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Matsuoka H, Yoshida KI, Nakai S, Suzuki R, Imura Y, Takami H, Watanabe M, Wakamatsu T, Tamiya H, Outani H, Yagi T, Kakunaga S, Takenaka S. Successful pazopanib treatment of undifferentiated pleomorphic sarcoma with coamplification of PDGFRA, VEGFR2 and KIT: A case report. Mol Clin Oncol 2024; 21:69. [PMID: 39113850 PMCID: PMC11304161 DOI: 10.3892/mco.2024.2767] [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: 02/06/2024] [Accepted: 06/03/2024] [Indexed: 08/10/2024] Open
Abstract
Undifferentiated pleomorphic sarcoma (UPS) is a high-grade, aggressive soft tissue sarcoma (STS) with a poor prognosis, and no definitive or effective treatment is currently available for it. Pazopanib, an orally available multiple tyrosine kinase inhibitor, has been approved for the treatment of advanced STS. The present study documents the case of a 51-year-old man with advanced UPS with coamplification of platelet-derived growth factor receptor A (PDGFRA), vascular endothelial growth factor receptor 2 (VEGFR2) and stem cell factor receptor (KIT) genes. The patient exhibited a marked and sustained response to pazopanib. The patient presented with a retroperitoneal tumour with pancreatic head lymph node metastasis, and bone metastases in the second/fifth thoracic vertebrae and left femur. Based on the histological analysis of the retroperitoneal tumour and femoral mass, the patient was diagnosed with UPS. Palliative radiation therapy was administered to the left femur and second/fifth thoracic vertebrae to prevent fractures. After radiation therapy, the patient achieved a partial response after eight courses of doxorubicin. A comprehensive genomic profiling analysis (FoundationOne® CDx) revealed coamplification of PDGFRA, VEGFR2 and KIT genes. Hence, pazopanib was initiated as a second-line treatment. Notably, the retroperitoneal tumour shrank, and no new lesions developed for 3 years after the initiation of pazopanib treatment. This response suggests that the coamplification of PDGFRA, VEGFR2 and KIT may predict favourable outcomes in response to pazopanib.
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Affiliation(s)
- Haruki Matsuoka
- Musculoskeletal Oncology Service, Osaka International Cancer Institute, Osaka 541-8567, Japan
- Department of Orthopaedic Surgery, Osaka Police Hospital, Osaka 543-0035, Japan
| | - Ken-Ichi Yoshida
- Department of Diagnostic Pathology and Cytology, Osaka International Cancer Institute, Osaka 541-8567, Japan
| | - Sho Nakai
- Musculoskeletal Oncology Service, Osaka International Cancer Institute, Osaka 541-8567, Japan
- Department of Orthopaedic Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Rie Suzuki
- Musculoskeletal Oncology Service, Osaka International Cancer Institute, Osaka 541-8567, Japan
| | - Yoshinori Imura
- Department of Orthopaedic Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Haruna Takami
- Department of Orthopaedic Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Makiyo Watanabe
- Musculoskeletal Oncology Service, Osaka International Cancer Institute, Osaka 541-8567, Japan
| | - Toru Wakamatsu
- Musculoskeletal Oncology Service, Osaka International Cancer Institute, Osaka 541-8567, Japan
| | - Hironari Tamiya
- Musculoskeletal Oncology Service, Osaka International Cancer Institute, Osaka 541-8567, Japan
| | - Hidetatsu Outani
- Department of Orthopaedic Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Toshinari Yagi
- Musculoskeletal Oncology Service, Osaka International Cancer Institute, Osaka 541-8567, Japan
| | - Shigeki Kakunaga
- Musculoskeletal Oncology Service, Osaka International Cancer Institute, Osaka 541-8567, Japan
| | - Satoshi Takenaka
- Musculoskeletal Oncology Service, Osaka International Cancer Institute, Osaka 541-8567, Japan
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de Queiroz RM, Efe G, Guzman A, Hashimoto N, Kawashima Y, Tanaka T, Rustgi AK, Prives C. Mdm2 requires Sprouty4 to regulate focal adhesion formation and metastasis independent of p53. Nat Commun 2024; 15:7132. [PMID: 39164253 PMCID: PMC11336179 DOI: 10.1038/s41467-024-51488-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/07/2024] [Indexed: 08/22/2024] Open
Abstract
Although the E3 ligase Mdm2 and its homologue and binding partner MdmX are the major regulators of the p53 tumor suppressor protein, it is now evident that Mdm2 and MdmX have multiple functions that do not involve p53. As one example, it is known that Mdm2 can regulate cell migration, although mechanistic insight into this function is still lacking. Here we show in cells lacking p53 expression that knockdown of Mdm2 or MdmX, as well as pharmacological inhibition of the Mdm2/MdmX complex, not only reduces cell migration and invasion, but also impairs cell spreading and focal adhesion formation. In addition, Mdm2 knockdown decreases metastasis in vivo. Interestingly, Mdm2 downregulates the expression of Sprouty4, which is required for the Mdm2 mediated effects on cell migration, focal adhesion formation and metastasis. Further, our findings indicate that Mdm2 dampening of Sprouty4 is a prerequisite for maintaining RhoA levels in the cancer cells that we have studied. Taken together we describe a molecular mechanism whereby the Mdm2/MdmX complex through Sprouty4 regulates cellular processes leading to increase metastatic capability independently of p53.
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Affiliation(s)
| | - Gizem Efe
- Herbert Irving Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Asja Guzman
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Naoko Hashimoto
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
- Research Institute of Disaster Medicine, Chiba University, Chiba, Japan
| | - Yusuke Kawashima
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Tomoaki Tanaka
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
- Research Institute of Disaster Medicine, Chiba University, Chiba, Japan
| | - Anil K Rustgi
- Herbert Irving Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Carol Prives
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA.
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Papouliakos S, Chrysovergis A, Papanikolaou V, Spyropoulou D, Papanastasiou G, Asimakopoulos AD, Mastronikoli S, Stathopoulos P, Roukas D, Adamopoulou M, Tsiambas E, Peschos D, Pantos P, Ragos V, Mastronikolis N, Kyrodimos E. Clinical Impact of C-myc Oncogenic Diversity on Solid and Lymphoid Malignancies. MAEDICA 2024; 19:355-359. [PMID: 39188831 PMCID: PMC11345059 DOI: 10.26574/maedica.2024.19.2.355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
INTRODUCTION Onset and progression of malignant tumors is a multistep process including a variety of gross chromosomal and specific genes' deregulation. Among oncogenes that are frequently altered in solid and also in hematological malignancies, the C-myc (gene locus: 8q24.21) plays a pivotal role. C-myc is a proto-oncogene encoding for a nuclear phosphoprotein implicated in cell cycle progression, apoptosis and cellular differentiation and transformation. OBJECTIVE The purpose of the current molecular review was to explore the differences of C-myc oncogenic activity in solid and lymphoid malignancies that modify its clinical impact on them. MATERIAL AND METHOD A systematic review of the literature in the international database PubMed was carried out. The year 2010 was set as a prominent time limit for the publication date of articles in the majority of them, whereas specific references of great importance and historical value in the field of C-myc gene discovery and analysis were also included. The following keywords were used: C-myc, oncogene, signaling pathway, malignancies, carcinoma, lymphoma. A pool of 43 important articles were selected for the present study at the basis of combining molecular knowledge with new targeted therapeutic strategies. RESULTS C-myc oncogene demonstrates two different mechanisms of deregulation: amplification, mutation and translocation patterns. These particular aspects of gene alteration are unique for solid and non-solid (hematological) malignancies, respectively. CONCLUSIONS C-myc is characterized by diversity regarding its deregulation mechanisms in malignancies derived from different tissues. C-myc translocation is sporadically combined with amplification ("complicon" formation) or mutations creating exotic genetic signatures. This "bi-phasic" C-myc deregulation model in the corresponding malignant tumor categories clinically affects the corresponding patients, also modifying the targeted therapeutic strategies on them.
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Affiliation(s)
| | | | | | - Despoina Spyropoulou
- Department of Radiation Oncology, Medical School, University of Patras, Patras, Greece
| | - Georgios Papanastasiou
- Department of Otorhinolaryngology, Head and Neck Surgery, Lausanne University Hospital, Lausanne, Switzerland; Department of Maxillofacial Surgery, Medical School, University of Ioannina, Ioannina, Greece
| | - Asimakis D Asimakopoulos
- Department of Otorhinolaryngology, Head and Neck Surgery, Lausanne University Hospital, Lausanne, Switzerland; Department of Maxillofacial Surgery, Medical School, University of Ioannina, Ioannina, Greece
| | | | | | - Dimitrios Roukas
- Department of Psychiatry, 417 Veterans Army Hospital, Athens, Greece
| | - Maria Adamopoulou
- Biomedical Sciences Program, Department of Science and Mathematics, Deree American College, Athens, Greece
| | | | - Dimitrios Peschos
- Department of Physiology, Medical School, University of Ioannina, Greece
| | - Pavlos Pantos
- First Department of Otolaryngology, "Hippocration" Hospital, Medical school, National and Kapodistrian University of Athens, Athens, Greece
| | - Vasileios Ragos
- Department of Otorhinolaryngology, Head and Neck Surgery, Lausanne University Hospital, Lausanne, Switzerland; Department of Maxillofacial Surgery, Medical School, University of Ioannina, Ioannina, Greece
| | | | - Efthymios Kyrodimos
- First Department of Otolaryngology, "Hippocration" Hospital, Medical school, National and Kapodistrian University of Athens, Athens, Greece
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Wu H, Geng Q, Shi W, Qiu C. Comprehensive pan-cancer analysis reveals CCDC58 as a carcinogenic factor related to immune infiltration. Apoptosis 2024; 29:536-555. [PMID: 38066393 DOI: 10.1007/s10495-023-01919-0] [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] [Accepted: 11/06/2023] [Indexed: 02/18/2024]
Abstract
CCDC58, a member of the CCDC protein family, has been primarily associated with the malignant progression of hepatocellular carcinoma (HCC) and breast cancer, with limited research conducted on its involvement in other tumor types. We aimed to assess the significance of CCDC58 in pan-cancer. We utilized the TCGA, GTEx, and UALCAN databases to perform the differential expression of CCDC58 at both mRNA and protein levels. Prognostic value was evaluated through univariate Cox regression and Kaplan-Meier methods. Mutation and methylation analyses were conducted using the cBioPortal and SMART databases. We identified genes interacting with and correlated to CCDC58 through STRING and GEPIA2, respectively. Subsequently, we performed GO and KEGG enrichment analyses. To gain insights into the functional status of CCDC58 at the single-cell level, we utilized CancerSEA. We explored the correlation between CCDC58 and immune infiltration as well as immunotherapy using the ESTIMATE package, TIMER2.0, TISIDB, TIDE, TIMSO, and TCIA. We examined the relationship between CCDC58 and tumor heterogeneity, stemness, DNA methyltransferases, and MMR genes. Lastly, we constructed a nomogram based on CCDC58 in HCC and investigated its association with drug sensitivity. CCDC58 expression was significantly upregulated and correlated with poor prognosis across various tumor types. The mutation frequency of CCDC58 was found to be increased in 25 tumors. We observed a negative correlation between CCDC58 expression and the methylation sites in the majority of tumors. CCDC58 showed negative correlations with immune and stromal scores, as well as with NK T cells, Tregs, CAFs, endothelial cells, and immunomodulators. Its value in immunotherapy was comparable to that of tumor mutational burden. CCDC58 exhibited positive correlations with tumor heterogeneity, stemness, DNA methyltransferase genes, and MMR genes. In HCC, CCDC58 was identified as an independent risk factor and demonstrated potential associations with multiple drugs. CCDC58 demonstrates significant clinical value as a prognostic marker and indicator of immune response across various tumor types. Its comprehensive analysis provides insights into its potential implications in pan-cancer research.
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Affiliation(s)
- Huili Wu
- Department of Endodontics, Zhonglou Hospital, Changzhou Hospital of Traditional Chinese Medicine, Changzhou, China
| | - Qing Geng
- School of Exercise and Health, Shanghai University of Sport, Shanghai, China
| | - Wenxiang Shi
- Department of Pediatric Cardiology, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Chenjie Qiu
- Department of General Surgery, Changzhou Hospital of Traditional Chinese Medicine, Changzhou, China.
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Hu MZ, Dai ZZ, Ji HY, Zheng AQ, Liang H, Shen MM, Liu JN, Tang KF, Zhu SJ, Wang KJ. Upregulation of FAM50A promotes cancer development. Med Oncol 2023; 40:217. [PMID: 37393403 DOI: 10.1007/s12032-023-02072-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/24/2023] [Indexed: 07/03/2023]
Abstract
FAM50A encodes a nuclear protein involved in mRNA processing; however, its role in cancer development remains unclear. Herein, we conducted an integrative pan-cancer analysis using The Cancer Genome Atlas, Genotype-Tissue Expression, and the Clinical Proteomic Tumor Analysis Consortium databases. Based on the gene expression data from TCGA and GTEx databases, we compared FAM50A mRNA levels in 33 types of human cancer tissues to those in corresponding normal tissues and found that FAM50A mRNA level was upregulated in 20 of the 33 types of common cancer tissues. Then, we compared the DNA methylation status of the FAM50A promoter in tumor tissues to that in corresponding normal tissues. FAM50A upregulation was accompanied by promoter hypomethylation in 8 of the 20 types of tumor tissues, suggesting that promoter hypomethylation contributes to the upregulation of FAM50A in these cancer tissues. Elevated FAM50A expression in 10 types of cancer tissues was associated with poor prognosis in patients with cancer. FAM50A expression was positively correlated with CD4+ T-lymphocyte and dendritic cell infiltration in cancer tissues but was negatively correlated with CD8+ T-cell infiltration in cancer tissues. FAM50A knockdown caused DNA damage, induced interferon beta and interleukin-6 expression, and repressed the proliferation, invasion, and migration of cancer cells. Our findings indicate that FAM50A might be useful in cancer detection, reveal insights into its role in cancer development, and may contribute to the development of cancer diagnostics and treatments.
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Affiliation(s)
- Mei-Zhen Hu
- Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Zhi-Zheng Dai
- Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Hong-Yu Ji
- Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - An-Qi Zheng
- The First Affiliated Hospital of Wenzhou Medical University, Zhejiang, 325015, People's Republic of China
| | - Hang Liang
- School of Basic Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Mei-Mei Shen
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Choqing, 400016, People's Republic of China
| | - Jun-Nan Liu
- School of Basic Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Kai-Fu Tang
- Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Shu-Juan Zhu
- School of Basic Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China.
| | - Ke-Jian Wang
- School of Basic Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China.
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6
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Schnöller LE, Piehlmaier D, Weber P, Brix N, Fleischmann DF, Nieto AE, Selmansberger M, Heider T, Hess J, Niyazi M, Belka C, Lauber K, Unger K, Orth M. Systematic in vitro analysis of therapy resistance in glioblastoma cell lines by integration of clonogenic survival data with multi-level molecular data. Radiat Oncol 2023; 18:51. [PMID: 36906590 PMCID: PMC10007763 DOI: 10.1186/s13014-023-02241-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 03/06/2023] [Indexed: 03/13/2023] Open
Abstract
Despite intensive basic scientific, translational, and clinical efforts in the last decades, glioblastoma remains a devastating disease with a highly dismal prognosis. Apart from the implementation of temozolomide into the clinical routine, novel treatment approaches have largely failed, emphasizing the need for systematic examination of glioblastoma therapy resistance in order to identify major drivers and thus, potential vulnerabilities for therapeutic intervention. Recently, we provided proof-of-concept for the systematic identification of combined modality radiochemotherapy treatment vulnerabilities via integration of clonogenic survival data upon radio(chemo)therapy with low-density transcriptomic profiling data in a panel of established human glioblastoma cell lines. Here, we expand this approach to multiple molecular levels, including genomic copy number, spectral karyotyping, DNA methylation, and transcriptome data. Correlation of transcriptome data with inherent therapy resistance on the single gene level yielded several candidates that were so far underappreciated in this context and for which clinically approved drugs are readily available, such as the androgen receptor (AR). Gene set enrichment analyses confirmed these results, and identified additional gene sets, including reactive oxygen species detoxification, mammalian target of rapamycin complex 1 (MTORC1) signaling, and ferroptosis/autophagy-related regulatory circuits to be associated with inherent therapy resistance in glioblastoma cells. To identify pharmacologically accessible genes within those gene sets, leading edge analyses were performed yielding candidates with functions in thioredoxin/peroxiredoxin metabolism, glutathione synthesis, chaperoning of proteins, prolyl hydroxylation, proteasome function, and DNA synthesis/repair. Our study thus confirms previously nominated targets for mechanism-based multi-modal glioblastoma therapy, provides proof-of-concept for this workflow of multi-level data integration, and identifies novel candidates for which pharmacological inhibitors are readily available and whose targeting in combination with radio(chemo)therapy deserves further examination. In addition, our study also reveals that the presented workflow requires mRNA expression data, rather than genomic copy number or DNA methylation data, since no stringent correlation between these data levels could be observed. Finally, the data sets generated in the present study, including functional and multi-level molecular data of commonly used glioblastoma cell lines, represent a valuable toolbox for other researchers in the field of glioblastoma therapy resistance.
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Affiliation(s)
- Leon Emanuel Schnöller
- Department of Radiation Oncology, University Hospital, LMU München, Marchioninistrasse 15, 81377, Munich, Germany
| | - Daniel Piehlmaier
- Research Unit Radiation Cytogenetics (ZYTO), Helmholtz Center Munich, German Research Center for Environmental Health GmbH, 85764, Neuherberg, Germany
| | - Peter Weber
- Research Unit Radiation Cytogenetics (ZYTO), Helmholtz Center Munich, German Research Center for Environmental Health GmbH, 85764, Neuherberg, Germany.,Clinical Cooperation Group 'Personalized Radiotherapy in Head and Neck Cancer' Helmholtz Center Munich, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Nikko Brix
- Department of Radiation Oncology, University Hospital, LMU München, Marchioninistrasse 15, 81377, Munich, Germany
| | - Daniel Felix Fleischmann
- Department of Radiation Oncology, University Hospital, LMU München, Marchioninistrasse 15, 81377, Munich, Germany.,German Cancer Consortium (DKTK), Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alexander Edward Nieto
- Department of Radiation Oncology, University Hospital, LMU München, Marchioninistrasse 15, 81377, Munich, Germany
| | - Martin Selmansberger
- Research Unit Radiation Cytogenetics (ZYTO), Helmholtz Center Munich, German Research Center for Environmental Health GmbH, 85764, Neuherberg, Germany
| | - Theresa Heider
- Research Unit Radiation Cytogenetics (ZYTO), Helmholtz Center Munich, German Research Center for Environmental Health GmbH, 85764, Neuherberg, Germany
| | - Julia Hess
- Research Unit Radiation Cytogenetics (ZYTO), Helmholtz Center Munich, German Research Center for Environmental Health GmbH, 85764, Neuherberg, Germany.,Clinical Cooperation Group 'Personalized Radiotherapy in Head and Neck Cancer' Helmholtz Center Munich, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Maximilian Niyazi
- Department of Radiation Oncology, University Hospital, LMU München, Marchioninistrasse 15, 81377, Munich, Germany.,German Cancer Consortium (DKTK), Munich, Germany.,Bavarian Cancer Research Center (BKFZ), Munich, Germany
| | - Claus Belka
- Department of Radiation Oncology, University Hospital, LMU München, Marchioninistrasse 15, 81377, Munich, Germany.,Clinical Cooperation Group 'Personalized Radiotherapy in Head and Neck Cancer' Helmholtz Center Munich, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,German Cancer Consortium (DKTK), Munich, Germany.,Bavarian Cancer Research Center (BKFZ), Munich, Germany
| | - Kirsten Lauber
- Department of Radiation Oncology, University Hospital, LMU München, Marchioninistrasse 15, 81377, Munich, Germany.,Clinical Cooperation Group 'Personalized Radiotherapy in Head and Neck Cancer' Helmholtz Center Munich, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,German Cancer Consortium (DKTK), Munich, Germany
| | - Kristian Unger
- Research Unit Radiation Cytogenetics (ZYTO), Helmholtz Center Munich, German Research Center for Environmental Health GmbH, 85764, Neuherberg, Germany. .,Clinical Cooperation Group 'Personalized Radiotherapy in Head and Neck Cancer' Helmholtz Center Munich, German Research Center for Environmental Health GmbH, Neuherberg, Germany.
| | - Michael Orth
- Department of Radiation Oncology, University Hospital, LMU München, Marchioninistrasse 15, 81377, Munich, Germany.
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Wang X, Liu Y, Liu H, Pan W, Ren J, Zheng X, Tan Y, Chen Z, Deng Y, He N, Chen H, Li S. Recent advances and application of whole genome amplification in molecular diagnosis and medicine. MedComm (Beijing) 2022; 3:e116. [PMID: 35281794 PMCID: PMC8906466 DOI: 10.1002/mco2.116] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 11/30/2022] Open
Abstract
Whole genome amplification (WGA) is a technology for non-selective amplification of the whole genome sequence, first appearing in 1992. Its primary purpose is to amplify and reflect the whole genome of trace tissues and single cells without sequence bias and to provide sufficient DNA template for subsequent multigene and multilocus analysis, along with comprehensive genome research. WGA provides a method to obtain a large amount of genetic information from a small amount of DNA and provides a valuable tool for preserving limited samples in molecular biology. WGA technology is especially suitable for forensic identification and genetic disease research, along with new technologies such as next-generation sequencing (NGS). In addition, WGA is also widely used in single-cell sequencing. Due to the small amount of DNA in a single cell, it is often unable to meet the amount of samples needed for sequencing, so WGA is generally used to achieve the amplification of trace samples. This paper reviews WGA methods based on different principles, summarizes both amplification principle and amplification quality, and discusses the application prospects and challenges of WGA technology in molecular diagnosis and medicine.
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Affiliation(s)
- Xiaoyu Wang
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Yapeng Liu
- School of Early‐Childhood Education, Nanjing Xiaozhuang UniversityNanjingChina
| | - Hongna Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Wenjing Pan
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Jie Ren
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Xiangming Zheng
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Yimin Tan
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Nongyue He
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
- State Key Laboratory of BioelectronicsSoutheast UniversityNanjingChina
| | - Hui Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
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8
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Quantification of protein-protein interactions and activation dynamics: A new path to predictive biomarkers. Biophys Chem 2022; 283:106768. [DOI: 10.1016/j.bpc.2022.106768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/08/2022] [Accepted: 01/24/2022] [Indexed: 12/27/2022]
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9
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Makani VKK, Mendonza JJ, Edathara PM, Yerramsetty S, Pal Bhadra M. BORIS/CTCFL expression activates the TGFβ signaling cascade and induces Drp1 mediated mitochondrial fission in neuroblastoma. Free Radic Biol Med 2021; 176:62-72. [PMID: 34534628 DOI: 10.1016/j.freeradbiomed.2021.09.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/03/2021] [Accepted: 09/13/2021] [Indexed: 11/19/2022]
Abstract
The cancer-testis antigen CTCFL/BORIS (Brother of Regulator of Imprinted Sites) also known, as a paralog of CTCF -the "master weaver of the genome" is a key transcriptional regulator. Both CTCF and BORIS can bind to the same promoter sequence and recruit diverse proteins. BORIS is also known to be associated with actively translating ribosomes suggesting new roles of BORIS in gene expression. Various studies have attempted to elucidate the role of BORIS in different cell types for the development of targeted therapy depending on molecular signatures and genetic aberrations associated with the disease type. The current study is focused on its role in neuroblastoma. Here, we have deciphered the role of BORIS on TGFβ1 pathway which is highly affected by embryonic CTCFL expression. BORIS stabilized the SMAD3 and SMAD4 transcripts leading to prolonged TGFβ activation. Further, loss of BORIS abrogated both the canonical and non-canonical TGFβ signaling suggesting the dependency of TGFβ on BORIS. The effect on the metabolic profile of the neuroblastoma cells were analyzed with change in BORIS expression levels. Also, ectopic expression of BORIS leads to Drp1 phosphorylation (Ser616) enhancing mitochondrial fission followed by a switch in cellular metabolism towards glycolysis. This cellular metabolism switch was in turn supported with a reduction in oxygen consumption rate upon BORIS expression. Interestingly methylome analysis revealed patterns of global histone methylation, a mechanism that regulate important signaling pathways in neuroblastoma. This study analyzes the consequence of BORIS expression in neuroblastoma cells and thereby elucidate its downstream targets, which could help in designing effective therapeutic for treating neuroblastoma. Similar results were obtained in both MYCN amplified and non-MYCN neuroblastoma cell lines, indicating a common mechanism of BORIS/CTCFL action in neuroblastoma.
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Affiliation(s)
- Venkata Krishna Kanth Makani
- Department of Applied Biology, CSIR- Indian Institute of Chemical Technology (IICT), Tarnaka, Hyderabad, 50007, India; Academy of Scientific and Innovative Research (AcSIR), CSIR- Human Resource Development Centre, (CSIR-HRDC) Campus, Ghaziabad, Uttar Pradesh, 201 002, India
| | - Jolly Janette Mendonza
- Department of Applied Biology, CSIR- Indian Institute of Chemical Technology (IICT), Tarnaka, Hyderabad, 50007, India; Academy of Scientific and Innovative Research (AcSIR), CSIR- Human Resource Development Centre, (CSIR-HRDC) Campus, Ghaziabad, Uttar Pradesh, 201 002, India
| | - Prajitha Mohandas Edathara
- Department of Applied Biology, CSIR- Indian Institute of Chemical Technology (IICT), Tarnaka, Hyderabad, 50007, India
| | - Suresh Yerramsetty
- Department of Applied Biology, CSIR- Indian Institute of Chemical Technology (IICT), Tarnaka, Hyderabad, 50007, India
| | - Manika Pal Bhadra
- Department of Applied Biology, CSIR- Indian Institute of Chemical Technology (IICT), Tarnaka, Hyderabad, 50007, India.
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10
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Fejzo MS, Chen HW, Anderson L, McDermott MS, Karlan B, Konecny GE, Slamon DJ. Analysis in epithelial ovarian cancer identifies KANSL1 as a biomarker and target gene for immune response and HDAC inhibition. Gynecol Oncol 2020; 160:539-546. [PMID: 33229045 DOI: 10.1016/j.ygyno.2020.11.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 11/08/2020] [Indexed: 02/06/2023]
Abstract
OBJECTIVE There is an immunoreactive subtype of ovarian cancer with a favorable prognosis, but the majority of ovarian cancers have limited immune reactivity. The reason for this is poorly understood. This study aimed to approach this question by identifying prognostically relevant genes whose prognostic mRNA expression levels correlated with a genomic event. METHODS Expression microarray and 5-year survival data on 170 ovarian tumors and aCGH data on 45 ovarian cancer cell lines were used to identify amplified/deleted genes associated with prognosis. Three immune-response genes were identified mapping to epigenetically modified chromosome 6p21.3. Genes were searched for roles in epigenetic modification, identifying KANSL1. Genome-wide association studies were searched to identify genetic variants in KANSL1 associated with altered immune profile. Sensitivity to HDAC inhibition in cell lines with KANSL1 amplification/rearrangement was studied. RESULTS Expression of 196 genes was statistically significantly associated with survival, and expression levels correlated with copy number variations for 82 of them. Among these, 3 immune-response genes (HCP5, PSMB8, PSMB9) clustered together at epigenetically modified chromosome 6p21.3 and their expression was inversely correlated to epigenetic modification gene KANSL1. KANSL1 is amplified/rearranged in ovarian cancer, associated with lymphocyte profile, a biomarker for response to HDAC inhibition, and may drive expression of immune-response genes. CONCLUSION This study identifies 82 genes with prognostic relevance and genomic alteration in ovarian cancer. Among these, immune-response genes have correlated expression which is associated with 5-year survival. KANSL1 may be a master gene altering immune-response gene expression at 6p21.3 and drive response to HDAC inhibitors. Future research should investigate KANSL1 and determine whether targeting it alters the immune profile of ovarian cancer and improves survival, HDAC inhibition, and/or immunotherapy response.
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Affiliation(s)
- Marlena S Fejzo
- David Geffen School of Medicine at UCLA, Los Angeles, CA 90024, USA.
| | - Hsiao-Wang Chen
- David Geffen School of Medicine at UCLA, Los Angeles, CA 90024, USA
| | - Lee Anderson
- David Geffen School of Medicine at UCLA, Los Angeles, CA 90024, USA
| | | | - Beth Karlan
- David Geffen School of Medicine at UCLA, Los Angeles, CA 90024, USA
| | | | - Dennis J Slamon
- David Geffen School of Medicine at UCLA, Los Angeles, CA 90024, USA
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11
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Fernandes SG, Dsouza R, Pandya G, Kirtonia A, Tergaonkar V, Lee SY, Garg M, Khattar E. Role of Telomeres and Telomeric Proteins in Human Malignancies and Their Therapeutic Potential. Cancers (Basel) 2020; 12:E1901. [PMID: 32674474 PMCID: PMC7409176 DOI: 10.3390/cancers12071901] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 12/19/2022] Open
Abstract
Telomeres are the ends of linear chromosomes comprised of repetitive nucleotide sequences in humans. Telomeres preserve chromosomal stability and genomic integrity. Telomere length shortens with every cell division in somatic cells, eventually resulting in replicative senescence once telomere length becomes critically short. Telomere shortening can be overcome by telomerase enzyme activity that is undetectable in somatic cells, while being active in germline cells, stem cells, and immune cells. Telomeres are bound by a shelterin complex that regulates telomere lengthening as well as protects them from being identified as DNA damage sites. Telomeres are transcribed by RNA polymerase II, and generate a long noncoding RNA called telomeric repeat-containing RNA (TERRA), which plays a key role in regulating subtelomeric gene expression. Replicative immortality and genome instability are hallmarks of cancer and to attain them cancer cells exploit telomere maintenance and telomere protection mechanisms. Thus, understanding the role of telomeres and their associated proteins in cancer initiation, progression and treatment is very important. The present review highlights the critical role of various telomeric components with recently established functions in cancer. Further, current strategies to target various telomeric components including human telomerase reverse transcriptase (hTERT) as a therapeutic approach in human malignancies are discussed.
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Affiliation(s)
- Stina George Fernandes
- Sunandan Divatia School of Science, SVKM’s NMIMS (Deemed to be University), Vile Parle West, Mumbai 400056, India; (S.G.F.); (R.D.)
| | - Rebecca Dsouza
- Sunandan Divatia School of Science, SVKM’s NMIMS (Deemed to be University), Vile Parle West, Mumbai 400056, India; (S.G.F.); (R.D.)
| | - Gouri Pandya
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University Uttar Pradesh, Noida 201313, India; (G.P.); (A.K.)
| | - Anuradha Kirtonia
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University Uttar Pradesh, Noida 201313, India; (G.P.); (A.K.)
| | - Vinay Tergaonkar
- Laboratory of NF-κB Signaling, Institute of Molecular and Cell Biology (IMCB), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore; (V.T.); (S.Y.L.)
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore 117597, Singapore
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore 117597, Singapore
| | - Sook Y. Lee
- Laboratory of NF-κB Signaling, Institute of Molecular and Cell Biology (IMCB), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore; (V.T.); (S.Y.L.)
| | - Manoj Garg
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University Uttar Pradesh, Noida 201313, India; (G.P.); (A.K.)
| | - Ekta Khattar
- Sunandan Divatia School of Science, SVKM’s NMIMS (Deemed to be University), Vile Parle West, Mumbai 400056, India; (S.G.F.); (R.D.)
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12
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Disel U, Madison R, Abhishek K, Chung JH, Trabucco SE, Matos AO, Frampton GM, Albacker LA, Reddy V, Karadurmus N, Benson A, Webster J, Paydas S, Cabanillas R, Nangia C, Ozturk M, Millis SZ, Pal SK, Wilky B, Sokol ES, Gay LM, Soman S, Ganesan S, Janeway K, Stephens PJ, Zhu VW, Ou SI, Lovly CM, Gounder M, Schrock AB, Ross JS, Miller VA, Klempner SJ, Ali SM. The Pan-Cancer Landscape of Coamplification of the Tyrosine Kinases KIT, KDR, and PDGFRA. Oncologist 2020; 25:e39-e47. [PMID: 31604903 PMCID: PMC6964135 DOI: 10.1634/theoncologist.2018-0528] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 05/03/2019] [Indexed: 12/23/2022] Open
Abstract
PURPOSE Amplifications of receptor tyrosine kinases (RTKS) are therapeutic targets in multiple tumor types (e.g. HER2 in breast cancer), and amplification of the chromosome 4 segment harboring the three RTKs KIT, PDGFRA, and KDR (4q12amp) may be similarly targetable. The presence of 4q12amp has been sporadically reported in small tumor specific series but a large-scale analysis is lacking. We assess the pan-cancer landscape of 4q12amp and provide early clinical support for the feasibility of targeting this amplicon. EXPERIMENTAL DESIGN Tumor specimens from 132,872 patients with advanced cancer were assayed with hybrid capture based comprehensive genomic profiling which assays 186-315 genes for all classes of genomic alterations, including amplifications. Baseline demographic data were abstracted, and presence of 4q12amp was defined as 6 or more copies of KIT/KDR/PDGFRA. Concurrent alterations and treatment outcomes with matched therapies were explored in a subset of cases. RESULTS Overall 0.65% of cases harbored 4q12amp at a median copy number of 10 (range 6-344). Among cancers with >100 cases in this series, glioblastomas, angiosarcomas, and osteosarcomas were enriched for 4q12amp at 4.7%, 4.8%, and 6.4%, respectively (all p < 0.001), giving an overall sarcoma (n = 6,885) incidence of 1.9%. Among 99 pulmonary adenocarcinoma cases harboring 4q12amp, 50 (50%) lacked any other known driver of NSLCC. Four index cases plus a previously reported case on treatment with empirical TKIs monotherapy had stable disease on average exceeding 20 months. CONCLUSION We define 4q12amp as a significant event across the pan-cancer landscape, comparable to known pan-cancer targets such as NTRK and microsatellite instability, with notable enrichment in several cancers such as osteosarcoma where standard treatment is limited. The responses to available TKIs observed in index cases strongly suggest 4q12amp is a druggable oncogenic target across cancers that warrants a focused drug development strategy. IMPLICATIONS FOR PRACTICE Coamplification of the receptor tyrosine kinases (rtks) KIT/KDR/PDGFRA (4q12amp) is present broadly across cancers (0.65%), with enrichment in osteosarcoma and gliomas. Evidence for this amplicon having an oncogenic role is the mutual exclusivity of 4q12amp to other known drivers in 50% of pulmonary adenocarcinoma cases. Furthermore, preliminary clinical evidence for driver status comes from four index cases of patients empirically treated with commercially available tyrosine kinase inhibitors with activity against KIT/KDR/PDGFRA who had stable disease for 20 months on average. The sum of these lines of evidence suggests further clinical and preclinical investigation of 4q12amp is warranted as the possible basis for a pan-cancer drug development strategy.
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Affiliation(s)
- Umut Disel
- Acibadem University, Acibadem Hospital Medical OncologyAdanaTurkey
| | | | | | - Jon H. Chung
- Foundation Medicine, Inc.CambridgeMassachusettsUSA
| | | | | | | | | | | | - Nuri Karadurmus
- Saglik Bilimleri Universities Gülhane Tıp FakültesiAnkaraTurkey
| | - Adam Benson
- Foundation Medicine, Inc.CambridgeMassachusettsUSA
| | | | - Semra Paydas
- Department of Medical Oncology, Cukurova University School of MedicineAdanaTurkey
| | - Ruben Cabanillas
- Instituto de Medicina Oncológica y Molecular de AsturiasAsturiasSpain
| | - Chaitali Nangia
- Chao Family Comprehensive Cancer Center, University of California, Irvine School of MedicineOrangeCaliforniaUSA
| | - M.A. Ozturk
- Department of Medical Oncology, Marmara University School of MedicineIstanbulTurkey
| | | | | | - Breelyn Wilky
- University of Miami School of MedicineMiamiFloridaUSA
| | | | | | - Salil Soman
- Beth Israel Deaconess Medical CenterBostonMassachusettsUSA
| | | | - Katherine Janeway
- Boston Children's Hospital and Dana‐Farber Cancer InstituteBostonMassachusettsUSA
| | | | - Viola W. Zhu
- Chao Family Comprehensive Cancer Center, University of California, Irvine School of MedicineOrangeCaliforniaUSA
| | - Sai‐Hong Ignatius Ou
- Chao Family Comprehensive Cancer Center, University of California, Irvine School of MedicineOrangeCaliforniaUSA
| | | | - Mrinal Gounder
- Memorial Sloan Kettering Cancer CenterNew YorkNew YorkUSA
| | | | - Jeffrey S. Ross
- Foundation Medicine, Inc.CambridgeMassachusettsUSA
- SUNY Upstate Medical UniversitySyracuseNew YorkUSA
| | | | | | - Siraj M. Ali
- Foundation Medicine, Inc.CambridgeMassachusettsUSA
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13
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Benstead-Hume G, Wooller SK, Downs JA, Pearl FMG. Defining Signatures of Arm-Wise Copy Number Change and Their Associated Drivers in Kidney Cancers. Int J Mol Sci 2019; 20:E5762. [PMID: 31744086 PMCID: PMC6887958 DOI: 10.3390/ijms20225762] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/13/2019] [Accepted: 11/14/2019] [Indexed: 01/15/2023] Open
Abstract
Using pan-cancer data from The Cancer Genome Atlas (TCGA), we investigated how patterns in copy number alterations in cancer cells vary both by tissue type and as a function of genetic alteration. We find that patterns in both chromosomal ploidy and individual arm copy number are dependent on tumour type. We highlight for example, the significant losses in chromosome arm 3p and the gain of ploidy in 5q in kidney clear cell renal cell carcinoma tissue samples. We find that specific gene mutations are associated with genome-wide copy number changes. Using signatures derived from non-negative factorisation, we also find gene mutations that are associated with particular patterns of ploidy change. Finally, utilising a set of machine learning classifiers, we successfully predicted the presence of mutated genes in a sample using arm-wise copy number patterns as features. This demonstrates that mutations in specific genes are correlated and may lead to specific patterns of ploidy loss and gain across chromosome arms. Using these same classifiers, we highlight which arms are most predictive of commonly mutated genes in kidney renal clear cell carcinoma (KIRC).
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Affiliation(s)
- Graeme Benstead-Hume
- Bioinformatics Lab, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK; (G.B.-H.); (S.K.W.)
| | - Sarah K. Wooller
- Bioinformatics Lab, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK; (G.B.-H.); (S.K.W.)
| | - Jessica A Downs
- Division of Cancer Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK;
| | - Frances M. G. Pearl
- Bioinformatics Lab, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK; (G.B.-H.); (S.K.W.)
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14
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Ramírez-Ramírez R, Gutiérrez-Angulo M, Peregrina-Sandoval J, Moreno-Ortiz JM, Franco-Topete RA, Cerda-Camacho FDJ, Ayala-Madrigal MDLL. Somatic deletion of KDM1A/LSD1 gene is associated to advanced colorectal cancer stages. J Clin Pathol 2019; 73:107-111. [PMID: 31471467 PMCID: PMC7027028 DOI: 10.1136/jclinpath-2019-206128] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/20/2019] [Accepted: 08/20/2019] [Indexed: 01/08/2023]
Abstract
Aims KDM1A/LSD1 and ZNF217 are involved in a protein complex that participates in transcriptional regulation. ZNF217 has been analysed in numerous cancers and its amplification has been associated with advanced stages of disease; however, a similar role for KDM1A/LSD1 has not been uncovered. In this study, we estimated the number of KDM1A/LSD1 and ZNF217 gene copies in tissue samples from patients diagnosed with colorectal cancer (CRC), as well as its association with clinicopathological features in patients with CRC. Methods Paraffin-embedded tumour samples from 50 patients with CRC with a histopathological diagnosis of CRC were included. The number of copies of KDM1A/LSD1 and ZNF217 genes was determined by fluorescence in situ hybridisation (FISH). We also analysed the association between copy numbers of selected genes and clinicopathological data based on multivariate analysis. Results Deletion of the KDM1A/LSD1 gene occurred in 19 samples (38%), whereas ZNF217 gene amplification was identified in 11 samples (22%). We found a significant association between lymph node metastasis or advanced tumour stage and KDM1A/LSD1 gene deletion (p value=0.0003 and p value=0.011, respectively). Conclusions KDM1A/LSD1 gene deletion could be considered a novel prognostic biomarker of late-stage CRC.
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Affiliation(s)
- Ruth Ramírez-Ramírez
- Laboratorio de Inmunología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan, México
| | - Melva Gutiérrez-Angulo
- Departamento de Clínicas, Centro Universitario de los Altos, Universidad de Guadalajara, Tepatitlán de Morelos, México.,Programa de Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, México
| | - Jorge Peregrina-Sandoval
- Laboratorio de Inmunología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan, México.,Laboratorio de Patología Clínica, Hospital Civil de Guadalajara "Fray Antonio Alcalde", Guadalajara, México
| | - José Miguel Moreno-Ortiz
- Programa de Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, México.,Instituto de Genética Humana "Dr. Enrique Corona Rivera", Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, México
| | - Ramon Antonio Franco-Topete
- Servicio de Anatomía Patológica, Hospital Civil de Guadalajara "Dr. Juan I Menchaca", Guadalajara, México.,Departamento de Microbiología y Patología, Universidad de Guadalajara, Guadalajara, México
| | | | - Maria de la Luz Ayala-Madrigal
- Programa de Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, México .,Instituto de Genética Humana "Dr. Enrique Corona Rivera", Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, México
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15
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Lauer S, Gresham D. An evolving view of copy number variants. Curr Genet 2019; 65:1287-1295. [PMID: 31076843 DOI: 10.1007/s00294-019-00980-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/17/2019] [Accepted: 04/20/2019] [Indexed: 01/08/2023]
Abstract
Copy number variants (CNVs) are regions of the genome that vary in integer copy number. CNVs, which comprise both amplifications and deletions of DNA sequence, have been identified across all domains of life, from bacteria and archaea to plants and animals. CNVs are an important source of genetic diversity, and can drive rapid adaptive evolution and progression of heritable and somatic human diseases, such as cancer. However, despite their evolutionary importance and clinical relevance, CNVs remain understudied compared to single-nucleotide variants (SNVs). This is a consequence of the inherent difficulties in detecting CNVs at low-to-intermediate frequencies in heterogeneous populations of cells. Here, we discuss molecular methods used to detect CNVs, the limitations associated with using these techniques, and the application of new and emerging technologies that present solutions to these challenges. The goal of this short review and perspective is to highlight aspects of CNV biology that are understudied and define avenues for further research that address specific gaps in our knowledge of these complex alleles. We describe our recently developed method for CNV detection in which a fluorescent gene functions as a single-cell CNV reporter and present key findings from our evolution experiments in Saccharomyces cerevisiae. Using a CNV reporter, we found that CNVs are generated at a high rate and undergo selection with predictable dynamics across independently evolving replicate populations. Many CNVs appear to be generated through DNA replication-based processes that are mediated by the presence of short, interrupted, inverted-repeat sequences. Our results have important implications for the role of CNVs in evolutionary processes and the molecular mechanisms that underlie CNV formation. We discuss the possible extension of our method to other applications, including tracking the dynamics of CNVs in models of human tumors.
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Affiliation(s)
- Stephanie Lauer
- Institute for Systems Genetics, New York University Langone Health, New York, NY, USA
| | - David Gresham
- Center for Genomics and System Biology, Department of Biology, New York University, New York, NY, USA.
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16
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Buhmeida A, Assidi M, Al-Maghrabi J, Dallol A, Sibiany A, Al-Ahwal M, Chaudhary A, Abuzenadah A, Al-Qahtani M. Membranous or Cytoplasmic HER2 Expression in Colorectal Carcinoma: Evaluation of Prognostic Value Using Both IHC & BDISH. Cancer Invest 2018; 36:129-140. [PMID: 29504811 DOI: 10.1080/07357907.2018.1439054] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND Human epidermal growth factor recptor-2 (HER2) was identified as a driver gene in several types of cancers with both prognostic and predictive value. However, the molecular association of HER2 gene mutation with HER2 gene amplification and/or protein expression in cancer tissues has not been clearly defined. Moreover, there is little information available on HER2 status role in tumor progression and metastasis in colorectal carcinoma (CRC) compared to other solid tumors. The aim of this study was to evaluate both HER2 amplification and protein expression profiles using immunohistochemistry (IHC) and bright-field dual in situ hybridization (BDISH) techniques, respectively. PATIENTS AND METHODS Tissue microarray (TMA) was constructed to accommodate a total of 243 CRC formalin-fixed paraffin embedded (FFPE) samples of consent patients and stained by IHC and BDISH methods. The expression patterns of HER2 protein status were evaluated and correlated to HER2 gene amplification status and then assessed for its prognostic value. RESULTS The expression profile of 58% samples showed cytoplasmic expression patterns of different categories. Interestingly, only 1% showed strong (+3) membranous expression pattern of HER2 with perfect match with their corresponding gene amplification status (>2). However, the cytoplasmic HER2 protein status did not show significant correlation with most clinicopathological features and survival outcomes except with age (p = 0.04) and tumor size (p = 0.03). CONCLUSION We demonstrated that the membranous HER2 gene/protein status is infrequent, while the main fraction of HER2 overexpression was cytoplasmic and lacking prognostic value. This cytoplasmic HER2 overexpression was induced through a gene-amplification independent pathway, making the HER2 gene status evaluation approach in those cases not worthy. Further investigations about the molecular pathways of the cytoplasmic HER2 protein in CRC and its associations with survival outcomes are required to allow either a breakthrough in CRC management; or to confirm the hypothesis of a marginal role in CRC onset and progression.
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Affiliation(s)
- Abdelbaset Buhmeida
- a Center of Excellence in Genomic Medicine Research , King Abdulaziz University , Jeddah , Saudi Arabia
| | - Mourad Assidi
- a Center of Excellence in Genomic Medicine Research , King Abdulaziz University , Jeddah , Saudi Arabia.,b KACST Technology Innovation Center in Personalized Medicine , King Abdulaziz University , Jeddah , Saudi Arabia
| | - Jaudah Al-Maghrabi
- c Department of Pathology, Faculty of Medicine , King Abdulaziz University , Jeddah , Saudi Arabia
| | - Ashraf Dallol
- a Center of Excellence in Genomic Medicine Research , King Abdulaziz University , Jeddah , Saudi Arabia.,b KACST Technology Innovation Center in Personalized Medicine , King Abdulaziz University , Jeddah , Saudi Arabia
| | - Abdulrahman Sibiany
- d Department of Surgery, Faculty of Medicine , King Abdulaziz University , Jeddah , Saudi Arabia
| | - Mahmoud Al-Ahwal
- e Department of Internal Medicine, Faculty of Medicine , King Abdulaziz University , Jeddah , Saudi Arabia
| | - Adeel Chaudhary
- a Center of Excellence in Genomic Medicine Research , King Abdulaziz University , Jeddah , Saudi Arabia
| | - Adel Abuzenadah
- a Center of Excellence in Genomic Medicine Research , King Abdulaziz University , Jeddah , Saudi Arabia.,b KACST Technology Innovation Center in Personalized Medicine , King Abdulaziz University , Jeddah , Saudi Arabia
| | - Mohammed Al-Qahtani
- a Center of Excellence in Genomic Medicine Research , King Abdulaziz University , Jeddah , Saudi Arabia
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17
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Liu R, Qu Y, Chen L, Pu J, Ma S, Zhang X, Yang Q, Shi B, Hou P, Ji M. Genomic copy number gains of ErbB family members predict poor clinical outcomes in glioma patients. Oncotarget 2017; 8:92275-92288. [PMID: 29190914 PMCID: PMC5696180 DOI: 10.18632/oncotarget.21228] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/17/2017] [Indexed: 11/25/2022] Open
Abstract
The aim of this study was to investigate copy number of ErbB family members (including EGFR, HER2, HER3 and HER4) in a cohort of gliomas and benign meningiomas (control subjects), and explore the associations of their copy number with clinicopathological characteristics and clinical outcomes of glioma patients. Using real-time quantitative PCR assay, we demonstrated that copy number of EGFR, HER2, HER3 and HER4 in glioma patients was significantly increased compared to control subjects. Moreover, our data also showed that the risk of cancer-related death was positively associated with copy number gain (CNG) of EGFR, HER3 and HER4, but not HER2. CNG of EGFR and HER2 was positively related to radiotherapy, while CNG of HER3 and HER4 was negatively related to chemotherapy. Importantly, EGFR CNG significantly shortened median survival times of glioma patients regardless of gender, tumor grade and therapeutic regimens. Stratified analysis showed that CNG of HER2-4 almost did not influence the survival of male patients, patients with high-grade tumors and patients receiving chemotherapy, but dramatically shortened median survival times of female patients, those with low-grade tumors and those receiving radiotherapy. Collectively, our data not only demonstrate that the members of ErbB family are frequently amplified in gliomas, but also suggest that these common genetic events may be prognostic factors for poor clinical outcomes in glioma patients.
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Affiliation(s)
- Rui Liu
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University School of Medicine, Xi'an 710061, P. R. China.,Department of Radio-Oncology, The First Affiliated Hospital of Xi'an Jiaotong University School of Medicine, Xi'an 710061, P. R. China
| | - Yiping Qu
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University School of Medicine, Xi'an 710061, P. R. China
| | - Lihong Chen
- Department of Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, P. R. China
| | - Jun Pu
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University School of Medicine, Xi'an 710061, P. R. China
| | - Sharui Ma
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University School of Medicine, Xi'an 710061, P. R. China
| | - Xiaozhi Zhang
- Department of Radio-Oncology, The First Affiliated Hospital of Xi'an Jiaotong University School of Medicine, Xi'an 710061, P. R. China
| | - Qi Yang
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University School of Medicine, Xi'an 710061, P. R. China
| | - Bingyin Shi
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University School of Medicine, Xi'an 710061, P. R. China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, P. R. China
| | - Peng Hou
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University School of Medicine, Xi'an 710061, P. R. China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, P. R. China
| | - Meiju Ji
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, P.R. China
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18
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Jia Y, Chen L, Jia Q, Dou X, Xu N, Liao DJ. The well-accepted notion that gene amplification contributes to increased expression still remains, after all these years, a reasonable but unproven assumption. J Carcinog 2016; 15:3. [PMID: 27298590 PMCID: PMC4895059 DOI: 10.4103/1477-3163.182809] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 04/25/2016] [Indexed: 02/06/2023] Open
Abstract
“Gene amplification causes overexpression” is a longstanding and well-accepted concept in cancer genetics. However, raking the whole literature, we find only statistical analyses showing a positive correlation between gene copy number and expression level, but do not find convincing experimental corroboration for this notion, for most of the amplified oncogenes in cancers. Since an association does not need to be an actual causal relation, in our opinion, this widespread notion still remains a reasonable but unproven assumption awaiting experimental verification.
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Affiliation(s)
- Yuping Jia
- Animal Facilities, Shandong Academy of Pharmaceutical Sciences, Ji'nan, Shandong 250101, USA
| | - Lichan Chen
- Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Qingwen Jia
- Animal Facilities, Shandong Academy of Pharmaceutical Sciences, Ji'nan, Shandong 250101, USA
| | - Xixi Dou
- Animal Facilities, Shandong Academy of Pharmaceutical Sciences, Ji'nan, Shandong 250101, USA
| | - Ningzhi Xu
- Laboratory of Cell and Molecular Biology, Cancer Institute, Chinese Academy of Medical Science, Beijing 100021, China
| | - Dezhong Joshua Liao
- Department of Pathology, Guizhou Medical University Hospital, Guizhou, Guiyang 550004, P.R. China
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