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Dutriaux A, Diazzi S, Bresesti C, Hardouin S, Deshayes F, Collignon J, Flagiello D. LADON, a Natural Antisense Transcript of NODAL, Promotes Tumour Progression and Metastasis in Melanoma. Noncoding RNA 2023; 9:71. [PMID: 37987367 PMCID: PMC10661258 DOI: 10.3390/ncrna9060071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/02/2023] [Accepted: 11/10/2023] [Indexed: 11/22/2023] Open
Abstract
The TGFβ family member NODAL, repeatedly required during embryonic development, has also been associated with tumour progression. Our aim was to clarify the controversy surrounding its involvement in melanoma tumour progression. We found that the deletion of the NODAL exon 2 in a metastatic melanoma cell line impairs its ability to form tumours and colonize distant tissues. However, we show that this phenotype does not result from the absence of NODAL, but from a defect in the expression of a natural antisense transcript of NODAL, here called LADON. We show that LADON expression is specifically activated in metastatic melanoma cell lines, that its transcript is packaged in exosomes secreted by melanoma cells, and that, via its differential impact on the expression of oncogenes and tumour suppressors, it promotes the mesenchymal to amoeboid transition that is critical for melanoma cell invasiveness. LADON is, therefore, a new player in the regulatory network governing tumour progression in melanoma and possibly in other types of cancer.
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Affiliation(s)
| | | | | | | | | | - Jérôme Collignon
- Institut Jacques Monod, Université Paris Cité, CNRS, F-75013 Paris, France; (A.D.); (S.D.)
| | - Domenico Flagiello
- Institut Jacques Monod, Université Paris Cité, CNRS, F-75013 Paris, France; (A.D.); (S.D.)
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Hou R, Hon CC, Huang Y. CamoTSS: analysis of alternative transcription start sites for cellular phenotypes and regulatory patterns from 5' scRNA-seq data. Nat Commun 2023; 14:7240. [PMID: 37945584 PMCID: PMC10636040 DOI: 10.1038/s41467-023-42636-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 10/16/2023] [Indexed: 11/12/2023] Open
Abstract
Five-prime single-cell RNA-seq (scRNA-seq) has been widely employed to profile cellular transcriptomes, however, its power of analysing transcription start sites (TSS) has not been fully utilised. Here, we present a computational method suite, CamoTSS, to precisely identify TSS and quantify its expression by leveraging the cDNA on read 1, which enables effective detection of alternative TSS usage. With various experimental data sets, we have demonstrated that CamoTSS can accurately identify TSS and the detected alternative TSS usages showed strong specificity in different biological processes, including cell types across human organs, the development of human thymus, and cancer conditions. As evidenced in nasopharyngeal cancer, alternative TSS usage can also reveal regulatory patterns including systematic TSS dysregulations.
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Affiliation(s)
- Ruiyan Hou
- School of Biomedical Sciences, University of Hong Kong, Hong Kong, SAR, China
| | - Chung-Chau Hon
- RIKEN Center for Integrative Medical Sciences, Yokohama City, Kanagawa, 230-0045, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Yuanhua Huang
- School of Biomedical Sciences, University of Hong Kong, Hong Kong, SAR, China.
- Department of Statistics and Actuarial Science, University of Hong Kong, Hong Kong, AR, China.
- Center for Translational Stem Cell Biology, Hong Kong Science and Technology Park, Hong Kong, SAR, China.
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Zhang Q, Bhatia M, Park T, Ott J. A multi-threaded approach to genotype pattern mining for detecting digenic disease genes. Front Genet 2023; 14:1222517. [PMID: 37693313 PMCID: PMC10483394 DOI: 10.3389/fgene.2023.1222517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 07/31/2023] [Indexed: 09/12/2023] Open
Abstract
To locate disease-causing DNA variants on the human gene map, the customary approach has been to carry out a genome-wide association study for one variant after another by testing for genotype frequency differences between individuals affected and unaffected with disease. So-called digenic traits are due to the combined effects of two variants, often on different chromosomes, while individual variants may have little or no effect on disease. Machine learning approaches have been developed to find variant pairs underlying digenic traits. However, many of these methods have large memory requirements so that only small datasets can be analyzed. The increasing availability of desktop computers with large numbers of processors and suitable programming to distribute the workload evenly over all processors in a machine make a new and relatively straightforward approach possible, that is, to evaluate all existing variant and genotype pairs for disease association. We present a prototype of such a method with two components, Vpairs and Gpairs, and demonstrate its advantages over existing implementations of such well-known algorithms as Apriori and FP-growth. We apply these methods to published case-control datasets on age-related macular degeneration and Parkinson disease and construct an ROC curve for a large set of genotype patterns.
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Affiliation(s)
- Qingrun Zhang
- Department of Mathematics and Statistics, University of Calgary, Calgary, AB, Canada
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
| | - Muskan Bhatia
- Amity Institute of Biotechnology, Amity University Madhya Pradesh, Gwalior, India
| | - Taesung Park
- Department of Statistics, Seoul National University, Seoul, Republic of Korea
| | - Jurg Ott
- Laboratory of Statistical Genetics, Rockefeller University, New York, NY, United States
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Tala JA, Polikoff LA, Pinto MG, Li S, Trakas E, Miksa M, Gertz S, Faustino EVS. Protein biomarkers for incident deep venous thrombosis in critically ill adolescents: An exploratory study. Pediatr Blood Cancer 2020; 67:e28159. [PMID: 31904170 DOI: 10.1002/pbc.28159] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/18/2019] [Accepted: 12/11/2019] [Indexed: 12/21/2022]
Abstract
BACKGROUND There are no tests to identify critically ill children at high risk of deep venous thrombosis (DVT). In this exploratory study, we aimed to identify proteins that are associated with incident DVT in critically ill adolescents. PROCEDURE Plasma samples were obtained from critically ill adolescents within 24 hours after initiation of cardiopulmonary support. The adolescents were followed with ultrasound to detect the development of DVT of the lower extremity and clinically for bleeding. Thrombin-antithrombin complex and prothrombin fragment 1+2 were measured using immunosorbent assays, whereas procoagulation and anticoagulation factors were measured using multiplex assays. Plasma samples were also analyzed using SOMAscan, an aptamer-based capture assay. The associations between DVT and the log-transformed level of the proteins were assessed using logistic regression adjusting for the presence of femoral venous catheter and severity of illness. Associations were expressed as odds ratio (OR) for every log-fold increase in level of the protein with 95% confidence interval (CI). RESULTS Plasma from 59 critically ill adolescents, of whom 9 developed incident DVT, was analyzed. The median age of the adolescents was 15.1 years (interquartile range, 14.0-16.7 years). Higher levels of thrombin-antithrombin complex (OR: 31.54; 95% CI: 2.09-475.92) and lower levels of factor XIII (OR: 0.03; 95% CI: 0.002-0.44) were associated with DVT. CD36, MIC-1, and EpoR were marginally associated with DVT. Only factor XIII was associated with clinically relevant bleeding (OR: 0.27; 95% CI: 0.08-0.97). CONCLUSIONS We identified candidate protein biomarkers for incident DVT. We plan to validate our findings in adequately powered studies.
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Affiliation(s)
- Joana A Tala
- Yale-New Haven Children's Hospital, New Haven, Connecticut
| | - Lee A Polikoff
- The Warren Alpert School of Medicine at Brown University, Providence, Rhode Island
| | | | - Simon Li
- New York Medical College, Valhalla, New York
| | - Erin Trakas
- University of Rochester Golisano Children's Hospital, Rochester, New York
| | - Michael Miksa
- Children's Hospital at Montefiore, New York City, New York
| | - Shira Gertz
- Saint Barnabas Medical Center, Livingston, New Jersey
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Chien CW, Lo YS, Wu HY, Hsuan Y, Lin CK, Chen YJ, Lin W, Han CL. Transcriptomic and Proteomic Profiling of Human Mesenchymal Stem Cell Derived from Umbilical Cord in the Study of Preterm Birth. Proteomics Clin Appl 2019; 14:e1900024. [PMID: 31520560 DOI: 10.1002/prca.201900024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 08/10/2019] [Indexed: 12/26/2022]
Abstract
OBJECTIVE Mesenchymal stem cells (MSCs) hold great therapeutic potential in morbidities associated with preterm birth. However, the molecular expressions of MSCs in preterm birth infants are not systematically evaluated. In this study, the dual-omics analyses of umbilical-cord (UC)-derived MSCs to identify the dysregulated cellular functions are presented. MATERIALS AND METHODS The UC-MSCs are collected from ten full-term and eight preterm birth infants for microarray and iTRAQ-based proteome profiling. RESULTS The integrative analysis of dual-omics data discovered 5615 commonly identified genes/proteins of which 29 genes/proteins show consistent up- or downregulation in preterm birth. The Gene Ontology analysis reveals that dysregulation of mitochondrial translation and cellular response to oxidative stress are mainly enriched in 290 differential expression proteins (DEPs) while the 412 differential expression genes (DEGs) are majorly involved in single-organism biosynthetic process, cellular response to stress, and mitotic cell cycle in preterm birth. Besides, a 13-protein module involving CUL2 and CUL3 is identified, which plays an important role in cullin-RING-based ubiquitin ligase complex, as potential mechanism for preterm birth. CONCLUSION The dual-omics data not only provide new insights to the molecular mechanism but also identify panel of candidate markers associated with preterm birth.
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Affiliation(s)
- Chih-Wei Chien
- Research and Development Division, Meribank Biotech Co. Ltd., Taipei, 11493, Taiwan
| | - Yu-Shu Lo
- Research and Development Division, Meribank Biotech Co. Ltd., Taipei, 11493, Taiwan
| | - Hsin-Yi Wu
- Instrumentation Center, National Taiwan University, Taipei, 10617, Taiwan
| | - Yogi Hsuan
- Meridigen Biotech Co. Ltd., Taipei, 11493, Taiwan
| | - Chi-Kang Lin
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, National Defense Medical Center, Taipei, 11490, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Willie Lin
- Meridigen Biotech Co. Ltd., Taipei, 11493, Taiwan
| | - Chia-Li Han
- Master Program in Clinical Pharmacogenomics and Pharmacoproteomics, College of Pharmacy, Taipei Medical University, Taipei, 11031, Taiwan
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Yoshimura H, Otsuka A, Michishita M, Yamamoto M, Ashizawa M, Zushi M, Moriya M, Azakami D, Ochiai K, Matsuda Y, Ishiwata T, Kamiya S, Takahashi K. Expression and Roles of S100A4 in Anaplastic Cells of Canine Mammary Carcinomas. Vet Pathol 2019; 56:389-398. [DOI: 10.1177/0300985818823772] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
S100A4 (metastasin), a member of the S100 protein family, was initially identified in metastatic cells and is well established as a marker of aggressive human cancer. However, expression and roles of S100A4 in canine mammary tumors have not been clarified. In this study, expression of S100A4 was examined immunohistochemically in normal, hyperplastic, and neoplastic mammary glands of dogs. In all normal and benign lesions, S100A4 was restricted to a few stromal fibroblasts and inflammatory cells. However, in 7 of 57 (12%) of the malignant tumors examined, cytoplasmic and nuclear expression of S100A4 was observed in epithelial tumor cells and stromal cells. Particularly, the frequency of S100A4-positive anaplastic carcinomas was high (4/8 cases, 50%). Next, we established a novel cell line, named NV-CML, from a S100A4-positive canine mammary carcinoma. The cultured NV-CML cells and the tumors that developed in the immunodeficient mice after subcutaneous injection of the cells maintained the immunophenotype of the original tumor, including S100A4 expression. Using this cell line, we examined the cellular functions of S100A4 using RNA interference. S100A4 expression level in NV-CML cells transfected with small interfering RNA (siRNA) targeting canine S100A4 (siS100A4) was reduced to about one-fifth of those with negative-control siRNA (siNeg). Cell proliferation in WST-8 assay and cell migration in Boyden chamber assay were significantly decreased in siS100A4-transfected cells compared with siNeg-transfected cells. These findings suggest that S100A4 may be related to progression of canine mammary carcinomas via its influence on cell growth and motility.
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Affiliation(s)
- Hisashi Yoshimura
- Division of Physiological Pathology, Department of Applied Science, School of Veterinary Nursing and Technology, Nippon Veterinary and Life Science University, Tokyo, Japan
| | - Aya Otsuka
- Department of Veterinary Pathology, School of Veterinary Medicine, Nippon Veterinary and Life Science University, Tokyo, Japan
| | - Masaki Michishita
- Department of Veterinary Pathology, School of Veterinary Medicine, Nippon Veterinary and Life Science University, Tokyo, Japan
| | - Masami Yamamoto
- Division of Physiological Pathology, Department of Applied Science, School of Veterinary Nursing and Technology, Nippon Veterinary and Life Science University, Tokyo, Japan
| | - Minori Ashizawa
- Division of Physiological Pathology, Department of Applied Science, School of Veterinary Nursing and Technology, Nippon Veterinary and Life Science University, Tokyo, Japan
| | - Manami Zushi
- Division of Physiological Pathology, Department of Applied Science, School of Veterinary Nursing and Technology, Nippon Veterinary and Life Science University, Tokyo, Japan
| | - Maiko Moriya
- Division of Physiological Pathology, Department of Applied Science, School of Veterinary Nursing and Technology, Nippon Veterinary and Life Science University, Tokyo, Japan
| | - Daigo Azakami
- Department of Veterinary Nursing, School of Veterinary Nursing and Technology, Nippon Veterinary and Life Science University, Tokyo, Japan
| | - Kazuhiko Ochiai
- Department of Basic Science, School of Veterinary Nursing and Technology, Nippon Veterinary and Life Science University, Tokyo, Japan
| | - Yoko Matsuda
- Department of Pathology, Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Tokyo, Japan
| | - Toshiyuki Ishiwata
- Division of Aging and Carcinogenesis, Research Team for Geriatric Pathology, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Shinji Kamiya
- Division of Animal Higher Function, Department of Applied Science, School of Veterinary Nursing and Technology, Nippon Veterinary and Life Science University, Tokyo, Japan
| | - Kimimasa Takahashi
- Department of Veterinary Pathology, School of Veterinary Medicine, Nippon Veterinary and Life Science University, Tokyo, Japan
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Bian Y, Guo J, Qiao L, Sun X. miR-3189-3p Mimics Enhance the Effects of S100A4 siRNA on the Inhibition of Proliferation and Migration of Gastric Cancer Cells by Targeting CFL2. Int J Mol Sci 2018; 19:ijms19010236. [PMID: 29342841 PMCID: PMC5796184 DOI: 10.3390/ijms19010236] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/27/2017] [Accepted: 01/08/2018] [Indexed: 12/17/2022] Open
Abstract
GDF15 is a downstream gene of S100A4. miR-3189 is embedded in the intron of GDF15—and coexpressed with it. miR-3189-3p functions to inhibit the proliferation and migration of glioblastoma cells. We speculated that S100A4 might regulate miR-3189-3p to affect its function in gastric cancer cells. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) showed that miR-3189-3p expression was significantly downregulated in MGC803 cells after S100A4 knockdown. Overexpression of miR-3189-3p significantly inhibited the proliferation and migration of the cells. Moreover, miR-3189-3p mimics enhanced the effects of an S100A4 siRNA on the inhibition of cell proliferation and migration. Dual luciferase reporter assays, qRT-PCR, and Western blotting verified that CFL2 is a direct target of miR-3189-3p. CFL2 mediates the regulation of miR-3189-3p on the proliferation and migration of MGC803 cells. Data mining based on Kaplan–Meier plots showed that high CFL2 expression is associated with poor overall survival and first progression in gastric cancer. These data suggested that miR-3189-3p mimics enhanced the effects of the S100A4 siRNA on the inhibition of gastric cancer cell proliferation and migration by targeting CFL2. The findings suggested that when targeting S100A4 to treat gastric cancer, consideration and correction for counteracting factors should obtain a satisfactory effect.
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Affiliation(s)
- Yue Bian
- Department of Medical Genetics, China Medical University, Shenyang 110122, China.
| | - Junfu Guo
- Department of Medical Genetics, China Medical University, Shenyang 110122, China.
- Teaching and Experiment Center, Liaoning University of Traditional Chinese Medicine, Shenyang110847, China.
| | - Linlin Qiao
- Department of Medical Genetics, China Medical University, Shenyang 110122, China.
| | - Xiuju Sun
- Department of Medical Genetics, China Medical University, Shenyang 110122, China.
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