451
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Cortés-Ciriano I, Lee JJK, Xi R, Jain D, Jung YL, Yang L, Gordenin D, Klimczak LJ, Zhang CZ, Pellman DS, Park PJ. Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. Nat Genet 2020; 52:331-341. [PMID: 32025003 PMCID: PMC7058534 DOI: 10.1038/s41588-019-0576-7] [Citation(s) in RCA: 370] [Impact Index Per Article: 92.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 12/20/2019] [Indexed: 01/12/2023]
Abstract
Chromothripsis is a mutational phenomenon characterized by massive, clustered genomic rearrangements that occurs in cancer and other diseases. Recent studies in selected cancer types have suggested that chromothripsis may be more common than initially inferred from low-resolution copy-number data. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we analyze patterns of chromothripsis across 2,658 tumors from 38 cancer types using whole-genome sequencing data. We find that chromothripsis events are pervasive across cancers, with a frequency of more than 50% in several cancer types. Whereas canonical chromothripsis profiles display oscillations between two copy-number states, a considerable fraction of events involve multiple chromosomes and additional structural alterations. In addition to non-homologous end joining, we detect signatures of replication-associated processes and templated insertions. Chromothripsis contributes to oncogene amplification and to inactivation of genes such as mismatch-repair-related genes. These findings show that chromothripsis is a major process that drives genome evolution in human cancer.
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Affiliation(s)
- Isidro Cortés-Ciriano
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Boston, MA, USA
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Jake June-Koo Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Boston, MA, USA
| | - Ruibin Xi
- School of Mathematical Sciences and Center for Statistical Science, Peking University, Beijing, China
| | - Dhawal Jain
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Youngsook L Jung
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Lixing Yang
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Dmitry Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Durham, NC, USA
| | - Leszek J Klimczak
- Integrative Bioinformatics Group, National Institute of Environmental Health Sciences, US National Institutes of Health, Durham, NC, USA
| | - Cheng-Zhong Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - David S Pellman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Blavatnik Institute, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Ludwig Center at Harvard, Boston, MA, USA.
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452
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Bosse KR, Majzner RG, Mackall CL, Maris JM. Immune-Based Approaches for the Treatment of Pediatric Malignancies. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2020; 4:353-370. [PMID: 34113750 PMCID: PMC8189419 DOI: 10.1146/annurev-cancerbio-030419-033436] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Immune-based therapies have now been credentialed for pediatric cancers with the robust efficacy of chimeric antigen receptor (CAR) T cells for pediatric B cell acute lymphocytic leukemia (ALL), offering a chance of a cure for children with previously lethal disease and a potentially more targeted therapy to limit treatment-related morbidities. The developmental origins of most pediatric cancers make them ideal targets for immune-based therapies that capitalize on the differential expression of lineage-specific cell surface molecules such as antibodies, antibody-drug conjugates, or CAR T cells, while the efficacy of other therapies that depend on tumor immunogenicity such as immune checkpoint inhibitors has been limited to date. Here we review the current status of immune-based therapies for childhood cancers, discuss challenges to developing immunotherapeutics for these diseases, and outline future directions of pediatric immunotherapy discovery and development.
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Affiliation(s)
- Kristopher R Bosse
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Robbie G Majzner
- Department of Pediatrics and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Crystal L Mackall
- Department of Pediatrics and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California 94305, USA
| | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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453
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Autry RJ, Paugh SW, Carter R, Shi L, Liu J, Ferguson DC, Lau CE, Bonten EJ, Yang W, McCorkle JR, Beard JA, Panetta JC, Diedrich JD, Crews KR, Pei D, Coke CJ, Natarajan S, Khatamian A, Karol SE, Lopez-Lopez E, Diouf B, Smith C, Gocho Y, Hagiwara K, Roberts KG, Pounds S, Kornblau SM, Stock W, Paietta EM, Litzow MR, Inaba H, Mullighan CG, Jeha S, Pui CH, Cheng C, Savic D, Yu J, Gawad C, Relling MV, Yang JJ, Evans WE. Integrative genomic analyses reveal mechanisms of glucocorticoid resistance in acute lymphoblastic leukemia. NATURE CANCER 2020; 1:329-344. [PMID: 32885175 PMCID: PMC7467080 DOI: 10.1038/s43018-020-0037-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 01/29/2020] [Indexed: 12/31/2022]
Abstract
Identification of genomic and epigenomic determinants of drug resistance provides important insights for improving cancer treatment. Using agnostic genome-wide interrogation of mRNA and miRNA expression, DNA methylation, SNPs, CNAs and SNVs/Indels in primary human acute lymphoblastic leukemia cells, we identified 463 genomic features associated with glucocorticoid resistance. Gene-level aggregation identified 118 overlapping genes, 15 of which were confirmed by genome-wide CRISPR screen. Collectively, this identified 30 of 38 (79%) known glucocorticoid-resistance genes/miRNAs and all 38 known resistance pathways, while revealing 14 genes not previously associated with glucocorticoid-resistance. Single cell RNAseq and network-based transcriptomic modelling corroborated the top previously undiscovered gene, CELSR2. Manipulation of CELSR2 recapitulated glucocorticoid resistance in human leukemia cell lines and revealed a synergistic drug combination (prednisolone and venetoclax) that mitigated resistance in mouse xenograft models. These findings illustrate the power of an integrative genomic strategy for elucidating genes and pathways conferring drug resistance in cancer cells.
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Affiliation(s)
- Robert J Autry
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Steven W Paugh
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Robert Carter
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lei Shi
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jingjing Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniel C Ferguson
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Calvin E Lau
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
- Pediatric Oncology Education Program, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Erik J Bonten
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wenjian Yang
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - J Robert McCorkle
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jordan A Beard
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - John C Panetta
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jonathan D Diedrich
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kristine R Crews
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Deqing Pei
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Christopher J Coke
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sivaraman Natarajan
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Alireza Khatamian
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Seth E Karol
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Elixabet Lopez-Lopez
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Barthelemy Diouf
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Colton Smith
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yoshihiro Gocho
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kohei Hagiwara
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kathryn G Roberts
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Steven M Kornblau
- Department of Leukemia, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wendy Stock
- Hematopoiesis and Hematological Malignancies Program, University of Chicago, Chicago, IL, USA
| | - Elisabeth M Paietta
- Department of Medicine, Albert Einstein College of Medicine, Montefiore Medical Center, North Division, Bronx, NY, USA
| | - Mark R Litzow
- Division of Hematology and Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Hiroto Inaba
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles G Mullighan
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sima Jeha
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ching-Hon Pui
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cheng Cheng
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniel Savic
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jiyang Yu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles Gawad
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mary V Relling
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jun J Yang
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - William E Evans
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, USA.
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454
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Date Y, Ito K. Oncogenic RUNX3: A Link between p53 Deficiency and MYC Dysregulation. Mol Cells 2020; 43:176-181. [PMID: 31991537 PMCID: PMC7057839 DOI: 10.14348/molcells.2019.0285] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 12/12/2019] [Indexed: 12/26/2022] Open
Abstract
The RUNX transcription factors serve as master regulators of development and are frequently dysregulated in human cancers. Among the three family members, RUNX3 is the least studied, and has long been considered to be a tumor-suppressor gene in human cancers. This idea is mainly based on the observation that RUNX3 is inactivated by genetic/epigenetic alterations or protein mislocalization during the initiation of tumorigenesis. Recently, this paradigm has been challenged, as several lines of evidence have shown that RUNX3 is upregulated over the course of tumor development. Resolving this paradox and understanding how a single gene can exhibit both oncogenic and tumor-suppressive properties is essential for successful drug targeting of RUNX. We propose a simple explanation for the duality of RUNX3: p53 status. In this model, p53 deficiency causes RUNX3 to become an oncogene, resulting in aberrant upregulation of MYC.
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Affiliation(s)
- Yuki Date
- Department of Molecular Bone Biology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8588, Japan
- Japan Society for the Promotion of Science, Tokyo 102-0083, Japan
| | - Kosei Ito
- Department of Molecular Bone Biology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8588, Japan
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455
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Przytycki PF, Singh M. Differential Allele-Specific Expression Uncovers Breast Cancer Genes Dysregulated by Cis Noncoding Mutations. Cell Syst 2020; 10:193-203.e4. [PMID: 32078798 PMCID: PMC7457951 DOI: 10.1016/j.cels.2020.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 12/04/2019] [Accepted: 01/22/2020] [Indexed: 01/23/2023]
Abstract
Identifying cancer-relevant mutations in noncoding regions is challenging due to the large numbers of such mutations, their low levels of recurrence, and difficulties in interpreting their functional impact. To uncover genes that are dysregulated due to somatic mutations in cis, we build upon the concept of differential allele-specific expression (ASE) and introduce methods to identify genes within an individual's cancer whose ASE differs from what is found in matched normal tissue. When applied to breast cancer tumor samples, our methods detect the known allele-specific effects of copy number variation and nonsense-mediated decay. Further, genes that are found to recurrently exhibit differential ASE across samples are cancer relevant. Genes with cis mutations are enriched for differential ASE, and we find 147 potentially functional noncoding mutations cis to genes that exhibit significant differential ASE. We conclude that differential ASE is a promising means for discovering gene dysregulation due to cis noncoding mutations.
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Affiliation(s)
- Pawel F Przytycki
- Department of Computer Science, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Mona Singh
- Department of Computer Science, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
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456
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Abstract
Limited clinical activity has been seen in osteosarcoma (OS) patients treated with immune checkpoint inhibitors (ICI). To gain insights into the immunogenic potential of these tumors, we conducted whole genome, RNA, and T-cell receptor sequencing, immunohistochemistry and reverse phase protein array profiling (RPPA) on OS specimens from 48 pediatric and adult patients with primary, relapsed, and metastatic OS. Median immune infiltrate level was lower than in other tumor types where ICI are effective, with concomitant low T-cell receptor clonalities. Neoantigen expression in OS was lacking and significantly associated with high levels of nonsense-mediated decay (NMD). Samples with low immune infiltrate had higher number of deleted genes while those with high immune infiltrate expressed higher levels of adaptive resistance pathways. PARP2 expression levels were significantly negatively associated with the immune infiltrate. Together, these data reveal multiple immunosuppressive features of OS and suggest immunotherapeutic opportunities in OS patients. The efficacy of immune checkpoint inhibitors (ICI) in osteosarcoma has been limited. Here, the authors investigate the immunogenomic landscape of osteosarcoma, and integrated analyses highlight features related to a suppressed immune microenvironment.
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457
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Amin SB, Anderson KJ, Boudreau CE, Martinez-Ledesma E, Kocakavuk E, Johnson KC, Barthel FP, Varn FS, Kassab C, Ling X, Kim H, Barter M, Lau CC, Ngan CY, Chapman M, Koehler JW, Long JP, Miller AD, Miller CR, Porter BF, Rissi DR, Mazcko C, LeBlanc AK, Dickinson PJ, Packer RA, Taylor AR, Rossmeisl JH, Woolard KD, Heimberger AB, Levine JM, Verhaak RGW. Comparative Molecular Life History of Spontaneous Canine and Human Gliomas. Cancer Cell 2020; 37:243-257.e7. [PMID: 32049048 PMCID: PMC7132629 DOI: 10.1016/j.ccell.2020.01.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 11/15/2019] [Accepted: 01/10/2020] [Indexed: 02/08/2023]
Abstract
Sporadic gliomas in companion dogs provide a window on the interaction between tumorigenic mechanisms and host environment. We compared the molecular profiles of canine gliomas with those of human pediatric and adult gliomas to characterize evolutionarily conserved mammalian mutational processes in gliomagenesis. Employing whole-genome, exome, transcriptome, and methylation sequencing of 83 canine gliomas, we found alterations shared between canine and human gliomas such as the receptor tyrosine kinases, TP53 and cell-cycle pathways, and IDH1 R132. Canine gliomas showed high similarity with human pediatric gliomas per robust aneuploidy, mutational rates, relative timing of mutations, and DNA-methylation patterns. Our cross-species comparative genomic analysis provides unique insights into glioma etiology and the chronology of glioma-causing somatic alterations.
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Affiliation(s)
- Samirkumar B Amin
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Kevin J Anderson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - C Elizabeth Boudreau
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Emmanuel Martinez-Ledesma
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Avenue Morones Prieto 3000, Monterrey, Nuevo Leon 64710, Mexico; Department of Neuro-Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Emre Kocakavuk
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; DKFZ Division of Translational Neurooncology at the West German Cancer Center (WTZ), German Cancer Consortium (DKTK) Partner Site & Department of Neurosurgery, University Hospital Essen, Essen, Germany
| | - Kevin C Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Floris P Barthel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Frederick S Varn
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Cynthia Kassab
- Department of Neurosurgery, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiaoyang Ling
- Department of Neurosurgery, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hoon Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Mary Barter
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Ching C Lau
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Connecticut Children's Medical Center, Hartford, CT 06106, USA; University of Connecticut School of Medicine, Farmington, CT 06032, USA
| | - Chew Yee Ngan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Margaret Chapman
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Jennifer W Koehler
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA
| | - James P Long
- Department of Neurosurgery, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Biostatistics, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andrew D Miller
- Department of Biomedical Sciences, Section of Anatomic Pathology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - C Ryan Miller
- Departments of Pathology and Laboratory Medicine, Neurology, and Pharmacology, Lineberger Comprehensive Cancer Center and Neuroscience Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Brian F Porter
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Daniel R Rissi
- Department of Pathology and Athens Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Christina Mazcko
- Comparative Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amy K LeBlanc
- Comparative Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Peter J Dickinson
- Department of Surgical and Radiological Sciences, UC Davis School of Veterinary Medicine, Davis, CA, USA
| | - Rebecca A Packer
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Amanda R Taylor
- Auburn University College of Veterinary Medicine, Auburn, AL, USA
| | | | - Kevin D Woolard
- Department of Surgical and Radiological Sciences, UC Davis School of Veterinary Medicine, Davis, CA, USA
| | - Amy B Heimberger
- Department of Neurosurgery, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jonathan M Levine
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
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458
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Affiliation(s)
- C Jones
- Division of Molecular Pathology, CRUK Childhood Brain Tumour Centre of Excellence, The Institute of Cancer Research, London, UK
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459
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Ney GM, Anderson B, Bender J, Kumar-Sinha C, Wu YM, Vats P, Cieslik M, Robinson DR, Li Q, Chinnaiyan AM, Mody R. Mutations predictive of hyperactive Ras signaling correlate with inferior survival across high-risk pediatric acute leukemia. Transl Pediatr 2020; 9:43-50. [PMID: 32154134 PMCID: PMC7036640 DOI: 10.21037/tp.2019.12.03] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Cancer remains the number one cause of disease-related mortality in children, and despite advances in the molecular understanding of leukemia and targeted therapies, refractory leukemia remains a leading cause of death. It therefore is essential to further define features, e.g., FLT3 alterations and KMT2A rearrangements, associated with inferior survival early to augment or alter therapeutic strategies to improve outcomes. METHODS To gain insights into the genetic drivers predictive of aggressive clinical behavior among pediatric leukemia patients, we performed comprehensive integrative clinical sequencing (ICS), including paired tumor/normal DNA sequencing and RNA-seq, for pediatric patients who presented at our institution over a period of five years with acute lymphoblastic or myelogenous leukemia (ALL and AML; n=43) and high-risk clinical features (high white blood cell count, extramedullary disease, or refractory and/or relapsed disease). RESULTS We found that RAS- and Ras-pathway aberrations, including N-RAS, NF1 and PTPN11, are frequent somatic mutations and, importantly, associated with decreased event free and overall survival (OS) (P=0.04, median event free survival 22.8 vs. 5.6 months; P=0.04, median OS 124 vs. 22.5 months). CONCLUSIONS We thus propose that hyperactive Ras signaling confers inferior survival in high-risk pediatric acute leukemia and that Ras pathways should be molecularly characterized to inform clinical decision making and to identify patients for experimental clinical trials and RAS-targeted therapy.
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Affiliation(s)
- Gina M Ney
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Bailey Anderson
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Jonathan Bender
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Chandan Kumar-Sinha
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yi-Mi Wu
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Pankaj Vats
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Marcin Cieslik
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Dan R Robinson
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Qing Li
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Arul M Chinnaiyan
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Rajen Mody
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA.,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
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460
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Abstract
PURPOSE OF REVIEW We provide an overview of the current landscape of drug development relevant to childhood cancers. We present recent and ongoing efforts to identify therapeutic targets in pediatric cancers. We describe efforts to improve the approach to clinical trials and highlight the role regulatory changes and multistakeholder platforms play in advancing pediatric cancer drug development. RECENT FINDINGS Expanding knowledge of the genetic landscape of pediatric malignancies through clinical genomics studies has yielded an increasing number of potential targets for intervention. In parallel, new therapies for children with cancer have shifted from cytotoxic agents to targeted therapy, with examples of striking activity in patients with tumors driven by oncogenic kinase fusions. Innovative trial designs and recent governmental policies provide opportunities for accelerating development of targeted therapies in pediatric oncology. SUMMARY Novel treatment strategies in pediatric oncology increasingly utilize molecularly targeted agents either as monotherapy or in combination with conventional cytotoxic agents. The interplay between new target identification, efforts to improve clinical trial design and new government regulations relevant to pediatric cancer drug development has the potential to advance novel agents into frontline care of children with cancer.
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461
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Abstract
PURPOSE OF REVIEW The current review aims to highlight the frequency of RAS mutations in pediatric leukemias and solid tumors and to propose strategies for targeting oncogenic RAS in pediatric cancers. RECENT FINDINGS The three RAS genes (HRAS, NRAS, and KRAS) comprise the most frequently mutated oncogene family in human cancer. RAS mutations are commonly observed in three of the leading causes of cancer death in the United States, namely lung cancer, pancreatic cancer, and colorectal cancer. The association of RAS mutations with these aggressive malignancies inspired the creation of the National Cancer Institute RAS initiative and spurred intense efforts to develop strategies to inhibit oncogenic RAS, with much recent success. RAS mutations are frequently observed in pediatric cancers; however, recent advances in anti-RAS drug development have yet to translate into pediatric clinical trials. SUMMARY We find that RAS is mutated in common and rare pediatric malignancies and that oncogenic RAS confers a functional dependency in these cancers. Many strategies for targeting RAS are being pursued for malignancies that primarily affect adults and there is a clear need for inclusion of pediatric patients in clinical trials of these agents.
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462
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Abstract
PURPOSE OF REVIEW Altered epigenetics is central to oncogenesis in many pediatric cancers. Aberrant epigenetic states are induced by mutations in histones or epigenetic regulatory genes, aberrant expression of genes regulating chromatin complexes, altered DNA methylation patterns, or dysregulated expression of noncoding RNAs. Developmental contexts of dysregulated epigenetic states are equally important for initiation and progression of many childhood cancers. As an improved understanding of disease-specific roles and molecular consequences of epigenetic alterations in oncogenesis is emerging, targeting these mechanisms of disease in childhood cancers is increasingly becoming important. RECENT FINDINGS In addition to disease-causing epigenetic events, DNA methylation patterns and specific oncohistone mutations are being utilized for the diagnosis of pediatric central nervous system (CNS) and solid tumors. These discoveries have improved the classification of poorly differentiated tumors and laid the foundation for future improved clinical management. On the therapeutic side, the first therapies targeting epigenetic alterations have recently entered clinical trials. Current clinical trials include pharmacological inhibition of histone and DNA modifiers in aggressive types of pediatric cancer. SUMMARY Targeting novel epigenetic vulnerabilities, either by themselves, or coupled with targeting altered transcriptional states, developmental cell states or immunomodulation will result in innovative approaches for treating deadly pediatric cancers.
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Affiliation(s)
- Eshini Panditharatna
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Broad Institute of Harvard and MIT, Cambridge, MA
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Broad Institute of Harvard and MIT, Cambridge, MA.,Boston Children's Cancer and Blood Disorder Center, Boston, Massachusetts, USA
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463
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Ghilu S, Li Q, Fontaine SD, Santi DV, Kurmasheva RT, Zheng S, Houghton PJ. Prospective use of the single-mouse experimental design for the evaluation of PLX038A. Cancer Chemother Pharmacol 2020; 85:251-263. [PMID: 31927611 PMCID: PMC7039322 DOI: 10.1007/s00280-019-04017-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 12/17/2019] [Indexed: 12/12/2022]
Abstract
PURPOSE Defining robust criteria for drug activity in preclinical studies allows for fewer animals per treatment group, and potentially allows for inclusion of additional cancer models that more accurately represent genetic diversity and, potentially, allows for tumor sensitivity biomarker identification. METHODS Using a single-mouse design, 32 pediatric xenograft tumor models representing diverse pediatric cancer types [Ewing sarcoma (9), brain (4), rhabdomyosarcoma (10), Wilms tumor (4), and non-CNS rhabdoid tumors (5)] were evaluated for response to a single administration of pegylated-SN38 (PLX038A), a controlled-release PEGylated formulation of SN-38. Endpoints measured were percent tumor regression, and event-free survival (EFS). The correlation between response to PLX038A was compared to that for ten models treated with irinotecan (2.5 mg/kg × 5 days × 2 cycles), using a traditional design (10 mice/group). Correlations between tumor sensitivity, genetic mutations and gene expression were sought. Models showing no disease at week 20 were categorized as 'extreme responders' to PLX038A, whereas those with EFS less than 5 weeks were categorized as 'resistant'. RESULTS The activity of PLX038A was evaluable in 31/32 models. PLX038A induced > 50% volume regressions in 25 models (78%). Initial tumor volume regression correlated only modestly with EFS (r2 = 0.238), but sensitivity to PLX038A was better correlated with response to irinotecan when one tumor hypersensitive to PLX038A was omitted (r2 = 0.6844). Mutations in 53BP1 were observed in three of six sensitive tumor models compared to none in resistant models (n = 6). CONCLUSIONS This study demonstrates the feasibility of using a single-mouse design for assessing the antitumor activity of an agent, while encompassing greater genetic diversity representative of childhood cancers. PLX038A was highly active in most xenograft models, and tumor sensitivity to PLX038A was correlated with sensitivity to irinotecan, validating the single-mouse design in identifying agents with the same mechanism of action. Biomarkers that correlated with model sensitivity included wild-type TP53, or mutant TP53 but with a mutation in 53BP1, thus a defect in DNA damage response. These results support the value of the single-mouse experimental design.
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Affiliation(s)
- Samson Ghilu
- Greehey Children's Cancer Research Institute, UT Health San Antonio, 8403 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Qilin Li
- Greehey Children's Cancer Research Institute, UT Health San Antonio, 8403 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Shaun D Fontaine
- ProLynx LLC, 455 Mission Bay Blvd, South San Francisco, CA, 94158, USA
| | - Daniel V Santi
- ProLynx LLC, 455 Mission Bay Blvd, South San Francisco, CA, 94158, USA
| | - Raushan T Kurmasheva
- Greehey Children's Cancer Research Institute, UT Health San Antonio, 8403 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Siyuan Zheng
- Greehey Children's Cancer Research Institute, UT Health San Antonio, 8403 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Peter J Houghton
- Greehey Children's Cancer Research Institute, UT Health San Antonio, 8403 Floyd Curl Drive, San Antonio, TX, 78229, USA.
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464
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Major A, Cox SM, Volchenboum SL. Using big data in pediatric oncology: Current applications and future directions. Semin Oncol 2020; 47:56-64. [DOI: 10.1053/j.seminoncol.2020.02.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/10/2020] [Accepted: 02/11/2020] [Indexed: 12/13/2022]
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465
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Subramanian I, Verma S, Kumar S, Jere A, Anamika K. Multi-omics Data Integration, Interpretation, and Its Application. Bioinform Biol Insights 2020; 14:1177932219899051. [PMID: 32076369 PMCID: PMC7003173 DOI: 10.1177/1177932219899051] [Citation(s) in RCA: 539] [Impact Index Per Article: 134.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 11/09/2019] [Indexed: 12/22/2022] Open
Abstract
To study complex biological processes holistically, it is imperative to take an integrative approach that combines multi-omics data to highlight the interrelationships of the involved biomolecules and their functions. With the advent of high-throughput techniques and availability of multi-omics data generated from a large set of samples, several promising tools and methods have been developed for data integration and interpretation. In this review, we collected the tools and methods that adopt integrative approach to analyze multiple omics data and summarized their ability to address applications such as disease subtyping, biomarker prediction, and deriving insights into the data. We provide the methodology, use-cases, and limitations of these tools; brief account of multi-omics data repositories and visualization portals; and challenges associated with multi-omics data integration.
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Affiliation(s)
| | | | | | - Abhay Jere
- Innovation Cell, Ministry of Human Resource Development, New Delhi, India
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466
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Dietz MS, Beach CZ, Barajas R, Parappilly MS, Sengupta SK, Baird LC, Ciporen JN, Han SJ, Loret de Mola R, Cho YJ, Nazemi KJ, McClelland S, Wong MH, Jaboin JJ. Measure Twice: Promise of Liquid Biopsy in Pediatric High-Grade Gliomas. Adv Radiat Oncol 2020; 5:152-162. [PMID: 32280814 PMCID: PMC7136635 DOI: 10.1016/j.adro.2019.12.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/07/2019] [Accepted: 12/17/2019] [Indexed: 12/20/2022] Open
Abstract
Purpose To review and critique the current state of liquid biopsy in pHGG. Materials and Methods Published literature was reviewed for articles related to liquid biopsy in pediatric glioma and adult glioma with a focus on high-grade gliomas. Results This review discusses the current state of liquid biomarkers of pHGG and their potential applications for liquid biopsy development. Conclusions While nascent, the progress toward identifying circulating analytes of pHGG primes the field of neuro-oncoogy for liquid biopsy development.
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Affiliation(s)
- Matthew S Dietz
- Department of Pediatrics, Oregon Health & Science University, Portland, Oregon
| | - Catherine Z Beach
- Department of Radiation Medicine, Oregon Health & Science University, Portland, Oregon
| | - Ramon Barajas
- Department of Diagnostic Radiology, Oregon Health & Science University, Portland, Oregon.,Advanced Imaging Research Center, Oregon Health & Science University, Portland, Oregon
| | - Michael S Parappilly
- Department of Diagnostic Radiology, Oregon Health & Science University, Portland, Oregon
| | - Sidharth K Sengupta
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, Oregon
| | - Lissa C Baird
- Department of Neurological Surgery, Oregon Health & Science University, Portland, Oregon
| | - Jeremy N Ciporen
- Department of Neurological Surgery, Oregon Health & Science University, Portland, Oregon
| | - Seunggu J Han
- Department of Neurological Surgery, Oregon Health & Science University, Portland, Oregon
| | | | - Yoon Jae Cho
- Department of Neurology, Oregon Health & Science University, Portland, Oregon.,The Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Kellie J Nazemi
- Department of Pediatrics, Oregon Health & Science University, Portland, Oregon
| | - Shearwood McClelland
- Department of Radiation Oncology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Melissa H Wong
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, Oregon.,The Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Jerry J Jaboin
- Department of Radiation Medicine, Oregon Health & Science University, Portland, Oregon.,The Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
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467
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Depicting the genetic architecture of pediatric cancers through an integrative gene network approach. Sci Rep 2020; 10:1224. [PMID: 31988326 PMCID: PMC6985191 DOI: 10.1038/s41598-020-58179-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 12/18/2019] [Indexed: 12/21/2022] Open
Abstract
The genetic etiology of childhood cancers still remains largely unknown. It is therefore essential to develop novel strategies to unravel the spectrum of pediatric cancer genes. Statistical network modeling techniques have emerged as powerful methodologies for enabling the inference of gene-disease relationship and have been performed on adult but not pediatric cancers. We performed a deep multi-layer understanding of pan-cancer transcriptome data selected from the Treehouse Childhood Cancer Initiative through a co-expression network analysis. We identified six modules strongly associated with pediatric tumor histotypes that were functionally linked to developmental processes. Topological analyses highlighted that pediatric cancer predisposition genes and potential therapeutic targets were central regulators of cancer-histotype specific modules. A module was related to multiple pediatric malignancies with functions involved in DNA repair and cell cycle regulation. This canonical oncogenic module gathered most of the childhood cancer predisposition genes and clinically actionable genes. In pediatric acute leukemias, the driver genes were co-expressed in a module related to epigenetic and post-transcriptional processes, suggesting a critical role of these pathways in the progression of hematologic malignancies. This integrative pan-cancer study provides a thorough characterization of pediatric tumor-associated modules and paves the way for investigating novel candidate genes involved in childhood tumorigenesis.
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468
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Malone ER, Oliva M, Sabatini PJB, Stockley TL, Siu LL. Molecular profiling for precision cancer therapies. Genome Med 2020; 12:8. [PMID: 31937368 PMCID: PMC6961404 DOI: 10.1186/s13073-019-0703-1] [Citation(s) in RCA: 440] [Impact Index Per Article: 110.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/04/2019] [Indexed: 02/07/2023] Open
Abstract
The number of druggable tumor-specific molecular aberrations has grown substantially in the past decade, with a significant survival benefit obtained from biomarker matching therapies in several cancer types. Molecular pathology has therefore become fundamental not only to inform on tumor diagnosis and prognosis but also to drive therapeutic decisions in daily practice. The introduction of next-generation sequencing technologies and the rising number of large-scale tumor molecular profiling programs across institutions worldwide have revolutionized the field of precision oncology. As comprehensive genomic analyses become increasingly available in both clinical and research settings, healthcare professionals are faced with the complex tasks of result interpretation and translation. This review summarizes the current and upcoming approaches to implement precision cancer medicine, highlighting the challenges and potential solutions to facilitate the interpretation and to maximize the clinical utility of molecular profiling results. We describe novel molecular characterization strategies beyond tumor DNA sequencing, such as transcriptomics, immunophenotyping, epigenetic profiling, and single-cell analyses. We also review current and potential applications of liquid biopsies to evaluate blood-based biomarkers, such as circulating tumor cells and circulating nucleic acids. Last, lessons learned from the existing limitations of genotype-derived therapies provide insights into ways to expand precision medicine beyond genomics.
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Affiliation(s)
- Eoghan R Malone
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Department of Medicine, University Avenue, University of Toronto, Toronto, Ontario, M5G 1Z5, Canada
| | - Marc Oliva
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Department of Medicine, University Avenue, University of Toronto, Toronto, Ontario, M5G 1Z5, Canada
| | - Peter J B Sabatini
- Department of Clinical Laboratory Genetics, University Health Network, and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Tracy L Stockley
- Department of Clinical Laboratory Genetics, University Health Network, and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Lillian L Siu
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Department of Medicine, University Avenue, University of Toronto, Toronto, Ontario, M5G 1Z5, Canada.
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469
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Kuzniar A, Maassen J, Verhoeven S, Santuari L, Shneider C, Kloosterman WP, de Ridder J. sv-callers: a highly portable parallel workflow for structural variant detection in whole-genome sequence data. PeerJ 2020; 8:e8214. [PMID: 31934500 PMCID: PMC6951283 DOI: 10.7717/peerj.8214] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 11/14/2019] [Indexed: 12/19/2022] Open
Abstract
Structural variants (SVs) are an important class of genetic variation implicated in a wide array of genetic diseases including cancer. Despite the advances in whole genome sequencing, comprehensive and accurate detection of SVs in short-read data still poses some practical and computational challenges. We present sv-callers, a highly portable workflow that enables parallel execution of multiple SV detection tools, as well as provide users with example analyses of detected SV callsets in a Jupyter Notebook. This workflow supports easy deployment of software dependencies, configuration and addition of new analysis tools. Moreover, porting it to different computing systems requires minimal effort. Finally, we demonstrate the utility of the workflow by performing both somatic and germline SV analyses on different high-performance computing systems.
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Affiliation(s)
| | | | | | - Luca Santuari
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, Netherlands
| | - Carl Shneider
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, Netherlands
| | - Wigard P Kloosterman
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, Netherlands
| | - Jeroen de Ridder
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, Netherlands
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470
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Li B, Brady SW, Ma X, Shen S, Zhang Y, Li Y, Szlachta K, Dong L, Liu Y, Yang F, Wang N, Flasch DA, Myers MA, Mulder HL, Ding L, Liu Y, Tian L, Hagiwara K, Xu K, Zhou X, Sioson E, Wang T, Yang L, Zhao J, Zhang H, Shao Y, Sun H, Sun L, Cai J, Sun HY, Lin TN, Du L, Li H, Rusch M, Edmonson MN, Easton J, Zhu X, Zhang J, Cheng C, Raphael BJ, Tang J, Downing JR, Alexandrov LB, Zhou BBS, Pui CH, Yang JJ, Zhang J. Therapy-induced mutations drive the genomic landscape of relapsed acute lymphoblastic leukemia. Blood 2020; 135:41-55. [PMID: 31697823 PMCID: PMC6940198 DOI: 10.1182/blood.2019002220] [Citation(s) in RCA: 158] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 10/10/2019] [Indexed: 12/23/2022] Open
Abstract
To study the mechanisms of relapse in acute lymphoblastic leukemia (ALL), we performed whole-genome sequencing of 103 diagnosis-relapse-germline trios and ultra-deep sequencing of 208 serial samples in 16 patients. Relapse-specific somatic alterations were enriched in 12 genes (NR3C1, NR3C2, TP53, NT5C2, FPGS, CREBBP, MSH2, MSH6, PMS2, WHSC1, PRPS1, and PRPS2) involved in drug response. Their prevalence was 17% in very early relapse (<9 months from diagnosis), 65% in early relapse (9-36 months), and 32% in late relapse (>36 months) groups. Convergent evolution, in which multiple subclones harbor mutations in the same drug resistance gene, was observed in 6 relapses and confirmed by single-cell sequencing in 1 case. Mathematical modeling and mutational signature analysis indicated that early relapse resistance acquisition was frequently a 2-step process in which a persistent clone survived initial therapy and later acquired bona fide resistance mutations during therapy. In contrast, very early relapses arose from preexisting resistant clone(s). Two novel relapse-specific mutational signatures, one of which was caused by thiopurine treatment based on in vitro drug exposure experiments, were identified in early and late relapses but were absent from 2540 pan-cancer diagnosis samples and 129 non-ALL relapses. The novel signatures were detected in 27% of relapsed ALLs and were responsible for 46% of acquired resistance mutations in NT5C2, PRPS1, NR3C1, and TP53. These results suggest that chemotherapy-induced drug resistance mutations facilitate a subset of pediatric ALL relapses.
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Affiliation(s)
- Benshang Li
- Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center-National Children's Medical Center, and
- Pediatric Translational Medicine Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Samuel W Brady
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN
| | - Shuhong Shen
- Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center-National Children's Medical Center, and
- Pediatric Translational Medicine Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingchi Zhang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital-Center for Stem Cell Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Yongjin Li
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN
| | - Karol Szlachta
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN
| | - Li Dong
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN
| | - Yu Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN
| | - Fan Yang
- Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center-National Children's Medical Center, and
- Pediatric Translational Medicine Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ningling Wang
- Department of Pediatrics, the Second Hospital of Anhui Medical University, Hefei, China
| | - Diane A Flasch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN
| | - Matthew A Myers
- Department of Computer Science, Princeton University, Princeton, NJ
| | - Heather L Mulder
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN
| | - Lixia Ding
- Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center-National Children's Medical Center, and
- Pediatric Translational Medicine Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanling Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN
| | - Liqing Tian
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN
| | - Kohei Hagiwara
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN
| | - Ke Xu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN
| | - Edgar Sioson
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN
| | - Tianyi Wang
- Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center-National Children's Medical Center, and
| | - Liu Yang
- Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center-National Children's Medical Center, and
| | - Jie Zhao
- Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center-National Children's Medical Center, and
| | - Hui Zhang
- Department of Pediatric Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Ying Shao
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN
| | | | - Lele Sun
- WuXi NextCODE Co., Ltd, Shanghai, China
| | - Jiaoyang Cai
- Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center-National Children's Medical Center, and
| | - Hui-Ying Sun
- Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center-National Children's Medical Center, and
| | | | - Lijuan Du
- Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center-National Children's Medical Center, and
- Pediatric Translational Medicine Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui Li
- Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center-National Children's Medical Center, and
- Pediatric Translational Medicine Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN
| | - Michael N Edmonson
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN
| | - Xiaofan Zhu
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital-Center for Stem Cell Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Jingliao Zhang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital-Center for Stem Cell Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | | | | | - Jingyan Tang
- Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center-National Children's Medical Center, and
| | - James R Downing
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, TN
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA; and
| | - Bin-Bing S Zhou
- Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center-National Children's Medical Center, and
- Pediatric Translational Medicine Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | | | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN
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471
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Evans WE, Pui CH, Yang JJ. The Promise and the Reality of Genomics to Guide Precision Medicine in Pediatric Oncology: The Decade Ahead. Clin Pharmacol Ther 2020; 107:176-180. [PMID: 31563145 PMCID: PMC6925646 DOI: 10.1002/cpt.1660] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 07/01/2019] [Indexed: 12/18/2022]
Abstract
Much has been written about the promise of "precision medicine," especially in oncology, where somatic mutations can influence the response of cancer cells to "targeted therapy." There have been successful examples of targeted therapy improving the outcome of some childhood cancers, such as the addition of an ABL class tyrosine kinase inhibitor to conventional chemotherapy substantially improving the cure rate for patients with BCR-ABL1 positive acute lymphoblastic leukemia. Although there are other mutations serving as putative targets in various childhood leukemias and solid tumors, effective targeted therapy has yet to be established for them in prospective clinical trials. There are also uncertainties about which "targeted therapy" to use when patients have multiple targetable genomic lesions in their cancer cells, given the paucity of data upon which to develop evidence-based guidelines for selecting and integrating targeted agents for individual patients. There are also multiple examples of inherited germline variants for which evidence-based guidelines have been developed by the Clinical Pharmacogenetics Implementation Consortium to guide the selection and dosing of medications in children with cancer. Clinical pharmacology is poised to play a critical role in both the discovery and development of new targeted anticancer agents and their evidence-based translation into better treatment for children with cancer. To embrace these challenges and opportunities of "precision medicine," clinical and basic pharmacologists must expand the depth of our science and the bandwidth of our translational capacity if we are to optimize precision medicine and advance the treatment of cancer in children and adults.
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Affiliation(s)
- William E Evans
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Hematological Malignancies Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Ching-Hon Pui
- Hematological Malignancies Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Hematological Malignancies Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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472
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Computational Deconvolution of Tumor-Infiltrating Immune Components with Bulk Tumor Gene Expression Data. Methods Mol Biol 2020; 2120:249-262. [PMID: 32124325 DOI: 10.1007/978-1-0716-0327-7_18] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Tumor-infiltrating immune cells play critical roles in immune-mediated tumor rejection and/or progression, and are key targets of immunotherapies. Estimation of different immune subsets becomes increasingly important with the decreased cost of high-throughput molecular profiling and the rapidly growing amount of cancer genomics data. Here, we present Tumor IMmune Estimation Resource (TIMER), an in silico deconvolution method for inference of tumor-infiltrating immune components. TIMER takes bulk tissue gene expression profiles measured with RNA-seq or microarray to evaluate the abundance of six immune cell types in the tumor microenvironment: B cell, CD4+ T cell, CD8+ T cell, neutrophil, macrophage, and dendritic cell. We further introduce its associated webserver for convenient, user-friendly analysis of tumor immune infiltrates across multiple cancer types.
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473
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Targeting the Cancer Epigenome with Histone Deacetylase Inhibitors in Osteosarcoma. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1258:55-75. [PMID: 32767234 DOI: 10.1007/978-3-030-43085-6_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Epigenetic deregulation is an emerging hallmark of cancer that enables tumor cells to escape surveillance by tumor suppressors and ultimately progress. The structure of the epigenome consists of covalent modifications of chromatin components, including acetylation by histone acetyltransferases (HATs) and deacetylation by histone deacetylases (HDACs). Targeting these enzymes with inhibitors to restore epigenetic homeostasis has been explored for many cancers. Osteosarcoma, an aggressive bone malignancy that primarily affects children and young adults, is notable for widespread genetic and epigenetic instability. This may explain why therapy directed at unique molecular pathways has failed to substantially improve outcomes in osteosarcoma over the past four decades. In this review, we discuss the potential of targeting the cancer epigenome, with a focus on histone deacetylase inhibitors (HDACi) for osteosarcoma. We additionally highlight the safety and tolerance of HDACi, combination chemotherapy with HDACi, and the ongoing challenges in the development of these agents.
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474
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Murphy AJ, Chen X, Pinto EM, Williams JS, Clay MR, Pounds SB, Cao X, Shi L, Lin T, Neale G, Morton CL, Woolard MA, Mulder HL, Gil HJ, Rehg JE, Billups CA, Harlow ML, Dome JS, Houghton PJ, Easton J, Zhang J, George RE, Zambetti GP, Davidoff AM. Forty-five patient-derived xenografts capture the clinical and biological heterogeneity of Wilms tumor. Nat Commun 2019; 10:5806. [PMID: 31862972 PMCID: PMC6925259 DOI: 10.1038/s41467-019-13646-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 11/19/2019] [Indexed: 12/22/2022] Open
Abstract
The lack of model systems has limited the preclinical discovery and testing of therapies for Wilms tumor (WT) patients who have poor outcomes. Herein, we establish 45 heterotopic WT patient-derived xenografts (WTPDX) in CB17 scid-/- mice that capture the biological heterogeneity of Wilms tumor (WT). Among these 45 total WTPDX, 6 from patients with diffuse anaplastic tumors, 9 from patients who experienced disease relapse, and 13 from patients with bilateral disease are included. Early passage WTPDX show evidence of clonal selection, clonal evolution and enrichment of blastemal gene expression. Favorable histology WTPDX are sensitive, whereas unfavorable histology WTPDX are resistant to conventional chemotherapy with vincristine, actinomycin-D, and doxorubicin given singly or in combination. This WTPDX library is a unique scientific resource that retains the spectrum of biological heterogeneity present in WT and provides an essential tool to test targeted therapies for WT patient groups with poor outcomes. The progress in pre-clinical drug discovery for Wilms tumor (WT) is limited by a lack of disease models. Here, the authors develop 45 heterotopic WT patient-derived xenografts including several anaplastic models that recapitulate the biological heterogeneity of WT, and propose this as a resource for evaluating future therapeutics for WT.
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Affiliation(s)
- Andrew J Murphy
- Department of Surgery, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA. .,Division of Pediatric Surgery, Department of Surgery, University of Tennessee Health Science Center, 910 Madison Ave. 2nd floor, Memphis, TN, 38163, USA.
| | - Xiang Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Emilia M Pinto
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Justin S Williams
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Michael R Clay
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Stanley B Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Xueyuan Cao
- Department of Biostatistics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.,College of Nursing, University of Tennessee Health Science Center, 920 Madison Ave, Memphis, TN, 38163, USA
| | - Lei Shi
- Department of Biostatistics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Tong Lin
- Department of Biostatistics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Geoffrey Neale
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Christopher L Morton
- Department of Surgery, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Mary A Woolard
- Department of Surgery, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Heather L Mulder
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Hyea Jin Gil
- Department of Surgery, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Jerold E Rehg
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Catherine A Billups
- Department of Biostatistics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Matthew L Harlow
- Department of Pediatric Hematology and Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, 450 Brookline Avenue, Room D640E, Boston, MA, 02215, USA
| | - Jeffrey S Dome
- Division of Oncology, Children's National Medical Center, 111 Michigan Avenue NW, Washington, DC, 20010, USA
| | - Peter J Houghton
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, 8403 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Rani E George
- Department of Pediatric Hematology and Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, 450 Brookline Avenue, Room D640E, Boston, MA, 02215, USA
| | - Gerard P Zambetti
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Andrew M Davidoff
- Department of Surgery, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.,Division of Pediatric Surgery, Department of Surgery, University of Tennessee Health Science Center, 910 Madison Ave. 2nd floor, Memphis, TN, 38163, USA
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475
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MacFarland SP, Zelley K, Surrey LF, Gallo D, Luo M, Raman P, Wertheim G, Hunger SP, Li MM, Brodeur GM. Pediatric Somatic Tumor Sequencing Identifies Underlying Cancer Predisposition. JCO Precis Oncol 2019; 3. [PMID: 32783018 DOI: 10.1200/po.19.00062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE The diagnosis of cancer predisposition in pediatric patients with cancer is vital for treatment decisions, surveillance, and management of at-risk family members. Somatic tumor testing can identify potential underlying constitutional variants that confer increased cancer risk. Here, we report the characteristics of constitutional variants identified through tumor testing. MATERIALS AND METHODS Data were abstracted from medical record review of 1,023 patients who received inhouse somatic tumor testing over a 28-month period. Patients were identified for testing using referral criteria developed as a collaboration between genomic diagnostics, pathology, and oncology. Characteristics of patients who underwent constitutional testing, including family history and variant loss of heterozygosity, were tracked. RESULTS From 1,023 patients who underwent somatic tumor sequencing in a 28-month period, 210 variants were identified in 141 patients (13.8%) that were concerning for cancer predisposition syndromes requiring intervention. A total of 73 variants in 41 patients have undergone clinical confirmatory testing thus far. Of these, 26 variants were confirmed to be constitutionally present (35.6%). Among patients tested, 23 (56.1%) of 41 total patients were diagnosed with a cancer predisposition syndrome. CONCLUSION Our data demonstrate that more than one third of variants in tumor somatic sequencing that were concerning for underlying cancer predisposition were constitutionally confirmed. Overall, somatic tumor testing identified potential cancer predisposition syndromes in pediatric patients, and some would not have been identified on the basis of clinical history alone.
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Affiliation(s)
- Suzanne P MacFarland
- Division of Oncology, Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Kristin Zelley
- Division of Oncology, Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Lea F Surrey
- Department of Pathology and Laboratory Medicine, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA.,Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Daniel Gallo
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Minjie Luo
- Department of Pathology and Laboratory Medicine, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA.,Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Pichai Raman
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA.,Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Gerald Wertheim
- Department of Pathology and Laboratory Medicine, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Stephen P Hunger
- Division of Oncology, Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA.,Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pediatrics, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Marilyn M Li
- Department of Pathology and Laboratory Medicine, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA.,Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pediatrics, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Garrett M Brodeur
- Division of Oncology, Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA.,Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pediatrics, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
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476
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Epigenetic deregulation of GATA3 in neuroblastoma is associated with increased GATA3 protein expression and with poor outcomes. Sci Rep 2019; 9:18934. [PMID: 31831790 PMCID: PMC6908619 DOI: 10.1038/s41598-019-55382-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 11/19/2019] [Indexed: 01/04/2023] Open
Abstract
To discover epigenetic changes that may underly neuroblastoma pathogenesis, we identified differentially methylated genes in neuroblastoma cells compared to neural crest cells, the presumptive precursors cells for neuroblastoma, by using genome-wide DNA methylation analysis. We previously described genes that were hypermethylated in neuroblastoma; in this paper we report on 67 hypomethylated genes, which were filtered to select genes that showed transcriptional over-expression and an association with poor prognosis in neuroblastoma, highlighting GATA3 for detailed studies. Specific methylation assays confirmed the hypomethylation of GATA3 in neuroblastoma, which correlated with high expression at both the RNA and protein level. Demethylation with azacytidine in cultured sympathetic ganglia cells led to increased GATA3 expression, suggesting a mechanistic link between GATA3 expression and DNA methylation. Neuroblastomas that had completely absent GATA3 methylation and/or very high levels of protein expression, were associated with poor prognosis. Knock-down of GATA3 in neuroblastoma cells lines inhibited cell proliferation and increased apoptosis but had no effect on cellular differentiation. These results identify GATA3 as an epigenetically regulated component of the neuroblastoma transcriptional control network, that is essential for neuroblastoma proliferation. This suggests that the GATA3 transcriptional network is a promising target for novel neuroblastoma therapies.
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477
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de Kanter JK, Lijnzaad P, Candelli T, Margaritis T, Holstege FCP. CHETAH: a selective, hierarchical cell type identification method for single-cell RNA sequencing. Nucleic Acids Res 2019; 47:e95. [PMID: 31226206 PMCID: PMC6895264 DOI: 10.1093/nar/gkz543] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 06/05/2019] [Accepted: 06/08/2019] [Indexed: 01/06/2023] Open
Abstract
Cell type identification is essential for single-cell RNA sequencing (scRNA-seq) studies, currently transforming the life sciences. CHETAH (CHaracterization of cEll Types Aided by Hierarchical classification) is an accurate cell type identification algorithm that is rapid and selective, including the possibility of intermediate or unassigned categories. Evidence for assignment is based on a classification tree of previously available scRNA-seq reference data and includes a confidence score based on the variance in gene expression per cell type. For cell types represented in the reference data, CHETAH’s accuracy is as good as existing methods. Its specificity is superior when cells of an unknown type are encountered, such as malignant cells in tumor samples which it pinpoints as intermediate or unassigned. Although designed for tumor samples in particular, the use of unassigned and intermediate types is also valuable in other exploratory studies. This is exemplified in pancreas datasets where CHETAH highlights cell populations not well represented in the reference dataset, including cells with profiles that lie on a continuum between that of acinar and ductal cell types. Having the possibility of unassigned and intermediate cell types is pivotal for preventing misclassification and can yield important biological information for previously unexplored tissues.
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Affiliation(s)
- Jurrian K de Kanter
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Philip Lijnzaad
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Tito Candelli
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Thanasis Margaritis
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Frank C P Holstege
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
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478
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Abstract
The capacity of single-agent therapy with immune checkpoint inhibitors to control solid cancers by unleashing preexisting local antitumor T cell responses has renewed interest in the broader use of T cells as anticancer therapeutics. At the same time, durable responses of refractory B-lineage malignancies to chimeric-receptor engineered T cells illustrate that T cells can be effectively redirected to cancers that lack preexisting tumor antigen-specific T cells, as most typical childhood cancers. This review summarizes strategies by which T cells can be modified to recognize defined antigens, with a focus on chimeric-receptor engineering. We provide an overview of candidate target antigens currently investigated in advanced preclinical and early clinical trials in pediatric malignancies and discuss the prerequisites for an adequate in vivo function of engineered T cells in the microenvironment of solid tumors and intrinsic and extrinsic limitations of current redirected T cell therapies. We further address innovative solutions to recruit therapeutic T cells to tumors, overcome the unreliable and heterogenous expression of most known tumor-associated antigens, and prevent functional inactivation of T cells in the hostile microenvironment of solid childhood tumors.
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Affiliation(s)
- Kerstin K Rauwolf
- Department of Pediatric Hematology and Oncology Albert-Schweitzer Campus 1, University Children's Hospital Muenster, 48149, Münster, Germany
| | - Claudia Rossig
- Department of Pediatric Hematology and Oncology Albert-Schweitzer Campus 1, University Children's Hospital Muenster, 48149, Münster, Germany.
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479
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Infectious stimuli promote malignant B-cell acute lymphoblastic leukemia in the absence of AID. Nat Commun 2019; 10:5563. [PMID: 31804490 PMCID: PMC6895129 DOI: 10.1038/s41467-019-13570-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 11/15/2019] [Indexed: 02/06/2023] Open
Abstract
The prerequisite to prevent childhood B-cell acute lymphoblastic leukemia (B-ALL) is to decipher its etiology. The current model suggests that infection triggers B-ALL development through induction of activation-induced cytidine deaminase (AID; also known as AICDA) in precursor B-cells. This evidence has been largely acquired through the use of ex vivo functional studies. However, whether this mechanism governs native non-transplant B-ALL development is unknown. Here we show that, surprisingly, AID genetic deletion does not affect B-ALL development in Pax5-haploinsufficient mice prone to B-ALL upon natural infection exposure. We next test the effect of premature AID expression from earliest pro-B-cell stages in B-cell transformation. The generation of AID off-target mutagenic activity in precursor B-cells does not promote B-ALL. Likewise, known drivers of human B-ALL are not preferentially targeted by AID. Overall these results suggest that infections promote B-ALL through AID-independent mechanisms, providing evidence for a new model of childhood B-ALL development. Infection or chronic inflammation is a risk factor for childhood B-cell precursor acute lymphoblastic leukemia. Here, the authors show that the DNA editing enzyme AID is expressed in infected B cells but using genetic mouse models show that it does not contribute to leukemia pathogenesis.
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480
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van der Zwet JCG, Cordo' V, Canté-Barrett K, Meijerink JPP. Multi-omic approaches to improve outcome for T-cell acute lymphoblastic leukemia patients. Adv Biol Regul 2019; 74:100647. [PMID: 31523030 DOI: 10.1016/j.jbior.2019.100647] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/20/2019] [Accepted: 08/23/2019] [Indexed: 06/10/2023]
Abstract
In the last decade, tremendous progress in curative treatment has been made for T-ALL patients using high-intensive, risk-adapted multi-agent chemotherapy. Further treatment intensification to improve the cure rate is not feasible as it will increase the number of toxic deaths. Hence, about 20% of pediatric patients relapse and often die due to acquired therapy resistance. Personalized medicine is of utmost importance to further increase cure rates and is achieved by targeting specific initiation, maintenance or resistance mechanisms of the disease. Genomic sequencing has revealed mutations that characterize genetic subtypes of many cancers including T-ALL. However, leukemia may have various activated pathways that are not accompanied by the presence of mutations. Therefore, screening for mutations alone is not sufficient to identify all molecular targets and leukemic dependencies for therapeutic inhibition. We review the extent of the driving type A and the secondary type B genomic mutations in pediatric T-ALL that may be targeted by specific inhibitors. Additionally, we review the need for additional screening methods on the transcriptional and protein levels. An integrated 'multi-omic' screening will identify potential targets and biomarkers to establish significant progress in future individualized treatment of T-ALL patients.
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Affiliation(s)
| | - Valentina Cordo'
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
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481
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Capasso M, Lasorsa VA, Cimmino F, Avitabile M, Cantalupo S, Montella A, De Angelis B, Morini M, de Torres C, Castellano A, Locatelli F, Iolascon A. Transcription Factors Involved in Tumorigenesis Are Over-Represented in Mutated Active DNA-Binding Sites in Neuroblastoma. Cancer Res 2019; 80:382-393. [PMID: 31784426 DOI: 10.1158/0008-5472.can-19-2883] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/24/2019] [Accepted: 11/22/2019] [Indexed: 11/16/2022]
Abstract
The contribution of coding mutations to oncogenesis has been largely clarified, whereas little is known about somatic mutations in noncoding DNA and their role in driving tumors remains controversial. Here, we used an alternative approach to interpret the functional significance of noncoding somatic mutations in promoting tumorigenesis. Noncoding somatic mutations of 151 neuroblastomas were integrated with ENCODE data to locate somatic mutations in regulatory elements specifically active in neuroblastoma cells, nonspecifically active in neuroblastoma cells, and nonactive. Within these types of elements, transcription factors (TF) were identified whose binding sites were enriched or depleted in mutations. For these TFs, a gene expression signature was built to assess their implication in neuroblastoma. DNA- and RNA-sequencing data were integrated to assess the effects of those mutations on mRNA levels. The pathogenicity of mutations was significantly higher in transcription factor binding site (TFBS) of regulatory elements specifically active in neuroblastoma cells, as compared with the others. Within these elements, there were 18 over-represented TFs involved mainly in cell-cycle phase transitions and 15 under-represented TFs primarily regulating cell differentiation. A gene expression signature based on over-represented TFs correlated with poor survival and unfavorable prognostic markers. Moreover, recurrent mutations in TFBS of over-represented TFs such as EZH2 affected MCF2L and ADP-ribosylhydrolase like 1 expression, among the others. We propose a novel approach to study the involvement of regulatory variants in neuroblastoma that could be extended to other cancers and provide further evidence that alterations of gene expression may have relevant effects in neuroblastoma development. SIGNIFICANCE: These findings propose a novel approach to study regulatory variants in neuroblastoma and suggest that noncoding somatic mutations have relevant implications in neuroblastoma development.
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Affiliation(s)
- Mario Capasso
- Department of Molecular Medicine and Medical Biotechnology, Università degli Studi di Napoli Federico II, Napoli, Italy. .,CEINGE Biotecnologie Avanzate, Napoli, Italy.,IRCCS SDN, Napoli, Italy
| | - Vito Alessandro Lasorsa
- Department of Molecular Medicine and Medical Biotechnology, Università degli Studi di Napoli Federico II, Napoli, Italy.,CEINGE Biotecnologie Avanzate, Napoli, Italy
| | - Flora Cimmino
- Department of Molecular Medicine and Medical Biotechnology, Università degli Studi di Napoli Federico II, Napoli, Italy.,CEINGE Biotecnologie Avanzate, Napoli, Italy
| | - Marianna Avitabile
- Department of Molecular Medicine and Medical Biotechnology, Università degli Studi di Napoli Federico II, Napoli, Italy.,CEINGE Biotecnologie Avanzate, Napoli, Italy
| | | | - Annalaura Montella
- Department of Molecular Medicine and Medical Biotechnology, Università degli Studi di Napoli Federico II, Napoli, Italy.,CEINGE Biotecnologie Avanzate, Napoli, Italy
| | - Biagio De Angelis
- Department of Pediatric Haematology and Oncology, IRCCS Ospedale Pediatrico Bambino Gesù, Roma, Italy
| | - Martina Morini
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Carmen de Torres
- Developmental Tumor Biology Laboratory, Department of Oncology, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Aurora Castellano
- Department of Pediatric Haematology and Oncology, IRCCS Ospedale Pediatrico Bambino Gesù, Roma, Italy
| | - Franco Locatelli
- Department of Pediatric Haematology and Oncology, IRCCS Ospedale Pediatrico Bambino Gesù, Roma, Italy.,Department of Paediatrics, Sapienza University of Rome, Roma, Italy
| | - Achille Iolascon
- Department of Molecular Medicine and Medical Biotechnology, Università degli Studi di Napoli Federico II, Napoli, Italy. .,CEINGE Biotecnologie Avanzate, Napoli, Italy
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482
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Hasan N, Ahuja N. The Emerging Roles of ATP-Dependent Chromatin Remodeling Complexes in Pancreatic Cancer. Cancers (Basel) 2019; 11:E1859. [PMID: 31769422 PMCID: PMC6966483 DOI: 10.3390/cancers11121859] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 02/08/2023] Open
Abstract
Pancreatic cancer is an aggressive cancer with low survival rates. Genetic and epigenetic dysregulation has been associated with the initiation and progression of pancreatic tumors. Multiple studies have pointed to the involvement of aberrant chromatin modifications in driving tumor behavior. ATP-dependent chromatin remodeling complexes regulate chromatin structure and have critical roles in stem cell maintenance, development, and cancer. Frequent mutations and chromosomal aberrations in the genes associated with subunits of the ATP-dependent chromatin remodeling complexes have been detected in different cancer types. In this review, we summarize the current literature on the genomic alterations and mechanistic studies of the ATP-dependent chromatin remodeling complexes in pancreatic cancer. Our review is focused on the four main subfamilies: SWItch/sucrose non-fermentable (SWI/SNF), imitation SWI (ISWI), chromodomain-helicase DNA-binding protein (CHD), and INOsitol-requiring mutant 80 (INO80). Finally, we discuss potential novel treatment options that use small molecules to target these complexes.
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Affiliation(s)
| | - Nita Ahuja
- Department of Surgery, Yale University School of Medicine, New Haven, CT 06520, USA;
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483
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Geoerger B, Zwaan CM, Marshall LV, Michon J, Bourdeaut F, Casanova M, Corradini N, Rossato G, Farid-Kapadia M, Shemesh CS, Hutchinson KE, Donaldson F, Liao M, Caron H, Trippett T. Atezolizumab for children and young adults with previously treated solid tumours, non-Hodgkin lymphoma, and Hodgkin lymphoma (iMATRIX): a multicentre phase 1-2 study. Lancet Oncol 2019; 21:134-144. [PMID: 31780255 DOI: 10.1016/s1470-2045(19)30693-x] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 09/23/2019] [Accepted: 09/26/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND Atezolizumab is an inhibitor of PD-L1, which can lead to enhanced anticancer T-cell activity. We aimed to evaluate the safety, pharmacokinetics, and activity of atezolizumab in children and young adults with refractory or relapsed solid tumours, with known or expected PD-L1 expression. METHODS iMATRIX was a multicentre, open-label, phase 1-2 trial of patients (aged <30 years) with solid tumours or lymphomas recruited from 28 hospitals in ten countries (USA, France, Italy, UK, Spain, the Netherlands, Denmark, Israel, Switzerland, and Germany). Eligible patients younger than 18 years received 15 mg/kg atezolizumab (maximum 1200 mg); patients aged 18-29 years received the adult dose (1200 mg) until disease progression or loss of clinical benefit. Co-primary endpoints were safety (assessed by incidence of adverse events) and pharmacokinetics (assessed by serum atezolizumab concentrations). Secondary endpoints included the proportion of patients achieving an objective response. This trial is registered with ClinicalTrials.gov, number NCT02541604. FINDINGS Between Nov 5, 2015, and April 2, 2018, we screened 115 patients, 25 of whom did not meet the inclusion criteria. 90 patients, with a median age of 14 years (IQR 10-17), were enrolled. At the data cutoff (April 2, 2018), two patients remained on study treatment. 87 (97%) of 90 patients received at least one dose of atezolizumab at 15 mg/kg or 1200 mg and were evaluable for safety. Three patients were not treated owing to either poor clinical condition or withdrawal of consent. In the safety-evaluable population (n=87), the most common adverse events were pyrexia (36 [41%] patients) and fatigue (31 [36%]). The most common grade 3-4 adverse event was anaemia (19 [22%] patients). The most commonly reported serious adverse events were in the categories of infections and infestations; pyrexia was the only serious adverse event reported in more than two patients. 57 (66%) patients had at least one treatment-related adverse event (grade 1-4); fatigue was the most common treatment-related adverse event (17 patients [20%]). There were no fatal adverse events. Mean serum concentrations of atezolizumab were overlapping and comparable between children receiving 15 mg/kg and young adults receiving 1200 mg of atezolizumab every 3 weeks. Serum concentrations of atezolizumab were above the target exposure level in all patients. At 6 months, four patients (5%) achieved an objective response (all partial responses). INTERPRETATION Although response to atezolizumab was restricted, atezolizumab was well tolerated with generally comparable exposure across populations. Our findings might help to define future development strategies for immune checkpoint inhibitors either by focusing research to specific disease subpopulations that exhibit greater benefit from immune checkpoint inhibitors, or by providing the means to identify therapeutic combination partners that augment T-cell infiltration and proliferation in so-called immune cold tumour microenvironments. FUNDING F Hoffmann-La Roche.
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Affiliation(s)
- Birgit Geoerger
- Gustave Roussy Cancer Center, Department of Pediatric and Adolescent Oncology, Université Paris-Saclay, Villejuif, France.
| | - C Michel Zwaan
- Department of Pediatric Oncology, Erasmus MC-Sophia Children's Hospital, Rotterdam, Netherlands; Princess Máxima Center, Utrecht, Netherlands
| | - Lynley V Marshall
- Paediatric and Adolescent Oncology Drug Development Unit, The Royal Marsden NHS Foundation Trust, London, UK; The Institute of Cancer Research, London, UK
| | - Jean Michon
- Service de Pédiatrie, SIREDO Center, Curie Institute, Paris, France
| | - Franck Bourdeaut
- Service de Pédiatrie, SIREDO Center, Curie Institute, Paris, France
| | | | - Nadège Corradini
- Haematology and Oncology Paediatric Institut, Léon Bérard Centre, Lyon, France
| | | | | | | | | | | | | | | | - Tanya Trippett
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
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484
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Boloix A, Masanas M, Jiménez C, Antonelli R, Soriano A, Roma J, Sánchez de Toledo J, Gallego S, Segura MF. Long Non-coding RNA PVT1 as a Prognostic and Therapeutic Target in Pediatric Cancer. Front Oncol 2019; 9:1173. [PMID: 31781490 PMCID: PMC6853055 DOI: 10.3389/fonc.2019.01173] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 10/18/2019] [Indexed: 12/27/2022] Open
Abstract
In recent decades, biomedical research has focused on understanding the functionality of the human translated genome, which represents a minor part of all genetic information transcribed from the human genome. However, researchers have become aware of the importance of non-coding RNA species that constitute the vast majority of the transcriptome. In addition to their crucial role in tissue development and homeostasis, mounting evidence shows non-coding RNA to be deregulated and functionally contributing to the development and progression of different types of human disease including cancer both in adults and children. Small non-coding RNAs (i.e., microRNA) are in the vanguard of clinical research which revealed that RNA could be used as disease biomarkers or new therapeutic targets. Furthermore, many more expectations have been raised for long non-coding RNAs, by far the largest fraction of non-coding transcripts, and still fewer findings have been translated into clinical applications. In this review, we center on PVT1, a large and complex long non-coding RNA that usually confers oncogenic properties on different tumor types. We focus on the compilation of early advances in the field of pediatric tumors which often lags behind clinical improvements in adult tumors, and provide a rationale to continue studying PVT1 as a possible functional contributor to pediatric malignancies and as a potential prognostic marker or therapeutic target.
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Affiliation(s)
- Ariadna Boloix
- Group of Translational Research in Child and Adolescent Cancer, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Esfera UAB, Cerdanyola del Vallès, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain
| | - Marc Masanas
- Group of Translational Research in Child and Adolescent Cancer, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Carlos Jiménez
- Group of Translational Research in Child and Adolescent Cancer, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Roberta Antonelli
- Group of Translational Research in Child and Adolescent Cancer, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Aroa Soriano
- Group of Translational Research in Child and Adolescent Cancer, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Josep Roma
- Group of Translational Research in Child and Adolescent Cancer, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Josep Sánchez de Toledo
- Group of Translational Research in Child and Adolescent Cancer, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Soledad Gallego
- Group of Translational Research in Child and Adolescent Cancer, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Miguel F Segura
- Group of Translational Research in Child and Adolescent Cancer, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
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485
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Rokita JL, Rathi KS, Cardenas MF, Upton KA, Jayaseelan J, Cross KL, Pfeil J, Egolf LE, Way GP, Farrel A, Kendsersky NM, Patel K, Gaonkar KS, Modi A, Berko ER, Lopez G, Vaksman Z, Mayoh C, Nance J, McCoy K, Haber M, Evans K, McCalmont H, Bendak K, Böhm JW, Marshall GM, Tyrrell V, Kalletla K, Braun FK, Qi L, Du Y, Zhang H, Lindsay HB, Zhao S, Shu J, Baxter P, Morton C, Kurmashev D, Zheng S, Chen Y, Bowen J, Bryan AC, Leraas KM, Coppens SE, Doddapaneni H, Momin Z, Zhang W, Sacks GI, Hart LS, Krytska K, Mosse YP, Gatto GJ, Sanchez Y, Greene CS, Diskin SJ, Vaske OM, Haussler D, Gastier-Foster JM, Kolb EA, Gorlick R, Li XN, Reynolds CP, Kurmasheva RT, Houghton PJ, Smith MA, Lock RB, Raman P, Wheeler DA, Maris JM. Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design. Cell Rep 2019; 29:1675-1689.e9. [PMID: 31693904 PMCID: PMC6880934 DOI: 10.1016/j.celrep.2019.09.071] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 07/10/2019] [Accepted: 09/24/2019] [Indexed: 02/08/2023] Open
Abstract
Accelerating cures for children with cancer remains an immediate challenge as a result of extensive oncogenic heterogeneity between and within histologies, distinct molecular mechanisms evolving between diagnosis and relapsed disease, and limited therapeutic options. To systematically prioritize and rationally test novel agents in preclinical murine models, researchers within the Pediatric Preclinical Testing Consortium are continuously developing patient-derived xenografts (PDXs)-many of which are refractory to current standard-of-care treatments-from high-risk childhood cancers. Here, we genomically characterize 261 PDX models from 37 unique pediatric cancers; demonstrate faithful recapitulation of histologies and subtypes; and refine our understanding of relapsed disease. In addition, we use expression signatures to classify tumors for TP53 and NF1 pathway inactivation. We anticipate that these data will serve as a resource for pediatric oncology drug development and will guide rational clinical trial design for children with cancer.
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Affiliation(s)
- Jo Lynne Rokita
- Division of Oncology, Children's Hospital of Philadelphia, and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-4318, USA; Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Komal S Rathi
- Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Maria F Cardenas
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kristen A Upton
- Division of Oncology, Children's Hospital of Philadelphia, and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-4318, USA
| | - Joy Jayaseelan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Jacob Pfeil
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Laura E Egolf
- Division of Oncology, Children's Hospital of Philadelphia, and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-4318, USA; Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gregory P Way
- Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alvin Farrel
- Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nathan M Kendsersky
- Division of Oncology, Children's Hospital of Philadelphia, and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-4318, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Khushbu Patel
- Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Krutika S Gaonkar
- Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Apexa Modi
- Division of Oncology, Children's Hospital of Philadelphia, and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-4318, USA; Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Esther R Berko
- Division of Oncology, Children's Hospital of Philadelphia, and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-4318, USA
| | - Gonzalo Lopez
- Division of Oncology, Children's Hospital of Philadelphia, and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-4318, USA; Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Zalman Vaksman
- Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Chelsea Mayoh
- Children's Cancer Institute, School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Jonas Nance
- Cancer Center, Texas Tech University Health Sciences Center School of Medicine, Lubbock, TX 79430, USA
| | - Kristyn McCoy
- Cancer Center, Texas Tech University Health Sciences Center School of Medicine, Lubbock, TX 79430, USA
| | - Michelle Haber
- Children's Cancer Institute, School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Kathryn Evans
- Children's Cancer Institute, School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Hannah McCalmont
- Children's Cancer Institute, School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Katerina Bendak
- Children's Cancer Institute, School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Julia W Böhm
- Children's Cancer Institute, School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Glenn M Marshall
- Children's Cancer Institute, School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia; Sydney Children's Hospital, Sydney, NSW, Australia
| | | | - Karthik Kalletla
- Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Frank K Braun
- Texas Children's Cancer and Hematology Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lin Qi
- Preclinical Neurooncology Research Program, Texas Children's Cancer Research Center, Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yunchen Du
- Preclinical Neurooncology Research Program, Texas Children's Cancer Research Center, Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Huiyuan Zhang
- Preclinical Neurooncology Research Program, Texas Children's Cancer Research Center, Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Holly B Lindsay
- Preclinical Neurooncology Research Program, Texas Children's Cancer Research Center, Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sibo Zhao
- Preclinical Neurooncology Research Program, Texas Children's Cancer Research Center, Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jack Shu
- Preclinical Neurooncology Research Program, Texas Children's Cancer Research Center, Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Patricia Baxter
- Preclinical Neurooncology Research Program, Texas Children's Cancer Research Center, Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christopher Morton
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Dias Kurmashev
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Siyuan Zheng
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Yidong Chen
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Jay Bowen
- The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Anthony C Bryan
- The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Kristen M Leraas
- The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Sara E Coppens
- The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | | | - Zeineen Momin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wendong Zhang
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gregory I Sacks
- Division of Oncology, Children's Hospital of Philadelphia, and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-4318, USA
| | - Lori S Hart
- Division of Oncology, Children's Hospital of Philadelphia, and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-4318, USA
| | - Kateryna Krytska
- Division of Oncology, Children's Hospital of Philadelphia, and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-4318, USA
| | - Yael P Mosse
- Division of Oncology, Children's Hospital of Philadelphia, and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-4318, USA
| | - Gregory J Gatto
- Department of Global Health Technologies, RTI International, Research Triangle Park, NC 27709, USA
| | - Yolanda Sanchez
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA; Norris Cotton Cancer Center, Lebanon, NH 03766, USA
| | - Casey S Greene
- Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Philadelphia, PA 19102, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sharon J Diskin
- Division of Oncology, Children's Hospital of Philadelphia, and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-4318, USA; Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Olena Morozova Vaske
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - David Haussler
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Julie M Gastier-Foster
- The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA; The Ohio State University College of Medicine, Departments of Pathology and Pediatrics, Columbus, OH 43210, USA
| | - E Anders Kolb
- Department of Pediatrics, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA 19107, USA; Nemours Center for Cancer and Blood Disorders, Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA
| | - Richard Gorlick
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiao-Nan Li
- Preclinical Neurooncology Research Program, Texas Children's Cancer Research Center, Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Division of Hematology, Oncology, Neuro-oncology and Stem Cell Transplant, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - C Patrick Reynolds
- Cancer Center, Texas Tech University Health Sciences Center School of Medicine, Lubbock, TX 79430, USA
| | - Raushan T Kurmasheva
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Peter J Houghton
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | | | | | - Pichai Raman
- Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - John M Maris
- Division of Oncology, Children's Hospital of Philadelphia, and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-4318, USA.
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486
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Hernández-Lemus E, Reyes-Gopar H, Espinal-Enríquez J, Ochoa S. The Many Faces of Gene Regulation in Cancer: A Computational Oncogenomics Outlook. Genes (Basel) 2019; 10:E865. [PMID: 31671657 PMCID: PMC6896122 DOI: 10.3390/genes10110865] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/16/2019] [Accepted: 10/24/2019] [Indexed: 12/16/2022] Open
Abstract
Cancer is a complex disease at many different levels. The molecular phenomenology of cancer is also quite rich. The mutational and genomic origins of cancer and their downstream effects on processes such as the reprogramming of the gene regulatory control and the molecular pathways depending on such control have been recognized as central to the characterization of the disease. More important though is the understanding of their causes, prognosis, and therapeutics. There is a multitude of factors associated with anomalous control of gene expression in cancer. Many of these factors are now amenable to be studied comprehensively by means of experiments based on diverse omic technologies. However, characterizing each dimension of the phenomenon individually has proven to fall short in presenting a clear picture of expression regulation as a whole. In this review article, we discuss some of the more relevant factors affecting gene expression control both, under normal conditions and in tumor settings. We describe the different omic approaches that we can use as well as the computational genomic analysis needed to track down these factors. Then we present theoretical and computational frameworks developed to integrate the amount of diverse information provided by such single-omic analyses. We contextualize this within a systems biology-based multi-omic regulation setting, aimed at better understanding the complex interplay of gene expression deregulation in cancer.
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Affiliation(s)
- Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City 14610, Mexico.
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico.
| | - Helena Reyes-Gopar
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City 14610, Mexico.
| | - Jesús Espinal-Enríquez
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City 14610, Mexico.
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico.
| | - Soledad Ochoa
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City 14610, Mexico.
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487
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Abstract
Metastatic cancer is a major cause of death and is associated with poor treatment efficacy. A better understanding of the characteristics of late-stage cancer is required to help adapt personalized treatments, reduce overtreatment and improve outcomes. Here we describe the largest, to our knowledge, pan-cancer study of metastatic solid tumour genomes, including whole-genome sequencing data for 2,520 pairs of tumour and normal tissue, analysed at median depths of 106× and 38×, respectively, and surveying more than 70 million somatic variants. The characteristic mutations of metastatic lesions varied widely, with mutations that reflect those of the primary tumour types, and with high rates of whole-genome duplication events (56%). Individual metastatic lesions were relatively homogeneous, with the vast majority (96%) of driver mutations being clonal and up to 80% of tumour-suppressor genes being inactivated bi-allelically by different mutational mechanisms. Although metastatic tumour genomes showed similar mutational landscape and driver genes to primary tumours, we find characteristics that could contribute to responsiveness to therapy or resistance in individual patients. We implement an approach for the review of clinically relevant associations and their potential for actionability. For 62% of patients, we identify genetic variants that may be used to stratify patients towards therapies that either have been approved or are in clinical trials. This demonstrates the importance of comprehensive genomic tumour profiling for precision medicine in cancer.
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488
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Pediatric ALL relapses after allo-SCT show high individuality, clonal dynamics, selective pressure, and druggable targets. Blood Adv 2019; 3:3143-3156. [PMID: 31648313 DOI: 10.1182/bloodadvances.2019000051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 07/08/2019] [Indexed: 12/11/2022] Open
Abstract
Survival of patients with pediatric acute lymphoblastic leukemia (ALL) after allogeneic hematopoietic stem cell transplantation (allo-SCT) is mainly compromised by leukemia relapse, carrying dismal prognosis. As novel individualized therapeutic approaches are urgently needed, we performed whole-exome sequencing of leukemic blasts of 10 children with post-allo-SCT relapses with the aim of thoroughly characterizing the mutational landscape and identifying druggable mutations. We found that post-allo-SCT ALL relapses display highly diverse and mostly patient-individual genetic lesions. Moreover, mutational cluster analysis showed substantial clonal dynamics during leukemia progression from initial diagnosis to relapse after allo-SCT. Only very few alterations stayed constant over time. This dynamic clonality was exemplified by the detection of thiopurine resistance-mediating mutations in the nucleotidase NT5C2 in 3 patients' first relapses, which disappeared in the post-allo-SCT relapses on relief of selective pressure of maintenance chemotherapy. Moreover, we identified TP53 mutations in 4 of 10 patients after allo-SCT, reflecting acquired chemoresistance associated with selective pressure of prior antineoplastic treatment. Finally, in 9 of 10 children's post-allo-SCT relapse, we found alterations in genes for which targeted therapies with novel agents are readily available. We could show efficient targeting of leukemic blasts by APR-246 in 2 patients carrying TP53 mutations. Our findings shed light on the genetic basis of post-allo-SCT relapse and may pave the way for unraveling novel therapeutic strategies in this challenging situation.
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489
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Ahmed F. Integrated Network Analysis Reveals FOXM1 and MYBL2 as Key Regulators of Cell Proliferation in Non-small Cell Lung Cancer. Front Oncol 2019; 9:1011. [PMID: 31681566 PMCID: PMC6804573 DOI: 10.3389/fonc.2019.01011] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/20/2019] [Indexed: 12/21/2022] Open
Abstract
Background: Loss of control on cell division is an important factor for the development of non-small cell lung cancer (NSCLC), however, its molecular mechanism and gene regulatory network are not clearly understood. This study utilized the systems bioinformatics approach to reveal the “driver-network” involve in tumorigenic processes in NSCLC. Methods: A meta-analysis of gene expression data of NSCLC was integrated with protein-protein interaction (PPI) data to construct an NSCLC network. MCODE and iRegulone were used to identify the local clusters and its upstream transcription regulators involve in NSCLC. Pair-wise gene expression correlation was performed using GEPIA. The survival analysis was performed by the Kaplan-Meier plot. Results: This study identified a local “driver-network” with highest MCODE score having 26 up-regulated genes involved in the process of cell proliferation in NSCLC. Interestingly, the “driver-network” is under the regulation of TFs FOXM1 and MYBL2 as well as miRNAs. Furthermore, the overexpression of member genes in “driver-network” and the TFs are associated with poor overall survival (OS) in NSCLC patients. Conclusion: This study identified a local “driver-network” and its upstream regulators responsible for the cell proliferation in NSCLC, which could be promising biomarkers and therapeutic targets for NSCLC treatment.
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Affiliation(s)
- Firoz Ahmed
- Department of Biochemistry, University of Jeddah, Jeddah, Saudi Arabia.,University of Jeddah Center for Scientific and Medical Research, University of Jeddah, Jeddah, Saudi Arabia
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490
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Study on miRNAs in Pan-Cancer of the Digestive Tract Based on the Illumina HiSeq System Data Sequencing. BIOMED RESEARCH INTERNATIONAL 2019; 2019:8016120. [PMID: 31737678 PMCID: PMC6817930 DOI: 10.1155/2019/8016120] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 08/16/2019] [Accepted: 09/06/2019] [Indexed: 02/08/2023]
Abstract
Objective miRNA has gained attention as a therapeutic target in various malignancies. The proposal of this study was to investigate the biological functions of key miRNAs and target genes in cancers of the digestive tract which include esophageal carcinoma (ESCA), gastric adenocarcinoma (GAC), colon adenocarcinoma (COAD), and rectal adenocarcinoma (READ). Materials and Methods After screening differentially expressed miRNAs (DEMIs) and differentially expressed mRNAs (DEMs) in four digestive cancers from The Cancer Genome Atlas (TCGA) database, the diagnostic value of above DEMIs was evaluated by receiver-operating characteristic (ROC) curve analysis. Then, corresponding DEMIs' target genes were predicted by miRWalk 2.0. Intersection of predicted target genes and DEMs was taken as the target genes of DEMIs, and miRNA-mRNA regulatory networks between DEMIs and target genes were constructed. Meanwhile, the univariate Cox risk regression model was used to screen miRNAs with distinct prognostic value, and Kaplan-Meier analysis was used to determine their significance of prognosis. Furthermore, we performed bioinformatics methods including protein-protein interaction (PPI) networks, gene ontology (GO) annotation, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and gene group RIDA analysis by Gene-Cloud of Biotechnology Information (GCBI) to explore the function and molecular mechanisms of DEMIs and predicted target genes in tumor development. Results Eventually, 3 DEMIs (miR-7-3, miR-328, and miR-323a) with significant prognostic value were obtained. In addition, 3 DEMIs (miR-490-3p, miR-133a-3p, and miR-552-3p) and 281 target genes were identified, and the 3 DEMIs showed high diagnostic value in READ and moderate diagnostic value in ESCA, GAC, and COAD. Also, the miRNA-mRNA regulatory network with 3 DEMIs and 281 overlapping genes was successfully established. Functional enrichment analysis showed that 281 overlapping genes were mainly related to regulation of cell proliferation, cell migration, and PI3K-Akt signaling pathway. Conclusion The diagnostic value and prognostic value of significant DEMIs in cancers of the digestive tract were identified, which may provide a novel direction for treatment and prognosis improvement of cancers of the digestive tract.
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491
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Stahl D, Gentles AJ, Thiele R, Gütgemann I. Prognostic profiling of the immune cell microenvironment in Ewing´s Sarcoma Family of Tumors. Oncoimmunology 2019; 8:e1674113. [PMID: 31741777 DOI: 10.1080/2162402x.2019.1674113] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/25/2019] [Accepted: 09/25/2019] [Indexed: 12/15/2022] Open
Abstract
Ewing´s Sarcoma Family of Tumors (ESFT) are clinically aggressive bone and soft tissue tumors in children and young adults. Analysis of the immune tumor microenvironment (TME) provides insight into tumor evolution and novel treatment options. So far, the scarcity of immune cells in ESFT has hindered a comprehensive analysis of rare subtypes. We determined the relative fraction of 22 immune cell types using 197 microarray gene expression datasets of primary ESFT tumor samples by using CIBERSORT, a deconvolution algorithm enumerating infiltrating leucocytes in bulk tumor tissue. The most abundant cells were macrophages (mean 43% of total tumor-infiltrating leukocytes, TILs), predominantly immunosuppressive M2 type macrophages, followed by T cells (mean 23% of TILs). Increased neutrophils, albeit at low number, were associated with a poor overall survival (OS) (p = .038) and increased M2 macrophages predicted a shorter event-free survival (EFS) (p = .033). High frequency of T cells and activated NK cells correlated with prolonged OS (p = .044 and p = .007, respectively). A small patient population (9/32) with combined low infiltrating M2 macrophages, low neutrophils, and high total T cells was identified with favorable outcome. This finding was confirmed in a validation cohort of patients with follow up (11/38). When comparing the immune TME with expression of known stemness genes, hypoxia-inducible factor 1 α (HIF1α) correlated with high abundance of macrophages and neutrophils and decreased T cell levels. The immune TME in ESFTs shows a distinct composition including rare immune cell subsets that in part may be due to expression of HIF1α.
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Affiliation(s)
- David Stahl
- Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | - Andrew J Gentles
- Departments of Medicine and Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Ralf Thiele
- Department of Computer Science, Bonn-Rhine-Sieg University of Applied Sciences, Sankt Augustin, Germany
| | - Ines Gütgemann
- Institute of Pathology, University Hospital Bonn, Bonn, Germany
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492
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Zhang W, Meyfeldt J, Wang H, Kulkarni S, Lu J, Mandel JA, Marburger B, Liu Y, Gorka JE, Ranganathan S, Prochownik EV. β-Catenin mutations as determinants of hepatoblastoma phenotypes in mice. J Biol Chem 2019; 294:17524-17542. [PMID: 31597698 DOI: 10.1074/jbc.ra119.009979] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 10/03/2019] [Indexed: 12/14/2022] Open
Abstract
Hepatoblastoma (HB) is the most common pediatric liver cancer. Although long-term survival of HB is generally favorable, it depends on clinical stage, tumor histology, and a variety of biochemical and molecular features. HB appears almost exclusively before the age of 3 years, is represented by seven histological subtypes, and is usually associated with highly heterogeneous somatic mutations in the catenin β1 (CTNNB1) gene, which encodes β-catenin, a Wnt ligand-responsive transcriptional co-factor. Numerous recurring β-catenin mutations, not previously documented in HB, have also been identified in various other pediatric and adult cancer types. Little is known about the underlying factors that determine the above HB features and behaviors or whether non-HB-associated β-catenin mutations are tumorigenic when expressed in hepatocytes. Here, we investigated the oncogenic properties of 14 different HB- and non-HB-associated β-catenin mutants encoded by Sleeping Beauty vectors following their delivery into the mouse liver by hydrodynamic tail-vein injection. We show that all β-catenin mutations, as well as WT β-catenin, are tumorigenic when co-expressed with a mutant form of yes-associated protein (YAP). However, tumor growth rates, histologies, nuclear-to-cytoplasmic partitioning, and metabolic and transcriptional landscapes were strongly influenced by the identities of the β-catenin mutations. These findings provide a context for understanding at the molecular level the notable biological diversity of HB.
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Affiliation(s)
- Weiqi Zhang
- Division of Hematology/Oncology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania 15224.,Tsinghua University School of Medicine, Beijing 100084, China
| | - Jennifer Meyfeldt
- Division of Hematology/Oncology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania 15224
| | - Huabo Wang
- Division of Hematology/Oncology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania 15224
| | - Sucheta Kulkarni
- Division of Hematology/Oncology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania 15224
| | - Jie Lu
- Division of Hematology/Oncology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania 15224
| | - Jordan A Mandel
- Division of Hematology/Oncology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania 15224
| | - Brady Marburger
- Division of Hematology/Oncology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania 15224.,University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15224
| | - Ying Liu
- Division of Hematology/Oncology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania 15224.,University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15224
| | - Joanna E Gorka
- Division of Hematology/Oncology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania 15224
| | - Sarangarajan Ranganathan
- University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15224.,Department of Pathology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania 15224.,Pittsburgh Liver Research Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania 15213
| | - Edward V Prochownik
- Division of Hematology/Oncology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania 15224 .,University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15224.,Pittsburgh Liver Research Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania 15213.,Department of Microbiology and Molecular Genetics, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania 15213.,Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15232
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493
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Bacolla A, Ye Z, Ahmed Z, Tainer JA. Cancer mutational burden is shaped by G4 DNA, replication stress and mitochondrial dysfunction. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 147:47-61. [PMID: 30880007 PMCID: PMC6745008 DOI: 10.1016/j.pbiomolbio.2019.03.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 02/01/2023]
Abstract
A hallmark of cancer is genomic instability, which can enable cancer cells to evade therapeutic strategies. Here we employed a computational approach to uncover mechanisms underlying cancer mutational burden by focusing upon relationships between 1) translocation breakpoints and the thousands of G4 DNA-forming sequences within retrotransposons impacting transcription and exemplifying probable non-B DNA structures and 2) transcriptome profiling and cancer mutations. We determined the location and number of G4 DNA-forming sequences in the Genome Reference Consortium Human Build 38 and found a total of 358,605 covering ∼13.4 million bases. By analyzing >97,000 unique translocation breakpoints from the Catalogue Of Somatic Mutations In Cancer (COSMIC), we found that breakpoints are overrepresented at G4 DNA-forming sequences within hominid-specific SVA retrotransposons, and generally occur in tumors with mutations in tumor suppressor genes, such as TP53. Furthermore, correlation analyses between mRNA levels and exome mutational loads from The Cancer Genome Atlas (TCGA) encompassing >450,000 gene-mutation regressions revealed strong positive and negative associations, which depended upon tissue of origin. The strongest positive correlations originated from genes not listed as cancer genes in COSMIC; yet, these show strong predictive power for survival in most tumor types by Kaplan-Meier estimation. Thus, correlation analyses of DNA structure and gene expression with mutation loads complement and extend more traditional approaches to elucidate processes shaping genomic instability in cancer. The combined results point to G4 DNA, activation of cell cycle/DNA repair pathways, and mitochondrial dysfunction as three major factors driving the accumulation of somatic mutations in cancer cells.
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Affiliation(s)
- Albino Bacolla
- Departments of Cancer Biology and of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA.
| | - Zu Ye
- Departments of Cancer Biology and of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA.
| | - Zamal Ahmed
- Departments of Cancer Biology and of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA.
| | - John A Tainer
- Departments of Cancer Biology and of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA.
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494
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Hovhannisyan G, Harutyunyan T, Aroutiounian R, Liehr T. DNA Copy Number Variations as Markers of Mutagenic Impact. Int J Mol Sci 2019; 20:ijms20194723. [PMID: 31554154 PMCID: PMC6801639 DOI: 10.3390/ijms20194723] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/17/2019] [Accepted: 09/20/2019] [Indexed: 12/26/2022] Open
Abstract
DNA copy number variation (CNV) occurs due to deletion or duplication of DNA segments resulting in a different number of copies of a specific DNA-stretch on homologous chromosomes. Implications of CNVs in evolution and development of different diseases have been demonstrated although contribution of environmental factors, such as mutagens, in the origin of CNVs, is poorly understood. In this review, we summarize current knowledge about mutagen-induced CNVs in human, animal and plant cells. Differences in CNV frequencies induced by radiation and chemical mutagens, distribution of CNVs in the genome, as well as adaptive effects in plants, are discussed. Currently available information concerning impact of mutagens in induction of CNVs in germ cells is presented. Moreover, the potential of CNVs as a new endpoint in mutagenicity test-systems is discussed.
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Affiliation(s)
- Galina Hovhannisyan
- Department of Genetics and Cytology, Yerevan State University, Alex Manoogian 1, 0025 Yerevan, Armenia.
| | - Tigran Harutyunyan
- Department of Genetics and Cytology, Yerevan State University, Alex Manoogian 1, 0025 Yerevan, Armenia.
| | - Rouben Aroutiounian
- Department of Genetics and Cytology, Yerevan State University, Alex Manoogian 1, 0025 Yerevan, Armenia.
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, D-07747 Jena, Germany.
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495
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Driver mutations in Janus kinases in a mouse model of B-cell leukemia induced by deletion of PU.1 and Spi-B. Blood Adv 2019; 2:2798-2810. [PMID: 30355579 DOI: 10.1182/bloodadvances.2018019950] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 10/02/2018] [Indexed: 01/13/2023] Open
Abstract
Precursor B-cell acute lymphoblastic leukemia (B-ALL) is associated with recurrent mutations that occur in cancer-initiating cells. There is a need to understand how driver mutations influence clonal evolution of leukemia. The E26-transformation-specific (ETS) transcription factors PU.1 and Spi-B (encoded by Spi1 and Spib) execute a critical role in B-cell development and serve as complementary tumor suppressors. Here, we used a mouse model to conditionally delete Spi1 and Spib genes in developing B cells. These mice developed B-ALL with a median time to euthanasia of 18 weeks. We performed RNA and whole-exome sequencing (WES) on leukemias isolated from Mb1-CreΔPB mice and identified single nucleotide variants (SNVs) in Jak1, Jak3, and Ikzf3 genes, resulting in amino acid sequence changes. Jak3 mutations resulted in amino acid substitutions located in the pseudo-kinase (R653H, V670A) and in the kinase (T844M) domains. Introduction of Jak3 T844M into Spi1/Spib-deficient precursor B cells was sufficient to promote proliferation in response to low IL-7 concentrations in culture, and to promote proliferation and leukemia-like disease in transplanted mice. We conclude that mutations in Janus kinases represent secondary drivers of leukemogenesis that cooperate with Spi1/Spib deletion. This mouse model represents a useful tool to study clonal evolution in B-ALL.
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496
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Lowery CD, Blosser W, Dowless M, Renschler M, Perez LV, Stephens J, Pytowski B, Wasserstrom H, Stancato LF, Falcon B. Anti-VEGFR2 therapy delays growth of preclinical pediatric tumor models and enhances anti-tumor activity of chemotherapy. Oncotarget 2019; 10:5523-5533. [PMID: 31565186 PMCID: PMC6756863 DOI: 10.18632/oncotarget.27148] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/21/2019] [Indexed: 01/09/2023] Open
Abstract
Vascular endothelial growth factor receptor 2 (VEGFR2) is an attractive therapeutic target in solid malignancies due to its central role in tumor angiogenesis. Ramucirumab (Cyramza®, LY3009806) is a human monoclonal antibody specific for VEGFR2 approved for several adult indications and currently in a phase 1 clinical trial for pediatric patients with solid tumors (NCT02564198). Here, we evaluated ramucirumab in vitro and the anti-murine VEGFR2 antibody DC101 in vivo with or without chemotherapy across a range of pediatric cancer models. Ramucirumab abrogated in vitro endothelial cord formation driven by cancer cell lines representing multiple pediatric histologies; this response was independent of the origin of the tumor cell-line. Several pediatric cancer mouse models responded to single agent DC101-mediated VEGFR2 inhibition with tumor growth delay. Preclinical stable disease and partial xenograft regressions were observed in mouse models of Ewing’s sarcoma, synovial sarcoma, neuroblastoma, and desmoplastic small round cell tumor treated with DC101 and cytotoxic chemotherapy. In contrast, DC101 treatment in osteosarcoma models had limited efficacy alone or in combination with chemotherapeutics. Our data indicate differential efficacy of targeting the VEGFR2 pathway in pediatric models and support the continued evaluation of VEGFR2 inhibition in combination with cytotoxic chemotherapy in multiple pediatric indications.
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Affiliation(s)
- Caitlin D Lowery
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, USA
| | - Wayne Blosser
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, USA
| | - Michele Dowless
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, USA
| | - Matthew Renschler
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, USA
| | - Lisa V Perez
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, USA
| | - Jennifer Stephens
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, USA
| | | | | | - Louis F Stancato
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, USA
| | - Beverly Falcon
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, USA
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497
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Gao J, Van Meter M, Hernandez Lopez S, Chen G, Huang Y, Ren S, Zhao Q, Rojas J, Gurer C, Thurston G, Kuhnert F. Therapeutic targeting of Notch signaling and immune checkpoint blockade in a spontaneous, genetically heterogeneous mouse model of T-cell acute lymphoblastic leukemia. Dis Model Mech 2019; 12:dmm.040931. [PMID: 31399482 PMCID: PMC6765191 DOI: 10.1242/dmm.040931] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 07/29/2019] [Indexed: 01/05/2023] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic cancer derived from the malignant transformation of T-cell progenitors. Outcomes remain poor for T-ALL patients who have either primary resistance to standard-of-care chemotherapy or disease relapse. Notably, there are currently no targeted therapies available in T-ALL. This lack of next-generation therapies highlights the need for relevant preclinical disease modeling to identify and validate new targets and treatment approaches. Here, we adapted a spontaneously arising, genetically heterogeneous, thymic transplantation-based murine model of T-ALL, recapitulating key histopathological and genetic features of the human disease, to the preclinical testing of targeted and immune-directed therapies. Genetic engineering of the murine Notch1 locus aligned the spectrum of Notch1 mutations in the mouse model to that of human T-ALL and confirmed aberrant, recombination-activating gene (RAG)-mediated 5′ Notch1 recombination events as the preferred pathway in murine T-ALL development. Testing of Notch1-targeting therapeutic antibodies demonstrated T-ALL sensitivity to different classes of Notch1 blockers based on Notch1 mutational status. In contrast, genetic ablation of Notch3 did not impact T-ALL development. The T-ALL model was further applied to the testing of immunotherapeutic agents in fully immunocompetent, syngeneic mice. In line with recent clinical experience in T-cell malignancies, programmed cell death 1 (PD-1) blockade alone lacked anti-tumor activity against murine T-ALL tumors. Overall, the unique features of the spontaneous T-ALL model coupled with genetic manipulations and the application to therapeutic testing in immunocompetent backgrounds will be of great utility for the preclinical evaluation of novel therapies against T-ALL. Summary: Adapting a spontaneous, genetically heterogenous T-ALL model to preclinical testing demonstrated that response to therapeutic anti-Notch1 antibodies was determined by Notch1 mutational status and that PD-1 immune checkpoint blockade alone lacked anti-tumor activity.
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Affiliation(s)
- Jie Gao
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, NY 10591, USA
| | | | | | - Guoying Chen
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, NY 10591, USA
| | - Ying Huang
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, NY 10591, USA
| | - Shumei Ren
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, NY 10591, USA
| | - Qi Zhao
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, NY 10591, USA
| | - Jose Rojas
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, NY 10591, USA
| | - Cagan Gurer
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, NY 10591, USA
| | - Gavin Thurston
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, NY 10591, USA
| | - Frank Kuhnert
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, NY 10591, USA
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498
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Wang J, LaFramboise T. CytoConverter: a web-based tool to convert karyotypes to genomic coordinates. BMC Bioinformatics 2019; 20:467. [PMID: 31510921 PMCID: PMC6739950 DOI: 10.1186/s12859-019-3062-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/29/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Cytogenetic nomenclature is used to describe chromosomal aberrations (or lack thereof) in a collection of cells, referred to as the cells' karyotype. The nomenclature identifies locations on chromosomes using a system of cytogenetic bands, each with a unique name and region on a chromosome. Each band is microscopically visible after staining, and encompasses a large portion of the chromosome. More modern analyses employ genomic coordinates, which precisely specify a chromosomal location according to its distance from the end of the chromosome. Currently, there is no tool to convert cytogenetic nomenclature into genomic coordinates. Since locations of genes and other genomic features are usually specified by genomic coordinates, a conversion tool will facilitate the identification of the features that are harbored in the regions of chromosomal gain and loss that are implied by a karyotype. RESULTS Our tool, termed CytoConverter, takes as input either a single karyotype or a file consisting of multiple karyotypes from several individuals. All net chromosomal gains and losses implied by the karyotype are returned in standard genomic coordinates, along with the numbers of cells harboring each aberration if included in the input. CytoConverter also returns graphical output detailing areas of gains and losses of chromosomes and chromosomal segments. CONCLUSIONS CytoConverter is available as a web-based application at https://jxw773.shinyapps.io/Cytogenetic__software/ and as an R script at https://sourceforge.net/projects/cytoconverter/ . Supplemental Material detailing the underlying algorithms is available.
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Affiliation(s)
- Janet Wang
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Thomas LaFramboise
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA.
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499
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Chang F, Lin F, Cao K, Surrey LF, Aplenc R, Bagatell R, Resnick AC, Santi M, Storm PB, Tasian SK, Waanders AJ, Hunger SP, Li MM. Development and Clinical Validation of a Large Fusion Gene Panel for Pediatric Cancers. J Mol Diagn 2019; 21:873-883. [PMID: 31255796 PMCID: PMC6734859 DOI: 10.1016/j.jmoldx.2019.05.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 04/30/2019] [Accepted: 05/16/2019] [Indexed: 12/12/2022] Open
Abstract
Gene fusions are one of the most common genomic alterations in pediatric cancer. Many fusions encode oncogenic drivers and play important roles in cancer diagnosis, risk stratification, and treatment selection. We report the development and clinical validation of a large custom-designed RNA sequencing panel, CHOP Fusion panel, using anchored multiplex PCR technology. The panel interrogates 106 cancer genes known to be involved in nearly 600 different fusions reported in hematological malignancies and solid tumors. The panel works well with different types of samples, including formalin-fixed, paraffin-embedded samples. The panel demonstrated excellent analytic accuracy, with 100% sensitivity and specificity on 60 pediatric tumor validation samples. In addition to identifying all known fusions in the validation samples, three unrecognized, yet clinically significant, fusions were also detected. A total of 276 clinical cases were analyzed after the validation, and 51 different fusions were identified in 104 cases. Of these fusions, 16 were not previously reported at the time of discovery. These fusions provided genomic information useful for clinical management. Our experience demonstrates that CHOP Fusion panel can detect the vast majority of known and certain novel clinically relevant fusion genes in pediatric cancers accurately, efficiently, and cost-effectively; and the panel provides an excellent tool for new fusion gene discovery.
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Affiliation(s)
- Fengqi Chang
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Fumin Lin
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Kajia Cao
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Lea F Surrey
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Richard Aplenc
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Rochelle Bagatell
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Adam C Resnick
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Mariarita Santi
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Phillip B Storm
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Sarah K Tasian
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Angela J Waanders
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Stephen P Hunger
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Marilyn M Li
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.
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500
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Abstract
Developments over the past five years have significantly advanced our ability to use genome-scale analyses—including high-density genotyping, transcriptome sequencing, exome sequencing, and genome sequencing—to identify the genetic basis of childhood cancer. This article reviews several key results from an expanding number of genomic studies of pediatric cancer: ( a) Histopathologic subtypes of cancers can be associated with a high incidence of germline predisposition, ( b) neurodevelopmental disorders or highly penetrant cancer predisposition syndromes can result from specific patterns of variation in genes encoding the SMARC family of chromatin remodelers, ( c) genome-wide association studies with relatively small pediatric cancer cohorts have successfully identified single-nucleotide polymorphisms with large effect sizes and provided insight into population differences in cancer risk, and ( d) multiple exome or genome analyses of unselected childhood cancer cohorts have yielded a 7–10% incidence of pathogenic variants in cancer predisposition genes. This work supports the increasing use of genomic sequencing in the care of pediatric cancer patients and at-risk family members.
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Affiliation(s)
- Sharon E. Plon
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Texas Children's Cancer Center, Texas Children's Hospital, Houston, Texas 77030, USA
- Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Philip J. Lupo
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
- Texas Children's Cancer Center, Texas Children's Hospital, Houston, Texas 77030, USA
- Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
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