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Shaw TI, Pounds S, Cao X, Ma J, Palacios G, Mason J, Perkins S, Wu G, Fan Y, Wang J, Zhou X, Obermayer A, Kinney MC, Kraveka J, Gross T, Sandlund J, Zhang J, Mullighan C, Lim MS, Leventaki V. Comprehensive genomic analysis reveals molecular heterogeneity in pediatric ALK-positive anaplastic large cell lymphoma. RESEARCH SQUARE 2024:rs.3.rs-4145750. [PMID: 38585847 PMCID: PMC10996813 DOI: 10.21203/rs.3.rs-4145750/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Anaplastic large cell lymphoma (ALCL) is a mature T-cell lymphoma that accounts for for 10-15% of childhood lymphomas. Despite the observation that more than 90% of pediatric cases harbor the anaplastic lymphoma kinase (ALK) rearrangement resulting in aberrant ALK kinase expression, there is significant clinical, morphologic, and biological heterogeneity. To gain insights into the genomic aberrations and molecular heterogeneity within ALK-positive ALCL(ALK+ ALCL), we analyzed 46 pediatric ALK+ ALCLs by whole-exome sequencing, RNA-sequencing, and DNA methylation profiling. Whole-exome sequencing found on average 25 SNV/Indel events per sample with recurring genetic events in regulators of DNA damage (TP53, MDM4), transcription (JUNB), and epigenetic regulators (TET1, KMT2B, KMT2A, KMT2C, KMT2E). Gene expression and methylation profiling consistently subclassified ALK+ ALCLs into two groups characterized by diferential ALK expression levels. The ALK-low group showed enrichment of pathways associated with immune response, cytokine signaling, and a hypermethylated predominant pattern compared to the ALK- high group, which had more frequent copy number changes, and was enriched with pathways associated with cell growth, proliferation, metabolic pathways, and. Taken together, these findings suggest that there is molecular heterogeneity within pediatric ALK+ALCL, predicting distinct biological mechanisms that may provide novel insights into disease pathogenesis and represent prognostic markers.
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Affiliation(s)
- Timothy I. Shaw
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Xueyuan Cao
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, TN
- Department of Health Promotion and Disease Prevention, University of Tennessee Health Science Center, Memphis, TN
| | - Jing Ma
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Gustavo Palacios
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN
| | - John Mason
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Sherrie Perkins
- Department of Pathology, University of Utah Health Sciences, Salt Lake City, UT
| | - Gang Wu
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Jian Wang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Alyssa Obermayer
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL
| | - Marsha C. Kinney
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center, at San Antonio, San Antonio, TX
| | - Jacqueline Kraveka
- Division of Pediatric Hematology-Oncology, Medical University of South Carolina, Charleston, SC
| | - Thomas Gross
- Department of Pediatric Hematology-Oncology, Nationwide Children’s Hospital, Columbus, OH
| | - John Sandlund
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Charles Mullighan
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Megan S. Lim
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Vasiliki Leventaki
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX
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2
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Balendran T, Lim K, Hamilton JA, Achuthan AA. Targeting transcription factors for therapeutic benefit in rheumatoid arthritis. Front Immunol 2023; 14:1196931. [PMID: 37457726 PMCID: PMC10339812 DOI: 10.3389/fimmu.2023.1196931] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023] Open
Abstract
Rheumatoid arthritis (RA) is a destructive inflammatory autoimmune disease that causes pain and disability. Many of the currently available drugs for treating RA patients are aimed at halting the progression of the disease and alleviating inflammation. Further, some of these treatment options have drawbacks, including disease recurrence and adverse effects due to long-term use. These inefficiencies have created a need for a different approach to treating RA. Recently, the focus has shifted to direct targeting of transcription factors (TFs), as they play a vital role in the pathogenesis of RA, activating key cytokines, chemokines, adhesion molecules, and enzymes. In light of this, synthetic drugs and natural compounds are being explored to target key TFs or their signaling pathways in RA. This review discusses the role of four key TFs in inflammation, namely NF-κB, STATs, AP-1 and IRFs, and their potential for being targeted to treat RA.
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Affiliation(s)
- Thivya Balendran
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
| | - Keith Lim
- Department of Medicine, Western Health, The University of Melbourne, St Albans, VIC, Australia
| | - John A. Hamilton
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
| | - Adrian A. Achuthan
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
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3
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The Preventive Effect of Specific Collagen Peptides against Dexamethasone-Induced Muscle Atrophy in Mice. Molecules 2023; 28:molecules28041950. [PMID: 36838938 PMCID: PMC9960993 DOI: 10.3390/molecules28041950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/13/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Muscle atrophy, also known as muscle wasting, is the thinning of muscle mass due to muscle disuse, aging, or diseases such as cancer or neurological problems. Muscle atrophy is closely related to the quality of life and has high morbidity and mortality. However, therapeutic options for muscle atrophy are limited, so studies to develop therapeutic agents for muscle loss are always required. For this study, we investigated how orally administered specific collagen peptides (CP) affect muscle atrophy and elucidated its molecular mechanism using an in vivo model. We treated mice with dexamethasone (DEX) to induce a muscular atrophy phenotype and then administered CP (0.25 and 0.5 g/kg) for four weeks. In a microcomputed tomography analysis, CP (0.5 g/kg) intake significantly increased the volume of calf muscles in mice with DEX-induced muscle atrophy. In addition, the administration of CP (0.25 and 0.5 g/kg) restored the weight of the gluteus maximus and the fiber cross-sectional area (CSA) of the pectoralis major and calf muscles, which were reduced by DEX. CP significantly inhibited the mRNA expression of myostatin and the phosphorylation of Smad2, but it did not affect TGF-β, BDNF, or FNDC5 gene expression. In addition, AKT/mTOR, a central pathway for muscle protein synthesis and related to myostatin signaling, was enhanced in the groups that were administered CP. Finally, CP decreased serum albumin levels and increased TNF-α gene expression. Collectively, our in vivo results demonstrate that CP can alleviate muscle wasting through a multitude of mechanisms. Therefore, we propose CP as a supplement or treatment to prevent muscle atrophy.
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Garbin A, Lovisa F, Holmes AB, Damanti CC, Gallingani I, Carraro E, Accordi B, Veltri G, Pizzi M, d'Amore ESG, Pillon M, Biffi A, Basso K, Mussolin L. miR-939 acts as tumor suppressor by modulating JUNB transcriptional activity in pediatric anaplastic large cell lymphoma. Haematologica 2021; 106:610-613. [PMID: 32299901 PMCID: PMC7849582 DOI: 10.3324/haematol.2019.241307] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 04/09/2020] [Indexed: 12/13/2022] Open
Affiliation(s)
- Anna Garbin
- Dept Women's and Children's Health, Clinic of Pediatric Hemato-Oncology, University of Padua, Italy
| | - Federica Lovisa
- Dept Women's and Children's Health, Clinic of Pediatric Hemato-Oncology, University of Padua, Italy
| | - Antony B Holmes
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Carlotta C Damanti
- Dept Women's and Children's Health, Clinic of Pediatric Hemato-Oncology, University of Padua, Italy
| | - Ilaria Gallingani
- Dept Women's and Children's Health, Clinic of Pediatric Hemato-Oncology, University of Padua, Italy
| | - Elisa Carraro
- Dept Women's and Children's Health, Clinic of Pediatric Hemato-Oncology, University of Padua, Italy
| | - Benedetta Accordi
- Dept Women's and Children's Health, Clinic of Pediatric Hemato-Oncology, University of Padua, Italy
| | - Giulia Veltri
- Dept Women's and Children's Health, Clinic of Pediatric Hemato-Oncology, University of Padua, Italy
| | - Marco Pizzi
- Surgical Pathology and Cytopathology Unit, Department of Medicine, University of Padova, Italy
| | | | - Marta Pillon
- Dept Women's and Children's Health, Clinic of Pediatric Hemato-Oncology, University of Padua, Italy
| | - Alessandra Biffi
- Dept Women's and Children's Health, Clinic of Pediatric Hemato-Oncology, University of Padua, Italy
| | - Katia Basso
- Institute for Cancer Genetics and Dept of Pathology and Cell Biology, Columbia University, New York, USA
| | - Lara Mussolin
- Dept Women's and Children's Health, Clinic of Pediatric Hemato-Oncology, University of Padua, Italy
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5
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Wu Z, Nicoll M, Ingham RJ. AP-1 family transcription factors: a diverse family of proteins that regulate varied cellular activities in classical hodgkin lymphoma and ALK+ ALCL. Exp Hematol Oncol 2021; 10:4. [PMID: 33413671 PMCID: PMC7792353 DOI: 10.1186/s40164-020-00197-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 01/07/2023] Open
Abstract
Classical Hodgkin lymphoma (cHL) and anaplastic lymphoma kinase-positive, anaplastic large cell lymphoma (ALK+ ALCL) are B and T cell lymphomas respectively, which express the tumour necrosis factor receptor superfamily member, CD30. Another feature shared by cHL and ALK+ ALCL is the aberrant expression of multiple members of the activator protein-1 (AP-1) family of transcription factors which includes proteins of the Jun, Fos, ATF, and Maf subfamilies. In this review, we highlight the varied roles these proteins play in the pathobiology of these lymphomas including promoting proliferation, suppressing apoptosis, and evading the host immune response. In addition, we discuss factors contributing to the elevated expression of these transcription factors in cHL and ALK+ ALCL. Finally, we examine therapeutic strategies for these lymphomas that exploit AP-1 transcriptional targets or the signalling pathways they regulate.
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Affiliation(s)
- Zuoqiao Wu
- grid.17089.37Department of Medical Microbiology and Immunology, Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada ,grid.17063.330000 0001 2157 2938Present Address: Department of Medicine, University of Toronto, Toronto, Canada
| | - Mary Nicoll
- grid.17089.37Department of Medical Microbiology and Immunology, Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada ,grid.14709.3b0000 0004 1936 8649Present Address: Department of Biology, McGill University, Montreal, Canada
| | - Robert J. Ingham
- grid.17089.37Department of Medical Microbiology and Immunology, Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada
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6
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Fiore D, Cappelli LV, Broccoli A, Zinzani PL, Chan WC, Inghirami G. Peripheral T cell lymphomas: from the bench to the clinic. Nat Rev Cancer 2020; 20:323-342. [PMID: 32249838 DOI: 10.1038/s41568-020-0247-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/18/2020] [Indexed: 02/07/2023]
Abstract
Peripheral T cell lymphomas (PTCLs) are a heterogeneous group of orphan neoplasms. Despite the introduction of anthracycline-based chemotherapy protocols, with or without autologous haematopoietic transplantation and a plethora of new agents, the progression-free survival of patients with PTCLs needs to be improved. The rarity of these neoplasms, the limited knowledge of their driving defects and the lack of experimental models have impaired clinical successes. This scenario is now rapidly changing with the discovery of a spectrum of genomic defects that hijack essential signalling pathways and foster T cell transformation. This knowledge has led to new genomic-based stratifications, which are being used to establish objective diagnostic criteria, more effective risk assessment and target-based interventions. The integration of genomic and functional data has provided the basis for targeted therapies and immunological approaches that underlie individual tumour vulnerabilities. Fortunately, novel therapeutic strategies can now be rapidly tested in preclinical models and effectively translated to the clinic by means of well-designed clinical trials. We believe that by combining new targeted agents with immune regulators and chimeric antigen receptor-expressing natural killer and T cells, the overall survival of patients with PTCLs will dramatically increase.
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MESH Headings
- Epigenesis, Genetic/genetics
- Epigenesis, Genetic/physiology
- Humans
- Immunotherapy
- Lymphoma, T-Cell, Peripheral/drug therapy
- Lymphoma, T-Cell, Peripheral/genetics
- Lymphoma, T-Cell, Peripheral/immunology
- Lymphoma, T-Cell, Peripheral/metabolism
- Molecular Targeted Therapy
- Mutation
- Signal Transduction/genetics
- Signal Transduction/physiology
- T-Lymphocytes/physiology
- Transcription Factors/genetics
- Transcription Factors/physiology
- Tumor Microenvironment/genetics
- Tumor Microenvironment/immunology
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Affiliation(s)
- Danilo Fiore
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Luca Vincenzo Cappelli
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Alessandro Broccoli
- Institute of Hematology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
| | - Pier Luigi Zinzani
- Institute of Hematology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy.
| | - Wing C Chan
- Department of Pathology, City of Hope Medical Center, Duarte, CA, USA.
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
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Abstract
Anaplastic large cell lymphomas are a rare subtype of peripheral/mature T-cell lymphomas which are clinically, pathologically and genetically heterogeneous. Both ALK-positive (ALK+) and ALK-negative (ALK-) ALCL are composed of large lymphoid cells with abundant cytoplasm and pleomorphic features with horseshoe-shaped and reniform nuclei. ALK+ ALCL were considered as a definite entity in the 2008 World Health Organization classification of hematopoietic and lymphoid tissues. ALK-ALCL was included as a provisional entity in the WHO 2008 edition and in the most recent 2017 edition, it is now considered a distinct entity that includes cytogenetic subsets that appear to have prognostic implications (e.g. 6p25 rearrangements at IRF4/DUSP22 locus). ALK+ ALCLs are distinct in epidemiology and pathogenetic origin and should be distinguished from ALK-ALCL, cutaneous ALCL and breast implant associated ALCL which have distinct clinical course and pathogenetic features. Breast implant-associated ALCL is now recognized as a new provisional entity distinct from other ALK-ALCL; notably that it is a noninvasive disease associated with excellent outcome. In this article, we will provide an overview of the salient themes relevant to the pathology and genetic mechanisms in ALCL.
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Affiliation(s)
- Vasiliki Leventaki
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Siddharth Bhattacharyya
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA United States
| | - Megan S Lim
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA United States.
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8
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Huang W, Guo L, Zhao M, Zhang D, Xu H, Nie Q. The Inhibition on MDFIC and PI3K/AKT Pathway Caused by miR-146b-3p Triggers Suppression of Myoblast Proliferation and Differentiation and Promotion of Apoptosis. Cells 2019; 8:cells8070656. [PMID: 31261950 PMCID: PMC6678156 DOI: 10.3390/cells8070656] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 06/27/2019] [Accepted: 06/27/2019] [Indexed: 01/30/2023] Open
Abstract
Accumulating studies report that microRNAs (miRNAs) are actively involved in skeletal myogenesis. Previously, our study revealed that miR-146b-3p was related to the growth of skeletal muscle. Here, we further report that miR-146b-3p is essential for the proliferation, differentiation, and apoptosis of chicken myoblast. Elevated expression of miR-146b-3p can dramatically suppress proliferation and differentiation, and facilitate apoptosis of chicken myoblast. Besides, we identified two target genes of miR-146b-3p, AKT1 and MDFIC, and found that miR-146b-3p can inhibit the PI3K/AKT pathway. Our study also showed that both AKT1 and MDFIC can promote the proliferation and differentiation while inhibit the apoptosis of myoblast in chicken. Overall, our results demonstrate that miR-146b-3p, directly suppressing PI3K/AKT pathway and MDFIC, acts in the proliferation, differentiation, and apoptosis of myoblast in chicken.
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Affiliation(s)
- Weiling Huang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Lijin Guo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Minxing Zhao
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Dexiang Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Haiping Xu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Qinghua Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China.
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9
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The Role of Activator Protein-1 (AP-1) Family Members in CD30-Positive Lymphomas. Cancers (Basel) 2018; 10:cancers10040093. [PMID: 29597249 PMCID: PMC5923348 DOI: 10.3390/cancers10040093] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 03/21/2018] [Accepted: 03/25/2018] [Indexed: 12/14/2022] Open
Abstract
The Activator Protein-1 (AP-1) transcription factor (TF) family, composed of a variety of members including c-JUN, c-FOS and ATF, is involved in mediating many biological processes such as proliferation, differentiation and cell death. Since their discovery, the role of AP-1 TFs in cancer development has been extensively analysed. Multiple in vitro and in vivo studies have highlighted the complexity of these TFs, mainly due to their cell-type specific homo- or hetero-dimerization resulting in diverse transcriptional response profiles. However, as a result of the increasing knowledge of the role of AP-1 TFs in disease, these TFs are being recognized as promising therapeutic targets for various malignancies. In this review, we focus on the impact of deregulated expression of AP-1 TFs in CD30-positive lymphomas including Classical Hodgkin Lymphoma and Anaplastic Large Cell Lymphoma.
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10
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Identification of the functional alteration signatures across different cancer types with support vector machine and feature analysis. Biochim Biophys Acta Mol Basis Dis 2017; 1864:2218-2227. [PMID: 29277326 DOI: 10.1016/j.bbadis.2017.12.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/04/2017] [Accepted: 12/15/2017] [Indexed: 12/13/2022]
Abstract
Cancers are regarded as malignant proliferations of tumor cells present in many tissues and organs, which can severely curtail the quality of human life. The potential of using plasma DNA for cancer detection has been widely recognized, leading to the need of mapping the tissue-of-origin through the identification of somatic mutations. With cutting-edge technologies, such as next-generation sequencing, numerous somatic mutations have been identified, and the mutation signatures have been uncovered across different cancer types. However, somatic mutations are not independent events in carcinogenesis but exert functional effects. In this study, we applied a pan-cancer analysis to five types of cancers: (I) breast cancer (BRCA), (II) colorectal adenocarcinoma (COADREAD), (III) head and neck squamous cell carcinoma (HNSC), (IV) kidney renal clear cell carcinoma (KIRC), and (V) ovarian cancer (OV). Based on the mutated genes of patients suffering from one of the aforementioned cancer types, patients they were encoded into a large number of numerical values based upon the enrichment theory of gene ontology (GO) terms and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. We analyzed these features with the Monte-Carlo Feature Selection (MCFS) method, followed by the incremental feature selection (IFS) method to identify functional alteration features that could be used to build the support vector machine (SVM)-based classifier for distinguishing the five types of cancers. Our results showed that the optimal classifier with the selected 344 features had the highest Matthews correlation coefficient value of 0.523. Sixteen decision rules produced by the MCFS method can yield an overall accuracy of 0.498 for the classification of the five cancer types. Further analysis indicated that some of these features and rules were supported by previous experiments. This study not only presents a new approach to mapping the tissue-of-origin for cancer detection but also unveils the specific functional alterations of each cancer type, providing insight into cancer-specific functional aberrations as potential therapeutic targets. This article is part of a Special Issue entitled: Accelerating Precision Medicine through Genetic and Genomic Big Data Analysis edited by Yudong Cai & Tao Huang.
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11
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Chung IH, Lu PH, Lin YH, Tsai MM, Lin YW, Yeh CT, Lin KH. The long non-coding RNA LINC01013 enhances invasion of human anaplastic large-cell lymphoma. Sci Rep 2017; 7:295. [PMID: 28331184 PMCID: PMC5428265 DOI: 10.1038/s41598-017-00382-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 02/22/2017] [Indexed: 12/28/2022] Open
Abstract
Anaplastic large-cell lymphoma (ALCL) is a rare type of highly malignant, non-Hodgkin lymphoma (NHL). Currently, only studies on the chimeric oncogene NPM-ALK have reported a link to ALCL progression. However, the specific molecular mechanisms underlying the invasion of ALCL are still unclear. Here, we sought to investigate differentially expressed, long non-coding RNAs (lncRNAs) in ALCL and their potential biological function. Our microarray analyses revealed that LINC01013, a novel non-coding RNA gene, was highly expressed in clinical specimens of ALCL and was significantly upregulated in invasive ALCL cell lines. Knockdown of LINC01013 suppressed tumor cell invasion; conversely, its overexpression enhanced tumor cell invasion. LINC01013-induced invasion was mediated by activation of the epithelial-to-mesenchymal transition (EMT)-associated proteins, snail and fibronectin. Specifically, LINC01013 induced snail, resulting in activation of fibronectin and enhanced ALCL cell invasion. Collectively, these findings support a potential role for LINC01013 in cancer cell invasion through the snail-fibronectin activation cascade and suggest that LINC01013 could potentially be utilized as a metastasis marker in ALCL.
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Affiliation(s)
- I-Hsiao Chung
- Department of Biochemistry, College of Medicine, Chang Gung University, Taoyuan, Taiwan (R.O.C.)
| | - Pei-Hsuan Lu
- Department of Biochemistry, College of Medicine, Chang Gung University, Taoyuan, Taiwan (R.O.C.).,Department of Dermatology, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan (R.O.C.)
| | - Yang-Hsiang Lin
- Department of Biochemistry, College of Medicine, Chang Gung University, Taoyuan, Taiwan (R.O.C.)
| | - Ming-Ming Tsai
- Department of Nursing, Chang Gung University of Science and Technology, Taoyuan, Taiwan (R.O.C.).,Department of General Surgery, Chang Gung Memorial Hospital, Chiayi, Taiwan (R.O.C.)
| | - Yun-Wen Lin
- Department of Biochemistry, College of Medicine, Chang Gung University, Taoyuan, Taiwan (R.O.C.)
| | - Chau-Ting Yeh
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan (R.O.C.)
| | - Kwang-Huei Lin
- Department of Biochemistry, College of Medicine, Chang Gung University, Taoyuan, Taiwan (R.O.C.). .,Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan (R.O.C.). .,Research Center for Chinese Herbal Medicine, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan (R.O.C.).
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12
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Papoudou-Bai A, Hatzimichael E, Barbouti A, Kanavaros P. Expression patterns of the activator protein-1 (AP-1) family members in lymphoid neoplasms. Clin Exp Med 2016; 17:291-304. [PMID: 27600282 DOI: 10.1007/s10238-016-0436-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 08/23/2016] [Indexed: 12/22/2022]
Abstract
The activator protein-1 (AP-1) is a dimeric transcription factor composed of proteins belonging to the Jun (c-Jun, JunB and JunD), Fos (c-Fos, FosB, Fra1 and Fra2) and activating transcription factor protein families. AP-1 is involved in various cellular events including differentiation, proliferation, survival and apoptosis. Deregulated expression of AP-1 transcription factors is implicated in the pathogenesis of various lymphomas such as classical Hodgkin lymphomas, anaplastic large cell lymphomas, diffuse large B cell lymphomas and adult T cell leukemia/lymphoma. The main purpose of this review is the analysis of the expression patterns of AP-1 transcription factors in order to gain insight into the histophysiology of lymphoid tissues and the pathology of lymphoid malignancies.
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Affiliation(s)
| | | | - Alexandra Barbouti
- Department of Anatomy-Histology-Embryology, Faculty of Medicine, University of Ioannina, Ioannina, Greece
| | - Panagiotis Kanavaros
- Department of Anatomy-Histology-Embryology, Faculty of Medicine, University of Ioannina, Ioannina, Greece.
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Developmental transcriptome analysis and identification of genes involved in formation of intestinal air-breathing function of Dojo loach, Misgurnus anguillicaudatus. Sci Rep 2016; 6:31845. [PMID: 27545457 PMCID: PMC4992823 DOI: 10.1038/srep31845] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 07/26/2016] [Indexed: 11/17/2022] Open
Abstract
Dojo loach, Misgurnus anguillicaudatus is a freshwater fish species of the loach family Cobitidae, using its posterior intestine as an accessory air-breathing organ. Little is known about the molecular regulatory mechanisms in the formation of intestinal air-breathing function of M. anguillicaudatus. Here high-throughput sequencing of mRNAs was performed from six developmental stages of posterior intestine of M. anguillicaudatus: 4-Dph (days post hatch) group, 8-Dph group, 12-Dph group, 20-Dph group, 40-Dph group and Oyd (one-year-old) group. These six libraries were assembled into 81300 unigenes. Totally 40757 unigenes were annotated. Subsequently, 35291 differentially expressed genes (DEGs) were scanned among different developmental stages and clustered into 20 gene expression profiles. Finally, 15 key pathways and 25 key genes were mined, providing potential targets for candidate gene selection involved in formation of intestinal air-breathing function in M. anguillicaudatus. This is the first report of developmental transcriptome of posterior intestine in M. anguillicaudatus, offering a substantial contribution to the sequence resources for this species and providing a deep insight into the formation mechanism of its intestinal air-breathing function. This report demonstrates that M. anguillicaudatus is a good model for studies to identify and characterize the molecular basis of accessory air-breathing organ development in fish.
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Fan SJ, Li HB, Cui G, Kong XL, Sun LL, Zhao YQ, Li YH, Zhou J. miRNA-149* promotes cell proliferation and suppresses apoptosis by mediating JunB in T-cell acute lymphoblastic leukemia. Leuk Res 2015; 41:62-70. [PMID: 26725775 DOI: 10.1016/j.leukres.2015.11.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 11/03/2015] [Accepted: 11/28/2015] [Indexed: 12/29/2022]
Abstract
MicroRNA-149* (miRNA-149*) functions as an oncogenic regulator in human melanoma. However, the effect of miRNA-149* on T-cell acute lymphoblastic leukemia (T-ALL) is unclear. Here we aimed to analyze the effects of miRNA-149* on in vitro T-ALL cells and to uncover the target for miRNA-149* in these cells. The miRNA-149* level was determined in multiple cell lines and bone marrow cells derived from patients with T-ALL, B acute lymphoblastic leukemia (B-ALL), acute myelocytic leukemia (AML), and healthy donors. We found that miRNA-149* was highly expressed in T-ALL cell lines and T-ALL patients' bone marrow samples. JunB was identified as a direct target of miR-149*. miRNA-149* mimics downregulated JunB levels in Molt-4 and Jurkat cells, while miRNA-149* inhibitors dramatically upregulated JunB expression in these cells. miRNA-149* mimics promoted proliferation, decreased the proportion of cells in G1 phase, and reduced cell apoptosis in T-ALL cells, while miRNA-149* inhibitors prevented these effects. miRNA-149* mimics downregulated p21 and upregulated cyclinD1, 4EBP1, and p70s6k in Molt-4 and Jurkat cells. Again, inhibitors prevented these effects. Our findings demonstrate that miRNA-149* may serve as an oncogenic regulator in T-ALL by negatively regulating JunB.
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Affiliation(s)
- Sheng-Jin Fan
- Department of Hematology, The First Clinical Hospital Affiliated to Harbin Medical University, Harbin 150001, Heilongjiang, PR China
| | - Hui-Bo Li
- Department of Hematology, The First Clinical Hospital Affiliated to Harbin Medical University, Harbin 150001, Heilongjiang, PR China
| | - Gang Cui
- Department of Hematology, The First Clinical Hospital Affiliated to Harbin Medical University, Harbin 150001, Heilongjiang, PR China
| | - Xiao-Lin Kong
- Department of Hematology, The First Clinical Hospital Affiliated to Harbin Medical University, Harbin 150001, Heilongjiang, PR China
| | - Li-Li Sun
- Department of Hematology, The First Clinical Hospital Affiliated to Harbin Medical University, Harbin 150001, Heilongjiang, PR China
| | - Yan-Qiu Zhao
- Department of Hematology, The First Clinical Hospital Affiliated to Harbin Medical University, Harbin 150001, Heilongjiang, PR China
| | - Ying-Hua Li
- Department of Hematology, The First Clinical Hospital Affiliated to Harbin Medical University, Harbin 150001, Heilongjiang, PR China.
| | - Jin Zhou
- Department of Hematology, The First Clinical Hospital Affiliated to Harbin Medical University, Harbin 150001, Heilongjiang, PR China
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Muschter D, Schäfer N, Stangl H, Straub RH, Grässel S. Sympathetic Neurotransmitters Modulate Osteoclastogenesis and Osteoclast Activity in the Context of Collagen-Induced Arthritis. PLoS One 2015; 10:e0139726. [PMID: 26431344 PMCID: PMC4592252 DOI: 10.1371/journal.pone.0139726] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 09/16/2015] [Indexed: 12/14/2022] Open
Abstract
Excessive synovial osteoclastogenesis is a hallmark of rheumatoid arthritis (RA). Concomitantly, local synovial changes comprise neuronal components of the peripheral sympathetic nervous system. Here, we wanted to analyze if collagen-induced arthritis (CIA) alters bone marrow-derived macrophage (BMM) osteoclastogenesis and osteoclast activity, and how sympathetic neurotransmitters participate in this process. Therefore, BMMs from Dark Agouti rats at different CIA stages were differentiated into osteoclasts in vitro and osteoclast number, cathepsin K activity, matrix resorption and apoptosis were analyzed in the presence of acetylcholine (ACh), noradrenaline (NA) vasoactive intestinal peptide (VIP) and assay-dependent, adenylyl cyclase activator NKH477. We observed modulation of neurotransmitter receptor mRNA expression in CIA osteoclasts without affecting protein level. CIA stage-dependently altered marker gene expression associated with osteoclast differentiation and activity without affecting osteoclast number or activity. Neurotransmitter stimulation modulated osteoclast differentiation, apoptosis and activity. VIP, NA and adenylyl cyclase activator NKH477 inhibited cathepsin K activity and osteoclastogenesis (NKH477, 10(-6) M NA) whereas ACh mostly acted pro-osteoclastogenic. We conclude that CIA alone does not affect metabolism of in vitro generated osteoclasts whereas stimulation with NA, VIP plus specific activation of adenylyl cyclase induced anti-resorptive effects probably mediated via cAMP signaling. Contrary, we suggest pro-osteoclastogenic and pro-resorptive properties of ACh mediated via muscarinic receptors.
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Affiliation(s)
- Dominique Muschter
- Department of Orthopedic Surgery, Experimental Orthopedics, University Hospital Regensburg, Regensburg, Bavaria, Germany
- Center for Medical Biotechnology, BioPark I, Regensburg, Bavaria, Germany
| | - Nicole Schäfer
- Department of Orthopedic Surgery, Experimental Orthopedics, University Hospital Regensburg, Regensburg, Bavaria, Germany
| | - Hubert Stangl
- Department of Internal Medicine I, Laboratory of Experimental Rheumatology and Neuroendocrine Immunology, University Hospital Regensburg, Regensburg, Bavaria, Germany
| | - Rainer H. Straub
- Department of Internal Medicine I, Laboratory of Experimental Rheumatology and Neuroendocrine Immunology, University Hospital Regensburg, Regensburg, Bavaria, Germany
| | - Susanne Grässel
- Department of Orthopedic Surgery, Experimental Orthopedics, University Hospital Regensburg, Regensburg, Bavaria, Germany
- Center for Medical Biotechnology, BioPark I, Regensburg, Bavaria, Germany
- * E-mail:
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