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Kacsoh DB, Diaz MJ, Gozlan EC, Sahoo A, Song JJ, Yeagley M, Chobrutskiy A, Chobrutskiy BI, Blanck G. Blood-based T cell receptor anti-viral CDR3s are associated with worse overall survival for neuroblastoma. J Cancer Res Clin Oncol 2023; 149:12047-12056. [PMID: 37421457 DOI: 10.1007/s00432-023-05059-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 06/28/2023] [Indexed: 07/10/2023]
Abstract
With the advent of large collections of adaptive immune receptor recombination reads representing cancer, there is the opportunity to further investigate the adaptive immune response to viruses in the cancer setting. This is a particularly important goal due to longstanding but still not well-resolved questions about viral etiologies in cancer and viral infections as comorbidities. In this report, we assessed the T cell receptor complementarity determining region-3 (CDR3) amino acid (AA) sequences, for blood-sourced TCRs from neuroblastoma (NBL) cases, for exact AA sequence matches to previously identified anti-viral TCR CDR3 AA sequences. Results indicated the presence of anti-viral TCR CDR3 AA sequences in the NBL blood samples highly significantly correlated with worse overall survival. Furthermore, the TCR CDR3 AA sequences demonstrating chemical complementarity to many cytomegalovirus antigens represented cases with a worse outcome, including cases where such CDR3s were obtained from tumor samples. Overall, these results indicate a significant need for, and provide a novel strategy for assessing viral infection complications in NBL patients.
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Affiliation(s)
- Dorottya B Kacsoh
- College of Medicine, University of Central Florida, Orlando, FL, 32827, USA
| | - Michael J Diaz
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, 33612, USA
| | - Etienne C Gozlan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, 33612, USA
| | - Arpan Sahoo
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, 33612, USA
| | - Joanna J Song
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, 33612, USA
| | - Michelle Yeagley
- University of Pittsburgh Medical Center, Pittsburgh, PA, 15261, USA
| | - Andrea Chobrutskiy
- Department of Pediatrics, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Boris I Chobrutskiy
- Department of Internal Medicine, Oregon Health and Science University Hospital, Portland, OR, 97239, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, 33612, USA.
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA.
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Zhang HF, Delaidelli A, Javed S, Turgu B, Morrison T, Hughes CS, Yang X, Pachva M, Lizardo MM, Singh G, Hoffmann J, Huang YZ, Patel K, Shraim R, Kung SH, Morin GB, Aparicio S, Martinez D, Maris JM, Bosse KR, Williams KC, Sorensen PH. A MYCN-independent mechanism mediating secretome reprogramming and metastasis in MYCN-amplified neuroblastoma. SCIENCE ADVANCES 2023; 9:eadg6693. [PMID: 37611092 PMCID: PMC10446492 DOI: 10.1126/sciadv.adg6693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 07/21/2023] [Indexed: 08/25/2023]
Abstract
MYCN amplification (MNA) is a defining feature of high-risk neuroblastoma (NB) and predicts poor prognosis. However, whether genes within or in close proximity to the MYCN amplicon also contribute to MNA+ NB remains poorly understood. Here, we identify that GREB1, a transcription factor encoding gene neighboring the MYCN locus, is frequently coexpressed with MYCN and promotes cell survival in MNA+ NB. GREB1 controls gene expression independently of MYCN, among which we uncover myosin 1B (MYO1B) as being highly expressed in MNA+ NB and, using a chick chorioallantoic membrane (CAM) model, as a crucial regulator of invasion and metastasis. Global secretome and proteome profiling further delineates MYO1B in regulating secretome reprogramming in MNA+ NB cells, and the cytokine MIF as an important pro-invasive and pro-metastatic mediator of MYO1B activity. Together, we have identified a putative GREB1-MYO1B-MIF axis as an unconventional mechanism promoting aggressive behavior in MNA+ NB and independently of MYCN.
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Affiliation(s)
- Hai-Feng Zhang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Alberto Delaidelli
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Sumreen Javed
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - Busra Turgu
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Taylor Morrison
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Christopher S. Hughes
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Xiaqiu Yang
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Manideep Pachva
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Michael M. Lizardo
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Gurdeep Singh
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Jennifer Hoffmann
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yue Zhou Huang
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Khushbu Patel
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rawan Shraim
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | | | - Gregg B. Morin
- Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC V5Z4S6, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Samuel Aparicio
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Daniel Martinez
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John M. Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kristopher R. Bosse
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Karla C. Williams
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - Poul H. Sorensen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
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Single nCounter assay for prediction of MYCN amplification and molecular classification of medulloblastomas: a multicentric study. J Neurooncol 2022; 157:27-35. [PMID: 35166989 DOI: 10.1007/s11060-022-03965-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/04/2022] [Indexed: 10/19/2022]
Abstract
PURPOSE Medulloblastoma is the most frequent pediatric malignant brain tumor, and is divided into four main subgroups: WNT, SHH, group 3, and group 4. MYCN amplification is an important medulloblastoma prognostic biomarker. We aimed to molecular classify and predict MYCN amplification in a single assay. METHODS It was included 209 medulloblastomas from 205 patients (Brazil, Argentina, and Portugal), divided into training (n = 50) and validation (n = 159) sets. A nCounter assay was carried out using a custom panel for molecular classification, with additional genes, including MYCN. nSolver 4.0 software and the R environment were used for profiling and MYCN mRNA analysis. MYCN amplification by FISH was performed in 64 cases. RESULTS The 205 medulloblastomas were classified in SHH (44.9%), WNT (15.6%), group 3 (18.1%) and group 4 (21.4%). In the training set, MYCN amplification was detected in three SHH medulloblastomas by FISH, which showed significantly higher MYCN mRNA counts than non-FISH amplified cases, and a cutoff for MYCN amplification was established ([Formula: see text] + 4σ = 11,124.3). Applying this threshold value in the validation set, we identified MYCN mRNA counts above the cutoff in three cases, which were FISH validated. CONCLUSION We successfully stratified medulloblastoma molecular subgroups and predicted MYCN amplification using a single nCounter assay without the requirement of additional biological tissue, costs, or bench time.
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Bourdeaut F, Grison C, Maurage CA, Laquerriere A, Vasiljevic A, Delisle MB, Michalak S, Figarella-Branger D, Doz F, Richer W, Pierron G, Miquel C, Delattre O, Couturier J. MYC and MYCN amplification can be reliably assessed by aCGH in medulloblastoma. Cancer Genet 2013; 206:124-9. [PMID: 23578955 DOI: 10.1016/j.cancergen.2013.02.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 02/21/2013] [Accepted: 02/25/2013] [Indexed: 12/19/2022]
Abstract
As prognostic factors, MYC and MYCN amplifications are routinely assessed in medulloblastomas. Fluorescence in situ hybridization (FISH) is currently considered as the technique of reference. Recently, array comparative genomic hybridization (aCGH) has been developed as an alternative technique to evaluate genomic abnormalities in other tumor types; however, this technique has not been widely adopted as a replacement for FISH in medulloblastoma. In this study, 34 tumors were screened by both FISH and aCGH. In all cases showing amplification by FISH, aCGH also unambiguously revealed the abnormality. The aCGH technique was also performed on tumors showing no amplification by FISH, and the absence of amplification was confirmed in all cases. Interestingly, one tumor showed a subclonal MYC amplification by FISH. This subclonal amplification was observed in approximately 20% of tumor cells and was clearly evident on aCGH. In conclusion, our analysis confirms that aCGH is as safe as FISH for the detection of MYC/MYCN gene amplification. Given its cost efficiency in comparison to two FISH tests and the global genomic information additionally provided by an aCGH experiment, this reproducible technique can be safely retained as an alternative to FISH for routine investigation of medulloblastoma.
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Affiliation(s)
- Franck Bourdeaut
- INSERM U830, Laboratory of Genetics and Biology of Cancers, Curie Institute, Paris, France.
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Del Nagro CJ, Choi J, Xiao Y, Rangell L, Mohan S, Pandita A, Zha J, Jackson PK, O'Brien T. Chk1 inhibition in p53-deficient cell lines drives rapid chromosome fragmentation followed by caspase-independent cell death. Cell Cycle 2013; 13:303-14. [PMID: 24247149 PMCID: PMC3906246 DOI: 10.4161/cc.27055] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Activation of Checkpoint kinase 1 (Chk1) following DNA damage mediates cell cycle arrest to prevent cells with damaged DNA from entering mitosis. Here we provide a high-resolution analysis of cells as they undergo S- and G₂-checkpoint bypass in response to Chk1 inhibition with the selective Chk1 inhibitor GNE-783. Within 4-8 h of Chk1 inhibition following gemcitabine induced DNA damage, cells with both sub-4N and 4N DNA content prematurely enter mitosis. Coincident with premature transition into mitosis, levels of DNA damage dramatically increase and chromosomes condense and attempt to align along the metaphase plate. Despite an attempt to congress at the metaphase plate, chromosomes rapidly fragment and lose connection to the spindle microtubules. Gemcitabine mediated DNA damage promotes the formation of Rad51 foci; however, while Chk1 inhibition does not disrupt Rad51 foci that are formed in response to gemcitabine, these foci are lost as cells progress into mitosis. Premature entry into mitosis requires the Aurora, Cdk1/2 and Plk1 kinases and even though caspase-2 and -3 are activated upon mitotic exit, they are not required for cell death. Interestingly, p53, but not p21, deficiency enables checkpoint bypass and chemo-potentiation. Finally, we uncover a differential role for the Wee-1 checkpoint kinase in response to DNA damage, as Wee-1, but not Chk1, plays a more prominent role in the maintenance of S- and G₂-checkpoints in p53 proficient cells.
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Affiliation(s)
| | | | - Yang Xiao
- Discovery Oncology; Genentech; San Francisco, CA
| | - Linda Rangell
- Department of Pathology; Genentech; San Francisco, CA
| | - Sankar Mohan
- Department of Research Diagnostics; Genentech; San Francisco, CA
| | - Ajay Pandita
- Department of Research Diagnostics; Genentech; San Francisco, CA
| | - Jiping Zha
- Department of Pathology; Genentech; San Francisco, CA
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Abstract
Next-generation sequencing (NGS) has transformed genomic research by decreasing the cost of sequencing and increasing the throughput. Now, the focus is on using NGS technology for diagnostics and therapeutics. In this review, we discuss the possible clinical applications of NGS and the potential of some of the current systems to transition to the clinic. Clinical use of NGS technologies will enable the identification of causative mutations for rare genetic disorders through whole-genome or targeted genome resequencing, rapid pathogen screening and cancer diagnosis along with the identification of appropriate therapy. Routine clinical use of NGS technologies is appealing, but mandates high accuracy, simple assays, small inexpensive instruments, flexible throughput, short run times and most importantly, easy data analysis as well as interpretation. A number of NGS systems launched recently have least some of these characteristics, namely, small instruments, flexible throughput and short run time, but still face a few challenges. Moreover, simplified data analysis tools will need to be developed to minimize the requirement of sophisticated bioinformatics support in clinics. In summary, for successful transition of NGS to clinic, a sustained collaboration between research labs, clinical practitioners and vendors offering sequencing based genetic tests is required.
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Affiliation(s)
- A N Desai
- Persistent LABS, Persistent Systems Ltd., Erandwane, Pune.
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7
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Kitada K, Aida S, Aikawa S. Coamplification of multiple regions of chromosome 2, including MYCN, in a single patchwork amplicon in cancer cell lines. Cytogenet Genome Res 2011; 136:30-7. [PMID: 22123490 DOI: 10.1159/000334349] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2011] [Indexed: 11/19/2022] Open
Abstract
Coamplification of multiple segments of chromosome 2, including an MYCN-bearing segment, was examined in 2 cancer cell lines, NCI-H69 (lung cancer) and IMR-32 (neuroblastoma). High-resolution array-CGH analysis revealed 13 and 6 highly amplified segments located at different sites in chromosome 2 in NCI-H69 and IMR-32, respectively. FISH analysis demonstrated that these segments were co-localized in double minutes in NCI-H69 and in homogeneously staining regions in IMR-32. Connectivity of the segments was determined by a PCR assay using designed primer sets. It was found that all the segments were connected to each other irrespective of their order and orientation against the genome sequence, and a single chain-like cluster was configured in both cell lines. Such patchwork structures of the amplicons suggest the possibility that massive genomic rearrangements, explained by the single catastrophic event model, are involved in the formation of the amplicons, enabling the coamplification of different chromosomal regions including the MYCN locus. The model comprises massive fragmentation of chromosomes and random rejoining of the fragments.
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Affiliation(s)
- K Kitada
- Kamakura Research Laboratories, Chugai Pharmaceutical Co. Ltd., Kamakura, Japan.
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