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Pinto N, Naranjo A, Ding X, Zhang FF, Hibbitts E, Kennedy R, Tibbetts R, Wong-Michalak S, Craig DW, Manojlovic Z, Hogarty MD, Kreissman S, Bagatell R, Irwin MS, Park JR, Asgharzadeh S. Impact of Genomic and Clinical Factors on Outcome of Children ≥18 Months of Age with Stage 3 Neuroblastoma with Unfavorable Histology and without MYCN Amplification: A Children's Oncology Group (COG) Report. Clin Cancer Res 2023; 29:1546-1556. [PMID: 36749880 PMCID: PMC10106446 DOI: 10.1158/1078-0432.ccr-22-3032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/13/2022] [Accepted: 02/06/2023] [Indexed: 02/09/2023]
Abstract
PURPOSE Patients ≥18 months of age with International Neuroblastoma Staging System (INSS) stage 3 unfavorable histology (UH), MYCN-nonamplified (MYCN-NA) tumors have favorable survival rates compared with other high-risk neuroblastoma populations. The impact of select clinical and biological factors on overall survival (OS) and event-free survival (EFS) were evaluated. EXPERIMENTAL DESIGN Patients enrolled on Children's Oncology Group (COG) A3973 (n = 34), ANBL0532 (n = 27), and/or biology protocol ANBL00B1 (n = 72) were analyzed. Tumors with available DNA (n = 65) and RNA (n = 42) were subjected to whole-exome sequencing (WES) and RNA sequencing. WES analyses and gene expression profiling were evaluated for their impact on survival. Multivariate analyses of EFS/OS using significant factors from univariate analyses were performed. RESULTS 5-year EFS/OS for patients treated with high-risk therapy on A3973 and ANBL0532 were 73.0% ± 8.1%/87.9% ± 5.9% and 61.4% ± 10.2%/73.0% ± 9.2%, respectively (P = 0.1286 and P = 0.2180). In the A3973/ANBL0532 cohort, patients with less than partial response (PR; n = 5) at end-induction had poor outcomes (5-year EFS/OS: 0%/20.0% ± 17.9%. Univariate analyses of WES data revealed that subjects whose tumors had chromosome 1p or 11q loss/LOH and chromosome 5 or 9 segmental chromosomal aberrations had inferior EFS compared with those with tumors without these aberrations. Multivariate analysis revealed that 11q loss/LOH was an independent predictor of inferior OS [HR, 3.116 (95% confidence interval, 1.034-9.389), P = 0.0435]. CONCLUSIONS Patients ≥18 months of age at diagnosis who had tumors with UH and MYCN-NA INSS stage 3 neuroblastoma assigned to high-risk therapy had an 81.6% ± 5.3% 5-year OS. Less than PR to induction therapy and chromosome 11q loss/LOH are independent predictors of inferior outcome and identify patients who should be eligible for future high-risk clinical trials.
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Affiliation(s)
- Navin Pinto
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Arlene Naranjo
- Children’s Oncology Group Data and Statistics Center, Department of Biostatistics, University of Florida, Gainesville, Florida, USA
| | - Xiangming Ding
- Department of Pediatrics, University of Southern California, Los Angeles, California, USA
| | - Fan F. Zhang
- Children’s Oncology Group Data and Statistics Center, Monrovia, California, USA
| | - Emily Hibbitts
- Children’s Oncology Group Data and Statistics Center, Department of Biostatistics, University of Florida, Gainesville, Florida, USA
| | - Rebekah Kennedy
- Department of Pediatrics, University of Southern California, Los Angeles, California, USA
| | - Rachelle Tibbetts
- Department of Pediatrics, University of Southern California, Los Angeles, California, USA
| | - Shannon Wong-Michalak
- Department of Pediatrics, University of Southern California, Los Angeles, California, USA
| | - David W Craig
- Department of Pediatrics, University of Southern California, Los Angeles, California, USA
| | - Zarko Manojlovic
- Department of Pediatrics, University of Southern California, Los Angeles, California, USA
| | - Michael D. Hogarty
- Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Susan Kreissman
- Department of Pediatrics, Duke University, Durham, North Carolina, USA
| | - Rochelle Bagatell
- Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Meredith S. Irwin
- Department of Pediatrics, University of Toronto, Toronto, Ontario, CANADA
| | - Julie R. Park
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Shahab Asgharzadeh
- Department of Pediatrics, University of Southern California, Los Angeles, California, USA
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Caglar HO. Bioinformatics analysis of recurrent deletion regions in neuroblastoma. Med Oncol 2022; 39:31. [DOI: 10.1007/s12032-021-01639-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 12/23/2021] [Indexed: 01/09/2023]
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Amirkhani Namagerdi A, d'Angelo D, Ciani F, Iannuzzi CA, Napolitano F, Avallone L, De Laurentiis M, Giordano A. Triple-Negative Breast Cancer Comparison With Canine Mammary Tumors From Light Microscopy to Molecular Pathology. Front Oncol 2020; 10:563779. [PMID: 33282730 PMCID: PMC7689249 DOI: 10.3389/fonc.2020.563779] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 10/19/2020] [Indexed: 12/12/2022] Open
Abstract
Many similar characteristics in human and dog cancers including, spontaneous development, clinical presentation, tumor heterogeneity, disease progression, and response to standard therapies have promoted the approval of this comparative model as an alternative to mice. Breast cancer represents the second most frequent neoplasm in humans after lung cancer. Triple-negative breast cancers (TNBC) constitute around 15% of all cases of breast cancer and do not express estrogen receptor (ER), progesterone receptor (PR), and do not overexpress human epidermal growth factor receptor 2 (HER2). As a result, they do not benefit from hormonal or trastuzumab-based therapy. Patients with TNBC have worse overall survival than patients with non-TNBC. Lehmann and collaborators described six different molecular subtypes of TNBC which further demonstrated its transcriptional heterogeneity. This six TNBC subtype classification has therapeutic implications. Breast cancer is the second most frequent neoplasm in sexually intact female dogs after skin cancer. Canine mammary tumors are a naturally occurring heterogeneous group of cancers that have several features in common with human breast cancer (HBC). These similarities include etiology, signaling pathway activation, and histological classification. Molecularly CMTs are more like TNBCs, and therefore dogs are powerful spontaneous models of cancer to test new therapeutic approaches, particularly for human TNBCs. More malignant tumors of the breast are more often ER and PR negative in both humans and dogs. Promising breast cancer biomarkers in both humans and canines are cancer-associated stroma (CAS), circulating tumor cells and tumor DNA (ctDNA), exosomes and miRNAs, and metabolites.
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Affiliation(s)
| | - Danila d'Angelo
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy
| | - Francesca Ciani
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy
| | | | - Francesco Napolitano
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy.,CCEINGE, Biotecnologie Avanzate, Naples, Italy
| | - Luigi Avallone
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy
| | - Michelino De Laurentiis
- Breast Oncology Division, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Naples, Italy
| | - Antonio Giordano
- Center for Biotechnology, College of Science and Technology, Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, PA, United States.,Department of Medical Biotechnologies, University of Siena, Siena, Italy
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López-Carrasco A, Martín-Vañó S, Burgos-Panadero R, Monferrer E, Berbegall AP, Fernández-Blanco B, Navarro S, Noguera R. Impact of extracellular matrix stiffness on genomic heterogeneity in MYCN-amplified neuroblastoma cell line. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:226. [PMID: 33109237 PMCID: PMC7592549 DOI: 10.1186/s13046-020-01729-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 10/07/2020] [Indexed: 12/13/2022]
Abstract
Background Increased tissue stiffness is a common feature of malignant solid tumors, often associated with metastasis and poor patient outcomes. Vitronectin, as an extracellular matrix anchorage glycoprotein related to a stiff matrix, is present in a particularly increased quantity and specific distribution in high-risk neuroblastoma. Furthermore, as cells can sense and transform the proprieties of the extracellular matrix into chemical signals through mechanotransduction, genotypic changes related to stiffness are possible. Methods We applied high density SNPa and NGS techniques to in vivo and in vitro models (orthotropic xenograft vitronectin knock-out mice and 3D bioprinted hydrogels with different stiffness) using two representative neuroblastoma cell lines (the MYCN-amplified SK-N-BE(2) and the ALK-mutated SH-SY5Y), to discern how tumor genomics patterns and clonal heterogeneity of the two cell lines are affected. Results We describe a remarkable subclonal selection of genomic aberrations in SK-N-BE(2) cells grown in knock-out vitronectin xenograft mice that also emerged when cultured for long times in stiff hydrogels. In particular, we detected an enlarged subclonal cell population with chromosome 9 aberrations in both models. Similar abnormalities were found in human high-risk neuroblastoma with MYCN amplification. The genomics of the SH-SY5Y cell line remained stable when cultured in both models. Conclusions Focus on heterogeneous intratumor segmental chromosome aberrations and mutations, as a mirror image of tumor microenvironment, is a vital area of future research.
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Affiliation(s)
- Amparo López-Carrasco
- Department of Pathology, Medical School, University of Valencia/INCLIVA, Valencia, Spain.,CIBERONC, Madrid, Spain
| | - Susana Martín-Vañó
- Department of Pathology, Medical School, University of Valencia/INCLIVA, Valencia, Spain.,CIBERONC, Madrid, Spain
| | - Rebeca Burgos-Panadero
- Department of Pathology, Medical School, University of Valencia/INCLIVA, Valencia, Spain.,CIBERONC, Madrid, Spain
| | - Ezequiel Monferrer
- Department of Pathology, Medical School, University of Valencia/INCLIVA, Valencia, Spain.,CIBERONC, Madrid, Spain
| | - Ana P Berbegall
- Department of Pathology, Medical School, University of Valencia/INCLIVA, Valencia, Spain.,CIBERONC, Madrid, Spain
| | | | - Samuel Navarro
- Department of Pathology, Medical School, University of Valencia/INCLIVA, Valencia, Spain.,CIBERONC, Madrid, Spain
| | - Rosa Noguera
- Department of Pathology, Medical School, University of Valencia/INCLIVA, Valencia, Spain. .,CIBERONC, Madrid, Spain.
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Newcastle Disease Virus (NDV) Oncolytic Activity in Human Glioma Tumors Is Dependent on CDKN2A-Type I IFN Gene Cluster Codeletion. Cells 2020; 9:cells9061405. [PMID: 32516884 PMCID: PMC7349162 DOI: 10.3390/cells9061405] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/29/2020] [Accepted: 05/31/2020] [Indexed: 12/16/2022] Open
Abstract
Glioblastoma (GBM) is the most aggressive and frequent primary brain tumor in adults with a median overall survival of 15 months. Tumor recurrence and poor prognosis are related to cancer stem cells (CSCs), which drive resistance to therapies. A common characteristic in GBM is CDKN2A gene loss, located close to the cluster of type I IFN genes at Ch9p21. Newcastle disease virus (NDV) is an avian paramyxovirus with oncolytic and immunostimulatory properties that has been proposed for the treatment of GBM. We have analyzed the CDKN2A-IFN I gene cluster in 1018 glioma tumors and evaluated the NDV oncolytic effect in six GBM CSCs ex vivo and in a mouse model. Our results indicate that more than 50% of GBM patients have some IFN deletion. Moreover, GBM susceptibility to NDV is dependent on the loss of the type I IFN. Infection of GBM with an NDV-expressing influenza virus NS1 protein can overcome the resistance to oncolysis by NDV of type I-competent cells. These results highlight the potential of using NDV vectors in antitumor therapies.
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Abstract
The genetic concept of synthetic lethality has now been validated clinically through the demonstrated efficacy of poly(ADP-ribose) polymerase (PARP) inhibitors for the treatment of cancers in individuals with germline loss-of-function mutations in either BRCA1 or BRCA2. Three different PARP inhibitors have now been approved for the treatment of patients with BRCA-mutant ovarian cancer and one for those with BRCA-mutant breast cancer; these agents have also shown promising results in patients with BRCA-mutant prostate cancer. Here, we describe a number of other synthetic lethal interactions that have been discovered in cancer. We discuss some of the underlying principles that might increase the likelihood of clinical efficacy and how new computational and experimental approaches are now facilitating the discovery and validation of synthetic lethal interactions. Finally, we make suggestions on possible future directions and challenges facing researchers in this field.
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Affiliation(s)
- Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA.
| | - Christopher J Lord
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
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Cobrinik D, Ostrovnaya I, Hassimi M, Tickoo SK, Cheung IY, Cheung NKV. Recurrent pre-existing and acquired DNA copy number alterations, including focal TERT gains, in neuroblastoma central nervous system metastases. Genes Chromosomes Cancer 2013; 52:1150-66. [PMID: 24123354 DOI: 10.1002/gcc.22110] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 08/14/2013] [Indexed: 12/13/2022] Open
Abstract
Stage 4 neuroblastomas have a high rate of local and metastatic relapse and associated disease mortality. The central nervous system (CNS) is currently one of the most common isolated relapse sites, yet the genomic alterations that contribute to these metastases are unknown. This study sought to identify recurrent DNA copy number alterations (CNAs) and target genes relating to neuroblastoma CNS metastases by studying 19 pre-CNS primary tumors and 27 CNS metastases, including 12 matched pairs. SNP microarray analyses revealed that MYCN amplified (MYCNA) tumors had recurrent CNAs different from non-MYCNA cohorts. Several CNAs known to be prevalent among primary neuroblastomas occurred more frequently in CNS metastases, including 4p-, 7q+, 12q+, and 19q- in non-MYCNA metastases, and 9p- and 14q- irrespective of MYCNA status. In addition, novel CNS metastases-related CNAs included 18q22.1 gains in non-MYCNA pre-CNS primaries and 5p15.33 gains and 15q26.1→tel losses in non-MYCNA CNS metastases. Based on minimal common regions, gene expression, and biological properties, TERT (5p), NR2F2 (15q), ALDH1A3 (15q), CDKN2A (9p), and possibly CDH7 and CDH19 (18q) were candidate genes associated with the CNS metastatic process. Notably, the 5p15 minimal common region contained only TERT, and non-MYCNA CNS metastases with focal 5p15 gains had increased TERT expression, similar to MYCNA tumors. These findings suggest that a specific genomic lesion (18q22.1 gain) predisposes to CNS metastases and that distinct lesions are recurrently acquired during metastatic progression. Among the acquired lesions, increased TERT copy number and expression appears likely to function in lieu of MYCNA to promote CNS metastasis.
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Affiliation(s)
- David Cobrinik
- Department of Pediatrics, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065
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Garzón I, Roa A, Moreu G, Oliveira AC, Roda O, Alfonso-Rodríguez CA, González-Jaranay M, Sánchez-Quevedo MDC, Alaminos M. Development of a diagnostic algorithm in periodontal disease and identification of genetic expression patterns: A preliminary report. J Dent Sci 2012. [DOI: 10.1016/j.jds.2012.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Cavuoto P, Fenech MF. A review of methionine dependency and the role of methionine restriction in cancer growth control and life-span extension. Cancer Treat Rev 2012; 38:726-36. [PMID: 22342103 DOI: 10.1016/j.ctrv.2012.01.004] [Citation(s) in RCA: 202] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Revised: 12/22/2011] [Accepted: 01/15/2012] [Indexed: 01/11/2023]
Abstract
Methionine is an essential amino acid with many key roles in mammalian metabolism such as protein synthesis, methylation of DNA and polyamine synthesis. Restriction of methionine may be an important strategy in cancer growth control particularly in cancers that exhibit dependence on methionine for survival and proliferation. Methionine dependence in cancer may be due to one or a combination of deletions, polymorphisms or alterations in expression of genes in the methionine de novo and salvage pathways. Cancer cells with these defects are unable to regenerate methionine via these pathways. Defects in the metabolism of folate may also contribute to the methionine dependence phenotype in cancer. Selective killing of methionine dependent cancer cells in co-culture with normal cells has been demonstrated using culture media deficient in methionine. Several animal studies utilizing a methionine restricted diet have reported inhibition of cancer growth and extension of a healthy life-span. In humans, vegan diets, which can be low in methionine, may prove to be a useful nutritional strategy in cancer growth control. The development of methioninase which depletes circulating levels of methionine may be another useful strategy in limiting cancer growth. The application of nutritional methionine restriction and methioninase in combination with chemotherapeutic regimens is the current focus of clinical studies.
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Affiliation(s)
- Paul Cavuoto
- CSIRO Food and Nutritional Sciences, P.O. Box 10041, Adelaide BC, SA 5000, Australia.
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