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Maruhashi K, Kashima H, Miyano S, Park H. Meta graphical lasso: uncovering hidden interactions among latent mechanisms. Sci Rep 2024; 14:18105. [PMID: 39103384 PMCID: PMC11300637 DOI: 10.1038/s41598-024-68959-7] [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: 04/07/2024] [Accepted: 07/30/2024] [Indexed: 08/07/2024] Open
Abstract
In complex systems, it's crucial to uncover latent mechanisms and their context-dependent relationships. This is especially true in medical research, where identifying unknown cancer mechanisms and their impact on phenomena like drug resistance is vital. Directly observing these mechanisms is challenging due to measurement complexities, leading to an approach that infers latent mechanisms from observed variable distributions. Despite machine learning advancements enabling sophisticated generative models, their black-box nature complicates the interpretation of complex latent mechanisms. A promising method for understanding these mechanisms involves estimating latent factors through linear projection, though there's no assurance that inferences made under specific conditions will remain valid across contexts. We propose a novel solution, suggesting data, even from systems appearing complex, can often be explained by sparse dependencies among a few common latent factors, regardless of the situation. This simplification allows for modeling that yields significant insights across diverse fields. We demonstrate this with datasets from finance, where we capture societal trends from stock price movements, and medicine, where we uncover new insights into cancer drug resistance through gene expression analysis.
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Affiliation(s)
- Koji Maruhashi
- Fujitsu Research, 4-1-1 Kamikodanaka, Nakahara-ku, Kawasaki, 2118588, Kanagawa, Japan.
| | | | - Satoru Miyano
- M &D Data Science Center, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, Japan
| | - Heewon Park
- M &D Data Science Center, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, Japan.
- School of Mathematics, Statistics and Data Science, Sungshin Women's University, 2, Bomun-ro 34da-gil, Seongbuk-gu, Seoul, 02844, Republic of Korea.
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Choi H, Kim HD, Choi YW, Lim H, Kim KW, Kim KS, Lee YC, Kim CH. T7 phage display reveals NOLC1 as a GM3 binding partner in human breast cancer MCF-7 cells. Arch Biochem Biophys 2023; 750:109810. [PMID: 37939867 DOI: 10.1016/j.abb.2023.109810] [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: 07/27/2023] [Revised: 10/25/2023] [Accepted: 10/31/2023] [Indexed: 11/10/2023]
Abstract
Ganglioside GM3 is a simple monosialoganglioside (NeuAc-Gal-Glc-ceramide) that modulates cell adhesion, proliferation, and differentiation. Previously, we reported isolation of GM3-binding vascular endothelial growth factor receptor and transforming growth factor-β receptor by the T7 phage display method (Chung et al., 2009; Kim et al., 2013). To further identify novel proteins interacting with GM3, we extended the T7 phage display method in this study. After T7 phage display biopanning combined with immobilized biotin-labeled 3'-sialyllactose prepared on a streptavidin-coated microplate, we isolated 100 candidate sequences from the human lung cDNA library. The most frequently detected clones from the blast analysis were the human nucleolar and coiled-body phosphoprotein 1 (NOLC1) sequences. We initially identified NOLC1 as a molecule that possibly binds to GM3 and confirmed this binding ability using the glutathione S-transferase fusion protein. Herein, we report another GM3-interacting protein, NOLC1, that can be isolated by the T7 phage display method. These results are expected to be helpful for elucidating the functional roles of ganglioside GM3 with NOLC1. When human breast cancer MCF-7 cells were examined for subcellular localization of NOLC1, immunofluorescence of NOLC1 was observed in the intracellular region. In addition, NOLC1 expression was increased in the nucleolus after treatment with the anticancer drug doxorubicin. GM3 and NOLC1 levels in the doxorubicin-treated MCF-7 cells were correlated, indicating possible associations between GM3 and NOLC1. Therefore, direct interactions between carbohydrates and cellular proteins can pave the path for new signaling phenomena in biology.
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Affiliation(s)
- Hyunju Choi
- Molecular and Cellular Glycobiology Unit, Department of Biological Sciences, SungKyunKwan University, Seoburo 2066, Jangan-Gu, Suwon, 16419, South Korea.
| | - Hee-Do Kim
- Molecular and Cellular Glycobiology Unit, Department of Biological Sciences, SungKyunKwan University, Seoburo 2066, Jangan-Gu, Suwon, 16419, South Korea.
| | - Yeon-Woo Choi
- Molecular and Cellular Glycobiology Unit, Department of Biological Sciences, SungKyunKwan University, Seoburo 2066, Jangan-Gu, Suwon, 16419, South Korea.
| | - Hakseong Lim
- Molecular and Cellular Glycobiology Unit, Department of Biological Sciences, SungKyunKwan University, Seoburo 2066, Jangan-Gu, Suwon, 16419, South Korea.
| | - Kyung-Woon Kim
- Molecular and Cellular Glycobiology Unit, Department of Biological Sciences, SungKyunKwan University, Seoburo 2066, Jangan-Gu, Suwon, 16419, South Korea.
| | - Kyoung-Sook Kim
- Department of Medicinal Biotechnology, College of Health Sciences, Dong-A University, Saha-Gu, Busan, 604-714, South Korea
| | - Young-Choon Lee
- Department of Medicinal Biotechnology, College of Health Sciences, Dong-A University, Saha-Gu, Busan, 604-714, South Korea.
| | - Cheorl-Ho Kim
- Molecular and Cellular Glycobiology Unit, Department of Biological Sciences, SungKyunKwan University, Seoburo 2066, Jangan-Gu, Suwon, 16419, South Korea.
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Sun Z, Zhang Q, Lv J, Sun Y, Feng Z, Zhang M, Zhang F, Xia C, Gao Y, Zhang Z, Zuo YF, Ren SY. High expression of NOLC1 as an independent prognostic factor for survival in patients with colorectal cancer. J Cancer Res Clin Oncol 2023; 149:15697-15712. [PMID: 37670166 PMCID: PMC10620263 DOI: 10.1007/s00432-023-05297-7] [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: 06/16/2023] [Accepted: 08/14/2023] [Indexed: 09/07/2023]
Abstract
BACKGROUND As a phosphorylated protein, NOLC1 is mainly located in the nucleus and is highly expressed in a variety of tumors, participating in the regulation of cell proliferation and aging. This study further investigated the role of NOLC1 in colorectal cancer tumors, aiming to provide sufficient scientific evidence for the clinical treatment of colorectal cancer. METHODS We used TCGA, GEO, TNMplot, GEPIA, and other databases to explore the expression level of NOLC1 in colorectal cancer patients, as well as the correlation between the clinical characteristics of colorectal cancer patients and their expression, and conducted the prognostic analysis. Immunohistofluorescence (IHF) staining verified the analytical results. Subsequently, KEGG and GO enrichment analysis was used to identify the potential molecular mechanism of NOLC1 promoting the occurrence and development of colorectal cancer. The influence of NOLC1 expression on the immune microenvironment of colorectal cancer patients was further investigated using the TIMER database. GDSC database analysis was used to screen out possible anti-colorectal cancer drugs against NOLC1. Finally, we demonstrated the effect of NOLC1 on the activity and migration of colorectal cancer cells by Edu Cell proliferation assay and Wound Healing assay in vitro. RESULTS Our results suggest that NOLC1 is overexpressed in colorectal cancer, and that overexpression of NOLC1 is associated with relevant clinical features. NOLC1, as an independent risk factor affecting the prognosis of colorectal cancer patients, can lead to a poor prognosis of colorectal cancer. In addition, NOLC1 may be associated with MCM10, HELLS, NOC3L, and other genes through participating in Wnt signaling pathways and jointly regulate the occurrence and development of colorectal cancer under the influence of the tumor microenvironment and many other influencing factors. Related to NOLC1: Selumetinib, Imatinib, and targeted drugs such as Lapatinib have potential value in the clinical application of colorectal cancer. NOLC1 enhances the proliferation and migration of colorectal cancer cells. CONCLUSIONS High expression of NOLC1 as an independent prognostic factor for survival in patients with colorectal cancer. NOLC1 enhances the proliferation and migration of colorectal cancer cells. Further studies and clinical trials are needed to confirm the role of NOLC1 in the development and progression of colorectal cancer.
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Affiliation(s)
- Zhiwei Sun
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, 116023, China
| | - Qianshi Zhang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, 116023, China
| | - Jinjuan Lv
- Department of Clinical Biochemistry, College of Laboratory Diagnostic Medicine, Dalian Medical University, Dalian, China
| | - Yuzhu Sun
- Department of Clinical Biochemistry, College of Laboratory Diagnostic Medicine, Dalian Medical University, Dalian, China
| | - Zhen Feng
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, 116023, China
| | - Mengyan Zhang
- Department of Clinical Biochemistry, College of Laboratory Diagnostic Medicine, Dalian Medical University, Dalian, China
| | - Feifan Zhang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, 116023, China
| | - Cong Xia
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, 116023, China
| | - Yina Gao
- Department of Clinical Biochemistry, College of Laboratory Diagnostic Medicine, Dalian Medical University, Dalian, China
| | - Zhenyu Zhang
- Department of Clinical Biochemistry, College of Laboratory Diagnostic Medicine, Dalian Medical University, Dalian, China
| | - Yun-Fei Zuo
- Department of Clinical Biochemistry, College of Laboratory Diagnostic Medicine, Dalian Medical University, Dalian, China.
| | - Shuang-Yi Ren
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, 116023, China.
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Zhai F, Wang J, Luo X, Ye M, Jin X. Roles of NOLC1 in cancers and viral infection. J Cancer Res Clin Oncol 2023; 149:10593-10608. [PMID: 37296317 DOI: 10.1007/s00432-023-04934-5] [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: 04/15/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND The nucleolus is considered the center of metabolic control and an important organelle for the biogenesis of ribosomal RNA (rRNA). Nucleolar and coiled-body phosphoprotein 1(NOLC1), which was originally identified as a nuclear localization signal-binding protein is a nucleolar protein responsible for nucleolus construction and rRNA synthesis, as well as chaperone shuttling between the nucleolus and cytoplasm. NOLC1 plays an important role in a variety of cellular life activities, including ribosome biosynthesis, DNA replication, transcription regulation, RNA processing, cell cycle regulation, apoptosis, and cell regeneration. PURPOSE In this review, we introduce the structure and function of NOLC1. Then we elaborate its upstream post-translational modification and downstream regulation. Meanwhile, we describe its role in cancer development and viral infection which provide a direction for future clinical applications. METHODS The relevant literatures from PubMed have been reviewed for this article. CONCLUSION NOLC1 plays an important role in the progression of multiple cancers and viral infection. In-depth study of NOLC1 provides a new perspective for accurate diagnosis of patients and selection of therapeutic targets.
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Affiliation(s)
- Fengguang Zhai
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, China
- The Affiliated First Hospital, Ningbo University, Ningbo, 315020, China
| | - Jie Wang
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, China
- The Affiliated First Hospital, Ningbo University, Ningbo, 315020, China
| | - Xia Luo
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Meng Ye
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, China.
- The Affiliated First Hospital, Ningbo University, Ningbo, 315020, China.
| | - Xiaofeng Jin
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, China.
- The Affiliated First Hospital, Ningbo University, Ningbo, 315020, China.
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Ghafouri-Fard S, Safarzadeh A, Taheri M, Jamali E. Identification of diagnostic biomarkers via weighted correlation network analysis in colorectal cancer using a system biology approach. Sci Rep 2023; 13:13637. [PMID: 37604903 PMCID: PMC10442394 DOI: 10.1038/s41598-023-40953-5] [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: 04/11/2023] [Accepted: 08/18/2023] [Indexed: 08/23/2023] Open
Abstract
Colorectal cancer (CRC) is the third most frequent cancer to be diagnosed in both females and males necessitating identification of effective biomarkers. An in-silico system biology approach called weighted gene co-expression network analysis (WGCNA) can be used to examine gene expression in a complicated network of regulatory genes. In the current study, the co-expression network of DEGs connected to CRC and their target genes was built using the WGCNA algorithm. GO and KEGG pathway analysis were carried out to learn more about the biological role of the DEmRNAs. These findings revealed that the genes were mostly enriched in the biological processes that were involved in the regulation of hormone levels, extracellular matrix organization, and extracellular structure organization. The intersection of genes between hub genes and DEmRNAs showed that DKC1, PA2G4, LYAR and NOLC1 were the clinically final hub genes of CRC.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Arash Safarzadeh
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany.
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Elena Jamali
- Department of Pathology, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Yang J, Miao RR, Li YN, Pan T, Wu SH, Qu XJ, Cui SX. Atypical chemokine receptor 3 induces colorectal tumorigenesis in mice by promoting β-arrestin-NOLC1-fibrillarin-dependent rRNA biogenesis. Acta Pharmacol Sin 2022; 43:2967-2976. [PMID: 35365782 PMCID: PMC9622750 DOI: 10.1038/s41401-022-00901-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/13/2022] [Indexed: 01/27/2023] Open
Abstract
Atypical chemokine receptor 3 (ACKR3) has emerged as a key player in various biological processes. Its atypical "intercepting receptor" properties have established ACKR3 as the major regulator in the pathophysiological processes in many diseases. In this study, we investigated the role of ACKR3 activation in promoting colorectal tumorigenesis. We showed that ACKR3 expression levels were significantly increased in human colon cancer tissues, and high levels of ACKR3 predicted the increased severity of cancer. In Villin-ACKR3 transgenic mice with a high expression level of CKR3 in their intestinal epithelial cells, administration of AOM/DSS induced more severe colorectal tumorigenesis than their WT littermates. Cancer cells of Villin-ACKR3 transgenic mice were characterised by the nuclear β-arrestin-1 (β-arr1)-activated perturbation of rRNA biogenesis. In HCT116 cells, cotreatment with CXCL12 and AMD3100 selectively activated ACKR3 and induced nuclear translocation of β-arr1, leading to an interaction of β-arr1 with nucleolar and coiled-body phosphoprotein 1 (NOLC1). NOLC1, as the phosphorylated protein, further interacted with fibrillarin, a conserved nucleolar methyltransferase responsible for ribosomal RNA methylation in the nucleolus, thereby increasing the methylation in histone H2A and promoting rRNA transcription in ribosome biogenesis. In conclusion, ACKR3 promotes colorectal tumorigenesis through the perturbation of rRNA biogenesis by the β-arr1-induced interaction of NOLC1 with fibrillarin.
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Affiliation(s)
- Juan Yang
- Beijing Key Laboratory of Environmental Toxicology, Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, 100069, China
- Department of Comprehensive Ward, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Rong-Rong Miao
- Department of Pharmacology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Ya-Nan Li
- Beijing Key Laboratory of Environmental Toxicology, Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, 100069, China
| | - Ting Pan
- Beijing Key Laboratory of Environmental Toxicology, Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, 100069, China
| | - Shu-Hua Wu
- Department of Pathology, Hospital of Bin Zhou Medical College, Binzhou, 256603, China
| | - Xian-Jun Qu
- Department of Pharmacology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Shu-Xiang Cui
- Beijing Key Laboratory of Environmental Toxicology, Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, 100069, China.
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Li J, Yuan J, Li Y, Wang J, Gong D, Xie Q, Ma R, Wang J, Ren M, Lu D, Xu Z. d-Borneol enhances cisplatin sensitivity via p21/p27-mediated S-phase arrest and cell apoptosis in non-small cell lung cancer cells and a murine xenograft model. Cell Mol Biol Lett 2022; 27:61. [PMID: 35883026 PMCID: PMC9327246 DOI: 10.1186/s11658-022-00362-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 07/06/2022] [Indexed: 12/28/2022] Open
Abstract
Background Cisplatin (CDDP) is commonly used to treat non-small cell lung cancer (NSCLC), but the appearance of drug resistance greatly hinders its efficacy. Borneol may promote drug absorption; however, synergism between borneol and CDDP in suppressing NSCLC is not clearly understood. Hence, we investigated borneol as a novel chemosensitizer to support chemotherapeutic efficacy and reduce side effects. Methods We compared viability after exposure to d-borneol, l-borneol, and synthetic borneol in two NSCLC cell lines, A549 and H460, and selected the most sensitive cells. We then assessed synergy between borneol forms and CDDP in cisplatin-resistant NSCLC cells, H460/CDDP. Next, we identified effective concentrations and exposure times. Subsequently, we evaluated cell migration via wound healing and cell proliferation via clone formation assay. Then, we focused on P-glycoprotein (P-gp) function, cell cycle, apoptosis, and RNA sequencing to elucidate underlying molecular mechanisms for synergy. Finally, we used an H460/CDDP xenograft tumor model to verify antitumor activity and safety in vivo. Data were examined using one-way analysis of variance (ANOVA) for multiple datasets or t-test for comparisons between two variables. Results d-Borneol was more effective in H460 than A549 cells. d-Borneol combined with CDDP showed greater inhibition of cell proliferation, migration, and clone formation in H460/CDDP cells than CDDP alone. RNA sequencing (RNA-seq) analysis identified differentially expressed genes enriched in cell cycle pathways. The impact of d-borneol on CDDP chemosensitivity involved arrest of the cell cycle at S phase via p27/p21-mediated cyclinA2/D3-CDK2/6 signaling and activation of intrinsic apoptosis via p21-mediated Bax/Bcl-2/caspase3 signaling. Further, d-borneol ameliorated drug resistance by suppressing levels and activity of P-gp. Cotreatment with d-borneol and CDDP inhibited tumor growth in vivo and reduced CDDP-caused liver and kidney toxicity. Conclusions d-Borneol increased the efficacy of cisplatin and reduced its toxicity. This compound has the potential to become a useful chemosensitizer for drug-resistance NSCLC. Supplementary Information The online version contains supplementary material available at 10.1186/s11658-022-00362-4.
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Affiliation(s)
- Jinxiu Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jianmei Yuan
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yong Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jian Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China.
| | - Daoyin Gong
- Department of Pathology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China.
| | - Qian Xie
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Rong Ma
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jiajun Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Mihong Ren
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Danni Lu
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhuo Xu
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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Comparative Proteomic Analysis of Drug Trichosanthin Addition to BeWo Cell Line. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27051603. [PMID: 35268705 PMCID: PMC8911981 DOI: 10.3390/molecules27051603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/11/2022] [Accepted: 02/16/2022] [Indexed: 11/17/2022]
Abstract
Trichosanthin (TCS) is a traditional Chinese herbal medicine used to treat some gynecological diseases. Its effective component has diverse biological functions, including antineoplastic activity. The human trophoblast cell line BeWo was chosen as an experimental model for in vitro testing of a drug screen for anticancer properties of TCS. The MTT method was used in this study to get a primary screen result. The result showed that 100 mM had the best IC50 value. Proteomics analysis was then performed for further investigation of the drug effect of TCS on the BeWo cell line. In this differential proteomic expression analysis, the total proteins extracted from the BeWo cell line and their protein expression level after the drug treatment were compared by 2DE. Then, 24 unique three-fold differentially expressed proteins (DEPs) were successfully identified by MALDI-TOF/TOF MS. Label-free proteomics was run as a complemental method for the same experimental procedure. There are two proteins that were identified in both the 2DE and label-free methods. Among those identified proteins, bioinformatics analysis showed the importance of pathway and signal transduction and gives us the potential possibility for the disease treatment hypothesis.
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Hu Z, Lai Y, Ma C, Zuo L, Xiao G, Gao H, Xie B, Huang X, Gan H, Huang D, Yao N, Feng B, Ru J, Chen Y, Cai D. Cordyceps militaris extract induces apoptosis and pyroptosis via caspase-3/PARP/GSDME pathways in A549 cell line. Food Sci Nutr 2022; 10:21-38. [PMID: 35035907 PMCID: PMC8751435 DOI: 10.1002/fsn3.2636] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/17/2021] [Accepted: 10/01/2021] [Indexed: 12/19/2022] Open
Abstract
Cordyceps militaris (CM) is traditionally used as dietary therapy for lung cancer patients in China. CM extract (CME) is hydrosoluble fraction of CM and extensively investigated. Caspase-3-involved cell death is considered as its major anticancer mechanism but inconclusive. Therefore, we explore its caspase-3-dependent programmed cell death nature (apoptosis and pyroptosis) and validate its caspase-3-dependent property in loss-of-function experiment. Component profile of CME is detected by High Performance Liquid Chromatography- quadrupole time-of-flight mass spectrometry (HPLC-qTOF). Results show that CME causes pyroptosis-featured cell bubbling and cell lysis and inhibits cell proliferation in A549 cell. CME induces chromatin condensing and makes PI+/annexin V+ staining in bubbling cells, indicating genotoxicity, apoptosis, and pyroptosis cell death are caused by CME. High concentration of CME (200 μg/ml) exerts G2/M and G0 cell cycles arresting and suppresses P53-downstream proliferative proteins, including P53, P21, CDC25B, CyclinB1, Bcl-2, and BCL2 associated agonist of cell death (BAD), but 1-100 μg/ml of CME show less effect on proteins above. Correspondingly, caspase-3 activity and caspase-3 downstream proteins including pyroptotic effector gasdermin-E (GSDME) and apoptotic marker cleaved-poly-ADP-ribose polymerase (PARP) are significantly promoted by CME. Moreover, regarding membrane pore formation in pyroptotic cell, expression of membrane GSDME (GSDME antibody conjugated with PE-Cy7 for detection in flow cytometry) is remarkably increased by CME treatment. By contrast, other pyroptosis-related proteins such as P2X7, NLRP3, GSDMD, and Caspase-1 are not affected after CME treatment. Additionally, TET2 is unexpectedly raised by CME. In present of caspase-3 inhibitor Ac-DEVD-CHO (Ac-DC), CME-induced cytotoxicity, cell bubbling, and genotoxicity are reduced, and CME-induced upregulation of apoptosis (cleaved-PARP-1) and pyroptosis (GSDME-NT) proteins are reversed. Lastly, 22 components are identified in HPLC-qTOF experiment, and they are classified into trophism, neoadjuvant component, cytotoxic component, and cancer deterioration promoter according to previous references. Conclusively, CME causes caspase-3-dependent apoptosis and pyroptosis in A549 through caspase-3/PARP and caspase-3/GSDME pathways, and it provides basic insight into clinic application of CME for cancer patients.
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Affiliation(s)
- Zixuan Hu
- The Fifth Clinical Medical CollegeGuangzhou University of Chinese MedicineGuangzhouChina
- Guangdong Provincial Key Laboratory of Research and Development in Traditional Chinese MedicineGuangzhouChina
| | - Yijing Lai
- The Fifth Clinical Medical CollegeGuangzhou University of Chinese MedicineGuangzhouChina
- Guangdong Provincial Key Laboratory of Research and Development in Traditional Chinese MedicineGuangzhouChina
| | - Chaoya Ma
- Guangdong Provincial Key Laboratory of Occupational Disease Prevention and TreatmentDepartment of Science and EducationGuangdong Province Hospital for Occupational Disease Prevention and TreatmentGuangzhouChina
| | - Lina Zuo
- Health examination centerSun Yat‐sen Memorial Hospital, Sun Yat‐Sen UniversityGuangzhou510120China
| | - Guanlin Xiao
- The Fifth Clinical Medical CollegeGuangzhou University of Chinese MedicineGuangzhouChina
- Guangdong Provincial Key Laboratory of Research and Development in Traditional Chinese MedicineGuangzhouChina
| | - Haili Gao
- The Fifth Clinical Medical CollegeGuangzhou University of Chinese MedicineGuangzhouChina
| | - Biyuan Xie
- The Fifth Clinical Medical CollegeGuangzhou University of Chinese MedicineGuangzhouChina
| | - Xuejun Huang
- The Fifth Clinical Medical CollegeGuangzhou University of Chinese MedicineGuangzhouChina
- Guangdong Provincial Key Laboratory of Research and Development in Traditional Chinese MedicineGuangzhouChina
| | - Haining Gan
- The Fifth Clinical Medical CollegeGuangzhou University of Chinese MedicineGuangzhouChina
- Guangdong Provincial Key Laboratory of Research and Development in Traditional Chinese MedicineGuangzhouChina
| | - Dane Huang
- The Fifth Clinical Medical CollegeGuangzhou University of Chinese MedicineGuangzhouChina
- Guangdong Provincial Key Laboratory of Research and Development in Traditional Chinese MedicineGuangzhouChina
| | - Nan Yao
- The Fifth Clinical Medical CollegeGuangzhou University of Chinese MedicineGuangzhouChina
- Guangdong Provincial Key Laboratory of Research and Development in Traditional Chinese MedicineGuangzhouChina
| | - Baoguo Feng
- GENETERRA (Chinese) Research CenterGuangzhouChina
| | - JieXia Ru
- College of Materials and EnergySouth China Agricultural UniversityGuangzhouChina
| | - Yuxing Chen
- The Fifth Clinical Medical CollegeGuangzhou University of Chinese MedicineGuangzhouChina
- Guangdong Provincial Key Laboratory of Research and Development in Traditional Chinese MedicineGuangzhouChina
| | - Dake Cai
- The Fifth Clinical Medical CollegeGuangzhou University of Chinese MedicineGuangzhouChina
- Guangdong Provincial Key Laboratory of Research and Development in Traditional Chinese MedicineGuangzhouChina
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Yang M, Gao XR, Meng YN, Shen F, Chen YP. ETS1 Ameliorates Hyperoxia-Induced Alveolar Epithelial Cell Injury by Regulating the TGM2-Mediated Wnt/β-Catenin Pathway. Lung 2021; 199:681-690. [PMID: 34817668 DOI: 10.1007/s00408-021-00489-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 10/24/2021] [Indexed: 11/24/2022]
Abstract
PURPOSE Bronchopulmonary dysplasia (BPD) is a chronic lung disease that affects newborns who need oxygen therapy, and high-concentration oxygen therapy may cause neonatal morbidity and mortality in newborns. E26 oncogene homologue 1 (ETS1) and transglutaminase 2 (TGM2) have been reported to be associated with lung cell injury. However, the mechanism of ETS1 in regulating BPD is still unclear. METHODS Hyperoxia-induced A549 cells to simulate hyperoxia-induced alveolar epithelial cell injury. MTT assays and colony formation assays were performed to investigate the proliferation of A549 cells. Flow cytometry was carried out to quantify the apoptosis of A549 cells. The expression levels of ETS1 and TGM2 were quantified by qRT-PCR. The protein expression levels of ETS1, TGM2, β-catenin, c-Jun and MET were measured by western blot. Overexpression of ETS1, overexpression of TGM2, overexpression of ETS1 with downregulation of TGM2 and overexpression of TGM2 with inhibition of Wnt/β-catenin pathway were performed to investigate the role of ETS1, TGM2 and Wnt/β-catenin pathways in hyperoxia-induced alveolar epithelial cell injury. RESULTS Hyperoxia decreased the proliferation and promoted the apoptosis of cells in a time-dependent manner. Moreover, overexpression of ETS1 rescued the effect of hyperoxia on proliferation and apoptosis. In addition, overexpression of TGM2 participated in the regulation of hyperoxia-induced proliferation and apoptosis. ETS1 regulated hyperoxia-induced alveolar epithelial cell injury through the Wnt/β-catenin pathway via TGM2. CONCLUSION ETS1 ameliorates hyperoxia-induced alveolar epithelial cell injury through the TGM2-mediated Wnt/β-catenin pathway.
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Affiliation(s)
- Min Yang
- Department of Respiratory, Hunan Children's Hospital, No. 86 Ziyuan Road, Changsha, 410007, Hunan Province, China
| | - Xi-Rong Gao
- Neonate Department, Hunan Children's Hospital, Changsha, 410007, Hunan Province, China
| | - Yan-Ni Meng
- Department of Respiratory, Hunan Children's Hospital, No. 86 Ziyuan Road, Changsha, 410007, Hunan Province, China
| | - Fang Shen
- Research Institute of Children, Hunan Children's Hospital, Changsha, 410007, Hunan Province, China
| | - Yan-Ping Chen
- Department of Respiratory, Hunan Children's Hospital, No. 86 Ziyuan Road, Changsha, 410007, Hunan Province, China.
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Knockdown of NOLC1 Inhibits PI3K-AKT Pathway to Improve the Poor Prognosis of Esophageal Carcinoma. JOURNAL OF ONCOLOGY 2021; 2021:9944132. [PMID: 34046062 PMCID: PMC8128555 DOI: 10.1155/2021/9944132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 04/30/2021] [Indexed: 11/29/2022]
Abstract
Objective Esophageal carcinoma (ESCA) is a common malignant gastrointestinal tumor. The abnormal expression of NOLC1 is involved in the tumorigenesis of various human tumors, whereas the function and mechanism of NOLC1 in ESCA remain unclear. In this study, we explored the relationship between NOLC1 and poor prognosis of ESCA, and its role and mechanism in the occurrence of ESCA. Methods The NOLC1 expression in ESCA tissues and cell lines was determined by qRT-PCR, immunohistochemistry, or western blot. The Kaplan–Meier method was conducted to estimate the overall survival. Cox regression analysis was carried out to examine the association between patient characteristics and prognosis. A recombined lentiviral vector containing NOLC1 was applied for transfecting ESCA cells (Eca109 and TE-13) and established a stable cell line with low NOLC1 expression or high NOLC1 expression, in the absence or presence of PI3K inhibitor (LY294002) treatment. Cell proliferation, apoptosis rate, invasion ability, migration ability, and PI3K/AKT pathway were detected by CCK8 assay, flow cytometry, Transwell assay, wound-healing assay, and western blot. Results NOLC1 overexpression was observed in ESCA tissues and ESCA cell lines (EC9706, Eca109, TE-13, Kyse170, T.TN) compared with adjacent normal tissues and normal esophageal cell line HEEC. NOLC1 overexpression was markedly associated with bigger tumor size, lymph node metastasis, and advanced TNM stage. Patients with NOLC1 overexpression have shorter overall survival than that of those with low NOLC1 expression. NOLC1 overexpression was considered to be an independent poor prognostic factor affecting overall survival. NOLC1 knockdown inhibited proliferation, migration, invasion, and cyclin B1 expression and promoted the apoptosis and cleaved-caspase-3 expression of Eca109 and TE-13 cells. NOLC1 overexpression accelerated proliferation, migration, invasion, and cyclin B1 expression and inhibited the apoptosis and cleaved-caspase-3 expression of ESCA cells via activating PI3K/AKT pathway. Rescue experiments showed that PI3K inhibitor (LY294002) could reverse the phenomenon caused by NOLC1 overexpression. Conclusion NOLC1 may be a marker for poor prognosis. It can participate in the occurrence and development of ESCA via the PI3K/AKT pathway.
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A Zic2/Runx2/NOLC1 signaling axis mediates tumor growth and metastasis in clear cell renal cell carcinoma. Cell Death Dis 2021; 12:319. [PMID: 33767130 PMCID: PMC7994417 DOI: 10.1038/s41419-021-03617-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 12/26/2022]
Abstract
Clear cell renal cell carcinoma (ccRCC) is one of the most common malignancies with rapid growth and high metastasis, but lacks effective therapeutic targets. Here, using public sequencing data analyses, quantitative real-time PCR assay, western blotting, and IHC staining, we characterized that runt-related transcription factor 2 (Runx2) was significantly upregulated in ccRCC tissues than that in normal renal tissues, which was associated with the worse survival of ccRCC patients. Overexpression of Runx2 promoted malignant proliferation and migration of ccRCC cells, and inversely, interfering Runx2 with siRNA attenuates its oncogenic ability. RNA sequencing and functional studies revealed that Runx2 enhanced ccRCC cell growth and metastasis via downregulation of tumor suppressor nucleolar and coiled-body phosphoprotein 1 (NOLC1). Moreover, increased Zic family member 2 (Zic2) was responsible for the upregulation of Runx2 and its oncogenic functions in ccRCC. Kaplan-Meier survival analyses indicated that ccRCC patients with high Zic2/Runx2 and low NOLC1 had the worst outcome. Therefore, our study demonstrates that Zic2/Runx2/NOLC1 signaling axis promotes ccRCC progression, providing a set of potential targets and prognostic indicators for patients with ccRCC.
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Xu Z, Wei J, Qin F, Sun Y, Xiang W, Yuan L, Qin J, Deng K, Zheng T, Li S. Hypoxia-associated alternative splicing signature in lung adenocarcinoma. Epigenomics 2020; 13:47-63. [PMID: 33336585 DOI: 10.2217/epi-2020-0399] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Aim: To establish a signature based on hypoxia-related alternative splicing (AS) events for lung adenocarcinoma. Materials & methods: The least absolute shrinkage and selection operator Cox approach was used to construct a prognostic model. A nomogram that integrates the final AS predictor and stage was created. The network of the key AS events and splicing factors was created. Results: We created a prognostic signature of 11 AS events. Moreover, a nomogram that constitutes the pathological stage and risk was exhibited to be greatly effective in estimating the survival likelihood of lung adenocarcinoma patients. Conclusion: Herein we developed the first-ever signature based on hypoxia-related AS events with both prognostic predictive power and diagnostic efficacy.
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Affiliation(s)
- Zhanyu Xu
- Department of Thoracic & Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, 530021, PR China
| | - Jiangbo Wei
- Department of Thoracic & Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, 530021, PR China
| | - Fanglu Qin
- Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, 530021, PR China
| | - Yu Sun
- Department of Thoracic & Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, 530021, PR China
| | - Weiwei Xiang
- Department of Thoracic & Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, 530021, PR China
| | - Liqiang Yuan
- Department of Thoracic & Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, 530021, PR China
| | - Junqi Qin
- Department of Thoracic & Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, 530021, PR China
| | - Kun Deng
- Department of Thoracic & Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, 530021, PR China
| | - Tiaozhan Zheng
- Department of Thoracic & Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, 530021, PR China
| | - Shikang Li
- Department of Thoracic & Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, 530021, PR China
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Zhang X, Liu M, Zhang X, Wang Y, Dai L. Autoantibodies to tumor-associated antigens in lung cancer diagnosis. Adv Clin Chem 2020; 103:1-45. [PMID: 34229848 DOI: 10.1016/bs.acc.2020.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Lung cancer (LC) accounts for the majority of cancer-related deaths worldwide. Although screening the high-risk population by low-dose CT (LDCT) has reduced mortality, the cost and high false positivity rate has prevented its general diagnostic use. As such, better and more specific minimally invasive biomarkers are needed in general and for early LC detection, specifically. Autoantibodies produced by humoral immune response to tumor-associated antigens (TAA) are emerging as a promising noninvasive biomarker for LC. Given the low sensitivity of any one single autoantibody, a panel approach could provide a more robust and promising strategy to detect early stage LC. In this review, we summarize the background of TAA autoantibodies (TAAb) and the techniques currently used for identifying TAA, as well as recent findings of LC specific antigens and TAAb. This review provides guidance toward the development of accurate and reliable TAAb as immunodiagnostic biomarkers in the early detection of LC.
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Affiliation(s)
- Xiuzhi Zhang
- Department of Pathology, Henan Medical College, Zhengzhou, Henan, China
| | - Man Liu
- Henan Institute of Medical and Pharmaceutical Sciences in Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China; School of Basic Medical Sciences & Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China; Henan Key Laboratory of Tumor Epidemiology, Zhengzhou University, Zhengzhou, Henan, China
| | - Xue Zhang
- Henan Institute of Medical and Pharmaceutical Sciences in Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China; School of Basic Medical Sciences & Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China; Henan Key Laboratory of Tumor Epidemiology, Zhengzhou University, Zhengzhou, Henan, China
| | - Yulin Wang
- Henan Institute of Medical and Pharmaceutical Sciences in Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China; School of Basic Medical Sciences & Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China; Henan Key Laboratory of Tumor Epidemiology, Zhengzhou University, Zhengzhou, Henan, China
| | - Liping Dai
- Henan Institute of Medical and Pharmaceutical Sciences in Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China; School of Basic Medical Sciences & Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China; Henan Key Laboratory of Tumor Epidemiology, Zhengzhou University, Zhengzhou, Henan, China.
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Scherer M, Levin M, Butter F, Scheibe M. Quantitative Proteomics to Identify Nuclear RNA-Binding Proteins of Malat1. Int J Mol Sci 2020; 21:ijms21031166. [PMID: 32050583 PMCID: PMC7037011 DOI: 10.3390/ijms21031166] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/03/2020] [Accepted: 02/05/2020] [Indexed: 01/02/2023] Open
Abstract
The long non-coding RNA Malat1 has been implicated in several human cancers, while the mechanism of action is not completely understood. As RNAs in cells function together with RNA-binding proteins (RBPs), the composition of their RBP complex can shed light on their functionality. We here performed quantitative interactomics of 14 non-overlapping fragments covering the full length of Malat1 to identify possible nuclear interacting proteins. Overall, we identified 35 candidates including 14 already known binders, which are able to interact with Malat1 in the nucleus. Furthermore, the use of fragments along the full-length RNA allowed us to reveal two hotspots for protein binding, one in the 5′-region and one in the 3′-region of Malat1. Our results provide confirmation on previous RNA-protein interaction studies and suggest new candidates for functional investigations.
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