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Han GH, Kim HR, Yun H, Chung JY, Kim JH, Cho H. Developing a comprehensive molecular subgrouping model for cervical cancer using machine learning. Am J Cancer Res 2024; 14:3186-3197. [PMID: 39005664 PMCID: PMC11236797 DOI: 10.62347/mter1763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 06/17/2024] [Indexed: 07/16/2024] Open
Abstract
This study developed a molecular classification model for cervical cancer using machine learning, integrating prognosis related biomarkers with clinical features. Analyzing 281 specimens, 27 biomarkers were identified, associated with recurrence and treatment response. The model identified four molecular subgroups: group 1 (OALO) with Overexpression of ATP5H and LOw risk; group 2 (LASIM) with low expression of ATP5H and SCP, indicating InterMediate risk; group 3 (LASNIM) characterized by Low expression of ATP5H, SCP, and NANOG, also at InterMediate risk; and group 4 (LASONH), with Low expression of ATP5H, and SCP, Over expression of NANOG, indicating High risk, and potentially aggressive disease. This classification correlated with clinical outcomes such as tumor stage, lymph node metastasis, and response to treatment, demonstrating that combining molecular and clinical factors could significantly enhance the prediction of recurrence and aid in personalized treatment strategies for cervical cancer.
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Affiliation(s)
- Gwan Hee Han
- Department of Obstetrics and Gynecology, Sanggye Paik Hospital, Inje University College of MedicineSeoul 01757, Republic of Korea
| | - Hae-Rim Kim
- Department of Statistics, College of Natural Science, University of SeoulSeoul 02504, Republic of Korea
| | - Hee Yun
- Department of Obstetrics and Gynecology, Gangnam Severance Hospital, Yonsei University College of MedicineSeoul 06299, Republic of Korea
| | - Joon-Yong Chung
- Molecular Imaging Branch, Center for Cancer Research, National Cancer Institute, National Institutes of HealthBethesda, MD 20892, USA
| | - Jae-Hoon Kim
- Department of Obstetrics and Gynecology, Yonsei University College of MedicineSeoul 03722, Republic of Korea
- Institute of Women’s Life Medical Science, Yonsei University College of MedicineSeoul 03722, Republic of Korea
| | - Hanbyoul Cho
- Department of Obstetrics and Gynecology, Yonsei University College of MedicineSeoul 03722, Republic of Korea
- Institute of Women’s Life Medical Science, Yonsei University College of MedicineSeoul 03722, Republic of Korea
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Wang C, Chen Y, Yang X, Du Y, Xu Z, Zhou Y, Yang X, Wang X, Zhang C, Li S, Yang Y, Li W, Liu X. The porcine piRNA transcriptome response to Senecavirus a infection. Front Vet Sci 2023; 10:1126277. [PMID: 37323834 PMCID: PMC10265626 DOI: 10.3389/fvets.2023.1126277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 04/26/2023] [Indexed: 06/17/2023] Open
Abstract
Introduction Senecavirus A (SVA) belongs to the genus Senecavirus in the family Picornaviridae. PIWI-interacting RNAs (piRNAs) are a class of small Ribonucleic Acids (RNAs) that have been found in mammalian cells in recent years. However, the expression profile of piRNAs in the host during SVA infection and their roles are poorly understood. Methods Here, we found the significant differential expression of 173 piRNAs in SVA-infected porcine kidney (PK-15) cells using RNA-seq and 10 significant differentially expressed (DE) piRNAs were further verified by qRT-PCR. Results GO annotation analysis showed that metabolism, proliferation, and differentiation were significantly activated after SVA infection. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that significant DE piRNAs were mainly enriched in AMPK pathway, Rap1 pathway, circadian rhythm and VEGF pathway. It was suggested that piRNAs may regulated antiviral immunity, intracellular homeostasis, and tumor activities during SVA infection. In addition, we found that the expression levels of the major piRNA-generating genes BMAL1 and CRY1 were significantly downregulated after SVA infection. Discussion This suggests that SVA may affect circadian rhythm and promote apoptosis by inhibiting the major piRNA-generating genes BMAL1 and CRY1. The piRNA transcriptome in PK-15 cells has never been reported before, and this study will further the understanding of the piRNA regulatory mechanisms underlying SVA infections.
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Affiliation(s)
- Chen Wang
- Southwest University, College of Veterinary Medicine, Chongqing, China
| | - Yanxi Chen
- Southwest University, College of Veterinary Medicine, Chongqing, China
| | - Xiwang Yang
- Southwest University, College of Veterinary Medicine, Chongqing, China
| | - Yunsha Du
- Southwest University, College of Veterinary Medicine, Chongqing, China
| | - Zhiwen Xu
- Animal Biotechnology Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yuancheng Zhou
- Veterinary Biologicals Engineering and Technology Research Center of Sichuan Province, Animtech Bioengineering CO., LTD., Chengdu, China
- Livestock and Poultry Biological Products Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Xu Yang
- Veterinary Biologicals Engineering and Technology Research Center of Sichuan Province, Animtech Bioengineering CO., LTD., Chengdu, China
- Livestock and Poultry Biological Products Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Xuetao Wang
- Veterinary Biologicals Engineering and Technology Research Center of Sichuan Province, Animtech Bioengineering CO., LTD., Chengdu, China
- Livestock and Poultry Biological Products Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Chuanming Zhang
- Veterinary Biologicals Engineering and Technology Research Center of Sichuan Province, Animtech Bioengineering CO., LTD., Chengdu, China
- Livestock and Poultry Biological Products Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Shuwei Li
- Veterinary Biologicals Engineering and Technology Research Center of Sichuan Province, Animtech Bioengineering CO., LTD., Chengdu, China
- Livestock and Poultry Biological Products Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Yijun Yang
- Department of Infectious and Tropical Diseases, The Second Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Wenting Li
- Department of Infectious and Tropical Diseases, The Second Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Xiao Liu
- Southwest University, College of Veterinary Medicine, Chongqing, China
- State Key Laboratory of Silkworm Genome Biology, Chongqing, China
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Hosseini K, Beirami SM, Forouhandeh H, Vahed SZ, Eyvazi S, Ramazani F, Tarhriz V, Ardalan M. The role of circadian gene timeless in gastrointestinal cancers. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Sanford ABA, da Cunha LS, Machado CB, de Pinho Pessoa FMC, Silva ANDS, Ribeiro RM, Moreira FC, de Moraes Filho MO, de Moraes MEA, de Souza LEB, Khayat AS, Moreira-Nunes CA. Circadian Rhythm Dysregulation and Leukemia Development: The Role of Clock Genes as Promising Biomarkers. Int J Mol Sci 2022; 23:ijms23158212. [PMID: 35897788 PMCID: PMC9332415 DOI: 10.3390/ijms23158212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/08/2022] [Accepted: 07/19/2022] [Indexed: 12/04/2022] Open
Abstract
The circadian clock (CC) is a daily system that regulates the oscillations of physiological processes and can respond to the external environment in order to maintain internal homeostasis. For the functioning of the CC, the clock genes (CG) act in different metabolic pathways through the clock-controlled genes (CCG), providing cellular regulation. The CC’s interruption can result in the development of different diseases, such as neurodegenerative and metabolic disorders, as well as cancer. Leukemias correspond to a group of malignancies of the blood and bone marrow that occur when alterations in normal cellular regulatory processes cause the uncontrolled proliferation of hematopoietic stem cells. This review aimed to associate a deregulated CC with the manifestation of leukemia, looking for possible pathways involving CG and their possible role as leukemic biomarkers.
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Affiliation(s)
- Ana Beatriz Aguiar Sanford
- Unichristus University Center, Faculty of Biomedicine, Fortaleza 60430-275, CE, Brazil; (A.B.A.S.); (L.S.d.C.)
| | - Leidivan Sousa da Cunha
- Unichristus University Center, Faculty of Biomedicine, Fortaleza 60430-275, CE, Brazil; (A.B.A.S.); (L.S.d.C.)
| | - Caio Bezerra Machado
- Pharmacogenetics Laboratory, Department of Medicine, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (C.B.M.); (F.M.C.d.P.P.); (M.O.d.M.F.); (M.E.A.d.M.)
| | - Flávia Melo Cunha de Pinho Pessoa
- Pharmacogenetics Laboratory, Department of Medicine, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (C.B.M.); (F.M.C.d.P.P.); (M.O.d.M.F.); (M.E.A.d.M.)
| | - Abigail Nayara dos Santos Silva
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.N.d.S.S.); (F.C.M.); (A.S.K.)
| | | | - Fabiano Cordeiro Moreira
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.N.d.S.S.); (F.C.M.); (A.S.K.)
| | - Manoel Odorico de Moraes Filho
- Pharmacogenetics Laboratory, Department of Medicine, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (C.B.M.); (F.M.C.d.P.P.); (M.O.d.M.F.); (M.E.A.d.M.)
| | - Maria Elisabete Amaral de Moraes
- Pharmacogenetics Laboratory, Department of Medicine, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (C.B.M.); (F.M.C.d.P.P.); (M.O.d.M.F.); (M.E.A.d.M.)
| | - Lucas Eduardo Botelho de Souza
- Center for Cell-Based Therapy, Regional Blood Center of Ribeirão Preto, University of São Paulo, São Paulo 14051-140, SP, Brazil;
| | - André Salim Khayat
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.N.d.S.S.); (F.C.M.); (A.S.K.)
| | - Caroline Aquino Moreira-Nunes
- Unichristus University Center, Faculty of Biomedicine, Fortaleza 60430-275, CE, Brazil; (A.B.A.S.); (L.S.d.C.)
- Pharmacogenetics Laboratory, Department of Medicine, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (C.B.M.); (F.M.C.d.P.P.); (M.O.d.M.F.); (M.E.A.d.M.)
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.N.d.S.S.); (F.C.M.); (A.S.K.)
- Northeast Biotechnology Network (RENORBIO), Itaperi Campus, Ceará State University, Fortaleza 60740-903, CE, Brazil
- Correspondence:
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MSC-Derived Extracellular Vesicle-Delivered L-PGDS Inhibit Gastric Cancer Progression by Suppressing Cancer Cell Stemness and STAT3 Phosphorylation. Stem Cells Int 2022; 2022:9668239. [PMID: 35087591 PMCID: PMC8789473 DOI: 10.1155/2022/9668239] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/29/2021] [Accepted: 12/14/2021] [Indexed: 02/06/2023] Open
Abstract
Mesenchymal stem cell- (MSC-) derived extracellular vesicles (EVs) serving as delivery system have attracted extensive research interest, especially in cancer therapy. In our previous study, lipocalin-type prostaglandin D2 synthase (L-PGDS) showed inhibitory effects on gastric cancer growth. In this study, we aimed to explore whether MSC-EV-delivered L-PGDS (EVs-L-PGDS) could inhibit gastric cancer progression. EVs-L-PGDS were generated from MSCs transfected with adenovirus encoding L-PGDS. Cell colony-forming, migration, invasion, and flow cytometry assays were used to show the inhibitory effects of EVs on tumor cells in vitro, and the nude mouse subcutaneous tumor model was performed to show the inhibitory effect of EVs on tumor progression in vivo. In vitro, EVs-L-PGDS could be internalized and inhibit the colony-forming, migration, and invasion ability of gastric cancer cell SGC-7901 and promote cell apoptosis. In vivo, EVs-L-PGDS inhibited the tumor growth in nude mouse subcutaneous tumor-bearing model. Compared with the PBS and EVs containing empty vector (EVs-Vector) group, more apoptotic cells and higher L-PGDS expression were detected in tumor tissue of the EVs-L-PGDS treatment group. And these differences are significant. Mechanistically, EVs-L-PGDS reduced the expression of stem cell markers including Oct4, Nanog, and Sox2 and inhibited STAT3 phosphorylation in gastric cancer cell SGC-7901. In conclusion, our results imply that MSC-derived EVs could be utilized as an effective nanovehicle to deliver L-PGDS for gastric cancer treatment, which provides a novel idea for the EV-based cancer therapy.
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