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Mohan D, Nambirajan A, Malik R, Sharma A, Suri V, Kaur K, Doddamani R, Garg A, Gupta S, Mallick S, Sharma MC. MYCN immunohistochemistry as surrogate marker for MYCN-amplified spinal ependymomas. Hum Cell 2024; 37:704-713. [PMID: 38411836 DOI: 10.1007/s13577-024-01037-2] [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: 07/10/2023] [Accepted: 01/21/2024] [Indexed: 02/28/2024]
Abstract
MYCN (master regulator of cell cycle entry and proliferative metabolism) gene amplification defines a molecular subgroup of spinal cord ependymomas that show high-grade morphology and aggressive behavior. Demonstration of MYCN amplification by DNA methylation or fluorescence-in situ hybridization (FISH) is required for diagnosis. We aimed to (i) assess prevalence and clinicopathological features of MYCN-amplified spinal ependymomas and (ii) evaluate utility of immunohistochemistry (IHC) for MYCN protein as a surrogate for molecular testing. A combined retrospective-prospective study spanning 8 years was designed during which all spinal cord ependymomas with adequate tissue were subjected to MYCN FISH and MYCN IHC. Among 77 spinal cord ependymomas included, MYCN amplification was identified in 4 samples from 3 patients (3/74, 4%) including two (1st and 2nd recurrences) from the same patient. All patients were adults (median age at diagnosis of 32 years) including two females and one male. The index tumors were located in thoracic (n = 2) and lumbar (n = 1) spinal cord. One of the female patients had neurofibromatosis type 2 (NF2). All four tumors showed anaplastic histology. Diffuse expression of MYCN protein was seen in all four MYCN-amplified samples but in none of the non-amplified cases, thus showing 100% concordance with FISH results. On follow-up, the NF2 patient developed widespread spinal dissemination while another developed recurrence proximal to the site of previous excision. To conclude, MYCN-amplified spinal ependymomas are rare tumors, accounting for ~ 4% of spinal cord ependymomas. Within the limitation of small sample size, MYCN IHC showed excellent concordance with MYCN gene amplification.
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Affiliation(s)
- Divya Mohan
- Departments of Pathology, Neurosurgery, Neuroradiology and Radiation Oncology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Aruna Nambirajan
- Departments of Pathology, Neurosurgery, Neuroradiology and Radiation Oncology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Rafat Malik
- Departments of Pathology, Neurosurgery, Neuroradiology and Radiation Oncology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Agrima Sharma
- Departments of Pathology, Neurosurgery, Neuroradiology and Radiation Oncology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Vaishali Suri
- Departments of Pathology, Neurosurgery, Neuroradiology and Radiation Oncology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Kavneet Kaur
- Departments of Pathology, Neurosurgery, Neuroradiology and Radiation Oncology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Ramesh Doddamani
- Departments of Pathology, Neurosurgery, Neuroradiology and Radiation Oncology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Ajay Garg
- Departments of Pathology, Neurosurgery, Neuroradiology and Radiation Oncology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Subhash Gupta
- Departments of Pathology, Neurosurgery, Neuroradiology and Radiation Oncology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Supriya Mallick
- Departments of Pathology, Neurosurgery, Neuroradiology and Radiation Oncology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Mehar Chand Sharma
- Departments of Pathology, Neurosurgery, Neuroradiology and Radiation Oncology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India.
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Do AD, Wu KS, Chu SS, Giang LH, Lin YL, Chang CC, Wong TT, Hsieh CL, Sung SY. LOXL1-AS1 contributes to metastasis in sonic-hedgehog medulloblastoma by promoting cancer stem-like phenotypes. J Exp Clin Cancer Res 2024; 43:130. [PMID: 38689348 PMCID: PMC11059759 DOI: 10.1186/s13046-024-03057-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 04/22/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Medulloblastomas (MBs) are one of the most common malignant brain tumor types in children. MB prognosis, despite improvement in recent years, still depends on clinical and biological risk factors. Metastasis is the leading cause of MB-related deaths, which highlights an unmet need for risk stratification and targeted therapy to improve clinical outcomes. Among the four molecular subgroups, sonic-hedgehog (SHH)-MB harbors clinical and genetic heterogeneity with a subset of high-risk cases. Recently, long non-coding (lnc)RNAs were implied to contribute to cancer malignant progression, but their role in MB remains unclear. This study aimed to identify pro-malignant lncRNAs that have prognostic and therapeutic significance in SHH-MB. METHODS The Daoy SHH-MB cell line was engineered for ectopic expression of MYCN, a genetic signature of SHH-MB. MYCN-associated lncRNA genes were identified using RNA-sequencing data and were validated in SHH-MB cell lines, MB tissue samples, and patient cohort datasets. SHH-MB cells with genetic manipulation of the candidate lncRNA were evaluated for metastatic phenotypes in vitro, including cell migration, invasion, sphere formation, and expressions of stemness markers. An orthotopic xenograft mouse model was used to evaluate metastasis occurrence and survival. Finally, bioinformatic screening and in vitro assays were performed to explore downstream mechanisms. RESULTS Elevated lncRNA LOXL1-AS1 expression was identified in MYCN-expressing Daoy cells and MYCN-amplified SHH-MB tumors, and was significantly associated with lower survival in SHH-MB patients. Functionally, LOXL1-AS1 promoted SHH-MB cell migration and cancer stemness in vitro. In mice, MYCN-expressing Daoy cells exhibited a high metastatic rate and adverse effects on survival, both of which were suppressed under LOLX1-AS1 perturbation. Integrative bioinformatic analyses revealed associations of LOXL1-AS1 with processes of cancer stemness, cell differentiation, and the epithelial-mesenchymal transition. LOXL1-AS1 positively regulated the expression of transforming growth factor (TGF)-β2. Knockdown of TGF-β2 in SHH-MB cells significantly abrogated their LOXL1-AS1-mediated prometastatic functions. CONCLUSIONS This study proved the functional significance of LOXL1-AS1 in SHH-MB metastasis by its promotion of TGF-β2-mediated cancer stem-like phenotypes, providing both prognostic and therapeutic potentials for targeting SHH-MB metastasis.
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Affiliation(s)
- Anh Duy Do
- International Ph.D. Program for Translational Science, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan
- Department of Physiology, Pathophysiology and Immunology, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, 700000, Vietnam
| | - Kuo-Sheng Wu
- Graduate Institute of Clinical Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, 11031, Taiwan
| | - Shing-Shung Chu
- Graduate Institute of Clinical Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, 11031, Taiwan
| | - Le Hien Giang
- International Ph.D. Program for Translational Science, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan
- Department of Biology and Genetics, Hai Phong University of Medicine and Pharmacy, Hai Phong, 180000, Vietnam
| | - Yu-Ling Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Che-Chang Chang
- International Ph.D. Program for Translational Science, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan
- Neuroscience Research Center, Taipei Medical University Hospital, Taipei, 11031, Taiwan
| | - Tai-Tong Wong
- Graduate Institute of Clinical Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, 11031, Taiwan
- Neuroscience Research Center, Taipei Medical University Hospital, Taipei, 11031, Taiwan
- Pediatric Brain Tumor Program, Taipei Cancer Center, Taipei Medical University, Taipei, 11031, Taiwan
- Division of Pediatric Neurosurgery, Department of Neurosurgery, Taipei Neuroscience Institute, Taipei Medical University Hospital, Taipei Medical University, Taipei, 11031, Taiwan
| | - Chia-Ling Hsieh
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan.
- Neuroscience Research Center, Taipei Medical University Hospital, Taipei, 11031, Taiwan.
- Institute for Drug Evaluation Platform, Development Center for Biotechnology, Taipei, 11571, Taiwan.
| | - Shian-Ying Sung
- International Ph.D. Program for Translational Science, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan.
- Graduate Institute of Clinical Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, 11031, Taiwan.
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan.
- Neuroscience Research Center, Taipei Medical University Hospital, Taipei, 11031, Taiwan.
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, 11031, Taiwan.
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Sharma S, Kumar P. Dissecting the functional significance of HSP90AB1 and other heat shock proteins in countering glioblastomas and ependymomas using omics analysis and drug prediction using virtual screening. Neuropeptides 2023; 102:102383. [PMID: 37729687 DOI: 10.1016/j.npep.2023.102383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/07/2023] [Accepted: 09/10/2023] [Indexed: 09/22/2023]
Abstract
Heat shock proteins (HSPs) are the evolutionary family of proteins that are highly conserved and present widely in various organisms and play an array of important roles and cellular functions. Currently, very few or no studies are based on the systematic analysis of the HSPs in Glioblastoma (GBMs) and ependymomas. We performed an integrated omics analysis to predict the mutual regulatory differential HSP signatures that were associated with both glioblastoma and ependymomas. Further, we explored the various common dysregulated biological processes operating in both the tumors, and were analyzed using functional enrichment, gene ontology along with the pathway analysis of the predicted HSPs. We established an interactome network of protein-protein interaction (PPIN) to identify the hub HSPs that were commonly associated with GBMs and ependymoma. To understand the mutual molecular mechanism of the HSPs in both malignancies, transcription factors, and miRNAs overlapping with both diseases were explored. Moreover, a transcription factor-miRNAs-HSPs coregulatory network was constructed along with the prediction of potential candidate drugs that were based on perturbation-induced gene expression analysis. Based on the RNA-sequencing data, HSP90AB1 was identified as the most promising target among other predicted HSPs. Finally, the ranking of the drugs was arranged based on various drug scores. In conclusion, this study gave a spotlight on the mutual targetable HSPs, biological pathways, and regulatory signatures associated with GBMs and ependymoma with an improved understanding of crosstalk involved. Additionally, the role of therapeutics was also explored against HSP90AB1. These findings could potentially be able to explain the interplay of HSP90AB1 and other HSPs within these two malignancies.
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Affiliation(s)
- Sudhanshu Sharma
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University, Shahabad Daulatpur, Bawana Road, Delhi 110042, India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University, Shahabad Daulatpur, Bawana Road, Delhi 110042, India.
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Sanghrajka RM, Koche R, Medrano H, El Nagar S, Stephen DN, Lao Z, Bayin NS, Ge K, Joyner AL. KMT2D suppresses Sonic hedgehog-driven medulloblastoma progression and metastasis. iScience 2023; 26:107831. [PMID: 37822508 PMCID: PMC10562805 DOI: 10.1016/j.isci.2023.107831] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 03/29/2023] [Accepted: 09/01/2023] [Indexed: 10/13/2023] Open
Abstract
The major cause of treatment failure and mortality among medulloblastoma patients is metastasis intracranially or along the spinal cord. The molecular mechanisms driving tumor metastasis in Sonic hedgehog-driven medulloblastoma (SHH-MB) patients, however, remain largely unknown. In this study we define a tumor suppressive role of KMT2D (MLL2), a gene frequently mutated in the most metastatic β-subtype. Strikingly, genetic mouse models of SHH-MB demonstrate that heterozygous loss of Kmt2d in conjunction with activation of the SHH pathway causes highly penetrant disease with decreased survival, increased hindbrain invasion and spinal cord metastasis. Loss of Kmt2d attenuates neural differentiation and shifts the transcriptional/chromatin landscape of primary and metastatic tumors toward a decrease in differentiation genes and tumor suppressors and an increase in genes/pathways implicated in advanced stage cancer and metastasis (TGFβ, Notch, Atoh1, Sox2, and Myc). Thus, secondary heterozygous KMT2D mutations likely have prognostic value for identifying SHH-MB patients prone to develop metastasis.
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Affiliation(s)
- Reeti Mayur Sanghrajka
- Developmental Biology Program, Sloan Kettering Institute of Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Biochemistry, Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Richard Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hector Medrano
- Developmental Biology Program, Sloan Kettering Institute of Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Salsabiel El Nagar
- Developmental Biology Program, Sloan Kettering Institute of Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel N. Stephen
- Developmental Biology Program, Sloan Kettering Institute of Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zhimin Lao
- Developmental Biology Program, Sloan Kettering Institute of Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - N. Sumru Bayin
- Developmental Biology Program, Sloan Kettering Institute of Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kai Ge
- Adipocyte Biology and Gene Regulation Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Alexandra L. Joyner
- Developmental Biology Program, Sloan Kettering Institute of Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Biochemistry, Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
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Damodharan S, Puccetti D. Pediatric Central Nervous System Tumor Overview and Emerging Treatment Considerations. Brain Sci 2023; 13:1106. [PMID: 37509034 PMCID: PMC10377074 DOI: 10.3390/brainsci13071106] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Pediatric central nervous system (CNS) tumors are the most common solid tumor in children, with the majority being glial in origin. These tumors are classified by the World Health Organization (WHO) as either being low grade (WHO grade 1 and 2) or high grade (WHO grade 3 and 4). Our knowledge of the molecular landscape of pediatric brain tumors has advanced over the last decade, which has led to newer categorizations along with an expansion of therapeutic targets and options. In this review, we will give an overview of common CNS tumors seen in children along with a focus on treatment options and future considerations.
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Affiliation(s)
- Sudarshawn Damodharan
- Department of Pediatrics, Division of Pediatric Hematology, Oncology and Bone Marrow Transplant, University of Wisconsin School of Medicine & Public Health, Madison, WI 53792, USA
| | - Diane Puccetti
- Department of Pediatrics, Division of Pediatric Hematology, Oncology and Bone Marrow Transplant, University of Wisconsin School of Medicine & Public Health, Madison, WI 53792, USA
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Ntenti C, Lallas K, Papazisis G. Clinical, Histological, and Molecular Prognostic Factors in Childhood Medulloblastoma: Where Do We Stand? Diagnostics (Basel) 2023; 13:diagnostics13111915. [PMID: 37296767 DOI: 10.3390/diagnostics13111915] [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: 03/30/2023] [Revised: 05/26/2023] [Accepted: 05/28/2023] [Indexed: 06/12/2023] Open
Abstract
Medulloblastomas, highly aggressive neoplasms of the central nervous system (CNS) that present significant heterogeneity in clinical presentation, disease course, and treatment outcomes, are common in childhood. Moreover, patients who survive may be diagnosed with subsequent malignancies during their life or could develop treatment-related medical conditions. Genetic and transcriptomic studies have classified MBs into four subgroups: wingless type (WNT), Sonic Hedgehog (SHH), Group 3, and Group 4, with distinct histological and molecular profiles. However, recent molecular findings resulted in the WHO updating their guidelines and stratifying medulloblastomas into further molecular subgroups, changing the clinical stratification and treatment management. In this review, we discuss most of the histological, clinical, and molecular prognostic factors, as well the feasibility of their application, for better characterization, prognostication, and treatment of medulloblastomas.
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Affiliation(s)
- Charikleia Ntenti
- First Department of Pharmacology, School of Medicine, Aristotle University of Thessaloniki, 54621 Thessaloniki, Greece
| | - Konstantinos Lallas
- Department of Medical Oncology, School of Medicine, Aristotle University of Thessaloniki, 54621 Thessaloniki, Greece
| | - Georgios Papazisis
- Clinical Research Unit, Special Unit for Biomedical Research and Education (BRESU), School of Medicine, Aristotle University of Thessaloniki, 54621 Thessaloniki, Greece
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Bhardwaj N, Das G, Srinivasan R. Neuroblastoma-derived v-myc avian myelocytomatosis viral related oncogene or MYCN gene. J Clin Pathol 2023:jcp-2022-208476. [PMID: 37221048 DOI: 10.1136/jcp-2022-208476] [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: 09/06/2022] [Accepted: 04/13/2023] [Indexed: 05/25/2023]
Abstract
The MYCN gene belongs to the MYC family of transcription factors. Amplification of MYCN, first discovered in neuroblastoma cells, ushered in the era of cancer genomics. The MYCN gene and MYCN protein are extensively studied in the context of neuroblastoma. As demonstrated in transgenic mouse models, MYCN gene shows a restricted spatiotemporal expression predominantly in the neural crest cells which explains the associated neoplasms including neuroblastoma and central nervous system tumours. In neuroblastoma, MYCN amplification is a marker of aggressive tumours with poor prognosis and survival and forms the basis of risk stratification classifications.MYCN dysregulated expression occurs by several mechanisms at the transcriptional, translational and post-translational levels. These include massive gene amplification which occurs in an extrachromosomal location, upregulated transcription and stabilisation of the protein increasing its half-life. MYCN protein, a basic loop-helix-loop leucine zipper transcription factor, has many regions which bind to several proteins foremost of which is MAX forming the MYC:MAX heterodimer. Overall, MYCN controls multiple aspects of cell fate, foremost of which is cellular proliferation besides cell differentiation, apoptosis and cellular metabolism, all of which are the focus of this brief review. In addition to amplification, other mechanisms of MYCN overexpression include activating missense mutations as reported in basal cell carcinoma and Wilms tumour. A better understanding of this molecule will help in the discovery of novel strategies for its indirect targeting to improve the outcomes of patients with neuroblastoma and other MYCN-associated neoplasms.
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Affiliation(s)
- Neha Bhardwaj
- Department of Pathology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Gargi Das
- Medical Oncology (Pediatric Oncology), Cancer Institute-WIA, Chennai, Tamil Nadu, India
| | - Radhika Srinivasan
- Pathology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
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Saeed H, Leibowitz BJ, Zhang L, Yu J. Targeting Myc-driven stress addiction in colorectal cancer. Drug Resist Updat 2023; 69:100963. [PMID: 37119690 DOI: 10.1016/j.drup.2023.100963] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 04/06/2023] [Accepted: 04/17/2023] [Indexed: 05/01/2023]
Abstract
MYC is a proto-oncogene that encodes a powerful regulator of transcription and cellular programs essential for normal development, as well as the growth and survival of various types of cancer cells. MYC rearrangement and amplification is a common cause of hematologic malignancies. In epithelial cancers such as colorectal cancer, genetic alterations in MYC are rare. Activation of Wnt, ERK/MAPK, and PI3K/mTOR pathways dramatically increases Myc levels through enhanced transcription, translation, and protein stability. Elevated Myc promotes stress adaptation, metabolic reprogramming, and immune evasion to drive cancer development and therapeutic resistance through broad changes in transcriptional and translational landscapes. Despite intense interest and effort, Myc remains a difficult drug target. Deregulation of Myc and its targets has profound effects that vary depending on the type of cancer and the context. Here, we summarize recent advances in the mechanistic understanding of Myc-driven oncogenesis centered around mRNA translation and proteostress. Promising strategies and agents under development to target Myc are also discussed with a focus on colorectal cancer.
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Affiliation(s)
- Haris Saeed
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, 5117 Centre Ave., Pittsburgh, PA 15213, USA; Dept. of Pathology, University of Pittsburgh School of Medicine, 5117 Centre Ave., Pittsburgh, PA 15213, USA
| | - Brian J Leibowitz
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, 5117 Centre Ave., Pittsburgh, PA 15213, USA; Dept. of Pathology, University of Pittsburgh School of Medicine, 5117 Centre Ave., Pittsburgh, PA 15213, USA
| | - Lin Zhang
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, 5117 Centre Ave., Pittsburgh, PA 15213, USA; Dept. of Chemical Biology and Pharmacology, University of Pittsburgh School of Medicine, 5117 Centre Ave., Pittsburgh, PA 15213, USA
| | - Jian Yu
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, 5117 Centre Ave., Pittsburgh, PA 15213, USA; Dept. of Pathology, University of Pittsburgh School of Medicine, 5117 Centre Ave., Pittsburgh, PA 15213, USA; Dept. of Radiation Oncology, University of Pittsburgh School of Medicine, 5117 Centre Ave., Pittsburgh, PA 15213, USA.
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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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