KH. Nanomaterials for detection of biomolecules and delivering therapeutic agents in theragnosis: A review. Int J Biol Macromol 2024; 254:127904. [PMID: 37939770 DOI: 10.1016/j.ijbiomac.2023.127904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 10/30/2023] [Accepted: 11/03/2023] [Indexed: 11/10/2023]
Abstract
Nanomaterials are emerging facts used to deliver therapeutic agents in living systems. Nanotechnology is used as a compliment by implementing different kinds of nanotechnological applications such as nano-porous structures, functionalized nanomaterials, quantum dots, carbon nanomaterials, and polymeric nanostructures. The applications are in the initial stage, which led to achieving several diagnoses and therapy in clinical practice. This review conveys the importance of nanomaterials in post-genomic employment, which includes the design of immunosensors, immune assays, and drug delivery. In this view, genomics is a molecular tool containing large databases that are useful in choosing an apt molecular inhibitor such as drug, ligand and antibody target in the drug delivery process. This study identifies the expression of genes and proteins in analysis and classification of diseases. Experimentally, the study analyses the design of a disease model. In particular, drug delivery is a boon area to treat cancer. The identified drugs enter different phase trails (Trails I, II, and III). The genomic information conveys more essential entities to the phase I trials and helps to move further for other trails such as trails-II and III. In such cases, the biomarkers play a crucial role by monitoring the unique pathological process. Genetic engineering with recombinant DNA techniques can be employed to develop genetically engineered disease models. Delivering drugs in a specific area is one of the challenging issues achieved using nanoparticles. Therefore, genomics is considered as a vast molecular tool to identify drugs in personalized medicine for cancer therapy.
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Affiliation(s)
- Gokul Paramasivam
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical & Technical Sciences (SIMATS), Saveetha Nagar, Thandalam, Chennai 602105, Tamil Nadu, India.
| | - Anandhavelu Sanmugam
- Department of Applied Chemistry, Sri Venkateswara College of Engineering, Pennalur, Sriperumbudur 602117, Tamil Nadu, India
| | - Vishnu Vardhan Palem
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical & Technical Sciences (SIMATS), Saveetha Nagar, Thandalam, Chennai 602105, Tamil Nadu, India
| | - Murugan Sevanan
- Department of Biotechnology, Karunya Institute of Technology and Sciences, Karunya Nagar, Coimbatore 641114, Tamil Nadu, India
| | - Ananda Babu Sairam
- Department of Applied Chemistry, Sri Venkateswara College of Engineering, Pennalur, Sriperumbudur 602117, Tamil Nadu, India
| | - Nachiappan Nachiappan
- Department of Applied Chemistry, Sri Venkateswara College of Engineering, Pennalur, Sriperumbudur 602117, Tamil Nadu, India
| | - BuHyun Youn
- Department of Biological Sciences, Pusan National University, Busan 46241, Republic of Korea
| | - Jung Sub Lee
- Department of Orthopaedic Surgery, Biomedical Research Institute, Pusan National University Hospital, Busan 46241, Republic of Korea; School of Medicine, Pusan National University, Busan 46241, Republic of Korea
| | - Muthuchamy Nallal
- Department of Chemistry, Pusan National University, Busan 46241, Republic of Korea.
| | - Kang Hyun Park
- Department of Chemistry, Pusan National University, Busan 46241, Republic of Korea.
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16
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Blackburn PR, McGee RB, Mostafavi R, Carroll AJ, Mikhail FM, Armstrong GT, Furtado LV, Chiang J, Wheeler DA, Carey SS, Nichols KE, Upadhyaya SA. Constitutional balanced translocations involving SMARCB1: A rare cause of rhabdoid tumor predisposition syndrome. Genes Chromosomes Cancer 2024; 63:e23195. [PMID: 37548271 DOI: 10.1002/gcc.23195] [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: 04/24/2023] [Revised: 07/19/2023] [Accepted: 07/28/2023] [Indexed: 08/08/2023] Open
Abstract
Rhabdoid Tumor Predisposition Syndrome 1 (RTPS1) confers an increased risk of developing rhabdoid tumors and is caused by germline mutations in SMARCB1. RTPS1 should be evaluated in all individuals with rhabdoid tumor and is more likely in those with a young age at presentation (occasionally congenital presentation), multiple primary tumors, or a family history of rhabdoid tumor or RTPS1. Proband genetic testing is the standard method for diagnosing RTPS1. Most known RTPS1-related SMARCB1 gene mutations are copy number variants (CNVs) or single nucleotide variants/indels, but structural variant analysis (SVA) is not usually included in the molecular evaluation. Here, we report two children with RTPS1 presenting with atypical teratoid/rhabdoid tumor (ATRT) who had constitutional testing showing balanced chromosome translocations involving SMARCB1. Patient 1 is a 23-year-old female diagnosed with pineal region ATRT at 7 months who was found to have a de novo, constitutional t(16;22)(p13.3;q11.2). Patient 2 is a 24-month-old male diagnosed with a posterior fossa ATRT at 14 months, with subsequent testing showing a constitutional t(5;22)(q14.1;q11.23). These structural rearrangements have not been previously reported in RTPS1. While rare, these cases suggest that structural variants should be considered in the evaluation of children with rhabdoid tumors to provide more accurate genetic counseling on the risks of developing tumors, the need for surveillance, and the risks of passing the disorder on to future children. Further research is needed to understand the prevalence, clinical features, and tumor risks associated with RTPS1-related constitutional balanced translocations.
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Affiliation(s)
- Patrick R Blackburn
- Department of Pathology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Rose B McGee
- Division of Cancer Predisposition, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Roya Mostafavi
- Division of Cancer Predisposition, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Andrew J Carroll
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Gregory T Armstrong
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Larissa V Furtado
- Department of Pathology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jason Chiang
- Department of Pathology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - David A Wheeler
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Steven S Carey
- Department of Hospitalist Medicine, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Kim E Nichols
- Division of Cancer Predisposition, St Jude Children's Research Hospital, Memphis, Tennessee, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Santhosh A Upadhyaya
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
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17
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Furtado LV, Santiago T, Shi Z, Wang L, Liu YC, Gartrell J, Ruiz RE. Novel HNRNPM::LEUTX fusion resulting from chromothripsis of chromosome 19 in a pediatric undifferentiated small round cell neoplasm. Genes Chromosomes Cancer 2023; 62:740-745. [PMID: 37366242 DOI: 10.1002/gcc.23187] [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: 03/08/2023] [Revised: 06/08/2023] [Accepted: 06/12/2023] [Indexed: 06/28/2023] Open
Abstract
Small round cell neoplasms comprise a diverse group of tumors characterized by a primitive/undifferentiated appearance. Although several entities are associated with recurrent gene fusions, many of these neoplasms have not been fully characterized, and novel molecular alterations are being discovered. Here, we report an undifferentiated small round cell neoplasm arising in the anterior mediastinum of a 17-month-old female. The tumor harbored a novel HNRNPM::LEUTX fusion resulting from chromothripsis of chromosome 19, which was identified by whole transcriptome sequencing, but not by targeted sequencing. The structural variations caused by the chromothripsis event also challenged the interpretation of the targeted sequencing findings. This report expands the spectrum of gene partners involved in LEUTX fusions and underscores the value of whole transcriptome sequencing in the diagnostic workup of undifferentiated small round cell tumors. It also highlights the interpretive challenges associated with complex genomic alterations. A careful evidence-based analysis of sequencing data along with histopathologic correlation is essential to ensure correct categorization of fusions.
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Affiliation(s)
- Larissa V Furtado
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Teresa Santiago
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Zonggao Shi
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Lu Wang
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Yen-Chun Liu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jessica Gartrell
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Robert E Ruiz
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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18
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Horackova K, Janatova M, Kleiblova P, Kleibl Z, Soukupova J. Early-Onset Ovarian Cancer <30 Years: What Do We Know about Its Genetic Predisposition? Int J Mol Sci 2023; 24:17020. [PMID: 38069345 PMCID: PMC10707471 DOI: 10.3390/ijms242317020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
Ovarian cancer (OC) is one of the leading causes of cancer-related deaths in women. Most patients are diagnosed with advanced epithelial OC in their late 60s, and early-onset adult OC diagnosed ≤30 years is rare, accounting for less than 5% of all OC cases. The most significant risk factor for OC development are germline pathogenic/likely pathogenic variants (GPVs) in OC predisposition genes (including BRCA1, BRCA2, BRIP1, RAD51C, RAD51D, Lynch syndrome genes, or BRIP1), which contribute to the development of over 20% of all OC cases. GPVs in BRCA1/BRCA2 are the most prevalent. The presence of a GPV directs tailored cancer risk-reducing strategies for OC patients and their relatives. Identification of OC patients with GPVs can also have therapeutic consequences. Despite the general assumption that early cancer onset indicates higher involvement of hereditary cancer predisposition, the presence of GPVs in early-onset OC is rare (<10% of patients), and their heritability is uncertain. This review summarizes the current knowledge on the genetic predisposition to early-onset OC, with a special focus on epithelial OC, and suggests other alternative genetic factors (digenic, oligogenic, polygenic heritability, genetic mosaicism, imprinting, etc.) that may influence the development of early-onset OC in adult women lacking GPVs in known OC predisposition genes.
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Affiliation(s)
- Klara Horackova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic; (K.H.); (M.J.); (P.K.); (Z.K.)
| | - Marketa Janatova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic; (K.H.); (M.J.); (P.K.); (Z.K.)
| | - Petra Kleiblova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic; (K.H.); (M.J.); (P.K.); (Z.K.)
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic
| | - Zdenek Kleibl
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic; (K.H.); (M.J.); (P.K.); (Z.K.)
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, 128 00 Prague, Czech Republic
| | - Jana Soukupova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic; (K.H.); (M.J.); (P.K.); (Z.K.)
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19
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Kirkham JK, Liu YC, Foy SG, Ma J, Gheorghe G, Furtado LV, Popescu MI, Klco JM, Karol SE, Blackburn PR. Clinical and genomic characterization of an ATRA-insensitive acute promyelocytic leukemia variant with a FNDC3B::RARB fusion. Genes Chromosomes Cancer 2023; 62:617-623. [PMID: 37283355 DOI: 10.1002/gcc.23180] [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: 04/06/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/08/2023] Open
Abstract
The promyelocytic leukemia-retinoic acid receptor-α (PML::RARA) fusion is the hallmark of acute promyelocytic leukemia (APL) and is observed in over 95% of APL cases. RARA and homologous receptors RARB and RARG are occasionally fused to other gene partners, which differentially affect sensitivity to targeted therapies. Most APLs without RARA fusions have rearrangements involving RARG or RARB, both of which frequently show resistance to all-trans-retinoic acid (ATRA) and/or multiagent chemotherapy for acute myeloid leukemia (AML). We present a 13-year-old male diagnosed with variant APL with a novel FNDC3B::RARB in-frame fusion that showed no response to ATRA but responded well to conventional AML therapy. While FNDC3B has been identified as a rare RARA translocation partner in ATRA-sensitive variant APL, it has never been reported as a fusion partner with RARB and it is only the second known fusion partner with RARB in variant APL. We also show that this novel fusion confers an RNA expression signature that is similar to APL, despite clinical resistance to ATRA monotherapy.
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MESH Headings
- Male
- Humans
- Adolescent
- Leukemia, Promyelocytic, Acute/drug therapy
- Leukemia, Promyelocytic, Acute/genetics
- Leukemia, Promyelocytic, Acute/metabolism
- Translocation, Genetic
- Tretinoin/therapeutic use
- Leukemia, Myeloid, Acute/genetics
- Retinoic Acid Receptor alpha/genetics
- Genomics
- Oncogene Proteins, Fusion/genetics
- Fibronectins/genetics
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Affiliation(s)
- Justin K Kirkham
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Yen-Chun Liu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Scott G Foy
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Gabriela Gheorghe
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Larissa V Furtado
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Marcela I Popescu
- Department of Pediatric Hematology and Oncology, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee, USA
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Seth E Karol
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Patrick R Blackburn
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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20
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Erdogan O, Özkaya ŞÇ, Erzik C, Bilguvar K, Arga KY, Bayraklı F. Toward Precision Oncology in Glioblastoma with a Personalized Cancer Genome Reporting Tool and Genetic Changes Identified by Whole Exome Sequencing. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:426-433. [PMID: 37669106 DOI: 10.1089/omi.2023.0117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Precision/personalized medicine in oncology has two key pillars: molecular profiling of the tumors and personalized reporting of the results in ways that are clinically contextualized and triangulated. Moreover, neurosurgery as a field stands to benefit from precision/personalized medicine and new tools for reporting of the molecular findings. In this context, glioblastoma (GBM) is a highly aggressive brain tumor with limited treatment options and poor prognosis. Precision/personalized medicine has emerged as a promising approach for personalized therapy in GBM. In this study, we performed whole exome sequencing of tumor tissue samples from six newly diagnosed GBM patients and matched nontumor control samples. We report here the genetic alterations identified in the tumors, including single nucleotide variations, insertions or deletions (indels), and copy number variations, and attendant mutational signatures. Additionally, using a personalized cancer genome-reporting tool, we linked genomic information to potential therapeutic targets and treatment options for each patient. Our findings revealed heterogeneity in genetic alterations and identified targetable pathways, such as the PI3K/AKT/mTOR pathway. This study demonstrates the prospects of precision/personalized medicine in GBM specifically, and neurosurgical oncology more generally, including the potential for genomic profiling coupled with personalized cancer genome reporting. Further research and larger studies are warranted to validate these findings and advance the treatment options and outcomes for patients with GBM.
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Affiliation(s)
- Onur Erdogan
- Department of Neurosurgery, School of Medicine, Marmara University, Istanbul, Turkey
- Institute of Neurological Sciences, Marmara University, Istanbul, Turkey
| | - Şeyma Çolakoğlu Özkaya
- Department of Medical Biology and Genetics, Institute of Health Sciences, Marmara University, Istanbul, Turkey
| | - Can Erzik
- Department of Medical Biology, School of Medicine, Marmara University, Istanbul, Turkey
| | - Kaya Bilguvar
- Department of Neurosurgery and Genetics, Yale Center for Genome Analysis, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Medical Biology, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Kazım Yalçın Arga
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
- Health Biotechnology Joint Research and Application Center of Excellence, Istanbul, Turkey
| | - Fatih Bayraklı
- Department of Neurosurgery, School of Medicine, Marmara University, Istanbul, Turkey
- Institute of Neurological Sciences, Marmara University, Istanbul, Turkey
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21
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Cupit-Link M, Hagiwara K, Zhang J, Federico SM. Clinical Response to a PARP Inhibitor and Chemotherapy in a Child with BARD1-Mutated Refractory Neuroblastoma: A Case Report. RESEARCH SQUARE 2023:rs.3.rs-3250117. [PMID: 37645774 PMCID: PMC10462232 DOI: 10.21203/rs.3.rs-3250117/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Despite advances in the treatment of high-risk neuroblastoma, approximately half of these patients die from the disease. Targeted therapy based on synthetic lethality associated with homologous recombination deficiency (HRD) caused by germline mutations in homologous recombination repair genes has shown great efficacy in several adult solid tumors. Here we report the first successful treatment of a pediatric patient with refractory neuroblastoma and a germline pathogenic mutation in BARD1 using a PARP inhibitor, talazoparib, in combination with cytotoxic chemotherapy and radiation therapy. Allele-specific expression in RNA-seq indicates bi-allelic loss of BARD1 in tumor; however, the HRD score was below the threshold currently used for HRD classification in adult cancers. Our study demonstrates that the use of PARP inhibition in combination with DNA-damaging agents should be considered in children with BARD1-mutated neuroblastoma and cautions against the use of HRD score alone as a biomarker for this pediatric population.
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Affiliation(s)
- Maggie Cupit-Link
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Kohei Hagiwara
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Sara M. Federico
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105
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22
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Goldberger Z, Hauert S, Chang K, Kurtanich T, Alpar AT, Repond G, Wang Y, Gomes S, Krishnakumar R, Siddarth P, Swartz MA, Hubbell JA, Briquez PS. Membrane-localized neoantigens predict the efficacy of cancer immunotherapy. Cell Rep Med 2023; 4:101145. [PMID: 37552990 PMCID: PMC10439248 DOI: 10.1016/j.xcrm.2023.101145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 12/24/2022] [Accepted: 07/13/2023] [Indexed: 08/10/2023]
Abstract
Immune checkpoint immunotherapy (ICI) can re-activate immune reactions against neoantigens, leading to remarkable remission in cancer patients. Nevertheless, only a minority of patients are responsive to ICI, and approaches for prediction of responsiveness are needed to improve the success of cancer treatments. While the tumor mutational burden (TMB) correlates positively with responsiveness and survival of patients undergoing ICI, the influence of the subcellular localizations of the neoantigens remains unclear. Here, we demonstrate in both a mouse melanoma model and human clinical datasets of 1,722 ICI-treated patients that a high proportion of membrane-localized neoantigens, particularly at the plasma membrane, correlate with responsiveness to ICI therapy and improved overall survival across multiple cancer types. We further show that combining membrane localization and TMB analyses can enhance the predictability of cancer patient response to ICI. Our results may have important implications for establishing future clinical guidelines to direct the choice of treatment toward ICI.
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Affiliation(s)
- Zoe Goldberger
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA; Department of Bioengineering, McGill University, Montreal, QC, Canada
| | - Sylvie Hauert
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Kevin Chang
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Trevin Kurtanich
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Aaron T Alpar
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Grégoire Repond
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Yue Wang
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Suzana Gomes
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | | | - Prabha Siddarth
- Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
| | - Melody A Swartz
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA; Ben May Department of Cancer Research, University of Chicago, Chicago, IL, USA; Committee on Immunology, University of Chicago, Chicago, IL, USA; Committee on Cancer Biology, University of Chicago, Chicago, IL, USA
| | - Jeffrey A Hubbell
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA; Committee on Immunology, University of Chicago, Chicago, IL, USA; Committee on Cancer Biology, University of Chicago, Chicago, IL, USA.
| | - Priscilla S Briquez
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA; Department of General and Visceral Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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23
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van Belzen IAEM, Cai C, van Tuil M, Badloe S, Strengman E, Janse A, Verwiel ETP, van der Leest DFM, Kester L, Molenaar JJ, Meijerink J, Drost J, Peng WC, Kerstens HHD, Tops BBJ, Holstege FCP, Kemmeren P, Hehir-Kwa JY. Systematic discovery of gene fusions in pediatric cancer by integrating RNA-seq and WGS. BMC Cancer 2023; 23:618. [PMID: 37400763 DOI: 10.1186/s12885-023-11054-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 03/08/2023] [Indexed: 07/05/2023] Open
Abstract
BACKGROUND Gene fusions are important cancer drivers in pediatric cancer and their accurate detection is essential for diagnosis and treatment. Clinical decision-making requires high confidence and precision of detection. Recent developments show RNA sequencing (RNA-seq) is promising for genome-wide detection of fusion products but hindered by many false positives that require extensive manual curation and impede discovery of pathogenic fusions. METHODS We developed Fusion-sq to overcome existing disadvantages of detecting gene fusions. Fusion-sq integrates and "fuses" evidence from RNA-seq and whole genome sequencing (WGS) using intron-exon gene structure to identify tumor-specific protein coding gene fusions. Fusion-sq was then applied to the data generated from a pediatric pan-cancer cohort of 128 patients by WGS and RNA sequencing. RESULTS In a pediatric pan-cancer cohort of 128 patients, we identified 155 high confidence tumor-specific gene fusions and their underlying structural variants (SVs). This includes all clinically relevant fusions known to be present in this cohort (30 patients). Fusion-sq distinguishes healthy-occurring from tumor-specific fusions and resolves fusions in amplified regions and copy number unstable genomes. A high gene fusion burden is associated with copy number instability. We identified 27 potentially pathogenic fusions involving oncogenes or tumor-suppressor genes characterized by underlying SVs, in some cases leading to expression changes indicative of activating or disruptive effects. CONCLUSIONS Our results indicate how clinically relevant and potentially pathogenic gene fusions can be identified and their functional effects investigated by combining WGS and RNA-seq. Integrating RNA fusion predictions with underlying SVs advances fusion detection beyond extensive manual filtering. Taken together, we developed a method for identifying candidate gene fusions that is suitable for precision oncology applications. Our method provides multi-omics evidence for assessing the pathogenicity of tumor-specific gene fusions for future clinical decision making.
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Affiliation(s)
| | - Casey Cai
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Marc van Tuil
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Shashi Badloe
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Eric Strengman
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Alex Janse
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | | | - Lennart Kester
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Jan J Molenaar
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Jules Meijerink
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Weng Chuan Peng
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - Bastiaan B J Tops
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - Patrick Kemmeren
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
- Center for Molecular Medicine, UMC Utrecht and Utrecht University, Utrecht, The Netherlands.
| | - Jayne Y Hehir-Kwa
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
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24
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Robbe P, Schuh A. Genomic Stratification of Hematological Malignancies. Hemasphere 2023; 7:e902. [PMID: 37251914 PMCID: PMC10219718 DOI: 10.1097/hs9.0000000000000902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 04/25/2023] [Indexed: 05/31/2023] Open
Affiliation(s)
- Pauline Robbe
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Anna Schuh
- Department of Oncology, University of Oxford, United Kingdom
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25
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Yan R, Shen Y, Zhang X, Xu P, Wang J, Li J, Ren F, Ye D, Zhou SK. Histopathological bladder cancer gene mutation prediction with hierarchical deep multiple-instance learning. Med Image Anal 2023; 87:102824. [PMID: 37126973 DOI: 10.1016/j.media.2023.102824] [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: 09/14/2022] [Revised: 03/13/2023] [Accepted: 04/17/2023] [Indexed: 05/03/2023]
Abstract
Gene mutation detection is usually carried out by molecular biological methods, which is expensive and has a long-time cycle. In contrast, pathological images are ubiquitous. If clinically significant gene mutations can be predicted only through pathological images, it will greatly promote the widespread use of gene mutation detection in clinical practice. However, current gene mutation prediction methods based on pathological images are ineffective because of the inability to identify mutated regions in gigapixel Whole Slide Image (WSI). To address this challenge, hereby we propose a carefully designed framework for WSI-based gene mutation prediction, which consists of three parts. (i) The first part of cancerous area segmentation, based on supervised learning, quickly filters out a large number of non-mutated regions; (ii) the second part of cancerous patch clustering, based on the representations derived from contrastive learning, ensures the comprehensiveness of patch selection; and (iii) the third part of mutation classification, based on the proposed hierarchical deep multi-instance learning method (HDMIL), ensures that sufficient patches are considered and inaccurate selections are ignored. In addition, benefiting from a two-stage attention mechanism in HDMIL, the patches that are highly correlated with gene mutations can be identified. This interpretability can help a pathologist to analyze the correlation between gene mutation and histopathological morphology. Experimental results demonstrate that the proposed gene mutation prediction framework significantly outperforms the state-of-the-art methods. In the TCGA bladder cancer dataset, five clinically relevant gene mutations are well predicted.
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Affiliation(s)
- Rui Yan
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yijun Shen
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Xueyuan Zhang
- Zhijian Life Technology Co., Ltd., Beijing, 100036, China
| | - Peihang Xu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Jun Wang
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Jintao Li
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China
| | - Fei Ren
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China; SKLP, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - S Kevin Zhou
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China; School of Biomedical Engineering & Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, 215123, China.
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26
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Liu Y, Klein J, Bajpai R, Dong L, Tran Q, Kolekar P, Smith JL, Ries RE, Huang BJ, Wang YC, Alonzo TA, Tian L, Mulder HL, Shaw TI, Ma J, Walsh MP, Song G, Westover T, Autry RJ, Gout AM, Wheeler DA, Wan S, Wu G, Yang JJ, Evans WE, Loh M, Easton J, Zhang J, Klco JM, Meshinchi S, Brown PA, Pruett-Miller SM, Ma X. Etiology of oncogenic fusions in 5,190 childhood cancers and its clinical and therapeutic implication. Nat Commun 2023; 14:1739. [PMID: 37019972 PMCID: PMC10076316 DOI: 10.1038/s41467-023-37438-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 03/16/2023] [Indexed: 04/07/2023] Open
Abstract
Oncogenic fusions formed through chromosomal rearrangements are hallmarks of childhood cancer that define cancer subtype, predict outcome, persist through treatment, and can be ideal therapeutic targets. However, mechanistic understanding of the etiology of oncogenic fusions remains elusive. Here we report a comprehensive detection of 272 oncogenic fusion gene pairs by using tumor transcriptome sequencing data from 5190 childhood cancer patients. We identify diverse factors, including translation frame, protein domain, splicing, and gene length, that shape the formation of oncogenic fusions. Our mathematical modeling reveals a strong link between differential selection pressure and clinical outcome in CBFB-MYH11. We discover 4 oncogenic fusions, including RUNX1-RUNX1T1, TCF3-PBX1, CBFA2T3-GLIS2, and KMT2A-AFDN, with promoter-hijacking-like features that may offer alternative strategies for therapeutic targeting. We uncover extensive alternative splicing in oncogenic fusions including KMT2A-MLLT3, KMT2A-MLLT10, C11orf95-RELA, NUP98-NSD1, KMT2A-AFDN and ETV6-RUNX1. We discover neo splice sites in 18 oncogenic fusion gene pairs and demonstrate that such splice sites confer therapeutic vulnerability for etiology-based genome editing. Our study reveals general principles on the etiology of oncogenic fusions in childhood cancer and suggests profound clinical implications including etiology-based risk stratification and genome-editing-based therapeutics.
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Affiliation(s)
- Yanling Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jonathon Klein
- Department of Cell and Molecular Biology and Center for Advanced Genome Editing, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Richa Bajpai
- Department of Cell and Molecular Biology and Center for Advanced Genome Editing, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Li Dong
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Quang Tran
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Pandurang Kolekar
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jenny L Smith
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Rhonda E Ries
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Benjamin J Huang
- Department of Pediatrics and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | | | - Todd A Alonzo
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Liqing Tian
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Heather L Mulder
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Timothy I Shaw
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael P Walsh
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Guangchun Song
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Tamara Westover
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Robert J Autry
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alexander M Gout
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David A Wheeler
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shibiao Wan
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jun J Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - William E Evans
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mignon Loh
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute and the Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | | | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology and Center for Advanced Genome Editing, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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27
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Fu F, Tao X, Jiang Z, Gao Z, Zhao Y, Li Y, Hu H, Shen L, Sun Y, Zhang Y. Identification of Germline Mutations in East-Asian Young Never-Smokers with Lung Adenocarcinoma by Whole-Exome Sequencing. PHENOMICS (CHAM, SWITZERLAND) 2023; 3:182-189. [PMID: 37197646 PMCID: PMC10110802 DOI: 10.1007/s43657-022-00062-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 05/19/2023]
Abstract
Recently, an increasing number of young never-smokers are diagnosed with lung cancer. The aim of this study is to investigate the genetic predisposition of lung cancer in these patients and discover candidate pathogenic variants for lung adenocarcinoma in young never-smokers. Peripheral blood was collected from 123 never-smoking east-Asian patients diagnosed with lung adenocarcinoma before the age of 40. Whole-exome sequencing (WES) was conducted on genomic DNA extracted from peripheral blood cells. As a result, 3,481 single nucleotide variants were identified. By bioinformatical tools and the published gene list associated with genetic predisposition of cancer, pathogenic variants were detected in ten germline genes: ATR, FANCD2, FANCE, GATA2, HFE, MSH2, PDGFRA, PMS2, SDHB, and WAS. Patients with pathogenic variants were more likely to occur in females (9/10, 90.0%) and have stage IV lung adenocarcinoma (4/10, 40%). Furthermore, germline mutations in 17 genes (ASB18, B3GALT5, CLEC4F, COL6A6, CYP4B1, C6orf132, EXO1, GATA4, HCK, KCP, NPHP4, PIGX, PPIL2, PPP1R3G, RRBP1, SALL4, and TTC28), which occurred in at least two patients, displayed potentially pathogenic effects. Gene ontology analysis further showed that these genes with germline mutations were mainly located in nucleoplasm and associated with DNA repair-related biological processes. The study provides spectrum of pathogenic variants and functional explanation for genetic predisposition of lung adenocarcinoma in young never-smokers, which sheds a light on prevention and early diagnosis of lung cancer. Supplementary Information The online version contains supplementary material available at 10.1007/s43657-022-00062-1.
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Affiliation(s)
- Fangqiu Fu
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai, 200032 China
- Institute of Thoracic Oncology, Fudan University, Shanghai, 200032 China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China
| | - Xiaoting Tao
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai, 200032 China
- Institute of Thoracic Oncology, Fudan University, Shanghai, 200032 China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China
| | - Zhonglin Jiang
- Key Laboratory of Systems Biology, Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031 China
| | - Zhendong Gao
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai, 200032 China
- Institute of Thoracic Oncology, Fudan University, Shanghai, 200032 China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China
| | - Yue Zhao
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai, 200032 China
- Institute of Thoracic Oncology, Fudan University, Shanghai, 200032 China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China
| | - Yuan Li
- Institute of Thoracic Oncology, Fudan University, Shanghai, 200032 China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032 China
| | - Hong Hu
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai, 200032 China
- Institute of Thoracic Oncology, Fudan University, Shanghai, 200032 China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China
| | - Libing Shen
- International Human Phenome Institutes (Shanghai), Shanghai, 200433 China
| | - Yihua Sun
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai, 200032 China
- Institute of Thoracic Oncology, Fudan University, Shanghai, 200032 China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China
| | - Yang Zhang
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai, 200032 China
- Institute of Thoracic Oncology, Fudan University, Shanghai, 200032 China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China
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Malhotra R, Javle V, Tanwar N, Gowda P, Varghese L, K A, Madhusudhan N, Jaiswal N, K. S. B, Chatterjee M, Prabhash K, Sreekanthreddy P, Rishi KD, Goswami HM, Veldore VH. An absolute approach to using whole exome DNA and RNA workflow for cancer biomarker testing. Front Oncol 2023; 13:1002792. [PMID: 36994199 PMCID: PMC10040847 DOI: 10.3389/fonc.2023.1002792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/24/2023] [Indexed: 03/16/2023] Open
Abstract
IntroductionThe concept of personalized medicine in cancer has emerged rapidly with the advancement of genome sequencing and the identification of clinically relevant variants that contribute to disease prognosis and facilitates targeted therapy options. In this study, we propose to validate a whole exome-based tumor molecular profiling for DNA and RNA from formalin-fixed paraffin-embedded (FFPE) tumor tissue.MethodsThe study included 166 patients across 17 different cancer types. The scope of this study includes the identification of single-nucleotide variants (SNVs), insertions/deletions (INDELS), copy number alterations (CNAs), gene fusions, tumor mutational burden (TMB), and microsatellite instability (MSI). The assay yielded a mean read depth of 200×, with >80% of on-target reads and a mean uniformity of >90%. Clinical maturation of whole exome sequencing (WES) (DNA and RNA)- based assay was achieved by analytical and clinical validations for all the types of genomic alterations in multiple cancers. We here demonstrate a limit of detection (LOD) of 5% for SNVs and 10% for INDELS with 97.5% specificity, 100% sensitivity, and 100% reproducibility.ResultsThe results were >98% concordant with other orthogonal techniques and appeared to be more robust and comprehensive in detecting all the clinically relevant alterations. Our study demonstrates the clinical utility of the exome-based approach of comprehensive genomic profiling (CGP) for cancer patients at diagnosis and disease progression.DiscussionThe assay provides a consolidated picture of tumor heterogeneity and prognostic and predictive biomarkers, thus helping in precision oncology practice. The primary intended use of WES (DNA+RNA) assay would be for patients with rare cancers as well as for patients with unknown primary tumors, and this category constitutes nearly 20–30% of all cancers. The WES approach may also help us understand the clonal evolution during disease progression to precisely plan the treatment in advanced stage disease.
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Affiliation(s)
| | - Vyomesh Javle
- 4baseCare Onco Solutions Pvt. Ltd., Bangalore, India
| | | | - Pooja Gowda
- 4baseCare Onco Solutions Pvt. Ltd., Bangalore, India
| | - Linu Varghese
- 4baseCare Onco Solutions Pvt. Ltd., Bangalore, India
| | - Anju K
- 4baseCare Onco Solutions Pvt. Ltd., Bangalore, India
| | | | - Nupur Jaiswal
- 4baseCare Onco Solutions Pvt. Ltd., Bangalore, India
| | | | | | - Kumar Prabhash
- Department of Medical Oncology, Tata Memorial Centre, Mumbai, India
| | | | | | | | - Vidya H. Veldore
- 4baseCare Onco Solutions Pvt. Ltd., Bangalore, India
- *Correspondence: Vidya H. Veldore,
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29
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Locher M, Jukic E, Vogi V, Keller MA, Kröll T, Schwendinger S, Oberhuber K, Verdorfer I, Mühlegger BE, Witsch-Baumgartner M, Nachbaur D, Willenbacher W, Gunsilius E, Wolf D, Zschocke J, Steiner N. Amp(1q) and tetraploidy are commonly acquired chromosomal abnormalities in relapsed multiple myeloma. Eur J Haematol 2023; 110:296-304. [PMID: 36433728 PMCID: PMC10107198 DOI: 10.1111/ejh.13905] [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: 08/20/2022] [Revised: 11/14/2022] [Accepted: 11/17/2022] [Indexed: 11/28/2022]
Abstract
Long-term disease control in multiple myeloma (MM) is typically an unmet medical need, and most patients experience multiple relapses. Fluorescence in situ hybridization (FISH) is the standard technique to detect chromosomal abnormalities (CAs), which are important to estimate the prognosis of MM and the allocation of risk adapted therapies. In advanced stages, the importance of CAs needs further investigation. From 148 MM patients, two or more paired samples, at least one of which was collected at relapse, were analyzed by FISH. Using targeted next-generation sequencing, we molecularly investigated samples harboring relapse-associated CAs. Sixty-one percent of the patients showed a change in the cytogenetic profile during the disease course, including 10% who acquired high-risk cytogenetics. Amp(1q) (≥4 copies of 1q21), driven by an additional increase in copy number in patients who already had 3 copies of 1q21, was the most common acquired CA with 16% affected patients. Tetraploidy, found in 10% of the samples collected at the last time-point, was unstable over the course of the disease and was associated with TP53 lesions. Our results indicate that cytogenetic progression is common in relapsed patients. The relatively high frequency of amp(1q) suggests an active role for this CA in disease progression.
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Affiliation(s)
- Maurus Locher
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Emina Jukic
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Verena Vogi
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Markus A Keller
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Teresa Kröll
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Simon Schwendinger
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Klaus Oberhuber
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Irmgard Verdorfer
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Beatrix E Mühlegger
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | | | - David Nachbaur
- Internal Medicine V (Hematology & Oncology), Medical University of Innsbruck, Innsbruck, Austria
| | - Wolfgang Willenbacher
- Internal Medicine V (Hematology & Oncology), Medical University of Innsbruck, Innsbruck, Austria.,syndena GmbH, connect to cure, Innsbruck, Austria
| | - Eberhard Gunsilius
- Internal Medicine V (Hematology & Oncology), Medical University of Innsbruck, Innsbruck, Austria
| | - Dominik Wolf
- Internal Medicine V (Hematology & Oncology), Medical University of Innsbruck, Innsbruck, Austria.,Medical Clinic 3, Oncology, Hematology, Immunoncology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Johannes Zschocke
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Normann Steiner
- Internal Medicine V (Hematology & Oncology), Medical University of Innsbruck, Innsbruck, Austria
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30
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Wen Z, Wang S, Yang DM, Xie Y, Chen M, Bishop J, Xiao G. Deep learning in digital pathology for personalized treatment plans of cancer patients. Semin Diagn Pathol 2023; 40:109-119. [PMID: 36890029 DOI: 10.1053/j.semdp.2023.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023]
Abstract
Over the past decade, many new cancer treatments have been developed and made available to patients. However, in most cases, these treatments only benefit a specific subgroup of patients, making the selection of treatment for a specific patient an essential but challenging task for oncologists. Although some biomarkers were found to associate with treatment response, manual assessment is time-consuming and subjective. With the rapid developments and expanded implementation of artificial intelligence (AI) in digital pathology, many biomarkers can be quantified automatically from histopathology images. This approach allows for a more efficient and objective assessment of biomarkers, aiding oncologists in formulating personalized treatment plans for cancer patients. This review presents an overview and summary of the recent studies on biomarker quantification and treatment response prediction using hematoxylin-eosin (H&E) stained pathology images. These studies have shown that an AI-based digital pathology approach can be practical and will become increasingly important in improving the selection of cancer treatments for patients.
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Affiliation(s)
- Zhuoyu Wen
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Shidan Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Donghan M Yang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yang Xie
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA; Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA; Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Mingyi Chen
- Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Justin Bishop
- Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA; Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA; Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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31
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Brayer KJ, Kang H, El-Naggar AK, Andreasen S, Homøe P, Kiss K, Mikkelsen L, Heegaard S, Pelaez D, Moeyersoms A, Tse DT, Guo Y, Lee DY, Ness SA. Dominant Gene Expression Profiles Define Adenoid Cystic Carcinoma (ACC) from Different Tissues: Validation of a Gene Signature Classifier for Poor Survival in Salivary Gland ACC. Cancers (Basel) 2023; 15:1390. [PMID: 36900183 PMCID: PMC10000625 DOI: 10.3390/cancers15051390] [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: 11/28/2022] [Revised: 02/11/2023] [Accepted: 02/17/2023] [Indexed: 02/25/2023] Open
Abstract
Adenoid cystic carcinoma (ACC) is an aggressive malignancy that most often arises in salivary or lacrimal glands but can also occur in other tissues. We used optimized RNA-sequencing to analyze the transcriptomes of 113 ACC tumor samples from salivary gland, lacrimal gland, breast or skin. ACC tumors from different organs displayed remarkedly similar transcription profiles, and most harbored translocations in the MYB or MYBL1 genes, which encode oncogenic transcription factors that may induce dramatic genetic and epigenetic changes leading to a dominant 'ACC phenotype'. Further analysis of the 56 salivary gland ACC tumors led to the identification of three distinct groups of patients, based on gene expression profiles, including one group with worse survival. We tested whether this new cohort could be used to validate a biomarker developed previously with a different set of 68 ACC tumor samples. Indeed, a 49-gene classifier developed with the earlier cohort correctly identified 98% of the poor survival patients from the new set, and a 14-gene classifier was almost as accurate. These validated biomarkers form a platform to identify and stratify high-risk ACC patients into clinical trials of targeted therapies for sustained clinical response.
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Affiliation(s)
- Kathryn J. Brayer
- Department of Internal Medicine, Division of Molecular Medicine, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131, USA
| | - Huining Kang
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131, USA
- Department of Internal Medicine, Division of Epidemiology, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA
| | - Adel K. El-Naggar
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Simon Andreasen
- Department of Otorhinolaryngology and Maxillofacial Surgery, Zealand University Hospital, 4600 Køge, Denmark
| | - Preben Homøe
- Department of Otorhinolaryngology and Maxillofacial Surgery, Zealand University Hospital, 4600 Køge, Denmark
| | - Katalin Kiss
- Department of Pathology, Rigshospitalet, University of Copenhagen, 1165 Copenhagen, Denmark
| | - Lauge Mikkelsen
- Department of Pathology, Rigshospitalet, University of Copenhagen, 1165 Copenhagen, Denmark
- Department of Ophthalmology, Rigshospitalet-Glostrup, University of Copenhagen, 1165 Copenhagen, Denmark
| | - Steffen Heegaard
- Department of Ophthalmology, Rigshospitalet-Glostrup, University of Copenhagen, 1165 Copenhagen, Denmark
| | - Daniel Pelaez
- Dr. Nasser Al-Rashid Orbital Vision Research Center, Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Acadia Moeyersoms
- Dr. Nasser Al-Rashid Orbital Vision Research Center, Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- The Sheila and David Fuente Graduate Program in Cancer Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - David T. Tse
- Dr. Nasser Al-Rashid Orbital Vision Research Center, Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Yan Guo
- Department of Internal Medicine, Division of Molecular Medicine, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131, USA
| | - David Y. Lee
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131, USA
- Department of Internal Medicine, Division of Hematology/Oncology, Section of Radiation Oncology, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA
| | - Scott A. Ness
- Department of Internal Medicine, Division of Molecular Medicine, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131, USA
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32
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Enhancing childhood cancer targetability. NATURE CANCER 2023; 4:153-155. [PMID: 36585448 DOI: 10.1038/s43018-022-00472-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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33
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Villani A, Davidson S, Kanwar N, Lo WW, Li Y, Cohen-Gogo S, Fuligni F, Edward LM, Light N, Layeghifard M, Harripaul R, Waldman L, Gallinger B, Comitani F, Brunga L, Hayes R, Anderson ND, Ramani AK, Yuki KE, Blay S, Johnstone B, Inglese C, Hammad R, Goudie C, Shuen A, Wasserman JD, Venier RE, Eliou M, Lorenti M, Ryan CA, Braga M, Gloven-Brown M, Han J, Montero M, Spatare F, Whitlock JA, Scherer SW, Chun K, Somerville MJ, Hawkins C, Abdelhaleem M, Ramaswamy V, Somers GR, Kyriakopoulou L, Hitzler J, Shago M, Morgenstern DA, Tabori U, Meyn S, Irwin MS, Malkin D, Shlien A. The clinical utility of integrative genomics in childhood cancer extends beyond targetable mutations. NATURE CANCER 2023; 4:203-221. [PMID: 36585449 PMCID: PMC9970873 DOI: 10.1038/s43018-022-00474-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 11/02/2022] [Indexed: 12/31/2022]
Abstract
We conducted integrative somatic-germline analyses by deeply sequencing 864 cancer-associated genes, complete genomes and transcriptomes for 300 mostly previously treated children and adolescents/young adults with cancer of poor prognosis or with rare tumors enrolled in the SickKids Cancer Sequencing (KiCS) program. Clinically actionable variants were identified in 56% of patients. Improved diagnostic accuracy led to modified management in a subset. Therapeutically targetable variants (54% of patients) were of unanticipated timing and type, with over 20% derived from the germline. Corroborating mutational signatures (SBS3/BRCAness) in patients with germline homologous recombination defects demonstrates the potential utility of PARP inhibitors. Mutational burden was significantly elevated in 9% of patients. Sequential sampling identified changes in therapeutically targetable drivers in over one-third of patients, suggesting benefit from rebiopsy for genomic analysis at the time of relapse. Comprehensive cancer genomic profiling is useful at multiple points in the care trajectory for children and adolescents/young adults with cancer, supporting its integration into early clinical management.
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Affiliation(s)
- Anita Villani
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Scott Davidson
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada.,Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Nisha Kanwar
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Winnie W Lo
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Yisu Li
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sarah Cohen-Gogo
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Fabio Fuligni
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Lisa-Monique Edward
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Nicholas Light
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Mehdi Layeghifard
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Ricardo Harripaul
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Larissa Waldman
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Cancer Genetics and High-Risk Program, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Bailey Gallinger
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Department of Genetic Counselling, University of Toronto, Toronto, Ontario, Canada.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Federico Comitani
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Ledia Brunga
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Reid Hayes
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Nathaniel D Anderson
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Arun K Ramani
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada.,Center for Computational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kyoko E Yuki
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Sasha Blay
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Brittney Johnstone
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Cancer Genetics and High-Risk Program, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Cara Inglese
- Department of Genetic Counselling, University of Toronto, Toronto, Ontario, Canada.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rawan Hammad
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Division of Hematology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Catherine Goudie
- Division of Hematology-Oncology, McGill University Health Centre, Montreal, Quebec, Canada.,Department of Pediatrics, McGill University, Montreal, Quebec, Canada
| | - Andrew Shuen
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Jonathan D Wasserman
- Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada.,Division of Endocrinology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rosemarie E Venier
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Department of Genetic Counselling, University of Toronto, Toronto, Ontario, Canada
| | - Marianne Eliou
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Miranda Lorenti
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Carol Ann Ryan
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael Braga
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Meagan Gloven-Brown
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jianan Han
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Maria Montero
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Famida Spatare
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - James A Whitlock
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Stephen W Scherer
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,McLaughlin Centre, University of Toronto, Toronto, Ontario, Canada
| | - Kathy Chun
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Martin J Somerville
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Cynthia Hawkins
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Mohamed Abdelhaleem
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Vijay Ramaswamy
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Gino R Somers
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Lianna Kyriakopoulou
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Johann Hitzler
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada.,Developmental and Stem Cell Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Mary Shago
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Daniel A Morgenstern
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Uri Tabori
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Stephen Meyn
- Center for Human Genomics and Precision Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Meredith S Irwin
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - David Malkin
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada. .,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada. .,Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada.
| | - Adam Shlien
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada. .,Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.
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34
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O’Donohue T, Sait SF, Bender JG. Progress in precision therapy in pediatric oncology. Curr Opin Pediatr 2023; 35:41-47. [PMID: 36377257 PMCID: PMC9812924 DOI: 10.1097/mop.0000000000001198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
PURPOSE OF REVIEW The fields of precision medicine and cancer genomics in pediatric oncology are rapidly evolving. Novel diagnostic tools are critical in refining cancer diagnoses, stratifying patient risk, and informing treatment decisions. This review is timely and relevant as it discusses advantages and drawbacks of common molecular profiling techniques and highlights novel platforms, which may address select limitations. We discuss recent publications demonstrating utility of large-scale molecular profiling and feasibility and logistics of matching targeted therapies to patients. RECENT FINDINGS We describe the increased accessibility of next-generation sequencing, complementary profiling methods, and strategies to guide treatment decisions. We describe curation and sharing of large genomic datasets and novel mechanisms to obtain matched targeted therapies. Importantly, we discuss relevant publications in distinct disease domains that support indications for evidence-based precision therapy. Lastly, we introduce the incremental analyses that can be obtained via whole-genome and transcriptome sequencing. SUMMARY Here we highlight high-yield clinical scenarios of precision medicine approaches and identify the ongoing challenges including universally defining clinical actionability, optimizing trial design to account for molecular heterogeneity while acknowledging limitations in patient accrual, expanding access to molecularly targeted therapies, and validating new tools and technology to aid in precision medicine therapeutic approaches.
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Affiliation(s)
- Tara O’Donohue
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sameer Farouk Sait
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Julia Glade Bender
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
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35
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Thatikonda V, Islam SMA, Autry RJ, Jones BC, Gröbner SN, Warsow G, Hutter B, Huebschmann D, Fröhling S, Kool M, Blattner-Johnson M, Jones DTW, Alexandrov LB, Pfister SM, Jäger N. Comprehensive analysis of mutational signatures reveals distinct patterns and molecular processes across 27 pediatric cancers. NATURE CANCER 2023; 4:276-289. [PMID: 36702933 PMCID: PMC9970869 DOI: 10.1038/s43018-022-00509-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 12/21/2022] [Indexed: 01/27/2023]
Abstract
Analysis of mutational signatures can reveal underlying molecular mechanisms of the processes that have imprinted the somatic mutations found in cancer genomes. Here, we analyze single base substitutions and small insertions and deletions in pediatric cancers encompassing 785 whole-genome sequenced tumors from 27 molecularly defined cancer subtypes. We identified only a small number of mutational signatures active in pediatric cancers, compared with previously analyzed adult cancers. Further, we report a significant difference in the proportion of pediatric tumors showing homologous recombination repair defect signatures compared with previous analyses. In pediatric leukemias, we identified an indel signature, not previously reported, characterized by long insertions in nonrepeat regions, affecting mainly intronic and intergenic regions, but also exons of known cancer genes. We provide a systematic overview of COSMIC v.3 mutational signatures active across pediatric cancers, which is highly relevant for understanding tumor biology and enabling future research in defining biomarkers of treatment response.
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Affiliation(s)
- Venu Thatikonda
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim RCV GmbH, Vienna, Austria
| | - S M Ashiqul Islam
- Department of Cellular and Molecular Medicine and Department of Bioengineering, Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - Robert J Autry
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Barbara C Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
- Pediatric Glioma Research Group, DKFZ, Heidelberg, Germany
| | - Susanne N Gröbner
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Gregor Warsow
- Omics IT and Data Management Core Facility (W610), DKFZ, Heidelberg, Germany
| | - Barbara Hutter
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Computational Oncology Group, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT) Heidelberg, DKFZ, Heidelberg, Germany
- Division of Applied Bioinformatics, DKFZ, Heidelberg, Germany
| | - Daniel Huebschmann
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Computational Oncology Group, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT) Heidelberg, DKFZ, Heidelberg, Germany
- Pattern Recognition and Digital Medicine, Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
| | - Stefan Fröhling
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Division of Translational Medical Oncology, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Mirjam Blattner-Johnson
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, DKFZ, Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Pediatric Glioma Research Group, DKFZ, Heidelberg, Germany
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine and Department of Bioengineering, Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany.
| | - Natalie Jäger
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
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36
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Ziegler N, Cortés-López M, Alt F, Sprang M, Ustjanzew A, Lehmann N, El Malki K, Wingerter A, Russo A, Beck O, Attig S, Roth L, König J, Paret C, Faber J. Analysis of RBP expression and binding sites identifies PTBP1 as a regulator of CD19 expression in B-ALL. Oncoimmunology 2023; 12:2184143. [PMID: 36875548 PMCID: PMC9980455 DOI: 10.1080/2162402x.2023.2184143] [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] [Indexed: 03/05/2023] Open
Abstract
Despite massive improvements in the treatment of B-ALL through CART-19 immunotherapy, a large number of patients suffer a relapse due to loss of the targeted epitope. Mutations in the CD19 locus and aberrant splicing events are known to account for the absence of surface antigen. However, early molecular determinants suggesting therapy resistance as well as the time point when first signs of epitope loss appear to be detectable are not enlightened so far. By deep sequencing of the CD19 locus, we identified a blast-specific 2-nucleotide deletion in intron 2 that exists in 35% of B-ALL samples at initial diagnosis. This deletion overlaps with the binding site of RNA binding proteins (RBPs) including PTBP1 and might thereby affect CD19 splicing. Moreover, we could identify a number of other RBPs that are predicted to bind to the CD19 locus being deregulated in leukemic blasts, including NONO. Their expression is highly heterogeneous across B-ALL molecular subtypes as shown by analyzing 706 B-ALL samples accessed via the St. Jude Cloud. Mechanistically, we show that downregulation of PTBP1, but not of NONO, in 697 cells reduces CD19 total protein by increasing intron 2 retention. Isoform analysis in patient samples revealed that blasts, at diagnosis, express increased amounts of CD19 intron 2 retention compared to normal B cells. Our data suggest that loss of RBP functionality by mutations altering their binding motifs or by deregulated expression might harbor the potential for the disease-associated accumulation of therapy-resistant CD19 isoforms.
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Affiliation(s)
- Nicole Ziegler
- Center for Pediatric and Adolescent Medicine, Department of Pediatric Hematology/Oncology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | | | - Francesca Alt
- Center for Pediatric and Adolescent Medicine, Department of Pediatric Hematology/Oncology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Maximilian Sprang
- Faculty of Biology, Johannes Gutenberg University Mainz, Biozentrum I, Mainz, Germany
| | - Arsenij Ustjanzew
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Nadine Lehmann
- Center for Pediatric and Adolescent Medicine, Department of Pediatric Hematology/Oncology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Khalifa El Malki
- Center for Pediatric and Adolescent Medicine, Department of Pediatric Hematology/Oncology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Arthur Wingerter
- Center for Pediatric and Adolescent Medicine, Department of Pediatric Hematology/Oncology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Alexandra Russo
- Center for Pediatric and Adolescent Medicine, Department of Pediatric Hematology/Oncology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Olaf Beck
- Center for Pediatric and Adolescent Medicine, Department of Pediatric Hematology/Oncology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Sebastian Attig
- Department of Translational Oncology and Immunology at the Institute of Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Lea Roth
- Center for Pediatric and Adolescent Medicine, Department of Pediatric Hematology/Oncology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Claudia Paret
- Center for Pediatric and Adolescent Medicine, Department of Pediatric Hematology/Oncology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,German Cancer Consortium (DKTK), Site Frankfurt/Mainz, Germany, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jörg Faber
- Center for Pediatric and Adolescent Medicine, Department of Pediatric Hematology/Oncology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,German Cancer Consortium (DKTK), Site Frankfurt/Mainz, Germany, German Cancer Research Center (DKFZ), Heidelberg, Germany
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37
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Muñoz-Barrera A, Rubio-Rodríguez LA, Díaz-de Usera A, Jáspez D, Lorenzo-Salazar JM, González-Montelongo R, García-Olivares V, Flores C. From Samples to Germline and Somatic Sequence Variation: A Focus on Next-Generation Sequencing in Melanoma Research. Life (Basel) 2022; 12:1939. [PMID: 36431075 PMCID: PMC9695713 DOI: 10.3390/life12111939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/12/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022] Open
Abstract
Next-generation sequencing (NGS) applications have flourished in the last decade, permitting the identification of cancer driver genes and profoundly expanding the possibilities of genomic studies of cancer, including melanoma. Here we aimed to present a technical review across many of the methodological approaches brought by the use of NGS applications with a focus on assessing germline and somatic sequence variation. We provide cautionary notes and discuss key technical details involved in library preparation, the most common problems with the samples, and guidance to circumvent them. We also provide an overview of the sequence-based methods for cancer genomics, exposing the pros and cons of targeted sequencing vs. exome or whole-genome sequencing (WGS), the fundamentals of the most common commercial platforms, and a comparison of throughputs and key applications. Details of the steps and the main software involved in the bioinformatics processing of the sequencing results, from preprocessing to variant prioritization and filtering, are also provided in the context of the full spectrum of genetic variation (SNVs, indels, CNVs, structural variation, and gene fusions). Finally, we put the emphasis on selected bioinformatic pipelines behind (a) short-read WGS identification of small germline and somatic variants, (b) detection of gene fusions from transcriptomes, and (c) de novo assembly of genomes from long-read WGS data. Overall, we provide comprehensive guidance across the main methodological procedures involved in obtaining sequencing results for the most common short- and long-read NGS platforms, highlighting key applications in melanoma research.
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Affiliation(s)
- Adrián Muñoz-Barrera
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Luis A. Rubio-Rodríguez
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Ana Díaz-de Usera
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | - David Jáspez
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - José M. Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Rafaela González-Montelongo
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Víctor García-Olivares
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando de Pessoa Canarias, 35450 Las Palmas de Gran Canaria, Spain
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38
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Chen Z, Li X, Yang M, Zhang H, Xu XS. Optimization of deep learning models for the prediction of gene mutations using unsupervised clustering. J Pathol Clin Res 2022; 9:3-17. [PMID: 36376239 PMCID: PMC9732687 DOI: 10.1002/cjp2.302] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 10/03/2022] [Accepted: 10/27/2022] [Indexed: 11/16/2022]
Abstract
Deep learning models are increasingly being used to interpret whole-slide images (WSIs) in digital pathology and to predict genetic mutations. Currently, it is commonly assumed that tumor regions have most of the predictive power. However, it is reasonable to assume that other tissues from the tumor microenvironment may also provide important predictive information. In this paper, we propose an unsupervised clustering-based multiple-instance deep learning model for the prediction of genetic mutations using WSIs of three cancer types obtained from The Cancer Genome Atlas. Our proposed model facilitates the identification of spatial regions related to specific gene mutations and exclusion of patches that lack predictive information through the use of unsupervised clustering. This results in a more accurate prediction of gene mutations when compared with models using all image patches on WSIs and two recently published algorithms for all three different cancer types evaluated in this study. In addition, our study validates the hypothesis that the prediction of gene mutations solely based on tumor regions on WSI slides may not always provide the best performance. Other tissue types in the tumor microenvironment could provide a better prediction ability than tumor tissues alone. These results highlight the heterogeneity in the tumor microenvironment and the importance of identification of predictive image patches in digital pathology prediction tasks.
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Affiliation(s)
- Zihan Chen
- School of Data ScienceUniversity of Science and Technology of ChinaHefeiPR China
| | - Xingyu Li
- Department of Statistics and Finance, School of ManagementUniversity of Science and Technology of ChinaHefeiPR China
| | - Miaomiao Yang
- Clinical Pathology CenterThe Fourth Affiliated Hospital of Anhui Medical UniversityHefeiPR China
| | - Hong Zhang
- Department of Statistics and Finance, School of ManagementUniversity of Science and Technology of ChinaHefeiPR China
| | - Xu Steven Xu
- Clinical Pharmacology and Quantitative ScienceGenmab Inc.PrincetonNJUSA
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39
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Langenberg KP, Meister MT, Bakhuizen JJ, Boer JM, van Eijkelenburg NK, Hulleman E, Ilan U, Looze EJ, Dierselhuis MP, van der Lugt J, Breunis W, Schild LG, Ober K, van Hooff SR, Scheijde-Vermeulen MA, Hiemcke-Jiwa LS, Flucke UE, Kranendonk ME, Wesseling P, Sonneveld E, Punt S, Boltjes A, van Dijk F, Verwiel ET, Volckmann R, Hehir-Kwa JY, Kester LA, Koudijs MM, Waanders E, Holstege FC, Vormoor HJ, Hoving EW, van Noesel MM, Pieters R, Kool M, Stumpf M, Blattner-Johnson M, Balasubramanian GP, Van Tilburg CM, Jones BC, Jones DT, Witt O, Pfister SM, Jongmans MC, Kuiper RP, de Krijger RR, Wijnen MH, den Boer ML, Zwaan CM, Kemmeren P, Koster J, Tops BB, Goemans BF, Molenaar JJ. Implementation of paediatric precision oncology into clinical practice: The Individualized Therapies for Children with cancer program ‘iTHER’. Eur J Cancer 2022; 175:311-325. [PMID: 36182817 PMCID: PMC9586161 DOI: 10.1016/j.ejca.2022.09.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 12/05/2022]
Abstract
iTHER is a Dutch prospective national precision oncology program aiming to define tumour molecular profiles in children and adolescents with primary very high-risk, relapsed, or refractory paediatric tumours. Between April 2017 and April 2021, 302 samples from 253 patients were included. Comprehensive molecular profiling including low-coverage whole genome sequencing (lcWGS), whole exome sequencing (WES), RNA sequencing (RNA-seq), Affymetrix, and/or 850k methylation profiling was successfully performed for 226 samples with at least 20% tumour content. Germline pathogenic variants were identified in 16% of patients (35/219), of which 22 variants were judged causative for a cancer predisposition syndrome. At least one somatic alteration was detected in 204 (90.3%), and 185 (81.9%) were considered druggable, with clinical priority very high (6.1%), high (21.3%), moderate (26.0%), intermediate (36.1%), and borderline (10.5%) priority. iTHER led to revision or refinement of diagnosis in 8 patients (3.5%). Temporal heterogeneity was observed in paired samples of 15 patients, indicating the value of sequential analyses. Of 137 patients with follow-up beyond twelve months, 21 molecularly matched treatments were applied in 19 patients (13.9%), with clinical benefit in few. Most relevant barriers to not applying targeted therapies included poor performance status, as well as limited access to drugs within clinical trial. iTHER demonstrates the feasibility of comprehensive molecular profiling across all ages, tumour types and stages in paediatric cancers, informing of diagnostic, prognostic, and targetable alterations as well as reportable germline variants. Therefore, WES and RNA-seq is nowadays standard clinical care at the Princess Máxima Center for all children with cancer, including patients at primary diagnosis. Improved access to innovative treatments within biology-driven combination trials is required to ultimately improve survival. Implementing comprehensive molecular profiling into standard of care is feasible. Temporal heterogeneity is observed, indicating the value of sequential analyses. Molecularly matched treatments are applied in a minority of patients despite clinical benefit. Poor performance status & limited access to drugs within trial hamper targeted treatment. The multidisciplinary tumour board is crucial in translating findings into clinical decision making.
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40
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How Genetics and Genomics Advances Are Rewriting Pediatric Cancer Research and Clinical Care. Medicina (B Aires) 2022; 58:medicina58101386. [PMID: 36295546 PMCID: PMC9610804 DOI: 10.3390/medicina58101386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/28/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022] Open
Abstract
In the last two decades, thanks to the data that have been obtained from the Human Genome Project and the development of next-generation sequencing (NGS) technologies, research in oncology has produced extremely important results in understanding the genomic landscape of pediatric cancers, which are the main cause of death during childhood. NGS has provided significant advances in medicine by detecting germline and somatic driver variants that determine the development and progression of many types of cancers, allowing a distinction between hereditary and non-hereditary cancers, characterizing resistance mechanisms that are also related to alterations of the epigenetic apparatus, and quantifying the mutational burden of tumor cells. A combined approach of next-generation technologies allows us to investigate the numerous molecular features of the cancer cell and the effects of the environment on it, discovering and following the path of personalized therapy to defeat an "ancient" disease that has had victories and defeats. In this paper, we provide an overview of the results that have been obtained in the last decade from genomic studies that were carried out on pediatric cancer and their contribution to the more accurate and faster diagnosis in the stratification of patients and the development of new precision therapies.
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41
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Chen PC, Han X, Shaw TI, Fu Y, Sun H, Niu M, Wang Z, Jiao Y, Teubner BJW, Eddins D, Beloate LN, Bai B, Mertz J, Li Y, Cho JH, Wang X, Wu Z, Liu D, Poudel S, Yuan ZF, Mancieri A, Low J, Lee HM, Patton MH, Earls LR, Stewart E, Vogel P, Hui Y, Wan S, Bennett DA, Serrano GE, Beach TG, Dyer MA, Smeyne RJ, Moldoveanu T, Chen T, Wu G, Zakharenko SS, Yu G, Peng J. Alzheimer's disease-associated U1 snRNP splicing dysfunction causes neuronal hyperexcitability and cognitive impairment. NATURE AGING 2022; 2:923-940. [PMID: 36636325 PMCID: PMC9833817 DOI: 10.1038/s43587-022-00290-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/01/2022] [Indexed: 11/05/2022]
Abstract
Recent proteome and transcriptome profiling of Alzheimer's disease (AD) brains reveals RNA splicing dysfunction and U1 small nuclear ribonucleoprotein (snRNP) pathology containing U1-70K and its N-terminal 40-KDa fragment (N40K). Here we present a causative role of U1 snRNP dysfunction to neurodegeneration in primary neurons and transgenic mice (N40K-Tg), in which N40K expression exerts a dominant-negative effect to downregulate full-length U1-70K. N40K-Tg recapitulates N40K insolubility, erroneous splicing events, neuronal degeneration and cognitive impairment. Specifically, N40K-Tg shows the reduction of GABAergic synapse components (e.g., the GABA receptor subunit of GABRA2), and concomitant postsynaptic hyperexcitability that is rescued by a GABA receptor agonist. Crossing of N40K-Tg and the 5xFAD amyloidosis model indicates that the RNA splicing defect synergizes with the amyloid cascade to remodel the brain transcriptome and proteome, deregulate synaptic proteins, and accelerate cognitive decline. Thus, our results support the contribution of U1 snRNP-mediated splicing dysfunction to AD pathogenesis.
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Affiliation(s)
- Ping-Chung Chen
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xian Han
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Timothy I. Shaw
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Yingxue Fu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Huan Sun
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Mingming Niu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Zhen Wang
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yun Jiao
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Brett J. W. Teubner
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Donnie Eddins
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Lauren N. Beloate
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Present address: Department of Biomedical Engineering and Electrical Engineering, Penn State University, State College, PA 16801, USA
| | - Bing Bai
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Present address: Department of Laboratory Medicine, Center for Precision Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, Jiangsu 210008, China
| | - Joseph Mertz
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Present address: GlaxoSmithKline, Rockville, MD 20850, USA
| | - Yuxin Li
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ji-Hoon Cho
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xusheng Wang
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Present address: Department of Biology, University of North Dakota, Grand Forks, ND 58202, USA
| | - Zhiping Wu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Danting Liu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Suresh Poudel
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Zuo-Fei Yuan
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ariana Mancieri
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jonathan Low
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hyeong-Min Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Mary H. Patton
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Laurie R. Earls
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Present address: Department of Biological Sciences, Loyola University of New Orleans, LA 70118, USA
| | - Elizabeth Stewart
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Peter Vogel
- Veterinary Pathology Core, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yawei Hui
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shibiao Wan
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - David A. Bennett
- Department of Neurological Sciences, Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL 60612, USA
| | | | - Thomas G. Beach
- Banner Sun Health Research Institute, Sun City, AZ 85351, USA
| | - Michael A. Dyer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Richard J. Smeyne
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Present address: Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Tudor Moldoveanu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Present address: Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AK 72205, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Gang Wu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Stanislav S. Zakharenko
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Gang Yu
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Present address: Department of Neuroscience, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Junmin Peng
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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42
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Sholl LM, Halmos B. Biomarker testing in cancer management- can one size fit all? Br J Cancer 2022; 127:1177-1179. [PMID: 36064588 PMCID: PMC9519751 DOI: 10.1038/s41416-022-01967-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 08/16/2022] [Accepted: 08/19/2022] [Indexed: 11/09/2022] Open
Abstract
Biomarker-guided treatment selection has transformed cancer management. Pruis et al. provide a powerful example of the challenges and promises of whole genome sequencing to match patients with advanced cancer for precision oncology studies and targeted therapies. Expanding genomic testing platforms are reviewed with a view towards future applications to inform clinical cancer research and practice.
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Affiliation(s)
- Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Balazs Halmos
- Department of Oncology, Montefiore Medical Center and Albert Einstein College of Medicine, New York, NY, USA.
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Pilheden M, Ahlgren L, Hyrenius-Wittsten A, Gonzalez-Pena V, Sturesson H, Hansen Marquart HV, Lausen B, Castor A, Pronk CJ, Barbany G, Pokrovskaja Tamm K, Fogelstrand L, Lohi O, Norén-Nyström U, Asklin J, Chen Y, Song G, Walsh M, Ma J, Zhang J, Saal LH, Gawad C, Hagström-Andersson AK. Duplex Sequencing Uncovers Recurrent Low-frequency Cancer-associated Mutations in Infant and Childhood KMT2A-rearranged Acute Leukemia. Hemasphere 2022; 6:e785. [PMID: 36204688 PMCID: PMC9529062 DOI: 10.1097/hs9.0000000000000785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/30/2022] [Indexed: 11/26/2022] Open
Abstract
Infant acute lymphoblastic leukemia (ALL) with KMT2A-gene rearrangements (KMT2A-r) have few mutations and a poor prognosis. To uncover mutations that are below the detection of standard next-generation sequencing (NGS), a combination of targeted duplex sequencing and NGS was applied on 20 infants and 7 children with KMT2A-r ALL, 5 longitudinal and 6 paired relapse samples. Of identified nonsynonymous mutations, 87 had been previously implicated in cancer and targeted genes recurrently altered in KMT2A-r leukemia and included mutations in KRAS, NRAS, FLT3, TP53, PIK3CA, PAX5, PIK3R1, and PTPN11, with infants having fewer such mutations. Of identified cancer-associated mutations, 62% were below the resolution of standard NGS. Only 33 of 87 mutations exceeded 2% of cellular prevalence and most-targeted PI3K/RAS genes (31/33) and typically KRAS/NRAS. Five patients only had low-frequency PI3K/RAS mutations without a higher-frequency signaling mutation. Further, drug-resistant clones with FLT3 D835H or NRAS G13D/G12S mutations that comprised only 0.06% to 0.34% of diagnostic cells, expanded at relapse. Finally, in longitudinal samples, the relapse clone persisted as a minor subclone from diagnosis and through treatment before expanding during the last month of disease. Together, we demonstrate that infant and childhood KMT2A-r ALL harbor low-frequency cancer-associated mutations, implying a vast subclonal genetic landscape.
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Affiliation(s)
- Mattias Pilheden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Louise Ahlgren
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Axel Hyrenius-Wittsten
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Veronica Gonzalez-Pena
- Division of Pediatric Hematology/Oncology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Helena Sturesson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | | | - Birgitte Lausen
- Department of Paediatrics and Adolescent Medicine, Rigshospitalet, University of Copenhagen, Denmark
| | - Anders Castor
- Childhood Cancer Center, Skane University Hospital, Lund, Sweden
| | | | - Gisela Barbany
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | | | - Linda Fogelstrand
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Sweden
| | - Olli Lohi
- Tampere Center for Child, Adolescent and Maternal Health Research and Tays Cancer Center, Tampere University and Tampere University Hospital, Tampere, Finland
| | | | | | | | - Guangchun Song
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Michael Walsh
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jing Ma
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Lao H. Saal
- SAGA Diagnostics, Lund, Sweden
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Charles Gawad
- Division of Pediatric Hematology/Oncology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Anna K. Hagström-Andersson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Center for Translational Genomics, Lund University, Lund, Sweden
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44
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Rosenquist R, Cuppen E, Buettner R, Caldas C, Dreau H, Elemento O, Frederix G, Grimmond S, Haferlach T, Jobanputra V, Meggendorfer M, Mullighan CG, Wordsworth S, Schuh A. Clinical utility of whole-genome sequencing in precision oncology. Semin Cancer Biol 2022; 84:32-39. [PMID: 34175442 DOI: 10.1016/j.semcancer.2021.06.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 06/02/2021] [Accepted: 06/22/2021] [Indexed: 12/14/2022]
Abstract
Precision diagnostics is one of the two pillars of precision medicine. Sequencing efforts in the past decade have firmly established cancer as a primarily genetically driven disease. This concept is supported by therapeutic successes aimed at particular pathways that are perturbed by specific driver mutations in protein-coding domains and reflected in three recent FDA tissue agnostic cancer drug approvals. In addition, there is increasing evidence from studies that interrogate the entire genome by whole-genome sequencing that acquired global and complex genomic aberrations including those in non-coding regions of the genome might also reflect clinical outcome. After addressing technical, logistical, financial and ethical challenges, national initiatives now aim to introduce clinical whole-genome sequencing into real-world diagnostics as a rational and potentially cost-effective tool for response prediction in cancer and to identify patients who would benefit most from 'expensive' targeted therapies and recruitment into clinical trials. However, so far, this has not been accompanied by a systematic and prospective evaluation of the clinical utility of whole-genome sequencing within clinical trials of uniformly treated patients of defined clinical outcome. This approach would also greatly facilitate novel predictive biomarker discovery and validation, ultimately reducing size and duration of clinical trials and cost of drug development. This manuscript is the third in a series of three to review and critically appraise the potential and challenges of clinical whole-genome sequencing in solid tumors and hematological malignancies.
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Affiliation(s)
- Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Solna, Sweden
| | - Edwin Cuppen
- Hartwig Medical Foundation, Amsterdam, The Netherlands; Center for Molecular Medicine and Oncode Institute, University Medical Center, Utrecht, The Netherlands
| | | | - Carlos Caldas
- Cancer Research UK Cambridge Institute and Department of Oncology, University of Cambridge, United Kingdom
| | - Helene Dreau
- NIHR Oxford Biomedical Research Centre and Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, United States; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, United States
| | - Geert Frederix
- Julius Center for Health Sciences and Primary Care, University Medical Center, Utrecht, The Netherlands
| | - Sean Grimmond
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | | | - Vaidehi Jobanputra
- New York Genome Center, 101 Avenue of the Americas, New York, NY 100132, United States; Columbia University Medical Center, 650 W 168th St, New York, NY 10032, United States
| | | | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, United States
| | - Sarah Wordsworth
- Nuffield Department of Population Health and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Anna Schuh
- NIHR Oxford Biomedical Research Centre and Department of Oncology, University of Oxford, Oxford, United Kingdom.
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45
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Jobanputra V, Wrzeszczynski KO, Buttner R, Caldas C, Cuppen E, Grimmond S, Haferlach T, Mullighan C, Schuh A, Elemento O. Clinical interpretation of whole-genome and whole-transcriptome sequencing for precision oncology. Semin Cancer Biol 2022; 84:23-31. [PMID: 34256129 DOI: 10.1016/j.semcancer.2021.07.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 07/01/2021] [Accepted: 07/07/2021] [Indexed: 02/08/2023]
Abstract
Whole-genome sequencing either alone or in combination with whole-transcriptome sequencing has started to be used to analyze clinical tumor samples to improve diagnosis, provide risk stratification, and select patient-specific therapies. Compared with current genomic testing strategies, largely focused on small number of genes tested individually or targeted panels, whole-genome and transcriptome sequencing (WGTS) provides novel opportunities to identify and report a potentially much larger number of actionable alterations with diagnostic, prognostic, and/or predictive impact. Such alterations include point mutations, indels, copy- number aberrations and structural variants, but also germline variants, fusion genes, noncoding alterations and mutational signatures. Nevertheless, these comprehensive tests are accompanied by many challenges ranging from the extent and diversity of sequence alterations detected by these methods to the complexity and limited existing standardization in interpreting them. We describe the challenges of WGTS interpretation and the opportunities with comprehensive genomic testing.
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Affiliation(s)
- Vaidehi Jobanputra
- New York Genome Center, 101 Avenue of the Americas, New York, NY 100132, United States; Columbia University Medical Center, 650 W 168th St, New York, NY 10032, United States.
| | | | | | - Carlos Caldas
- Cancer Research UK Cambridge Institute and Department of Oncology, University of Cambridge, United Kingdom
| | - Edwin Cuppen
- Hartwig Medical Foundation, Amsterdam, Netherlands; Center for Molecular Medicine and Oncode Institute, University Medical Center, Utrecht, Netherlands
| | - Sean Grimmond
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | | | - Charles Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, United States
| | - Anna Schuh
- NIHR Oxford Biomedical Research Centre and Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, United States; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, United States.
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46
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Mizuno K, Beltran H. Future directions for precision oncology in prostate cancer. Prostate 2022; 82 Suppl 1:S86-S96. [PMID: 35657153 PMCID: PMC9942493 DOI: 10.1002/pros.24354] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/28/2022] [Indexed: 11/06/2022]
Abstract
Clinical genomic testing is becoming routine in prostate cancer, as biomarker-driven therapies such as poly-ADP ribose polymerase (PARP) inhibitors and anti-PD1 immunotherapy are now approved for select men with castration-resistant prostate cancer harboring alterations in DNA repair genes. Challenges for precision medicine in prostate cancer include an overall low prevalence of actionable genomic alterations and a still limited understanding of the impact of tumor heterogeneity and co-occurring alterations on treatment response and outcomes across diverse patient populations. Expanded tissue-based technologies such as whole-genome sequencing, transcriptome analysis, epigenetic analysis, and single-cell RNA sequencing have not yet entered the clinical realm and could potentially improve upon our understanding of how molecular features of tumors, intratumoral heterogeneity, and the tumor microenvironment impact therapy response and resistance. Blood-based technologies including cell-free DNA, circulating tumor cells (CTCs), and extracellular vesicles (EVs) are less invasive molecular profiling resources that could also help capture intraindividual tumor heterogeneity and track dynamic changes that occur in the context of specific therapies. Furthermore, molecular imaging is an important biomarker tool within the framework of prostate cancer precision medicine with a capability to detect heterogeneity across metastases and potential therapeutic targets less invasively. Here, we review recent technological advances that may help promote the future implementation and value of precision oncology testing for patients with advanced prostate cancer.
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Affiliation(s)
- Kei Mizuno
- Department of Medical Oncology, Dana Farber Cancer Institute
| | - Himisha Beltran
- Department of Medical Oncology, Dana Farber Cancer Institute
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47
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Ramarao-Milne P, Kondrashova O, Patch AM, Nones K, Koufariotis LT, Newell F, Addala V, Lakis V, Holmes O, Leonard C, Wood S, Xu Q, Mukhopadhyay P, Naeini MM, Steinfort D, Williamson JP, Bint M, Pahoff C, Nguyen PT, Twaddell S, Arnold D, Grainge C, Basirzadeh F, Fielding D, Dalley AJ, Chittoory H, Simpson PT, Aoude LG, Bonazzi VF, Patel K, Barbour AP, Fennell DA, Robinson BW, Creaney J, Hollway G, Pearson JV, Waddell N. Comparison of actionable events detected in cancer genomes by whole-genome sequencing, in silico whole-exome and mutation panels. ESMO Open 2022; 7:100540. [PMID: 35849877 PMCID: PMC9463385 DOI: 10.1016/j.esmoop.2022.100540] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 06/07/2022] [Accepted: 06/19/2022] [Indexed: 12/14/2022] Open
Abstract
Background Next-generation sequencing is used in cancer research to identify somatic and germline mutations, which can predict sensitivity or resistance to therapies, and may be a useful tool to reveal drug repurposing opportunities between tumour types. Multigene panels are used in clinical practice for detecting targetable mutations. However, the value of clinical whole-exome sequencing (WES) and whole-genome sequencing (WGS) for cancer care is less defined, specifically as the majority of variants found using these technologies are of uncertain significance. Patients and methods We used the Cancer Genome Interpreter and WGS in 726 tumours spanning 10 cancer types to identify drug repurposing opportunities. We compare the ability of WGS to detect actionable variants, tumour mutation burden (TMB) and microsatellite instability (MSI) by using in silico down-sampled data to mimic WES, a comprehensive sequencing panel and a hotspot mutation panel. Results We reveal drug repurposing opportunities as numerous biomarkers are shared across many solid tumour types. Comprehensive panels identify the majority of approved actionable mutations, with WGS detecting more candidate actionable mutations for biomarkers currently in clinical trials. Moreover, estimated values for TMB and MSI vary when calculated from WGS, WES and panel data, and are dependent on whether all mutations or only non-synonymous mutations were used. Our results suggest that TMB and MSI thresholds should not only be tumour-dependent, but also be sequencing platform-dependent. Conclusions There is a large opportunity to repurpose cancer drugs, and these data suggest that comprehensive sequencing is an invaluable source of information to guide clinical decisions by facilitating precision medicine and may provide a wealth of information for future studies. Furthermore, the sequencing and analysis approach used to estimate TMB may have clinical implications if a hard threshold is used to indicate which patients may respond to immunotherapy. Genome analysis revealed that treatment biomarkers are shared across solid tumours, highlighting repurposing opportunities. Comprehensive panels detect most known biomarkers; however, WGS detects more biomarkers for treatments in clinical trials. TMB is well correlated between sequencing methods, but absolute values vary and are dependent on mutation types considered.
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Affiliation(s)
- P Ramarao-Milne
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia; Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia
| | - O Kondrashova
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - A-M Patch
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - K Nones
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - L T Koufariotis
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - F Newell
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - V Addala
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - V Lakis
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - O Holmes
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - C Leonard
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - S Wood
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Q Xu
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - P Mukhopadhyay
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - M M Naeini
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - D Steinfort
- Department of Thoracic Medicine, Royal Melbourne Hospital, Melbourne, Australia
| | - J P Williamson
- Department of Thoracic Medicine, Liverpool Hospital Sydney, Sydney, Australia
| | - M Bint
- Department of Thoracic Medicine, Sunshine Coast University Hospital, Birtinya, Australia
| | - C Pahoff
- Department of Respiratory Medicine, Gold Coast University Hospital, Southport, Australia
| | - P T Nguyen
- Department of Thoracic Medicine, Royal Adelaide Hospital, Adelaide, Australia
| | - S Twaddell
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, Australia
| | - D Arnold
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, Australia
| | - C Grainge
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, Australia
| | - F Basirzadeh
- Department of Thoracic Medicine, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - D Fielding
- Department of Thoracic Medicine, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - A J Dalley
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - H Chittoory
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - P T Simpson
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - L G Aoude
- The University of Queensland Diamantina Institute, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - V F Bonazzi
- The University of Queensland Diamantina Institute, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - K Patel
- The University of Queensland Diamantina Institute, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - A P Barbour
- The University of Queensland Diamantina Institute, Faculty of Medicine, University of Queensland, Brisbane, Australia; Upper Gastro-intestinal Surgical Unit, Department of Surgery, Princess Alexandra Hospital, Brisbane, Australia
| | - D A Fennell
- Cancer Research UK Centre Leicester, University of Leicester & University Hospitals of Leicester NHS Trust, Leicester, UK
| | - B W Robinson
- National Centre for Asbestos Related Disease, Institute of Respiratory Health, University of Western Australia, Nedlands, Australia; Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Australia
| | - J Creaney
- National Centre for Asbestos Related Disease, Institute of Respiratory Health, University of Western Australia, Nedlands, Australia; Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Australia
| | - G Hollway
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - J V Pearson
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - N Waddell
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
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Arthur C, Rezayee F, Mogensen N, Saft L, Rosenquist R, Nordenskjöld M, Harila-Saari A, Tham E, Barbany G. Patient-Specific Assays Based on Whole-Genome Sequencing Data to Measure Residual Disease in Children With Acute Lymphoblastic Leukemia: A Proof of Concept Study. Front Oncol 2022; 12:899325. [PMID: 35865473 PMCID: PMC9296121 DOI: 10.3389/fonc.2022.899325] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/23/2022] [Indexed: 01/24/2023] Open
Abstract
Risk-adapted treatment in acute lymphoblastic leukemia (ALL) relies on genetic information and measurable residual disease (MRD) monitoring. In this proof of concept study, DNA from diagnostic bone marrow (BM) of six children with ALL, without stratifying genetics or central nervous system (CNS) involvement, underwent whole-genome sequencing (WGS) to identify structural variants (SVs) in the leukemic blasts. Unique sequences generated by SVs were targeted with patient-specific droplet digital PCR (ddPCR) assays. Genomic DNA (gDNA) from BM and cell-free DNA (cfDNA) from plasma and cerebrospinal fluid (CSF) were analyzed longitudinally. WGS with 30× coverage enabled target identification in all cases. Limit of quantifiability (LoQ) and limit of detection (LoD) for the ddPCR assays (n = 15) were up to 10-5 and 10-6, respectively. All targets were readily detectable in a multiplexed ddPCR with minimal DNA input (1 ng of gDNA) at a 10-1 dilution, and targets for half of the patients were also detectable at a 10-2 dilution. The level of MRD in BM at end of induction and end of consolidation block 1 was in a comparable range between ddPCR and clinical routine methods for samples with detectable residual disease, although our approach consistently detected higher MRD values for patients with B-cell precursor ALL. Additionally, several samples with undetectable MRD by flow cytometry were MRD-positive by ddPCR. In plasma, the level of leukemic targets decreased in cfDNA over time following the MRD level detected in BM. cfDNA was successfully extracted from all diagnostic CSF samples (n = 6), and leukemic targets were detected in half of these. The results suggest that our approach to design molecular assays, together with ddPCR quantification, is a technically feasible option for accurate MRD quantification and that cfDNA may contribute valuable information regarding MRD and low-grade CNS involvement.
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Affiliation(s)
- Cecilia Arthur
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden,Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden,*Correspondence: Cecilia Arthur,
| | - Fatemah Rezayee
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden,Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Nina Mogensen
- Department of Pediatric Oncology, Karolinska University Hospital, Stockholm, Sweden,Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Leonie Saft
- Department of Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden,Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Richard Rosenquist
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden,Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Magnus Nordenskjöld
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden,Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Arja Harila-Saari
- Department of Women’s and Children’s Health, Uppsala University, Uppsala, Sweden
| | - Emma Tham
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden,Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Gisela Barbany
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden,Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
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Arunachalam S, Szlachta K, Brady SW, Ma X, Ju B, Shaner B, Mulder HL, Easton J, Raphael BJ, Myers M, Tinkle C, Allen SJ, Orr BA, Wetmore CJ, Baker SJ, Zhang J. Convergent evolution and multi-wave clonal invasion in H3 K27-altered diffuse midline gliomas treated with a PDGFR inhibitor. Acta Neuropathol Commun 2022; 10:80. [PMID: 35642016 PMCID: PMC9153212 DOI: 10.1186/s40478-022-01381-0] [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: 03/10/2022] [Accepted: 05/12/2022] [Indexed: 11/11/2022] Open
Abstract
The majority of diffuse midline gliomas, H3 K27-altered (DMG-H3 K27-a), are infiltrating pediatric brain tumors that arise in the pons with no effective treatment. To understand how clonal evolution contributes to the tumor’s invasive spread, we performed exome sequencing and SNP array profiling on 49 multi-region autopsy samples from 11 patients with pontine DMG-H3 K27-a enrolled in a phase I clinical trial of PDGFR inhibitor crenolanib. For each patient, a phylogenetic tree was constructed by testing multiple possible clonal evolution models to select the one consistent with somatic mutations and copy number variations across all tumor regions. The tree was then used to deconvolute subclonal composition and prevalence at each tumor region to study convergent evolution and invasion patterns. Somatic variants in the PI3K pathway, a late event, are enriched in our cohort, affecting 70% of patients. Convergent evolution of PI3K at distinct phylogenetic branches was detected in 40% of the patients. 24 (~ 50%) of tumor regions were occupied by subclones of mixed lineages with varying molecular ages, indicating multiple waves of invasion across the pons and extrapontine. Subclones harboring a PDGFRA amplicon, including one that amplified a PDGRFAY849C mutant allele, were detected in four patients; their presence in extrapontine tumor and normal brain samples imply their involvement in extrapontine invasion. Our study expands the current knowledge on tumor invasion patterns in DMG-H3 K27-a, which may inform the design of future clinical trials.
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Shukla N, Levine MF, Gundem G, Domenico D, Spitzer B, Bouvier N, Arango-Ossa JE, Glodzik D, Medina-Martínez JS, Bhanot U, Gutiérrez-Abril J, Zhou Y, Fiala E, Stockfisch E, Li S, Rodriguez-Sanchez MI, O'Donohue T, Cobbs C, Roehrl MHA, Benhamida J, Iglesias Cardenas F, Ortiz M, Kinnaman M, Roberts S, Ladanyi M, Modak S, Farouk-Sait S, Slotkin E, Karajannis MA, Dela Cruz F, Glade Bender J, Zehir A, Viale A, Walsh MF, Kung AL, Papaemmanuil E. Feasibility of whole genome and transcriptome profiling in pediatric and young adult cancers. Nat Commun 2022; 13:2485. [PMID: 35585047 PMCID: PMC9117241 DOI: 10.1038/s41467-022-30233-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 04/21/2022] [Indexed: 02/07/2023] Open
Abstract
The utility of cancer whole genome and transcriptome sequencing (cWGTS) in oncology is increasingly recognized. However, implementation of cWGTS is challenged by the need to deliver results within clinically relevant timeframes, concerns about assay sensitivity, reporting and prioritization of findings. In a prospective research study we develop a workflow that reports comprehensive cWGTS results in 9 days. Comparison of cWGTS to diagnostic panel assays demonstrates the potential of cWGTS to capture all clinically reported mutations with comparable sensitivity in a single workflow. Benchmarking identifies a minimum of 80× as optimal depth for clinical WGS sequencing. Integration of germline, somatic DNA and RNA-seq data enable data-driven variant prioritization and reporting, with oncogenic findings reported in 54% more patients than standard of care. These results establish key technical considerations for the implementation of cWGTS as an integrated test in clinical oncology. Cancer whole-genome and transcriptome sequencing (cWGTS) has been challenging to implement in clinical settings. Here, the authors develop a workflow to deliver robust cWGTS analyses and reports within clinically-relevant timeframes for paediatric, adolescent and young adult solid tumour patients.
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Affiliation(s)
- N Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M F Levine
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - G Gundem
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - D Domenico
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - B Spitzer
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - N Bouvier
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - J E Arango-Ossa
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - D Glodzik
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - J S Medina-Martínez
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - U Bhanot
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Precision Pathology Biobanking Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - J Gutiérrez-Abril
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Y Zhou
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - E Fiala
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - E Stockfisch
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - S Li
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - T O'Donohue
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - C Cobbs
- Integrated Genomics Operation Core, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M H A Roehrl
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Precision Pathology Biobanking Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - J Benhamida
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - F Iglesias Cardenas
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M Ortiz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M Kinnaman
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - S Roberts
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - S Modak
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - S Farouk-Sait
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - E Slotkin
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M A Karajannis
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - F Dela Cruz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - J Glade Bender
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A Viale
- Integrated Genomics Operation Core, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M F Walsh
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A L Kung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - E Papaemmanuil
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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