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Ognibene M, Parodi S, Amoroso L, Zara F, Pezzolo A. Overexpression of H2AFX gene in neuroblastoma is associated with worse prognosis. Pediatr Blood Cancer 2024; 71:e31146. [PMID: 38938078 DOI: 10.1002/pbc.31146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/22/2024] [Accepted: 05/31/2024] [Indexed: 06/29/2024]
Abstract
BACKGROUND Neuroblastoma (NB) is the most common solid tumour in childhood, and rises in the sympathetic nervous system. Here, we addressed the in silico analysis of the association between the expression of H2AFX gene involved in DNA damage response, and the survival of a cohort of 786 NB patients. METHODS In silico gene expression was retrieved from the publicly available dataset summarised by Cangelosi et al., including 13,696 gene expression profiles of 786 NB tumours at onset of disease. The prognostic value of H2AFX (H2A histone family member X) gene expression for event-free survival (EFS) and overall survival (OS) was evaluated by Kaplan-Meier and Cox regression analysis. The main results were validated on another openly accessible in silico database (NRC-283) containing 13,489 gene expressions in 283 NB patients. The expression of H2AFX protein was then tested by immunofluorescence on 48 primary NB samples of different tumour stages. H2AFX activity as an oncogene has been further validated in vitro by silencing the molecule in two NB cell lines, characterised by MYCN amplified or not, and performing cell growth and migration assays. RESULTS A strong inverse association between H2AFX expression and patients' survival was observed and confirmed by immunofluorescence results on primary NB tissue sections. Cox regression analysis also disclosed H2AFX as an independent predictor of EFS and OS. The gene-silencing experiments strongly suggested an oncogenic role for H2AFX on NB cells, regardless of MYCN amplification. CONCLUSIONS H2AFX is a prognostic marker for unfavourable NB and could be considered a target for therapeutic interventions.
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Affiliation(s)
- Marzia Ognibene
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Stefano Parodi
- Epidemiologia e Biostatistica, Direzione Scientifica, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Loredana Amoroso
- UOC Oncologia Pediatrica, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Federico Zara
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Genoa, Italy
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2
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Bianchini L, Sieber L, Hammad R, Schäfer R, Kutscher LM. Generation of two isogenic patient-derived human-induced pluripotent stem cell clones with 6q27 deletion. Stem Cell Res 2024; 80:103524. [PMID: 39106599 DOI: 10.1016/j.scr.2024.103524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Accepted: 07/30/2024] [Indexed: 08/09/2024] Open
Abstract
We generated two human induced pluripotent cell (hiPSC) isogenic clones from an 11-year-old patient with 6q27 deletion syndrome. The heterozygous deletion encompasses approximately 240 kilobases, affecting 6 genes (promoter region of WDR27, coding regions of C6orf120, PHF10, DYNLT2, ERMARD, LINC00242). The patient suffered from epilepsy, psychosocial retardation, and a metabolic disorder. The patient also had a history of SHH-medulloblastoma as an infant. The generated hiPSCs represent a useful tool for modelling 6q27 deletion syndrome in vitro and understanding the molecular basis of the disorder.
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Affiliation(s)
- Luca Bianchini
- Developmental Origins of Pediatric Cancer Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
| | - Laura Sieber
- Developmental Origins of Pediatric Cancer Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
| | - Ruba Hammad
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany; Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Freiburg, Germany; Freiburg iPS Core, Medical Center-University of Freiburg, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Richard Schäfer
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany; Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Freiburg, Germany; Freiburg iPS Core, Medical Center-University of Freiburg, Freiburg, Germany
| | - Lena M Kutscher
- Developmental Origins of Pediatric Cancer Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.
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Kang J, Jiang J, Xiang X, Zhang Y, Tang J, Li L. Identification of a new gene signature for prognostic evaluation in cervical cancer: based on cuproptosis-associated angiogenesis and multi-omics analysis. Cancer Cell Int 2024; 24:23. [PMID: 38200479 PMCID: PMC10782580 DOI: 10.1186/s12935-023-03189-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024] Open
Abstract
Patients with recurrent or metastatic cervical cancer are in urgent need of novel prognosis assessment or treatment approaches. In this study, a novel prognostic gene signature was discovered by utilizing cuproptosis-related angiogenesis (CuRA) gene scores obtained through weighted gene co-expression network analysis (WGCNA) of The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. To enhance its reliability, the gene signature was refined by integrating supplementary clinical variables and subjected to cross-validation. Meanwhile, the activation of the VEGF pathway was inferred from an analysis of cell-to-cell communication, based on the expression of ligands and receptors in cell transcriptomic datasets. High-CuRA patients had less infiltration of CD8 + T cells and reduced expression of most of immune checkpoint genes, which indicated greater difficulty in immunotherapy. Lower IC50 values of imatinib, pazopanib, and sorafenib in the high-CuRA group revealed the potential value of these drugs. Finally, we verified an independent prognostic gene SFT2D1 was highly expressed in cervical cancer and positively correlated with the microvascular density. Knockdown of SFT2D1 significantly inhibited ability of the proliferation, migration, and invasive in cervical cancer cells. CuRA gene signature provided valuable insights into the prediction of prognosis and immune microenvironment of cervical cancer, which could help develop new strategies for individualized precision therapy for cervical cancer patients.
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Affiliation(s)
- Jiawen Kang
- Department of Gynecologic Oncology, School of Medicine, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya, Central South University, Changsha, Hunan, China
- Department of Clinical Medicine, Medical College of Hunan Normal University, Changsha, Hunan, China
| | - Jingwen Jiang
- Department of Clinical Medicine, Medical College of Hunan Normal University, Changsha, Hunan, China
| | - Xiaoqing Xiang
- Department of Clinical Medicine, Medical College of Hunan Normal University, Changsha, Hunan, China
| | - Yong Zhang
- Department of Clinical Medicine, Medical College of Hunan Normal University, Changsha, Hunan, China.
| | - Jie Tang
- Department of Gynecologic Oncology, School of Medicine, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya, Central South University, Changsha, Hunan, China.
| | - Lesai Li
- Department of Gynecologic Oncology, School of Medicine, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya, Central South University, Changsha, Hunan, China.
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Bardhan A, Banerjee A, Pal DK, Ghosh A. HAGLR, A Long Non-coding RNA of Potential Tumor Suppressive Function in Clear Cell Renal Cell Carcinoma: Diagnostic and Prognostic Implications. Mol Biotechnol 2023:10.1007/s12033-023-00948-z. [PMID: 37955777 DOI: 10.1007/s12033-023-00948-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 10/16/2023] [Indexed: 11/14/2023]
Abstract
Research works suggested the role of long non-coding RNAs (lncRNAs) in pathogenesis of clear cell renal cell carcinoma (ccRCC). lncRNA HAGLR is studied in several malignancies, but not in ccRCC. From The Cancer Genome Atlas Kidney Renal Clear Cell Carcinoma (TCGA-KIRC) dataset, we analyzed molecular alterations of HAGLR and constructed a competitive endogenous RNA (ceRNA) network with related miRNAs and mRNAs. Gene Ontology analysis was done to identify important pathways enriched with HAGLR recovered mRNAs. Clinical importance of HAGLR and related mRNAs was assessed and, the impact of selected mRNA-encoding genes on tumor immune infiltration was studied using TIMER. HAGLR expression was reduced in ccRCC than in normal kidneys, and correlated significantly with gene promoter methylation. Low HAGLR level in tumors showed diagnostic potency, and was associated with clinicopathological parameters (stage/grade/metastasis) and poor patient survival. The HAGLR-associated ceRNA network constituted 13 miRNAs and 23 mRNAs differentially expressed in the TCGA-KIRC dataset. From HAGLR recovered mRNA-encoding genes, we developed a 5-gene (PAQR5, ARHGAP24, HABP4, PDLIM5, and RPS6KA2) prognostic signature in the training dataset and validated it in testing as well as entire datasets. The expression level of signature genes showed negative correlation with tumor infiltration of immune cells having adverse impact on ccRCC prognosis and also with tumor derived chemokines facilitating the infiltration. In conclusion, HAGLR seemed to play a tumor suppressive role in ccRCC. HAGLR and associated gene signature may have implementation in improving existing prognostic measure and developing effective immunotherapeutic strategies for ccRCC.
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Affiliation(s)
- Abhishek Bardhan
- Genetics of Non-communicable Diseases, Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, West Bengal, 700073, India
| | - Anwesha Banerjee
- Genetics of Non-communicable Diseases, Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, West Bengal, 700073, India
| | | | - Amlan Ghosh
- Genetics of Non-communicable Diseases, Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, West Bengal, 700073, India.
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Ognibene M, De Marco P, Amoroso L, Fragola M, Zara F, Parodi S, Pezzolo A. Neuroblastoma Patients' Outcome and Chromosomal Instability. Int J Mol Sci 2023; 24:15514. [PMID: 37958497 PMCID: PMC10648898 DOI: 10.3390/ijms242115514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/20/2023] [Accepted: 10/21/2023] [Indexed: 11/15/2023] Open
Abstract
Chromosomal instability (CIN) induces a high rate of losses or gains of whole chromosomes or parts of chromosomes. It is a hallmark of most human cancers and one of the causes of aneuploidy and intra-tumor heterogeneity. The present study aimed to evaluate the potential prognostic role of CIN in NB patients at diagnosis. We performed array comparative genomic hybridization analyses on 451 primary NB patients at the onset of the disease. To assess global chromosomal instability with high precision, we focused on the total number of DNA breakpoints of gains or losses of chromosome arms. For each tumor, an array-CGH-based breakpoint instability index (BPI) was assigned which defined the total number of chromosomal breakpoints per genome. This approach allowed us to quantify CIN related to whole genome disruption in all NB cases analyzed. We found differences in chromosomal breakages among the NB clinical risk groups. High BPI values are negatively associated with survival of NB patients. This association remains significant when correcting for stage, age, and MYCN status in the Cox model. Stratified analysis confirms the prognostic effect of BPI index in low-risk NB patients with non-amplified MYCN and with segmental chromosome aberrations.
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Affiliation(s)
- Marzia Ognibene
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (P.D.M.); (F.Z.)
| | - Patrizia De Marco
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (P.D.M.); (F.Z.)
| | - Loredana Amoroso
- U.O.C. Oncologia Pediatrica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy;
| | - Martina Fragola
- Epidemiologia e Biostatistica, Direzione Scientifica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (M.F.); (S.P.)
| | - Federico Zara
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (P.D.M.); (F.Z.)
| | - Stefano Parodi
- Epidemiologia e Biostatistica, Direzione Scientifica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (M.F.); (S.P.)
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Ognibene M, De Marco P, Amoroso L, Cangelosi D, Zara F, Parodi S, Pezzolo A. Multiple Genes with Potential Tumor Suppressive Activity Are Present on Chromosome 10q Loss in Neuroblastoma and Are Associated with Poor Prognosis. Cancers (Basel) 2023; 15:cancers15072035. [PMID: 37046696 PMCID: PMC10093755 DOI: 10.3390/cancers15072035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Neuroblastoma (NB) is a tumor affecting the peripheral sympathetic nervous system that substantially contributes to childhood cancer mortality. Despite recent advances in understanding the complexity of NB, the mechanisms determining its progression are still largely unknown. Some recurrent segmental chromosome aberrations (SCA) have been associated with poor survival. However, the prognostic role of most SCA has not yet been investigated. We examined a cohort of 260 NB primary tumors at disease onset for the loss of chromosome 10q, by array-comparative genomic hybridization (a-CGH) and Single Nucleotide Polymorphism (SNP) array and we found that 26 showed 10q loss, while the others 234 displayed different SCA. We observed a lower event-free survival for NB patients displaying 10q loss compared to patients with tumors carrying other SCA. Furthermore, analyzing the region of 10q loss, we identified a cluster of 75 deleted genes associated with poorer outcome. Low expression of six of these genes, above all CCSER2, was significantly correlated to worse survival using in silico data from 786 NB patients. These potential tumor suppressor genes can be partly responsible for the poor prognosis of NB patients with 10q loss.
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Amplification of CDK4 and MDM2: a detailed study of a high-risk neuroblastoma subgroup. Sci Rep 2022; 12:12420. [PMID: 35859155 PMCID: PMC9300649 DOI: 10.1038/s41598-022-16455-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 07/11/2022] [Indexed: 11/08/2022] Open
Abstract
In neuroblastoma, MYCN amplification and 11q-deletion are important, although incomplete, markers of high-risk disease. It is therefore relevant to characterize additional alterations that can function as prognostic and/or predictive markers. Using SNP-microarrays, a group of neuroblastoma patients showing amplification of one or multiple 12q loci was identified. Two loci containing CDK4 and MDM2 were commonly co-amplified, although amplification of either locus in the absence of the other was observed. Pharmacological inhibition of CDK4/6 with ribociclib or abemaciclib decreased proliferation in a broad set of neuroblastoma cell lines, including CDK4/MDM2-amplified, whereas MDM2 inhibition by Nutlin-3a was only effective in p53wild-type cells. Combined CDK4/MDM2 targeting had an additive effect in p53wild-type cell lines, while no or negative additive effect was observed in p53mutated cells. Most 12q-amplified primary tumors were of abdominal origin, including those of intrarenal origin initially suspected of being Wilms' tumor. An atypical metastatic pattern was also observed with low degree of bone marrow involvement, favoring other sites such as the lungs. Here we present detailed biological data of an aggressive neuroblastoma subgroup hallmarked by 12q amplification and atypical clinical presentation for which our in vitro studies indicate that CDK4 and/or MDM2 inhibition also could be beneficial.
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Ognibene M, De Marco P, Parodi S, Meli M, Di Cataldo A, Zara F, Pezzolo A. Genomic Analysis Made It Possible to Identify Gene-Driver Alterations Covering the Time Window between Diagnosis of Neuroblastoma 4S and the Progression to Stage 4. Int J Mol Sci 2022; 23:ijms23126513. [PMID: 35742955 PMCID: PMC9224358 DOI: 10.3390/ijms23126513] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/06/2022] [Accepted: 06/09/2022] [Indexed: 02/04/2023] Open
Abstract
Neuroblastoma (NB) is a tumor of the developing sympathetic nervous system. Despite recent advances in understanding the complexity of NB, the mechanisms that determine its regression or progression are still largely unknown. Stage 4S NB is characterized by a favorable course of disease and often by spontaneous regression, while progression to true stage 4 is a very rare event. Here, we focused on genomic analysis of an NB case that progressed from stage 4S to stage 4 with a very poor outcome. Array-comparative genomic hybridization (a-CGH) on tumor-tissue DNA, and whole-exome sequencing (WES) on exosomes DNA derived from plasma collected at the onset and at the tumor progression, pointed out relevant genetic changes that can explain this clinical worsening. The combination of a-CGH and WES data allowed for the identification iof somatic copy number aberrations and single-nucleotide variants in genes known to be responsible for aggressive NB. KLRB1, MAPK3 and FANCA genes, which were lost at the time of progression, were studied for their possible role in this event by analyzing in silico the impact of their expression on the outcome of 786 NB patients.
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Affiliation(s)
- Marzia Ognibene
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (P.D.M.); (F.Z.)
- Correspondence: ; Tel.: +39-010-5636-2601
| | - Patrizia De Marco
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (P.D.M.); (F.Z.)
| | - Stefano Parodi
- Scientific Directorate, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy;
| | - Mariaclaudia Meli
- U.O.C. Ematologia e Oncologia Pediatrica, Dipartimento di Medicina Clinica e Sperimentale, Università di Catania, 95123 Catania, Italy; (M.M.); (A.D.C.)
| | - Andrea Di Cataldo
- U.O.C. Ematologia e Oncologia Pediatrica, Dipartimento di Medicina Clinica e Sperimentale, Università di Catania, 95123 Catania, Italy; (M.M.); (A.D.C.)
| | - Federico Zara
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (P.D.M.); (F.Z.)
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High Grade of Amplification of Six Regions on Chromosome 2p in a Neuroblastoma Patient with Very Poor Outcome: The Putative New Oncogene TSSC1. Cancers (Basel) 2021; 13:cancers13225792. [PMID: 34830942 PMCID: PMC8616235 DOI: 10.3390/cancers13225792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 12/02/2022] Open
Abstract
Simple Summary Here, a case of neuroblastoma (NB) carrying a high-grade amplification of six loci besides MYCN is described. Since the patient had a very poor outcome, we postulated that these DNA co-amplifications might have a synergistic effect in increasing NB cell proliferation. In order to verify this hypothesis, we analyzed in silico the impact of high expression of the genes located within the amplifications on the NB patients’ outcome using a large dataset integrating three different platforms. These analyses disclosed that high expression of the TSSC1 gene was the most significantly associated with reduced overall survival of NB patients, suggesting that it may have a potential prognostic role in NB in both MYCN amplified and MYCN not amplified tumors. Further studies on TSSC1 interactions and functioning could lead to possible focused therapies for high-risk NB patients. Abstract We observed a case of high-risk neuroblastoma (NB) carried by a 28-month-old girl, displaying metastatic disease and a rapid decline of clinical conditions. By array-CGH analysis of the tumor tissue and of the metastatic bone marrow aspirate cells, we found a high-grade amplification of six regions besides MYCN on bands 2p25.3–p24.3. The genes involved in these amplifications were MYT1L, TSSC1, CMPK2, RSAD2, RNF144A, GREB1, NTSR2, LPIN1, NBAS, and the two intergenic non-protein coding RNAs LOC730811 and LOC339788. We investigated if these DNA co-amplifications may have an effect on enhancing tumor aggressiveness. We evaluated the association between the high expression of the amplified genes and NB patient’s outcome using the integration of gene expression data of 786 NB samples profiled with different public platforms from patients with at least five-year follow-up. NB patients with high expression of the TSSC1 gene were associated with a reduced survival rate. Immunofluorescence staining on primary tumor tissues confirmed that the TSSC1 protein expression was high in the relapsed or dead stage 4 cases, but it was generally low in NB patients in complete remission. TSSC1 appears as a putative new oncogene in NB.
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Integrating multiple genomic imaging data for the study of lung metastasis in sarcomas using multi-dimensional constrained joint non-negative matrix factorization. Inf Sci (N Y) 2021. [DOI: 10.1016/j.ins.2021.06.058] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Molecular Genetics in Neuroblastoma Prognosis. CHILDREN-BASEL 2021; 8:children8060456. [PMID: 34072462 PMCID: PMC8226597 DOI: 10.3390/children8060456] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/23/2021] [Accepted: 05/27/2021] [Indexed: 12/12/2022]
Abstract
In recent years, much research has been carried out to identify the biological and genetic characteristics of the neuroblastoma (NB) tumor in order to precisely define the prognostic subgroups for improving treatment stratification. This review will describe the major genetic features and the recent scientific advances, focusing on their impact on diagnosis, prognosis, and therapeutic solutions in NB clinical management.
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Degli Esposti C, Iadarola B, Maestri S, Beltrami C, Lavezzari D, Morini M, De Marco P, Erminio G, Garaventa A, Zara F, Delledonne M, Ognibene M, Pezzolo A. Exosomes from Plasma of Neuroblastoma Patients Contain Doublestranded DNA Reflecting the Mutational Status of Parental Tumor Cells. Int J Mol Sci 2021; 22:ijms22073667. [PMID: 33915956 PMCID: PMC8036333 DOI: 10.3390/ijms22073667] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 03/28/2021] [Accepted: 03/30/2021] [Indexed: 02/07/2023] Open
Abstract
Neuroblastoma (NB) is an aggressive infancy tumor, leading cause of death among preschool age diseases. Here we focused on characterization of exosomal DNA (exo-DNA) isolated from plasma cell-derived exosomes of neuroblastoma patients, and its potential use for detection of somatic mutations present in the parental tumor cells. Exosomes are small extracellular membrane vesicles secreted by most cells, playing an important role in intercellular communications. Using an enzymatic method, we provided evidence for the presence of double-stranded DNA in the NB exosomes. Moreover, by whole exome sequencing, we demonstrated that NB exo-DNA represents the entire exome and that it carries tumor-specific genetic mutations, including those occurring on known oncogenes and tumor suppressor genes in neuroblastoma (ALK, CHD5, SHANK2, PHOX2B, TERT, FGFR1, and BRAF). NB exo-DNA can be useful to identify variants responsible for acquired resistance, such as mutations of ALK, TP53, and RAS/MAPK genes that appear in relapsed patients. The possibility to isolate and to enrich NB derived exosomes from plasma using surface markers, and the quick and easy extraction of exo-DNA, gives this methodology a translational potential in the clinic. Exo-DNA can be an attractive non-invasive biomarker for NB molecular diagnostic, especially when tissue biopsy cannot be easily available.
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Affiliation(s)
- Chiara Degli Esposti
- Dipartimento di Biotecnologie, Università degli Studi di Verona, 37134 Verona, Italy; (C.D.E.); (B.I.); (S.M.); (C.B.); (D.L.); (M.D.)
| | - Barbara Iadarola
- Dipartimento di Biotecnologie, Università degli Studi di Verona, 37134 Verona, Italy; (C.D.E.); (B.I.); (S.M.); (C.B.); (D.L.); (M.D.)
| | - Simone Maestri
- Dipartimento di Biotecnologie, Università degli Studi di Verona, 37134 Verona, Italy; (C.D.E.); (B.I.); (S.M.); (C.B.); (D.L.); (M.D.)
| | - Cristina Beltrami
- Dipartimento di Biotecnologie, Università degli Studi di Verona, 37134 Verona, Italy; (C.D.E.); (B.I.); (S.M.); (C.B.); (D.L.); (M.D.)
| | - Denise Lavezzari
- Dipartimento di Biotecnologie, Università degli Studi di Verona, 37134 Verona, Italy; (C.D.E.); (B.I.); (S.M.); (C.B.); (D.L.); (M.D.)
| | - Martina Morini
- Laboratorio di Biologia Molecolare, IRCCS Giannina Gaslini, 16147 Genova, Italy;
| | - Patrizia De Marco
- U.O.C. Genetica Medica, IRCCS Giannina Gaslini, 16147 Genova, Italy; (P.D.M.); (F.Z.)
| | - Giovanni Erminio
- Epidemiologia e Biostatistica, IRCCS Giannina Gaslini, 16147 Genova, Italy;
| | - Alberto Garaventa
- Divisione di Oncologia, IRCCS Giannina Gaslini, 16147 Genova, Italy;
| | - Federico Zara
- U.O.C. Genetica Medica, IRCCS Giannina Gaslini, 16147 Genova, Italy; (P.D.M.); (F.Z.)
| | - Massimo Delledonne
- Dipartimento di Biotecnologie, Università degli Studi di Verona, 37134 Verona, Italy; (C.D.E.); (B.I.); (S.M.); (C.B.); (D.L.); (M.D.)
| | - Marzia Ognibene
- U.O.C. Genetica Medica, IRCCS Giannina Gaslini, 16147 Genova, Italy; (P.D.M.); (F.Z.)
- Correspondence: ; Tel.: +39-010-56362601
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Liu Z, Liang M, Grant CN, Spiegelman VS, Wang HG. Interpretable models for high-risk neuroblastoma stratification with multi-cohort copy number profiles. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Fransson S, Martinez-Monleon A, Johansson M, Sjöberg RM, Björklund C, Ljungman G, Ek T, Kogner P, Martinsson T. Whole-genome sequencing of recurrent neuroblastoma reveals somatic mutations that affect key players in cancer progression and telomere maintenance. Sci Rep 2020; 10:22432. [PMID: 33384420 PMCID: PMC7775426 DOI: 10.1038/s41598-020-78370-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 11/24/2020] [Indexed: 11/23/2022] Open
Abstract
Neuroblastoma is the most common and deadly childhood tumor. Relapsed or refractory neuroblastoma has a very poor prognosis despite recent treatment advances. To investigate genomic alterations associated with relapse and therapy resistance, whole-genome sequencing was performed on diagnostic and relapsed lesions together with constitutional DNA from seven children. Sequencing of relapsed tumors indicates somatic alterations in diverse genes, including those involved in RAS-MAPK signaling, promoting cell cycle progression or function in telomere maintenance and immortalization. Among recurrent alterations, CCND1-gain, TERT-rearrangements, and point mutations in POLR2A, CDK5RAP, and MUC16 were shown in ≥ 2 individuals. Our cohort contained examples of converging genomic alterations in primary-relapse tumor pairs, indicating dependencies related to specific genetic lesions. We also detected rare genetic germline variants in DNA repair genes (e.g., BARD1, BRCA2, CHEK2, and WRN) that might cooperate with somatically acquired variants in these patients with highly aggressive recurrent neuroblastoma. Our data indicate the importance of monitoring recurrent neuroblastoma through sequential genomic characterization and that new therapeutic approaches combining the targeting of MAPK signaling, cell cycle progression, and telomere activity are required for this challenging patient group.
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Affiliation(s)
- Susanne Fransson
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Box 445, 405 30, Gothenburg, Sweden.
| | - Angela Martinez-Monleon
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Box 445, 405 30, Gothenburg, Sweden
| | | | - Rose-Marie Sjöberg
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Box 445, 405 30, Gothenburg, Sweden
| | | | - Gustaf Ljungman
- Department of Women's and Children's Health, Children's University Hospital, University of Uppsala, Uppsala, Sweden
| | - Torben Ek
- Children's Cancer Center, Queen Silvia Children's Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Per Kogner
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Tommy Martinsson
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Box 445, 405 30, Gothenburg, Sweden
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15
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Ognibene M, Pezzolo A. Ezrin interacts with the tumor suppressor CHL1 and promotes neuronal differentiation of human neuroblastoma. PLoS One 2020; 15:e0244069. [PMID: 33326488 PMCID: PMC7743987 DOI: 10.1371/journal.pone.0244069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 12/02/2020] [Indexed: 11/30/2022] Open
Abstract
In a previous study, we demonstrated that CHL1, the neuronal cell adhesion molecule close homolog of L1, acts as a tumor suppressor in human neuroblastoma (NB), a still highly lethal childhood malignancy, influencing its differentiation and proliferation degree. Here we found that ezrin, one of the ERM (ezrin, radixin, moesin) proteins involved in cytoskeleton organization, strongly interacts with CHL1. The low expression of EZRIN, as well as the low expression of CHL1 and of the neuronal differentiation marker MAP2, correlates with poor outcome in NB patients. Knock-down of ezrin in HTLA-230 cell line induces neurite retraction, enhances cell proliferation and migration, and triggers anchorage-independent growth, with effects very similar to those already obtained by CHL1 silencing. Furthermore, lack of ezrin inhibits the expression of MAP2 and of the oncosuppressor molecule p53, whereas it enhances MAPK activation, all typical features of tumor aggressiveness. As already described, CHL1 overexpression in IMR-32 cell line provokes an opposite trend, but the co-silencing of ezrin reduces these effects, confirming the hypothesis that CHL1 acts in close connection with ezrin. Overall, our data show that ezrin reinforces the differentiating and oncosuppressive functions of CHL1, identifying this ERM protein as a new targetable molecule for NB therapy.
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Affiliation(s)
- Marzia Ognibene
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, Genova, Italy
- * E-mail:
| | - Annalisa Pezzolo
- Laboratorio Cellule Staminali Post Natali e Terapie Cellulari, IRCCS Istituto Giannina Gaslini, Genova, Italy
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16
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Liu D, Zhou D, Sun Y, Zhu J, Ghoneim D, Wu C, Yao Q, Gamazon ER, Cox NJ, Wu L. A Transcriptome-Wide Association Study Identifies Candidate Susceptibility Genes for Pancreatic Cancer Risk. Cancer Res 2020; 80:4346-4354. [PMID: 32907841 PMCID: PMC7572664 DOI: 10.1158/0008-5472.can-20-1353] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/25/2020] [Accepted: 08/14/2020] [Indexed: 12/13/2022]
Abstract
Pancreatic cancer is among the most well-characterized cancer types, yet a large proportion of the heritability of pancreatic cancer risk remains unclear. Here, we performed a large transcriptome-wide association study to systematically investigate associations between genetically predicted gene expression in normal pancreas tissue and pancreatic cancer risk. Using data from 305 subjects of mostly European descent in the Genotype-Tissue Expression Project, we built comprehensive genetic models to predict normal pancreas tissue gene expression, modifying the UTMOST (unified test for molecular signatures). These prediction models were applied to the genetic data of 8,275 pancreatic cancer cases and 6,723 controls of European ancestry. Thirteen genes showed an association of genetically predicted expression with pancreatic cancer risk at an FDR ≤ 0.05, including seven previously reported genes (INHBA, SMC2, ABO, PDX1, RCCD1, CFDP1, and PGAP3) and six novel genes not yet reported for pancreatic cancer risk [6q27: SFT2D1 OR (95% confidence interval (CI), 1.54 (1.25-1.89); 13q12.13: MTMR6 OR (95% CI), 0.78 (0.70-0.88); 14q24.3: ACOT2 OR (95% CI), 1.35 (1.17-1.56); 17q12: STARD3 OR (95% CI), 6.49 (2.96-14.27); 17q21.1: GSDMB OR (95% CI), 1.94 (1.45-2.58); and 20p13: ADAM33 OR (95% CI): 1.41 (1.20-1.66)]. The associations for 10 of these genes (SFT2D1, MTMR6, ACOT2, STARD3, GSDMB, ADAM33, SMC2, RCCD1, CFDP1, and PGAP3) remained statistically significant even after adjusting for risk SNPs identified in previous genome-wide association study. Collectively, this analysis identified novel candidate susceptibility genes for pancreatic cancer that warrant further investigation. SIGNIFICANCE: A transcriptome-wide association analysis identified seven previously reported and six novel candidate susceptibility genes for pancreatic cancer risk.
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Affiliation(s)
- Duo Liu
- Department of Pharmacy, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, P.R. China
- Division of Cancer Epidemiology, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Dan Zhou
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yanfa Sun
- Division of Cancer Epidemiology, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii
- College of Life Science, Longyan University, Longyan, Fujian, P.R. China
- Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan, Fujian, P.R. China
- Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Fujian Province University, Longyan, Fujian, P.R. China
| | - Jingjing Zhu
- Division of Cancer Epidemiology, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Dalia Ghoneim
- Division of Cancer Epidemiology, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Chong Wu
- Department of Statistics, Florida State University, Tallahassee, Florida
| | - Qizhi Yao
- Division of Surgical Oncology, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas
- Center for Translational Research on Inflammatory Diseases (CTRID), Michael E. DeBakey VA Medical Center, Houston, Texas
| | - Eric R Gamazon
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Clare Hall, University of Cambridge, Cambridge, United Kingdom
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Nancy J Cox
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Lang Wu
- Division of Cancer Epidemiology, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii.
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