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Zhong W, Fu J, Liao J, Ouyang S, Yin W, Liang Y, Liu K. A protective role of nintedanib in peritoneal fibrosis through H19-EZH2-KLF2 axis via impeding mesothelial-to-mesenchymal transition. Int Urol Nephrol 2024; 56:1987-1999. [PMID: 38097887 DOI: 10.1007/s11255-023-03892-8] [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: 04/24/2023] [Accepted: 11/16/2023] [Indexed: 05/14/2024]
Abstract
BACKGROUND Peritoneal fibrosis (PF), a common complication of long-term peritoneal dialysis, accounts for peritoneal ultrafiltration failure to develop into increased mortality. Nintedanib has previously been shown to protect against multi-organ fibrosis, including PF. Unfortunately, the precise molecular mechanism underlying nintedanib in the pathogenesis of PF remains elusive. METHODS The mouse model of PF was generated by chlorhexidine gluconate (CG) injection with or without nintedanib administration, either with the simulation for the cell model of PF by constructing high-glucose (HG)-treated human peritoneal mesothelial cells (HPMCs). HE and Masson staining were applied to assess the histopathological changes of peritoneum and collagen deposition. FISH, RT-qPCR, western blot and immunofluorescence were employed to examine distribution or expression of targeted genes. Cell viability was detected using CCK-8 assay. Cell morphology was observed under a microscope. RNA immunoprecipitation (RIP) and chromatin immunoprecipitation (ChIP) assays were applied to validate the H19-EZH2-KLF2 regulatory axis. RESULTS Aberrantly overexpressed H19 was observed in both the mouse and cell model of PF, of which knockdown significantly blocked HG-induced mesothelial-to-mesenchymal transition (MMT) of HPMCs. Moreover, loss of H19 further strengthened nintedanib-mediated suppressive effects against MMT process in a mouse model of PF. Mechanistically, H19 could epigenetically repressed KLF2 via recruiting EZH2. Furthermore, TGF-β/Smad pathway was inactivated by nintedanib through mediating H19/KLF2 axis. CONCLUSION In summary, nintedanib disrupts MMT process through regulating H19/EZH2/KLF2 axis and TGF-β/Smad pathway, which laid the experimental foundation for nintedanib in the treatment of PF.
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Affiliation(s)
- Wei Zhong
- Department of Nephrology and Laboratory of Kidney Disease, Changsha Clinical Research Center for Kidney Disease, Hunan Clinical Research Center for Chronic Kidney Disease, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), No.61, Jiefangxi Road, Changsha, 410002, Hunan, People's Republic of China
| | - Jia Fu
- Department of Oncology, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha, 410002, Hunan, People's Republic of China
| | - Jin Liao
- Department of Nephrology and Laboratory of Kidney Disease, Changsha Clinical Research Center for Kidney Disease, Hunan Clinical Research Center for Chronic Kidney Disease, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), No.61, Jiefangxi Road, Changsha, 410002, Hunan, People's Republic of China
| | - Shaxi Ouyang
- Department of Nephrology and Laboratory of Kidney Disease, Changsha Clinical Research Center for Kidney Disease, Hunan Clinical Research Center for Chronic Kidney Disease, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), No.61, Jiefangxi Road, Changsha, 410002, Hunan, People's Republic of China
| | - Wei Yin
- Department of Nephrology and Laboratory of Kidney Disease, Changsha Clinical Research Center for Kidney Disease, Hunan Clinical Research Center for Chronic Kidney Disease, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), No.61, Jiefangxi Road, Changsha, 410002, Hunan, People's Republic of China
| | - Yumei Liang
- Department of Nephrology and Laboratory of Kidney Disease, Changsha Clinical Research Center for Kidney Disease, Hunan Clinical Research Center for Chronic Kidney Disease, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), No.61, Jiefangxi Road, Changsha, 410002, Hunan, People's Republic of China
| | - Kanghan Liu
- Department of Nephrology and Laboratory of Kidney Disease, Changsha Clinical Research Center for Kidney Disease, Hunan Clinical Research Center for Chronic Kidney Disease, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), No.61, Jiefangxi Road, Changsha, 410002, Hunan, People's Republic of China.
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Okado S, Kato T, Hanamatsu Y, Emoto R, Imamura Y, Watanabe H, Kawasumi Y, Kadomatsu Y, Ueno H, Nakamura S, Mizuno T, Takeuchi T, Matsui S, Chen-Yoshikawa TF. CHST4 Gene as a Potential Predictor of Clinical Outcome in Malignant Pleural Mesothelioma. Int J Mol Sci 2024; 25:2270. [PMID: 38396947 PMCID: PMC10889779 DOI: 10.3390/ijms25042270] [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] [Received: 01/11/2024] [Revised: 02/07/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024] Open
Abstract
Malignant pleural mesothelioma (MPM) develops primarily from asbestos exposures and has a poor prognosis. In this study, The Cancer Genome Atlas was used to perform a comprehensive survival analysis, which identified the CHST4 gene as a potential predictor of favorable overall survival for patients with MPM. An enrichment analysis of favorable prognostic genes, including CHST4, showed immune-related ontological terms, whereas an analysis of unfavorable prognostic genes indicated cell-cycle-related terms. CHST4 mRNA expression in MPM was significantly correlated with Bindea immune-gene signatures. To validate the relationship between CHST4 expression and prognosis, we performed an immunohistochemical analysis of CHST4 protein expression in 23 surgical specimens from surgically treated patients with MPM who achieved macroscopic complete resection. The score calculated from the proportion and intensity staining was used to compare the intensity of CHST4 gene expression, which showed that CHST4 expression was stronger in patients with a better postoperative prognosis. The median overall postoperative survival was 107.8 months in the high-expression-score group and 38.0 months in the low-score group (p = 0.044, log-rank test). Survival after recurrence was also significantly improved by CHST4 expression. These results suggest that CHST4 is useful as a prognostic biomarker in MPM.
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Affiliation(s)
- Shoji Okado
- Department of Thoracic Surgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan; (S.O.); (T.K.); (Y.I.); (H.W.); (Y.K.); (Y.K.); (H.U.); (S.N.); (T.M.)
| | - Taketo Kato
- Department of Thoracic Surgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan; (S.O.); (T.K.); (Y.I.); (H.W.); (Y.K.); (Y.K.); (H.U.); (S.N.); (T.M.)
| | - Yuki Hanamatsu
- Department of Pathology and Translational Research, Gifu University Graduate School of Medicine, Yanagido 1-1, Gifu 501-1194, Japan; (Y.H.); (T.T.)
| | - Ryo Emoto
- Department of Biostatistics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan; (R.E.); (S.M.)
| | - Yoshito Imamura
- Department of Thoracic Surgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan; (S.O.); (T.K.); (Y.I.); (H.W.); (Y.K.); (Y.K.); (H.U.); (S.N.); (T.M.)
| | - Hiroki Watanabe
- Department of Thoracic Surgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan; (S.O.); (T.K.); (Y.I.); (H.W.); (Y.K.); (Y.K.); (H.U.); (S.N.); (T.M.)
| | - Yuta Kawasumi
- Department of Thoracic Surgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan; (S.O.); (T.K.); (Y.I.); (H.W.); (Y.K.); (Y.K.); (H.U.); (S.N.); (T.M.)
| | - Yuka Kadomatsu
- Department of Thoracic Surgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan; (S.O.); (T.K.); (Y.I.); (H.W.); (Y.K.); (Y.K.); (H.U.); (S.N.); (T.M.)
| | - Harushi Ueno
- Department of Thoracic Surgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan; (S.O.); (T.K.); (Y.I.); (H.W.); (Y.K.); (Y.K.); (H.U.); (S.N.); (T.M.)
| | - Shota Nakamura
- Department of Thoracic Surgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan; (S.O.); (T.K.); (Y.I.); (H.W.); (Y.K.); (Y.K.); (H.U.); (S.N.); (T.M.)
| | - Tetsuya Mizuno
- Department of Thoracic Surgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan; (S.O.); (T.K.); (Y.I.); (H.W.); (Y.K.); (Y.K.); (H.U.); (S.N.); (T.M.)
| | - Tamotsu Takeuchi
- Department of Pathology and Translational Research, Gifu University Graduate School of Medicine, Yanagido 1-1, Gifu 501-1194, Japan; (Y.H.); (T.T.)
| | - Shigeyuki Matsui
- Department of Biostatistics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan; (R.E.); (S.M.)
| | - Toyofumi Fengshi Chen-Yoshikawa
- Department of Thoracic Surgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan; (S.O.); (T.K.); (Y.I.); (H.W.); (Y.K.); (Y.K.); (H.U.); (S.N.); (T.M.)
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Li S, Cai X, Chen L, Lin M, Zhu Z, Xiao H, Nie P, Chen Q, Yang X. Inhibition of hepatocellular carcinoma growth via modulation of the miR-221/SOX11 axis by curcumin and berberine. PeerJ 2023; 11:e16593. [PMID: 38084140 PMCID: PMC10710771 DOI: 10.7717/peerj.16593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/14/2023] [Indexed: 12/18/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a fatal malignancy that has limited treatment options. This study focused on the potential therapeutic effects of curcumin (CUR) and berberine (BBR) on the miR-221/SRY-box transcription factor 11 (SOX11) axis in HCC. We investigated the combined effects of CUR and BBR on HEPG2 and Huh7 cell survival and miR-221 expression using Cell Counting Kit-8 assays and RT-qPCR, respectively. Western blotting was used to detect changes in the apoptosis-related caspase-3/9 protein levels. We performed bioinformatics analysis and dual-luciferase assays and measured apoptotic protein levels to assess the role of the miR-221/SOX11 axis in mediating the effects of CUR-BBR. Both CUR and BBR suppressed HCC cell growth in a dose-dependent manner, with the most potent combined effect observed at a 2:1 ratio. CUR-BBR treatment significantly downregulated miR-221 expression, and miR-221 overexpression partially reversed the CUR-BBR-mediated decrease in cell survival. In addition, SOX11 was found to be a direct target of miR-221. CUR-BBR treatment upregulated SOX11 expression, and overexpression of SOX11 restored the inhibitory effects of CUR-BBR on cell growth, migration, and invasion and promoted apoptosis in the presence of miR-221. Furthermore, CUR-BBR activated pro-apoptotic proteins caspase-3/9 through the miR-221/SOX11 axis. The combined effect of CUR-BBR played an important role in inhibiting the growth of HCC cells. This combined effect was achieved by regulating the miR-221/SOX11 axis and activating the synthesis of pro-apoptotic proteins. Our findings highlight a promising combined therapeutic approach for HCC and underscore the importance of targeting the miR-221/SOX11 axis.
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Affiliation(s)
- Sheng Li
- Department of Internal Medicine, Fuzhou Hospital of Traditional Chinese Medicine, Fuzhou, China
| | - Xiaoliang Cai
- Department of Internal Medicine, Fuzhou Hospital of Traditional Chinese Medicine, Fuzhou, China
| | - Liang Chen
- Department of Medical Oncology, Fuzhou Hospital of Traditional Chinese Medicine, Fuzhou, China
| | - Manbian Lin
- Department of Medical Oncology, Fuzhou Hospital of Traditional Chinese Medicine, Fuzhou, China
| | - Ziqi Zhu
- Department of Medical Oncology, Fuzhou Hospital of Traditional Chinese Medicine, Fuzhou, China
| | - Huihuang Xiao
- Department of Medical Oncology, Fuzhou Hospital of Traditional Chinese Medicine, Fuzhou, China
| | - Pingping Nie
- Department of Medical Oncology, Fuzhou Hospital of Traditional Chinese Medicine, Fuzhou, China
| | - Quanwen Chen
- Department of Medical Oncology, Fuzhou Hospital of Traditional Chinese Medicine, Fuzhou, China
| | - Xiaoyu Yang
- Fuzhou Hospital of Traditional Chinese Medicine, Fuzhou, China
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4
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Zhao R, Tang X, Lin H, Xing C, Xu N, Dai B, Wang P, Shao W, Liu M, Shen J, Deng S, Ren C. Knocking Down Gm16685 Decreases Liver Granuloma in Murine Schistosomiasis Japonica. Microorganisms 2023; 11:microorganisms11030796. [PMID: 36985369 PMCID: PMC10058064 DOI: 10.3390/microorganisms11030796] [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: 03/02/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) can regulate key genes and pathways in liver disease development. Moreover, macrophages are speculated to play an important role in regulating granulomatous inflammation during schistosomiasis. However, the role of lncRNAs in the formation of liver granulomas by influencing the polarization of macrophages in Schistosoma japonicum infection is unclear. Our study aimed to determine whether lncRNAs can play a role in S. japonicum-induced hepatic egg granulomas and elucidate their effect on macrophages. We established S. japonicum infection models and screened the target lncRNA Gm16685 highly expressed in schistosomiasis mice using high-throughput sequencing. Hematoxylin and eosin staining revealed that the knockdown of Gm16685 reduced the area of egg granulomas. Moreover, M1 macrophage factor genes were significantly downregulated in Gm16685 knockdown livers. Meanwhile, M2 macrophage factor genes were significantly upregulated, which was consistent with the protein detection results. Hepatocytes, hepatic stellate cells, and macrophages were isolated from mouse models infected with S. japonicum, with Gm16685 being significantly upregulated in macrophages. Moreover, the knockdown of Gm16685 in RAW264.7 cells revealed similar results to in liver tissue. RNA fluorescence in situ hybridization (FISH) and nucleocytoplasmic separation experiments revealed that Gm16685 was predominantly localized in the cytoplasm of cells. We found that miR-205-5p was upregulated after Gm16685 was knocked down. After overexpression of miR-205-5p, the expression of Gm16685 and inflammatory factors was significantly downregulated. These results indicate that Gm16685 can participate in the pathogenesis of hepatic disease in schistosomiasis and promote M1 macrophage polarization by regulating miR-205-5p. Thus, our study may provide a new target for schistosomiasis japonica treatment.
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Affiliation(s)
- Ruyu Zhao
- Department of Microbiology and Parasitology, Anhui Provincial Laboratory of Pathogen Biology, Anhui Key Laboratory of Zoonosis of High Institution, Laboratory of Tropical and Parasitic Diseases Control, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Xiaoxue Tang
- Department of Microbiology and Parasitology, Anhui Provincial Laboratory of Pathogen Biology, Anhui Key Laboratory of Zoonosis of High Institution, Laboratory of Tropical and Parasitic Diseases Control, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Huiyao Lin
- Department of Microbiology and Parasitology, Anhui Provincial Laboratory of Pathogen Biology, Anhui Key Laboratory of Zoonosis of High Institution, Laboratory of Tropical and Parasitic Diseases Control, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Chen Xing
- Department of Microbiology and Parasitology, Anhui Provincial Laboratory of Pathogen Biology, Anhui Key Laboratory of Zoonosis of High Institution, Laboratory of Tropical and Parasitic Diseases Control, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Na Xu
- Department of Microbiology and Parasitology, Anhui Provincial Laboratory of Pathogen Biology, Anhui Key Laboratory of Zoonosis of High Institution, Laboratory of Tropical and Parasitic Diseases Control, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Bingxin Dai
- Department of Microbiology and Parasitology, Anhui Provincial Laboratory of Pathogen Biology, Anhui Key Laboratory of Zoonosis of High Institution, Laboratory of Tropical and Parasitic Diseases Control, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Pingping Wang
- Department of Microbiology and Parasitology, Anhui Provincial Laboratory of Pathogen Biology, Anhui Key Laboratory of Zoonosis of High Institution, Laboratory of Tropical and Parasitic Diseases Control, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Wei Shao
- Department of Microbiology and Parasitology, Anhui Provincial Laboratory of Pathogen Biology, Anhui Key Laboratory of Zoonosis of High Institution, Laboratory of Tropical and Parasitic Diseases Control, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Miao Liu
- Department of Microbiology and Parasitology, Anhui Provincial Laboratory of Pathogen Biology, Anhui Key Laboratory of Zoonosis of High Institution, Laboratory of Tropical and Parasitic Diseases Control, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Jijia Shen
- Department of Microbiology and Parasitology, Anhui Provincial Laboratory of Pathogen Biology, Anhui Key Laboratory of Zoonosis of High Institution, Laboratory of Tropical and Parasitic Diseases Control, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Shengqun Deng
- Department of Microbiology and Parasitology, Anhui Provincial Laboratory of Pathogen Biology, Anhui Key Laboratory of Zoonosis of High Institution, Laboratory of Tropical and Parasitic Diseases Control, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Cuiping Ren
- Department of Microbiology and Parasitology, Anhui Provincial Laboratory of Pathogen Biology, Anhui Key Laboratory of Zoonosis of High Institution, Laboratory of Tropical and Parasitic Diseases Control, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
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Li C, Yue L, Ju Y, Wang J, Lu H, Li L, Chen M, Wang C, Li S, Liu T, Liu S, Lu T, Wang J, Hu X, Jiang C, Zhou D, Chen F. Transcriptomic analysis for the retested positive COVID-19 patients with long-term persistent SARS-CoV-2 but without symptoms in Wuhan. Clin Transl Med 2023; 13:e1172. [PMID: 36610051 PMCID: PMC9825106 DOI: 10.1002/ctm2.1172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/27/2022] [Accepted: 12/29/2022] [Indexed: 01/09/2023] Open
Affiliation(s)
- Cuidan Li
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina
| | - Liya Yue
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina
| | - Yingjiao Ju
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina,University of Chinese Academy of SciencesBeijingChina
| | - Jie Wang
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina,University of Chinese Academy of SciencesBeijingChina
| | - Hao Lu
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina,University of Chinese Academy of SciencesBeijingChina
| | - Lin Li
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Mengfan Chen
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina,University of Chinese Academy of SciencesBeijingChina
| | - Chenyang Wang
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina,University of Chinese Academy of SciencesBeijingChina
| | - Shuangshuang Li
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina,University of Chinese Academy of SciencesBeijingChina
| | - Tao Liu
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina,University of Chinese Academy of SciencesBeijingChina
| | - Sitong Liu
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina,University of Chinese Academy of SciencesBeijingChina
| | - Tianyi Lu
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina,University of Chinese Academy of SciencesBeijingChina
| | - Jing Wang
- State Key Laboratory of Pathogenesis, PreventionTreatment of High Incidence Diseases in Central AsiaXinjiangChina
| | - Xin Hu
- State Key Laboratory of Pathogenesis, PreventionTreatment of High Incidence Diseases in Central AsiaXinjiangChina
| | - Chunlai Jiang
- National Engineering Laboratory for AIDS Vaccine, School of Life ScienceJilin UniversityChangchunChina
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Fei Chen
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina,University of Chinese Academy of SciencesBeijingChina,State Key Laboratory of Pathogenesis, PreventionTreatment of High Incidence Diseases in Central AsiaXinjiangChina,Beijing Key Laboratory of Genome and Precision Medicine TechnologiesChinese Academy of Sciences and China National Center for BioinformationBeijingChina
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Qian SH, Chen L, Xiong YL, Chen ZX. Evolution and function of developmentally dynamic pseudogenes in mammals. Genome Biol 2022; 23:235. [PMID: 36348461 PMCID: PMC9641868 DOI: 10.1186/s13059-022-02802-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/23/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Pseudogenes are excellent markers for genome evolution, which are emerging as crucial regulators of development and disease, especially cancer. However, systematic functional characterization and evolution of pseudogenes remain largely unexplored. RESULTS To systematically characterize pseudogenes, we date the origin of human and mouse pseudogenes across vertebrates and observe a burst of pseudogene gain in these two lineages. Based on a hybrid sequencing dataset combining full-length PacBio sequencing, sample-matched Illumina sequencing, and public time-course transcriptome data, we observe that abundant mammalian pseudogenes could be transcribed, which contribute to the establishment of organ identity. Our analyses reveal that developmentally dynamic pseudogenes are evolutionarily conserved and show an increasing weight during development. Besides, they are involved in complex transcriptional and post-transcriptional modulation, exhibiting the signatures of functional enrichment. Coding potential evaluation suggests that 19% of human pseudogenes could be translated, thus serving as a new way for protein innovation. Moreover, pseudogenes carry disease-associated SNPs and conduce to cancer transcriptome perturbation. CONCLUSIONS Our discovery reveals an unexpectedly high abundance of mammalian pseudogenes that can be transcribed and translated, and these pseudogenes represent a novel regulatory layer. Our study also prioritizes developmentally dynamic pseudogenes with signatures of functional enrichment and provides a hybrid sequencing dataset for further unraveling their biological mechanisms in organ development and carcinogenesis in the future.
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Affiliation(s)
- Sheng Hu Qian
- grid.35155.370000 0004 1790 4137Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070 PR China ,grid.35155.370000 0004 1790 4137Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 PR China
| | - Lu Chen
- grid.35155.370000 0004 1790 4137Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070 PR China ,grid.35155.370000 0004 1790 4137Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 PR China
| | - Yu-Li Xiong
- grid.35155.370000 0004 1790 4137Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070 PR China ,grid.35155.370000 0004 1790 4137Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 PR China
| | - Zhen-Xia Chen
- grid.35155.370000 0004 1790 4137Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070 PR China ,grid.35155.370000 0004 1790 4137Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 PR China ,grid.35155.370000 0004 1790 4137Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan, 430070 PR China ,grid.35155.370000 0004 1790 4137Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518124 PR China ,grid.488316.00000 0004 4912 1102Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124 PR China
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7
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Zhang C, Sun C, Zhao Y, Wang Q, Guo J, Ye B, Yu G. Overview of MicroRNAs as Diagnostic and Prognostic Biomarkers for High-Incidence Cancers in 2021. Int J Mol Sci 2022; 23:ijms231911389. [PMID: 36232692 PMCID: PMC9570028 DOI: 10.3390/ijms231911389] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 12/24/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs (ncRNAs) about 22 nucleotides in size, which play an important role in gene regulation and are involved in almost all major cellular physiological processes. In recent years, the abnormal expression of miRNAs has been shown to be associated with human diseases including cancer. In the past ten years, the link between miRNAs and various cancers has been extensively studied, and the abnormal expression of miRNAs has been reported in various malignant tumors, such as lung cancer, gastric cancer, colorectal cancer, liver cancer, breast cancer, and prostate cancer. Due to the high malignancy grade of these cancers, it is more necessary to develop the related diagnostic and prognostic methods. According to the study of miRNAs, many potential cancer biomarkers have been proposed for the diagnosis and prognosis of diseases, especially cancer, thus providing a new theoretical basis and perspective for cancer screening. The use of miRNAs as biomarkers for diagnosis or prognosis of cancer has the advantages of being less invasive to patients, with better accuracy and lower price. In view of the important clinical significance of miRNAs in human cancer research, this article reviewed the research status of miRNAs in the above-mentioned cancers in 2021, especially in terms of diagnosis and prognosis, and provided some new perspectives and theoretical basis for the diagnosis and treatment of cancers.
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Affiliation(s)
- Chunyan Zhang
- State Key Laboratory Cell Differentiation and Regulation, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453007, China
- Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453007, China
- College of Life Science, Henan Normal University, Xinxiang 453007, China
- Institute of Biomedical Science, Henan Normal University, Xinxiang 453007, China
| | - Caifang Sun
- State Key Laboratory Cell Differentiation and Regulation, Henan Normal University, Xinxiang 453007, China
- College of Life Science, Henan Normal University, Xinxiang 453007, China
| | - Yabin Zhao
- State Key Laboratory Cell Differentiation and Regulation, Henan Normal University, Xinxiang 453007, China
- College of Life Science, Henan Normal University, Xinxiang 453007, China
| | - Qiwen Wang
- State Key Laboratory Cell Differentiation and Regulation, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453007, China
- Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453007, China
- College of Life Science, Henan Normal University, Xinxiang 453007, China
- Institute of Biomedical Science, Henan Normal University, Xinxiang 453007, China
| | - Jianlin Guo
- State Key Laboratory Cell Differentiation and Regulation, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453007, China
- Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453007, China
- College of Life Science, Henan Normal University, Xinxiang 453007, China
- Institute of Biomedical Science, Henan Normal University, Xinxiang 453007, China
| | - Bingyu Ye
- State Key Laboratory Cell Differentiation and Regulation, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453007, China
- Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453007, China
- College of Life Science, Henan Normal University, Xinxiang 453007, China
- Institute of Biomedical Science, Henan Normal University, Xinxiang 453007, China
- Correspondence: (B.Y.); (G.Y.)
| | - Guoying Yu
- State Key Laboratory Cell Differentiation and Regulation, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453007, China
- Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453007, China
- College of Life Science, Henan Normal University, Xinxiang 453007, China
- Institute of Biomedical Science, Henan Normal University, Xinxiang 453007, China
- Correspondence: (B.Y.); (G.Y.)
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8
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Long F, Tian L, Chai Z, Li J, Tang Y, Liu M. Identification of stage-associated exosome miRNAs in colorectal cancer by improved robust and corroborative approach embedded miRNA-target network. Front Med (Lausanne) 2022; 9:881788. [PMID: 36237545 PMCID: PMC9551196 DOI: 10.3389/fmed.2022.881788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 09/09/2022] [Indexed: 12/24/2022] Open
Abstract
Background Colorectal cancer (CRC) is a common gastrointestinal tumor with high morbidity and mortality. At the molecular level, patients at different stages present considerable heterogeneity. Although the miRNA in exosome is an effective biomarker to reveal tumor progression, studies based on stage-associated exosome miRNA regulatory network analysis still lacking. This study aims to identify CRC stage-associated exosome miRNAs and reveal their potential function in tumor progression. Methods In this study, serum and cellular exosome miRNA expression microarrays associated with CRC were downloaded from GEO database. Stage-common (SC) and stage-specific (SS) differentially expressed miRNAs were extracted and their targets were identified based on 11 databases. Furthermore, miRNA SC and SS regulatory function networks were built based on the CRC phenotypic relevance of miRNA targets, and the corresponding transcription factors were identified. Concurrently, the potential stage-associated miRNAs were identified by receiver-operating characteristic (ROC) curve analysis, survival analysis, drug response analysis, ceRNA analysis, pathway analysis and a comprehensive investigation of 159 publications. Results Ten candidate stage-associated miRNAs were identified, with three SC (miR-146a-5p, miR-22-3p, miR-23b-3p) and seven SS (I: miR-301a-3p, miR-548i; IIIA: miR-23a-3p; IV: miR-194-3p, miR-33a-3p, miR-485-3p, miR-194-5p) miRNAs. Additionally, their targets were enriched in several vital cancer-associated pathways such as TGF-beta, p53, and hippo signaling pathways. Moreover, five key hotspot target genes (CCNA2, MAPK1, PTPRD, MET, and CDKN1A) were demonstrated to associated with better overall survival in CRC patients. Finally, miR-23b-3p, miR-301a-3p and miR-194-3p were validated being the most stably expressed stage-associated miRNAs in CRC serum exosomes, cell exosomes and tissues. Conclusions These CRC stage-associated exosome miRNAs aid to further mechanism research of tumor progression and provide support for better clinical management in patients with different stages.
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9
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Wang G, Zheng H, Zhao X, Wang Y, Zeng Y, Du J. The Prognostic Model and Drug Sensitivity of LKB1-Mutant Lung Adenocarcinoma Based on Immune Landscape. Front Mol Biosci 2022; 9:756772. [PMID: 35720127 PMCID: PMC9201220 DOI: 10.3389/fmolb.2022.756772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Lung cancer is the most common cause of cancer-related deaths worldwide. LKB1-mutant lung adenocarcinoma (LUAD) is a unique subtype of this deadly cancer. LKB1 mutations cause functional changes in a variety of cell processes, including immune functions, that affect prognosis. To date, the potential role of immunity in the prognosis of LKB1-mutant LUAD is not well understood.Methods: We systematically analyzed immune-related genes in LUAD samples from The Cancer Genome Atlas (TCGA) database. ESTIMATE and CIBERSORT algorithms were used to explore the immune microenvironment. A prognostic risk model was constructed, and prognostic, immune function, drug sensitivity, and model specificity analyses were performed to identify the effectiveness of the model.Results: Our results showed that LKB1 mutations suppressed immune function in LUAD. A three-gene signature was constructed to stratify patients into two risk groups. The risk score was an independent predictor for overall survival (OS) in multivariate Cox regression analyses [hazard ratio (HR) > 1, p = 0.002]. Receiver operating characteristic (ROC) curve analyses confirmed that the risk score has better performance than clinicopathological characteristics. Functional analysis revealed that the immune status was different between the risk groups. ZM.447439 was an appropriate treatment for the high-risk group of patients. This risk model is only suitable for LKB1-mutant tumors; it performed poorly in LUAD patients with wild-type LKB1.Conclusion: Our findings indicate the potential role of immunity in LKB1-mutant LUAD, providing novel insights into prognosis and guiding effective immunotherapy.
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Affiliation(s)
- Guanghui Wang
- Institute of Oncology, Shandong Provincial Hospital, Shandong University, Jinan, China
- Department of Thoracic Surgery, Shandong Provincial Hospital, Shandong University, Jinan, China
| | - Haotian Zheng
- Institute of Oncology, Shandong Provincial Hospital, Shandong University, Jinan, China
| | - Xiaogang Zhao
- Department of Thoracic Surgery, The Second Hospital of Shandong University, Jinan, China
| | - Yadong Wang
- Institute of Oncology, Shandong Provincial Hospital, Shandong University, Jinan, China
| | - Yukai Zeng
- Institute of Oncology, Shandong Provincial Hospital, Shandong University, Jinan, China
| | - Jiajun Du
- Institute of Oncology, Shandong Provincial Hospital, Shandong University, Jinan, China
- Department of Thoracic Surgery, Shandong Provincial Hospital, Shandong University, Jinan, China
- *Correspondence: Jiajun Du,
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10
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Niu L, Geyer PE, Gupta R, Santos A, Meier F, Doll S, Wewer Albrechtsen NJ, Klein S, Ortiz C, Uschner FE, Schierwagen R, Trebicka J, Mann M. Dynamic human liver proteome atlas reveals functional insights into disease pathways. Mol Syst Biol 2022; 18:e10947. [PMID: 35579278 PMCID: PMC9112488 DOI: 10.15252/msb.202210947] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 12/12/2022] Open
Abstract
Deeper understanding of liver pathophysiology would benefit from a comprehensive quantitative proteome resource at cell type resolution to predict outcome and design therapy. Here, we quantify more than 150,000 sequence‐unique peptides aggregated into 10,000 proteins across total liver, the major liver cell types, time course of primary cell cultures, and liver disease states. Bioinformatic analysis reveals that half of hepatocyte protein mass is comprised of enzymes and 23% of mitochondrial proteins, twice the proportion of other liver cell types. Using primary cell cultures, we capture dynamic proteome remodeling from tissue states to cell line states, providing useful information for biological or pharmaceutical research. Our extensive data serve as spectral library to characterize a human cohort of non‐alcoholic steatohepatitis and cirrhosis. Dramatic proteome changes in liver tissue include signatures of hepatic stellate cell activation resembling liver cirrhosis and providing functional insights. We built a web‐based dashboard application for the interactive exploration of our resource (www.liverproteome.org).
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Affiliation(s)
- Lili Niu
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Philipp E Geyer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Rajat Gupta
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alberto Santos
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Center for Health Data Science, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.,Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Florian Meier
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sophia Doll
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Nicolai J Wewer Albrechtsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Biochemistry, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Sabine Klein
- Department of Internal Medicine I, Goethe University Clinic Frankfurt, Frankfurt, Germany.,Department of Internal Medicine B, WW University Münster, Münster, Germany
| | - Cristina Ortiz
- Department of Internal Medicine I, Goethe University Clinic Frankfurt, Frankfurt, Germany
| | - Frank E Uschner
- Department of Internal Medicine I, Goethe University Clinic Frankfurt, Frankfurt, Germany.,Department of Internal Medicine B, WW University Münster, Münster, Germany
| | - Robert Schierwagen
- Department of Internal Medicine I, Goethe University Clinic Frankfurt, Frankfurt, Germany.,Department of Internal Medicine B, WW University Münster, Münster, Germany
| | - Jonel Trebicka
- Department of Internal Medicine I, Goethe University Clinic Frankfurt, Frankfurt, Germany.,Department of Internal Medicine B, WW University Münster, Münster, Germany.,European Foundation for the Study of Chronic Failure, EFCLIF, Barcelona, Spain
| | - Matthias Mann
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
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11
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Stanniocalcin 2 (STC2): a universal tumour biomarker and a potential therapeutical target. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:161. [PMID: 35501821 PMCID: PMC9063168 DOI: 10.1186/s13046-022-02370-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/19/2022] [Indexed: 12/24/2022]
Abstract
Stanniocalcin 2 (STC2) is a glycoprotein which is expressed in a broad spectrum of tumour cells and tumour tissues derived from human breast, colorectum, stomach, esophagus, prostate, kidney, liver, bone, ovary, lung and so forth. The expression of STC2 is regulated at both transcriptional and post-transcriptional levels; particularly, STC2 is significantly stimulated under various stress conditions like ER stress, hypoxia and nutrient deprivation. Biologically, STC2 facilitates cells dealing with stress conditions and prevents apoptosis. Importantly, STC2 also promotes the development of acquired resistance to chemo- and radio- therapies. In addition, multiple groups have reported that STC2 overexpression promotes cell proliferation, migration and immune response. Therefore, the overexpression of STC2 is positively correlated with tumour growth, invasion, metastasis and patients' prognosis, highlighting its potential as a biomarker and a therapeutic target. This review focuses on discussing the regulation, biological functions and clinical importance of STC2 in human cancers. Future perspectives in this field will also be discussed.
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12
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Atyah M, Zhou C, Zhou Q, Chen W, Weng J, Wang P, Shi Y, Dong Q, Ren N. The Age-Specific Features and Clinical Significance of NRF2 and MAPK10 Expression in HCC Patients. Int J Gen Med 2022; 15:737-748. [PMID: 35082522 PMCID: PMC8786352 DOI: 10.2147/ijgm.s351263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/12/2022] [Indexed: 12/24/2022] Open
Abstract
Background Nuclear factor (erythroid-derived 2)-like 2 (NRF2) functions decline with age; however, cancer cells can hijack its pathways to ensure survival and aggressiveness. Yet, the role of NRF2 in hepatocellular carcinoma (HCC) is rarely investigated in an age-specific manner. This study investigates the expression of NRF2 and its activator (MAPK10) in different age groups of HCC patients, in addition to the age-specific features of NRF2 and MAPK10 interaction and their clinical significance. Methods Tumor and near-tumor tissue samples of 181 HCC patients were used to complete a protein expression analysis of NRF2 and MAPK10. Patients’ survival and clinical data were collected for clinical analysis. Global databases (TCGA, ICGC) were used to collect MAPK10 genetic mutation and mRNA expression data in patients with HCC, colorectal, stomach, and pancreatic cancers. Results Our findings revealed an increase in NRF2 protein expression but only in younger HCC patients, along with a decline in MAPK10 ability to activate NRF2 in older patients. We also found an increased MAPK10 genetic mutation rate and decreased mRNA expression in older patients. Low MAPK10 and NRF2 expression levels were associated with shorter survival and poorer prognosis due to positive correlation with microvascular invasion, tumor thrombus, elevated AFP levels, and larger tumor size. Conclusion NRF2 expression and oxidative stress mechanism in HCC patients are influenced by age. This magnifies the need to consider patients’ age in treatment strategies and guidelines and re-evaluates the application of studies’ age-standardized findings in older patients who are usually excluded from relevant research.
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Affiliation(s)
- Manar Atyah
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, 200032, People’s Republic of China
| | - Chenhao Zhou
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, 200032, People’s Republic of China
| | - Qiang Zhou
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, 200032, People’s Republic of China
| | - Wanyong Chen
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, 200032, People’s Republic of China
| | - Jialei Weng
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, 200032, People’s Republic of China
| | - Pengcheng Wang
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, 200032, People’s Republic of China
| | - Yi Shi
- Biomedical Research Centre, Zhongshan Hospital, Fudan University, Shanghai, 200032, People’s Republic of China
| | - Qiongzhu Dong
- Institute of Fudan Minhang Academic Health System, and Key Laboratory of Whole-period Monitoring and Precise Intervention of Digestive Cancer (SMHC), Minhang Hospital & AHS, Fudan University, Shanghai, 201199, People’s Republic of China
- Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, People’s Republic of China
- Qiongzhu Dong, Institute of Fudan Minhang Academic Health System, and Key Laboratory of Whole-period Monitoring and Precise Intervention of Digestive Cancer (SMHC), Minhang Hospital & AHS, Fudan University, Shanghai, 201199, People’s Republic of China, Tel +86-21- 64923400, Email
| | - Ning Ren
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, 200032, People’s Republic of China
- Institute of Fudan Minhang Academic Health System, and Key Laboratory of Whole-period Monitoring and Precise Intervention of Digestive Cancer (SMHC), Minhang Hospital & AHS, Fudan University, Shanghai, 201199, People’s Republic of China
- Correspondence: Ning Ren, Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, 200032, People’s Republic of China, Tel +86-21-64041990, Email
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13
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Zhang M, Wu K, Zhang P, Qiu Y, Bai F, Chen H. HOTAIR Facilitates Endocrine Resistance in Breast Cancer Through ESR1/ miR-130b-3p Axis: Comprehensive Analysis of mRNA-miRNA-lncRNA Network. Int J Gen Med 2021; 14:4653-4663. [PMID: 34434057 PMCID: PMC8380629 DOI: 10.2147/ijgm.s320998] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/27/2021] [Indexed: 12/21/2022] Open
Abstract
Background To summarize the regulatory role of mRNA-miRNA-lncRNA network associated with endocrine therapy resistance (ETR) in breast cancer. Methods We analyzed the differentially expressed genes (DEGs), differentially expressed lncRNAs (DELs), and differentially expressed miRNAs (DEMs) in long-term estrogen-deprived (LTED) estrogen receptor (ER)-positive breast cancer cells (LTED MCF7) (modeling relapse on endocrine therapy) and MCF7 cells in the presence of estrogen (E2) (modeling a patient at primary diagnosis) by mining GSE120929 and GSE120930 datasets. The mRNA-miRNA-lncRNA network was constructed by multiple bioinformatic tools. The prognosis of genes from the network was validated in breast cancer patients with following systemic treatment (endocrine therapy) by GEPIA, Kaplan–Meier plotter and UALCAN database. Results Totally, 769 DEGs, 33 DEMs, and 10 DELs were selected. The mRNA-miRNA-lncRNA network was established including 60 mRNA nodes, 6 miRNA nodes and 3 lncRNA nodes. A significant module containing 3 nodes and 3 edges was calculated based on the mRNA-miRNA-lncRNA network. The hub genes in the network are ABCG2, ESR1 and GJA1. ESR1/miR-130b-3p/HOTAIR are significantly correlated with the prognosis of breast cancer patients with endocrine therapy. Conclusion This study provides a novel ETR-related mRNA-miRNA-lncRNA network. Further, we suggest that ESR1/miR-130b-3p/HOTAIR may be promising targets for clinical treatment of endocrine therapy-resistant breast cancer.
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Affiliation(s)
- Mingdi Zhang
- Department of Breast Surgery, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, People's Republic of China
| | - Kejin Wu
- Department of Breast Surgery, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, People's Republic of China
| | - Peng Zhang
- Department of Breast Surgery, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, People's Republic of China
| | - Yiran Qiu
- Department of Breast Surgery, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, People's Republic of China
| | - Fang Bai
- Department of Breast Surgery, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, People's Republic of China
| | - Hongliang Chen
- Department of Breast Surgery, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, People's Republic of China
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14
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Lin Y, Wang L, Ge W, Hui Y, Zhou Z, Hu L, Pan H, Huang Y, Shen B. Multi-omics network characterization reveals novel microRNA biomarkers and mechanisms for diagnosis and subtyping of kidney transplant rejection. J Transl Med 2021; 19:346. [PMID: 34389032 PMCID: PMC8361655 DOI: 10.1186/s12967-021-03025-8] [Citation(s) in RCA: 3] [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: 05/24/2021] [Accepted: 08/05/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Kidney transplantation is an optimal method for treatment of end-stage kidney failure. However, kidney transplant rejection (KTR) is commonly observed to have negative effects on allograft function. MicroRNAs (miRNAs) are small non-coding RNAs with regulatory role in KTR genesis, the identification of miRNA biomarkers for accurate diagnosis and subtyping of KTR is therefore of clinical significance for active intervention and personalized therapy. METHODS In this study, an integrative bioinformatics model was developed based on multi-omics network characterization for miRNA biomarker discovery in KTR. Compared with existed methods, the topological importance of miRNA targets was prioritized based on cross-level miRNA-mRNA and protein-protein interaction network analyses. The biomarker potential of identified miRNAs was computationally validated and explored by receiver-operating characteristic (ROC) evaluation and integrated "miRNA-gene-pathway" pathogenic survey. RESULTS Three miRNAs, i.e., miR-145-5p, miR-155-5p, and miR-23b-3p, were screened as putative biomarkers for KTR monitoring. Among them, miR-155-5p was a previously reported signature in KTR, whereas the remaining two were novel candidates both for KTR diagnosis and subtyping. The ROC analysis convinced the power of identified miRNAs as single and combined biomarkers for KTR prediction in kidney tissue and blood samples. Functional analyses, including the latent crosstalk among HLA-related genes, immune signaling pathways and identified miRNAs, provided new insights of these miRNAs in KTR pathogenesis. CONCLUSIONS A network-based bioinformatics approach was proposed and applied to identify candidate miRNA biomarkers for KTR study. Biological and clinical validations are further needed for translational applications of the findings.
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Affiliation(s)
- Yuxin Lin
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, 215000 China
| | - Liangliang Wang
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, 215000 China
| | - Wenqing Ge
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, 215000 China
| | - Yu Hui
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, 215000 China
| | - Zheng Zhou
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, 215000 China
| | - Linkun Hu
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, 215000 China
| | - Hao Pan
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, 215000 China
| | - Yuhua Huang
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, 215000 China
| | - Bairong Shen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212 China
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